From 8c677bedd78660418e9b8c3d698c5055c3c4667b Mon Sep 17 00:00:00 2001 From: Thomas Purcell Date: Mon, 23 Oct 2023 16:17:23 +0200 Subject: [PATCH 01/30] Move FHI-aims io from atomate2 into pymatgen 1) parsers and AimsOuput ojbects moved over 2) All ASE Atoms objects removed in favor of pymatgen structures 3) TO DO: Check name schemes 4) Create an AimsInputs object in the future --- pymatgen/io/aims/__init__.py | 1 + pymatgen/io/aims/aims_output.py | 191 ++++++ pymatgen/io/aims/parsers.py | 1071 +++++++++++++++++++++++++++++++ 3 files changed, 1263 insertions(+) create mode 100644 pymatgen/io/aims/__init__.py create mode 100644 pymatgen/io/aims/aims_output.py create mode 100644 pymatgen/io/aims/parsers.py diff --git a/pymatgen/io/aims/__init__.py b/pymatgen/io/aims/__init__.py new file mode 100644 index 00000000000..d0d04312bee --- /dev/null +++ b/pymatgen/io/aims/__init__.py @@ -0,0 +1 @@ +"""IO interface for FHI-aims.""" diff --git a/pymatgen/io/aims/aims_output.py b/pymatgen/io/aims/aims_output.py new file mode 100644 index 00000000000..9975834ddf3 --- /dev/null +++ b/pymatgen/io/aims/aims_output.py @@ -0,0 +1,191 @@ +"""A representation of FHI-aims output (based on ASE output parser).""" +from __future__ import annotations + +from typing import TYPE_CHECKING, Any + +import numpy as np +from atomate2.aims.io.parsers import read_aims_header_info, read_aims_output +from monty.json import MontyDecoder, MSONable + +if TYPE_CHECKING: + from collections.abc import Sequence + from pathlib import Path + + from emmet.core.math import Matrix3D, Vector3D + + from pymatgen.core import Molecule, Structure + + +class AimsOutput(MSONable): + """The main output file for FHI-aims.""" + + def __init__( + self, + results: Sequence[Molecule | Structure], + metadata: dict[str, Any], + structure_summary: dict[str, Any], + ): + """AimsOutput object constructor. + + Parameters + ---------- + results: Sequence[.MSONableAtoms] + A list of all images in an output file + metadata: Dict[str, Any] + The metadata of the executable used to perform the calculation + structure_summary: Dict[str, Any] + The summary of the starting atomic structure + """ + self._results = results + self._metadata = metadata + self._structure_summary = structure_summary + + def as_dict(self) -> dict[str, Any]: + """Create a dict representation of the outputs for MSONable.""" + d: dict[str, Any] = { + "@module": self.__class__.__module__, + "@class": self.__class__.__name__, + } + + d["results"] = self._results + d["metadata"] = self._metadata + d["structure_summary"] = self._structure_summary + return d + + @classmethod + def from_outfile(cls, outfile: str | Path): + """Construct an AimsOutput from an output file. + + Parameters + ---------- + outfile: str or Path + The aims.out file to parse + """ + metadata, structure_summary = read_aims_header_info(outfile) + results = read_aims_output(outfile, index=slice(0, None)) + + return cls(results, metadata, structure_summary) + + @classmethod + def from_dict(cls, d: dict[str, Any]): + """Construct an AimsOutput from a dictionary. + + Parameters + ---------- + d: Dict[str, Any] + The dictionary used to create AimsOutput + """ + decoded = {k: MontyDecoder().process_decoded(v) for k, v in d.items() if not k.startswith("@")} + return cls(decoded["results"], decoded["metadata"], decoded["structure_summary"]) + + def get_results_for_image(self, image_ind: int) -> Structure | Molecule: + """Get the results dictionary for a particular image or slice of images. + + Parameters + ---------- + image_ind: int + The index of the image to get the results for + + Returns + ------- + The results for that image + """ + return self._results[image_ind] + + @property + def structure_summary(self) -> dict[str, Any]: + """The summary of the material/molecule that the calculations represent.""" + return self._structure_summary + + @property + def metadata(self) -> dict[str, Any]: + """The system metadata.""" + return self._metadata + + @property + def n_images(self) -> int: + """The number of images in results.""" + return len(self._results) + + @property + def initial_structure(self) -> Structure | Molecule: + """The initial structure for the calculations.""" + return self._structure_summary["initial_structure"] + + @property + def final_structure(self) -> Structure | Molecule: + """The final structure for the calculation.""" + return self._results[-1] + + @property + def structures(self) -> Sequence[Structure | Molecule]: + """All images in the output file.""" + return self._results + + @property + def fermi_energy(self) -> float: + """The Fermi energy for the final structure in the calculation.""" + return self.get_results_for_image(-1).properties["fermi_energy"] + + @property + def vbm(self) -> float: + """The HOMO level for the final structure in the calculation.""" + return self.get_results_for_image(-1).properties["vbm"] + + @property + def cbm(self) -> float: + """The LUMO level for the final structure in the calculation.""" + return self.get_results_for_image(-1).properties["cbm"] + + @property + def band_gap(self) -> float: + """The band gap for the final structure in the calculation.""" + return self.get_results_for_image(-1).properties["gap"] + + @property + def direct_band_gap(self) -> float: + """The direct band gap for the final structure in the calculation.""" + return self.get_results_for_image(-1).properties["direct_gap"] + + @property + def final_energy(self) -> float: + """The total energy for the final structure in the calculation.""" + return self.get_results_for_image(-1).properties["energy"] + + @property + def completed(self) -> bool: + """Did the calculation complete.""" + return len(self._results) > 0 + + @property + def aims_version(self) -> str: + """The version of FHI-aims used for the calculation.""" + return self._metadata["version_number"] + + @property + def forces(self) -> Sequence[Vector3D] | None: + """The forces for the final image of the calculation.""" + force_array = self.get_results_for_image(-1).site_properties.get("force", None) + if isinstance(force_array, np.ndarray): + return force_array.tolist() + + return force_array + + @property + def stress(self) -> Matrix3D: + """The stress for the final image of the calculation.""" + return self.get_results_for_image(-1).properties.get("stress", None) + + @property + def stresses(self) -> Sequence[Matrix3D] | None: + """The atomic virial stresses for the final image of the calculation.""" + stresses_array = self.get_results_for_image(-1).site_properties.get("atomic_virial_stress", None) + if isinstance(stresses_array, np.ndarray): + return stresses_array.tolist() + return stresses_array + + @property + def all_forces(self) -> list[list[Vector3D]]: + """The forces for all images in the calculation.""" + all_forces_array = [res.site_properties.get("force", None) for res in self._results] + return [af.tolist() if isinstance(af, np.ndarray) else af for af in all_forces_array] diff --git a/pymatgen/io/aims/parsers.py b/pymatgen/io/aims/parsers.py new file mode 100644 index 00000000000..8480a73c010 --- /dev/null +++ b/pymatgen/io/aims/parsers.py @@ -0,0 +1,1071 @@ +"""AIMS output parser, taken from ASE with modifications.""" +from __future__ import annotations + +import gzip +from dataclasses import dataclass, field +from pathlib import Path +from typing import TYPE_CHECKING, Any + +import numpy as np + +from pymatgen.core import Lattice, Molecule, Structure + +if TYPE_CHECKING: + from collections.abc import Sequence + + from emmet.core.math import Vector3D + + from pymatgen.core.structure import SiteCollection + +# TARP: Originally an object, but type hinting needs this to be an int +LINE_NOT_FOUND = -1000 +EV_PER_A3_TO_KBAR = 1.60217653e-19 * 1e22 + + +class ParseError(Exception): + """Parse error during reading of a file""" + + +class AimsParseError(Exception): + """Exception raised if an error occurs when parsing an Aims output file.""" + + def __init__(self, message): + self.message = message + super().__init__(self.message) + + +# Read aims.out files +scalar_property_to_line_key = { + "free_energy": ["| Electronic free energy"], + "number_of_iterations": ["| Number of self-consistency cycles"], + "magnetic_moment": ["N_up - N_down"], + "n_atoms": ["| Number of atoms"], + "n_bands": [ + "Number of Kohn-Sham states", + "Reducing total number of Kohn-Sham states", + "Reducing total number of Kohn-Sham states", + ], + "n_electrons": ["The structure contains"], + "n_kpts": ["| Number of k-points"], + "n_spins": ["| Number of spin channels"], + "electronic_temp": ["Occupation type:"], + "fermi_energy": ["| Chemical potential (Fermi level)"], +} + + +@dataclass +class AimsOutChunk: + """Base class for AimsOutChunks. + + Parameters + ---------- + lines: list[str] + The list of all lines in the aims.out file + """ + + lines: list[str] = field(default_factory=list) + + def reverse_search_for(self, keys: list[str], line_start: int = 0) -> int: + """Find the last time one of the keys appears in self.lines. + + Parameters + ---------- + keys: list[str] + The key strings to search for in self.lines + line_start: int + The lowest index to search for in self.lines + + Returns + ------- + int + The last time one of the keys appears in self.lines + """ + for ll, line in enumerate(self.lines[line_start:][::-1]): + if any(key in line for key in keys): + return len(self.lines) - ll - 1 + + return LINE_NOT_FOUND + + def search_for_all(self, key: str, line_start: int = 0, line_end: int = -1) -> list[int]: + """Find the all times the key appears in self.lines. + + Parameters + ---------- + key: str + The key string to search for in self.lines + line_start: int + The first line to start the search from + line_end: int + The last line to end the search at + + Returns + ------- + list[ints] + All times the key appears in the lines + """ + line_index = [] + for ll, line in enumerate(self.lines[line_start:line_end]): + if key in line: + line_index.append(ll + line_start) + return line_index + + def parse_scalar(self, property: str) -> float | None: + """Parse a scalar property from the chunk. + + Parameters + ---------- + property: str + The property key to parse + + Returns + ------- + float + The scalar value of the property + """ + line_start = self.reverse_search_for(scalar_property_to_line_key[property]) + + if line_start == LINE_NOT_FOUND: + return None + + line = self.lines[line_start] + return float(line.split(":")[-1].strip().split()[0]) + + +@dataclass +class AimsOutHeaderChunk(AimsOutChunk): + """The header of the aims.out file containing general information. + + Parameters + ---------- + lines: list[str] + The list of all lines in the aims.out file + _cache: dict[str, Any] + The cache storing previously calculated results + """ + + lines: list[str] = field(default_factory=list) + _cache: dict[str, Any] = field(default_factory=dict) + + @property + def commit_hash(self): + """Get the commit hash for the FHI-aims version.""" + line_start = self.reverse_search_for(["Commit number"]) + if line_start == LINE_NOT_FOUND: + raise AimsParseError("This file does not appear to be an aims-output file") + + return self.lines[line_start].split(":")[1].strip() + + @property + def aims_uuid(self): + """Get the aims-uuid for the calculation.""" + line_start = self.reverse_search_for(["aims_uuid"]) + if line_start == LINE_NOT_FOUND: + raise AimsParseError("This file does not appear to be an aims-output file") + + return self.lines[line_start].split(":")[1].strip() + + @property + def version_number(self): + """Get the commit hash for the FHI-aims version.""" + line_start = self.reverse_search_for(["FHI-aims version"]) + if line_start == LINE_NOT_FOUND: + raise AimsParseError("This file does not appear to be an aims-output file") + + return self.lines[line_start].split(":")[1].strip() + + @property + def fortran_compiler(self): + """Get the fortran compiler used to make FHI-aims.""" + line_start = self.reverse_search_for(["Fortran compiler :"]) + if line_start == LINE_NOT_FOUND: + raise AimsParseError("This file does not appear to be an aims-output file") + + return self.lines[line_start].split(":")[1].split("/")[-1].strip() + + @property + def c_compiler(self): + """Get the C compiler used to make FHI-aims.""" + line_start = self.reverse_search_for(["C compiler :"]) + if line_start == LINE_NOT_FOUND: + return None + + return self.lines[line_start].split(":")[1].split("/")[-1].strip() + + @property + def fortran_compiler_flags(self): + """Get the fortran compiler flags used to make FHI-aims.""" + line_start = self.reverse_search_for(["Fortran compiler flags"]) + if line_start == LINE_NOT_FOUND: + raise AimsParseError("This file does not appear to be an aims-output file") + + return self.lines[line_start].split(":")[1].strip() + + @property + def c_compiler_flags(self): + """Get the C compiler flags used to make FHI-aims.""" + line_start = self.reverse_search_for(["C compiler flags"]) + if line_start == LINE_NOT_FOUND: + return None + + return self.lines[line_start].split(":")[1].strip() + + @property + def build_type(self): + """Get the optional build flags passed to cmake.""" + line_end = self.reverse_search_for(["Linking against:"]) + line_inds = self.search_for_all("Using", line_end=line_end) + + return [" ".join(self.lines[ind].split()[1:]).strip() for ind in line_inds] + + @property + def linked_against(self): + """Get all libraries used to link the FHI-aims executable.""" + line_start = self.reverse_search_for(["Linking against:"]) + if line_start == LINE_NOT_FOUND: + return [] + + linked_libs = [self.lines[line_start].split(":")[1].strip()] + line_start += 1 + while "lib" in self.lines[line_start]: + linked_libs.append(self.lines[line_start].strip()) + line_start += 1 + + return linked_libs + + @property + def initial_lattice(self): + """Parse the initial lattice vectors from the aims.out file.""" + line_start = self.reverse_search_for(["| Unit cell:"]) + if line_start == LINE_NOT_FOUND: + return None + + return Lattice( + np.array( + [[float(inp) for inp in line.split()[-3:]] for line in self.lines[line_start + 1 : line_start + 4]] + ) + ) + + @property + def initial_structure(self): + """Create an SiteCollection object for the initial structure. + + Using the FHI-aims output file recreate the initial structure for + the calculation. + """ + lattice = self.initial_lattice + + line_start = self.reverse_search_for(["Atomic structure:"]) + if line_start == LINE_NOT_FOUND: + raise AimsParseError("No information about the structure in the chunk.") + + line_start += 2 + + coords = np.zeros((self.n_atoms, 3)) + species = [""] * self.n_atoms + for ll, line in enumerate(self.lines[line_start : line_start + self.n_atoms]): + inp = line.split() + coords[ll, :] = [float(pos) for pos in inp[4:7]] + species[ll] = inp[3] + + site_properties = {"charge": self.initial_charges} + if self.initial_magnetic_moments is not None: + site_properties["magmoms"] = self.initial_magnetic_moments + + if lattice: + return Structure(lattice, species, coords, np.sum(self.initial_charges), site_properties=site_properties) + + return Molecule(species, coords, np.sum(self.initial_charges), site_properties=site_properties) + + @property + def initial_charges(self): + if "initial_charges" not in self._cache: + self._parse_initial_charges_and_moments() + return self._cache["initial_charges"] + + @property + def initial_magnetic_moments(self): + if "initial_magnetic_moments" not in self._cache: + self._parse_initial_charges_and_moments() + return self._cache["initial_magnetic_moments"] + + def _parse_initial_charges_and_moments(self): + """Parse the initial charges and magnetic moments + + Once parsed store them in the cache + """ + charges = np.zeros(self.n_atoms) + magmoms = None + line_start = self.reverse_search_for(["Initial charges", "Initial moments and charges"]) + if line_start != LINE_NOT_FOUND: + line_start += 2 + magmoms = np.zeros(self.n_atoms) + for ll, line in enumerate(self.lines[line_start : line_start + self.n_atoms]): + inp = line.split() + if len(inp) == 4: + charges[ll] = float(inp[2]) + magmoms = None + else: + charges[ll] = float(inp[3]) + magmoms[ll] = float(inp[2]) + + self._cache["initial_charges"] = charges + self._cache["initial_magnetic_moments"] = magmoms + + @property + def is_md(self): + """Determine if calculation is a molecular dynamics calculation.""" + return self.reverse_search_for(["Complete information for previous time-step:"]) != LINE_NOT_FOUND + + @property + def is_relaxation(self): + """Determine if the calculation is a geometry optimization or not.""" + return self.reverse_search_for(["Geometry relaxation:"]) != LINE_NOT_FOUND + + def _parse_k_points(self): + """Get the list of k-points used in the calculation.""" + n_kpts = self.parse_scalar("n_kpts") + if n_kpts is None: + return { + "k_points": None, + "k_point_weights": None, + } + n_kpts = int(n_kpts) + + line_start = self.reverse_search_for(["| K-points in task"]) + line_end = self.reverse_search_for(["| k-point:"]) + if (line_start == LINE_NOT_FOUND) or (line_end == LINE_NOT_FOUND) or (line_end - line_start != n_kpts): + return { + "k_points": None, + "k_point_weights": None, + } + + k_points = np.zeros((n_kpts, 3)) + k_point_weights = np.zeros(n_kpts) + for kk, line in enumerate(self.lines[line_start + 1 : line_end + 1]): + k_points[kk] = [float(inp) for inp in line.split()[4:7]] + k_point_weights[kk] = float(line.split()[-1]) + + self._cache.update( + { + "k_points": k_points, + "k_point_weights": k_point_weights, + } + ) + return None + + @property + def n_atoms(self) -> int: + """The number of atoms for the material.""" + n_atoms = self.parse_scalar("n_atoms") + if n_atoms is None: + raise AimsParseError("No information about the number of atoms in the header.") + return int(n_atoms) + + @property + def n_bands(self): + """The number of Kohn-Sham states for the chunk.""" + line_start = self.reverse_search_for(scalar_property_to_line_key["n_bands"]) + + if line_start == LINE_NOT_FOUND: + raise AimsParseError("No information about the number of Kohn-Sham states in the header.") + + line = self.lines[line_start] + if "| Number of Kohn-Sham states" in line: + return int(line.split(":")[-1].strip().split()[0]) + + return int(line.split()[-1].strip()[:-1]) + + @property + def n_electrons(self): + """The number of electrons for the chunk.""" + line_start = self.reverse_search_for(scalar_property_to_line_key["n_electrons"]) + + if line_start == LINE_NOT_FOUND: + raise AimsParseError("No information about the number of electrons in the header.") + + line = self.lines[line_start] + return int(float(line.split()[-2])) + + @property + def n_k_points(self): + """The number of k_ppoints for the calculation.""" + n_kpts = self.parse_scalar("n_kpts") + if n_kpts is None: + return None + + return int(n_kpts) + + @property + def n_spins(self): + """The number of spin channels for the chunk.""" + n_spins = self.parse_scalar("n_spins") + if n_spins is None: + raise AimsParseError("No information about the number of spin channels in the header.") + return int(n_spins) + + @property + def electronic_temperature(self): + """The electronic temperature for the chunk.""" + line_start = self.reverse_search_for(scalar_property_to_line_key["electronic_temp"]) + if line_start == LINE_NOT_FOUND: + return 0.10 + + line = self.lines[line_start] + return float(line.split("=")[-1].strip().split()[0]) + + @property + def k_points(self): + """All k-points listed in the calculation.""" + if "k_points" not in self._cache: + self._parse_k_points() + + return self._cache["k_points"] + + @property + def k_point_weights(self): + """The k-point weights for the calculation.""" + if "k_point_weights" not in self._cache: + self._parse_k_points() + + return self._cache["k_point_weights"] + + @property + def header_summary(self): + """Dictionary summarizing the information inside the header.""" + return { + "initial_structure": self.initial_structure, + "initial_lattice": self.initial_lattice, + "is_relaxation": self.is_relaxation, + "is_md": self.is_md, + "n_atoms": self.n_atoms, + "n_bands": self.n_bands, + "n_electrons": self.n_electrons, + "n_spins": self.n_spins, + "electronic_temperature": self.electronic_temperature, + "n_k_points": self.n_k_points, + "k_points": self.k_points, + "k_point_weights": self.k_point_weights, + } + + @property + def metadata_summary(self) -> dict[str, str]: + """Dictionary containing all metadata for FHI-aims build.""" + return { + "commit_hash": self.commit_hash, + "aims_uuid": self.aims_uuid, + "version_number": self.version_number, + "fortran_compiler": self.fortran_compiler, + "c_compiler": self.c_compiler, + "fortran_compiler_flags": self.fortran_compiler_flags, + "c_compiler_flags": self.c_compiler_flags, + "build_type": self.build_type, + "linked_against": self.linked_against, + } + + +class AimsOutCalcChunk(AimsOutChunk): + """A part of the aims.out file corresponding to a single structure.""" + + def __init__(self, lines, header): + """Construct the AimsOutCalcChunk. + + Parameters + ---------- + lines: list[str] + The lines used for the structure + header: .AimsOutHeaderChunk + A summary of the relevant information from the aims.out header + """ + super().__init__(lines) + self._header = header.header_summary + self._cache = {} + + def _parse_structure(self): + """Parse a structure object from the file. + + For the given section of the aims output file generate the + calculated structure. + """ + lattice = self.lattice + velocities = self.velocities + species = self.species + coords = self.coords + + site_properties = dict() + if len(velocities) > 0: + site_properties["velocity"] = np.array(velocities) + + results = self.results + site_prop_keys = { + "forces": "force", + "stresses": "atomic_virial_stress", + "hirshfeld_charges": "hirshfeld_charge", + "hirshfeld_volumes": "hirshfeld_volume", + "hirshfeld_atomic_dipoles": "hirshfeld_atomic_dipole", + } + properties = {prop: results[prop] for prop in results if prop not in site_prop_keys} + for prop, site_key in site_prop_keys.items(): + if prop in results: + site_properties[site_key] = results[prop] + + if len(site_properties.keys()) == 0: + site_properties = None + + if lattice is not None: + return Structure(lattice, species, coords, site_properties=site_properties, properties=properties) + return Molecule(species, coords, site_properties=site_properties, properties=properties) + + @property + def _parse_lattice_atom_pos(self) -> tuple[list[str], list[Vector3D], list[Vector3D], Lattice | None]: + """Get the lattice of the structure + + Returns + ------- + species: list[str] + The species of all atoms + coords: list[Vector3D] + The cartesian coordinates of the atoms + velocities: list[Vector3D] + The velocities of all atoms + lattice: Lattice or None + The lattice of the system + """ + lattice_vectors = [] + velocities = [] + species = [] + coords = [] + + start_keys = [ + "Atomic structure (and velocities) as used in the preceding time step", + "Updated atomic structure", + "Atomic structure that was used in the preceding time step of the wrapper", + ] + line_start = self.reverse_search_for(start_keys) + if line_start == LINE_NOT_FOUND: + return self.initial_structure + + line_start += 1 + + line_end = self.reverse_search_for(['Writing the current geometry to file "geometry.in.next_step"'], line_start) + if line_end == LINE_NOT_FOUND: + line_end = len(self.lines) + + for line in self.lines[line_start:line_end]: + if "lattice_vector " in line: + lattice_vectors.append([float(inp) for inp in line.split()[1:]]) + elif "atom " in line: + line_split = line.split() + species.append(line_split[4]) + coords.append([float(inp) for inp in line_split[1:4]]) + elif "velocity " in line: + velocities.append([float(inp) for inp in line.split()[1:]]) + + return species, coords, velocities, Lattice(lattice_vectors) + + @property + def species(self): + if "species" not in self._cache: + self._cache.update(self._parse_lattice_atom_pos()) + return self._cache["species"] + + @property + def coords(self): + if "coords" not in self._cache: + self._cache.update(self._parse_lattice_atom_pos()) + return self._cache["coords"] + + @property + def velocities(self): + if "velocities" not in self._cache: + self._cache.update(self._parse_lattice_atom_pos()) + return self._cache["velocities"] + + @property + def lattice(self): + if "lattice" not in self._cache: + self._cache.update(self._parse_lattice_atom_pos()) + return self._cache["lattice"] + + @property + def forces(self): + """Parse the forces from the aims.out file.""" + line_start = self.reverse_search_for(["Total atomic forces"]) + if line_start == LINE_NOT_FOUND: + return None + + line_start += 1 + + return np.array( + [[float(inp) for inp in line.split()[-3:]] for line in self.lines[line_start : line_start + self.n_atoms]] + ) + + @property + def stresses(self): + """Parse the stresses from the aims.out file and convert to kbar.""" + line_start = self.reverse_search_for(["Per atom stress (eV) used for heat flux calculation"]) + if line_start == LINE_NOT_FOUND: + return None + line_start += 3 + stresses = [] + for line in self.lines[line_start : line_start + self.n_atoms]: + xx, yy, zz, xy, xz, yz = (float(d) for d in line.split()[2:8]) + stresses.append([xx, yy, zz, yz, xz, xy]) + + return np.array(stresses) * EV_PER_A3_TO_KBAR + + @property + def stress(self): + """Parse the stress from the aims.out file and convert to kbar.""" + from ase.stress import full_3x3_to_voigt_6_stress + + line_start = self.reverse_search_for( + [ + "Analytical stress tensor - Symmetrized", + "Numerical stress tensor", + ] + ) # Offset to relevant lines + if line_start == LINE_NOT_FOUND: + return None + + stress = [[float(inp) for inp in line.split()[2:5]] for line in self.lines[line_start + 5 : line_start + 8]] + return full_3x3_to_voigt_6_stress(stress) * EV_PER_A3_TO_KBAR + + @property + def is_metallic(self): + """Checks if the system is metallic.""" + line_start = self.reverse_search_for( + ["material is metallic within the approximate finite broadening function (occupation_type)"] + ) + return line_start != LINE_NOT_FOUND + + @property + def energy(self): + """Parse the energy from the aims.out file.""" + if self.initial_lattice is not None and self.is_metallic: + line_ind = self.reverse_search_for(["Total energy corrected"]) + else: + line_ind = self.reverse_search_for(["Total energy uncorrected"]) + if line_ind == LINE_NOT_FOUND: + raise AimsParseError("No energy is associated with the structure.") + + return float(self.lines[line_ind].split()[5]) + + @property + def dipole(self): + """Parse the electric dipole moment from the aims.out file.""" + line_start = self.reverse_search_for(["Total dipole moment [eAng]"]) + if line_start == LINE_NOT_FOUND: + return None + + line = self.lines[line_start] + return np.array([float(inp) for inp in line.split()[6:9]]) + + @property + def dielectric_tensor(self): + """Parse the dielectric tensor from the aims.out file.""" + line_start = self.reverse_search_for(["PARSE DFPT_dielectric_tensor"]) + if line_start == LINE_NOT_FOUND: + return None + + # we should find the tensor in the next three lines: + lines = self.lines[line_start + 1 : line_start + 4] + + # make ndarray and return + return np.array([np.fromstring(line, sep=" ") for line in lines]) + + @property + def polarization(self): + """Parse the polarization vector from the aims.out file.""" + line_start = self.reverse_search_for(["| Cartesian Polarization"]) + if line_start == LINE_NOT_FOUND: + return None + line = self.lines[line_start] + return np.array([float(s) for s in line.split()[-3:]]) + + def _parse_homo_lumo(self): + """Parse the HOMO/LUMO values and get band gap if periodic.""" + line_start = self.reverse_search_for(["Highest occupied state (VBM)"]) + homo = float(self.lines[line_start].split(" at ")[1].split("eV")[0].strip()) + + line_start = self.reverse_search_for(["Lowest unoccupied state (CBM)"]) + lumo = float(self.lines[line_start].split(" at ")[1].split("eV")[0].strip()) + + line_start = self.reverse_search_for(["verall HOMO-LUMO gap"]) + homo_lumo_gap = float(self.lines[line_start].split(":")[1].split("eV")[0].strip()) + + line_start = self.reverse_search_for(["Smallest direct gap"]) + if line_start == LINE_NOT_FOUND: + return { + "vbm": homo, + "cbm": lumo, + "gap": homo_lumo_gap, + "direct_gap": homo_lumo_gap, + } + + direct_gap = float(self.lines[line_start].split(":")[1].split("eV")[0].strip()) + return { + "vbm": homo, + "cbm": lumo, + "gap": homo_lumo_gap, + "direct_gap": direct_gap, + } + + def _parse_hirshfeld(self): + """Parse the Hirshfled charges volumes, and dipole moments.""" + line_start = self.reverse_search_for(["Performing Hirshfeld analysis of fragment charges and moments."]) + if line_start == LINE_NOT_FOUND: + return { + "charges": None, + "volumes": None, + "atomic_dipoles": None, + "dipole": None, + } + + line_inds = self.search_for_all("Hirshfeld charge", line_start, -1) + hirshfeld_charges = np.array([float(self.lines[ind].split(":")[1]) for ind in line_inds]) + + line_inds = self.search_for_all("Hirshfeld volume", line_start, -1) + hirshfeld_volumes = np.array([float(self.lines[ind].split(":")[1]) for ind in line_inds]) + + line_inds = self.search_for_all("Hirshfeld dipole vector", line_start, -1) + hirshfeld_atomic_dipoles = np.array( + [[float(inp) for inp in self.lines[ind].split(":")[1].split()] for ind in line_inds] + ) + + if self.lattice is None: + hirshfeld_dipole = np.sum( + hirshfeld_charges.reshape((-1, 1)) * self.coords, + axis=1, + ) + else: + hirshfeld_dipole = None + return { + "charges": hirshfeld_charges, + "volumes": hirshfeld_volumes, + "atomic_dipoles": hirshfeld_atomic_dipoles, + "dipole": hirshfeld_dipole, + } + + @property + def structure(self) -> Structure | Molecule: + """The pytmagen SiteCollection of the output file.""" + if "structure" not in self._cache: + self._cache["structure"] = self._parse_structure() + return self._cache["structure"] + + @property + def results(self): + """Convert an AimsOutChunk to a Results Dictionary.""" + results = { + "energy": self.energy, + "free_energy": self.free_energy, + "forces": self.forces, + "stress": self.stress, + "stresses": self.stresses, + "magmom": self.magmom, + "dipole": self.dipole, + "fermi_energy": self.E_f, + "n_iter": self.n_iter, + "hirshfeld_charges": self.hirshfeld_charges, + "hirshfeld_dipole": self.hirshfeld_dipole, + "hirshfeld_volumes": self.hirshfeld_volumes, + "hirshfeld_atomic_dipoles": self.hirshfeld_atomic_dipoles, + "dielectric_tensor": self.dielectric_tensor, + "polarization": self.polarization, + "vbm": self.vbm, + "cbm": self.cbm, + "gap": self.gap, + "direct_gap": self.direct_gap, + } + + return {key: value for key, value in results.items() if value is not None} + + # Properties from the aims.out header + @property + def initial_structure(self): + """Return the initial structure of the calculation.""" + return self._header["initial_structure"] + + @property + def initial_lattice(self): + """Return the initial lattice vectors for the structure.""" + return self._header["initial_lattice"] + + @property + def n_atoms(self): + """Return the number of atoms for the material.""" + return self._header["n_atoms"] + + @property + def n_bands(self): + """Return the number of Kohn-Sham states for the chunk.""" + return self._header["n_bands"] + + @property + def n_electrons(self): + """Return the number of electrons for the chunk.""" + return self._header["n_electrons"] + + @property + def n_spins(self): + """Return the number of spin channels for the chunk.""" + return self._header["n_spins"] + + @property + def electronic_temperature(self): + """Return the electronic temperature for the chunk.""" + return self._header["electronic_temperature"] + + @property + def n_k_points(self): + """Return the number of electrons for the chunk.""" + return self._header["n_k_points"] + + @property + def k_points(self): + """Return the number of spin channels for the chunk.""" + return self._header["k_points"] + + @property + def k_point_weights(self): + """Return tk_point_weights electronic temperature for the chunk.""" + return self._header["k_point_weights"] + + @property + def free_energy(self): + """Return the free energy for the chunk.""" + return self.parse_scalar("free_energy") + + @property + def n_iter(self): + """Return the number of SCF iterations. + + The number of steps needed to converge the SCF cycle for the chunk. + """ + return self.parse_scalar("number_of_iterations") + + @property + def magmom(self): + """Return the magnetic moment for the chunk.""" + return self.parse_scalar("magnetic_moment") + + @property + def E_f(self): + """Return he Fermi energy for the chunk.""" + return self.parse_scalar("fermi_energy") + + @property + def converged(self): + """Return True if the chunk is a fully converged final structure.""" + return (len(self.lines) > 0) and ("Have a nice day." in self.lines[-5:]) + + @property + def hirshfeld_charges(self): + """Return the Hirshfeld charges for the chunk.""" + return self._parse_hirshfeld()["charges"] + + @property + def hirshfeld_atomic_dipoles(self): + """Return the Hirshfeld atomic dipole moments for the chunk.""" + return self._parse_hirshfeld()["atomic_dipoles"] + + @property + def hirshfeld_volumes(self): + """Return the Hirshfeld volume for the chunk.""" + return self._parse_hirshfeld()["volumes"] + + @property + def hirshfeld_dipole(self): + """Return the Hirshfeld systematic dipole moment for the chunk.""" + if self.lattice is not None: + return self._parse_hirshfeld()["dipole"] + + return None + + @property + def vbm(self): + """Return the HOMO (VBM) of the calculation.""" + return self._parse_homo_lumo()["vbm"] + + @property + def cbm(self): + """Return the LUMO (CBM) of the calculation.""" + return self._parse_homo_lumo()["cbm"] + + @property + def gap(self): + """Return the HOMO-LUMO gap (band gap) of the calculation.""" + return self._parse_homo_lumo()["gap"] + + @property + def direct_gap(self): + """Return the direct band gap of the calculation.""" + return self._parse_homo_lumo()["direct_gap"] + + +def get_header_chunk(fd): + """Return the header information from the aims.out file.""" + header = [] + line = "" + + # Stop the header once the first SCF cycle begins + while ( + "Convergence: q app. | density | eigen (eV) | Etot (eV)" not in line + and "Begin self-consistency iteration #" not in line + ): + try: + line = next(fd).strip() # Raises StopIteration on empty file + except StopIteration: + raise ParseError("No SCF steps present, calculation failed at setup.") from None + + header.append(line) + return AimsOutHeaderChunk(header) + + +def get_aims_out_chunks(fd, header_chunk): + """Yield unprocessed chunks (header, lines) for each AimsOutChunk image.""" + try: + line = next(fd).strip() # Raises StopIteration on empty file + except StopIteration: + return + + # If the calculation is relaxation the updated structural information + # occurs before the re-initialization + if header_chunk.is_relaxation: + chunk_end_line = "Geometry optimization: Attempting to predict improved coordinates." + else: + chunk_end_line = "Begin self-consistency loop: Re-initialization" + + # If SCF is not converged then do not treat the next chunk_end_line as a + # new chunk until after the SCF is re-initialized + ignore_chunk_end_line = False + while True: + try: + line = next(fd).strip() # Raises StopIteration on empty file + except StopIteration: + break + + lines = [] + while chunk_end_line not in line or ignore_chunk_end_line: + lines.append(line) + # If SCF cycle not converged or numerical stresses are requested, + # don't end chunk on next Re-initialization + patterns = [ + ("Self-consistency cycle not yet converged - restarting mixer to attempt better convergence."), + ( + "Components of the stress tensor (for mathematical " + "background see comments in numerical_stress.f90)." + ), + "Calculation of numerical stress completed", + ] + if any(pattern in line for pattern in patterns): + ignore_chunk_end_line = True + elif "Begin self-consistency loop: Re-initialization" in line: + ignore_chunk_end_line = False + + try: + line = next(fd).strip() + except StopIteration: + break + yield AimsOutCalcChunk(lines, header_chunk) + + +def check_convergence(chunks: list[AimsOutCalcChunk], non_convergence_ok: bool = False) -> bool: + """Check if the aims output file is for a converged calculation. + + Parameters + ---------- + chunks: list[.AimsOutCalcChunk] + The list of chunks for the aims calculations + non_convergence_ok: bool + True if it is okay for the calculation to not be converged + + Returns + ------- + bool + True if the calculation is converged + """ + if not non_convergence_ok and not chunks[-1].converged: + raise ParseError("The calculation did not complete successfully") + return True + + +def read_aims_header_info( + filename: str | Path, +) -> tuple[dict[str, str], dict[str, Any]]: + """Read the FHI-aims header information. + + Parameters + ---------- + filename: str or Path + The file to read + + Returns + ------- + The calculation metadata and the system summary + """ + header_chunk = None + for path in [Path(filename), Path(f"{filename}.gz")]: + if not path.exists(): + continue + if path.suffix == ".gz": + with gzip.open(filename, "rt") as fd: + header_chunk = get_header_chunk(fd) + else: + with open(filename) as fd: + header_chunk = get_header_chunk(fd) + + if header_chunk is None: + raise FileNotFoundError(f"The requested output file {filename} does not exist.") + + system_summary = header_chunk.header_summary + metadata = header_chunk.metadata_summary + return metadata, system_summary + + +def read_aims_output( + filename: str | Path, + index: int | slice = -1, + non_convergence_ok: bool = False, +) -> SiteCollection | Sequence[SiteCollection]: + """Import FHI-aims output files with all data available. + + Includes all structures for relaxations and MD runs with FHI-aims + + Parameters + ---------- + filename: str or Path + The file to read + index: int or slice + The index of the images to read + non_convergence_ok: bool + True if the calculations do not have to be converged + + Returns + ------- + The selected Structure objects + """ + chunks = None + for path in [Path(filename), Path(f"{filename}.gz")]: + if not path.exists(): + continue + if path.suffix == ".gz": + with gzip.open(path, "rt") as fd: + header_chunk = get_header_chunk(fd) + chunks = list(get_aims_out_chunks(fd, header_chunk)) + else: + with open(path) as fd: + header_chunk = get_header_chunk(fd) + chunks = list(get_aims_out_chunks(fd, header_chunk)) + + if chunks is None: + raise FileNotFoundError(f"The requested output file {filename} does not exist.") + + check_convergence(chunks, non_convergence_ok) + + # Relaxations have an additional footer chunk due to how it is split + if header_chunk.is_relaxation: + images = [chunk.structure for chunk in chunks[:-1]] + else: + images = [chunk.structure for chunk in chunks] + return images[index] From 3b152d110985d4b9344e90d3ac890ca4c70e6c42 Mon Sep 17 00:00:00 2001 From: Thomas Purcell Date: Thu, 26 Oct 2023 17:48:42 +0200 Subject: [PATCH 02/30] Initial aims input files 1) remove aims_outputs naming convention 2) Add AimsGeometryIn and AimsControlIn classes --- pymatgen/io/aims/inputs.py | 441 ++++++++++++++++++ .../io/aims/{aims_output.py => output.py} | 0 2 files changed, 441 insertions(+) create mode 100644 pymatgen/io/aims/inputs.py rename pymatgen/io/aims/{aims_output.py => output.py} (100%) diff --git a/pymatgen/io/aims/inputs.py b/pymatgen/io/aims/inputs.py new file mode 100644 index 00000000000..ee70e0bdffc --- /dev/null +++ b/pymatgen/io/aims/inputs.py @@ -0,0 +1,441 @@ +"""Classes for reading/manipulating/writing FHI-aims input files. + +Works for geometry.in and control.in +""" + +from __future__ import annotations + +import time +from copy import deepcopy +from dataclasses import dataclass, field +from pathlib import Path +from typing import TYPE_CHECKING, Any + +import numpy as np +from monty.json import MontyDecoder, MSONable + +from pymatgen.core import Lattice, Structure + +if TYPE_CHECKING: + from collections.abc import Sequence + + +@dataclass +class AimsGeometryIn(MSONable): + """Class representing an aims geometry.in file""" + + _content: str + _structure: Structure + + @classmethod + def from_str(cls, contents: str): + """The contents of the input file + + self.__dict__ + ---------- + contents: str + The content of the string + """ + content_lines = [line.strip() for line in contents.split("\n") if line.strip()[0] != "#"] + + species = [] + coords = [] + is_frac = [] + lattice_vectors = [] + charges_dct = {} + moments_dct = {} + + for line in content_lines: + inp = line.split() + if (inp[0] == "atom") or (inp[0] == "atom_frac"): + coords.append([float(ii) for ii in line.split()[1:4]]) + species.append(inp[4]) + is_frac.append(inp[0] == "atom_frac") + if inp[0] == "lattice_vector": + lattice_vectors.append([float(ii) for ii in line.split()[1:4]]) + if inp[0] == "initial_moment": + charges_dct[len(coords) - 1] = float(inp[1]) + if inp[0] == "initial_charge": + moments_dct[len(coords) - 1] = float(inp[1]) + + charge = np.zeros(len(coords)) + for key, val in charges_dct.items(): + charge[key] = val + + magmom = np.zeros(len(coords)) + for key, val in moments_dct.items(): + magmom[key] = val + + if len(lattice_vectors) == 3: + lattice = Lattice(lattice_vectors) + for cc in range(len(coords)): + if is_frac[cc]: + coords[cc] = lattice.get_cartesian_coords(np.array(coords[cc]).reshape(3, 1)) + elif len(lattice_vectors) == 0: + lattice = None + if any(is_frac): + raise ValueError("Fractional coordinates given in file with no lattice vectors.") + else: + raise ValueError("Incorrect number of lattice vectors passed.") + + structure = Structure( + lattice, + species, + coords, + np.sum(charge), + coords_are_cartesian=True, + site_properties={"magmom": magmom, "charge": charge}, + ) + + return cls(_content="\n".join(content_lines), _structure=structure) + + @classmethod + def from_structure(cls, structure: Structure): + """The contents of the input file + + self.__dict__ + ---------- + structure: Structure + The structure for the file + """ + content_lines = [] + + if structure.lattice is not None: + for lv in structure.lattive.matrix: + content_lines.append(f"lattice_vector {lv[0]: .12e} {lv[1]: .12e} {lv[2]: .12e}") + + charges = structure.site_properties.get("charge", np.zeros(len(structure.species))) + magmoms = structure.site_properties.get("magmom", np.zeros(len(structure.species))) + for species, coord, charge, magmom in zip(structure.species, structure.cart_coords, charges, magmoms): + content_lines.append(f"atom {coord[0]: .12e} {coord[1]: .12e} {coord[2]: .12e} {species}") + if charge != 0: + content_lines.append(f" initial_charge {charge}") + if magmom != 0: + content_lines.append(f" initial_moment {magmom}") + + return cls(_content="\n".join(content_lines), _structure=structure) + + @property + def structure(self) -> Structure: + """Accses structure for the file""" + return self._structure + + @property + def content(self) -> str: + """Accses structure for the file""" + return self._content + + def write_file(self, directory: str | Path | None = None, overwrite: bool = False): + """Writes the geometry.in file + + self.__dict__ + ---------- + directory: str or Path + The directory to write the geometry.in file + overwrite: bool + If True allow to overwrite existing files + """ + if directory is None: + directory = Path.cwd() + + if not overwrite and (Path(directory) / "geometry.in").exists(): + raise ValueError(f"geometry.in file exists in {directory}") + + with open(f"{directory}/geometry.in", "w") as fd: + fd.write("#" + "=" * 72 + "\n") + fd.write(f"# FHI-aims geometry file: {directory}/geometry.in\n") + fd.write("# File generated from pymatgen\n") + fd.write(f"# {time.asctime()}\n") + fd.write(self.content) + + def as_dict(self) -> dict[str, Any]: + """Get a dictionary representation of the geometry.in file. + + Returns + ------- + The dictionary representation of the input file + """ + dct = {} + dct["@module"] = type(self).__module__ + dct["@class"] = type(self).__name__ + dct["content"] = self.content + dct["structure"] = self.structure + return dct + + @classmethod + def from_dict(cls, d: dict[str, Any]): + """Initialize from dictionary. + + self.__dict__ + ---------- + d: dict[str, Any] + The MontyEncoded dictionary + """ + decoded = {k: MontyDecoder().process_decoded(v) for k, v in d.items() if not k.startswith("@")} + + return cls( + content=decoded["content"], + structure=decoded["structure"], + ) + + +ALLOWED_AIMS_CUBE_TYPES = [ + "delta_density", + "spin_density", + "stm", + "total_density", + "total_density_integrable", + "long_range_potential", + "hartree_potential", + "xc_potential", + "delta_v", + "ion_dens", + "dielec_func", + "elf", +] + +ALLOWED_AIMS_CUBE_TYPES_STATE = [ + "first_order_density", + "eigenstate", + "eigenstate_imag", + "eigenstate_density", +] + +ALLOWED_AIMS_CUBE_FORMATS = [ + "cube", + "gOpenMol", + "xsf", +] + + +@dataclass +class AimsCube(MSONable): + """Class representing the FHI-aims cubes + + Parameters + ---------- + type: str + The value to be outputted as a cube file + origin: Sequence[float] | tuple[float, float, float] + The origin of the cube + edges: Sequence[Sequence[float]] + Specifies the edges of a cube: dx, dy, dz + dx (float): The length of the step in the x direction + dy (float): The length of the step in the y direction + dx (float): The length of the step in the x direction + points: Sequence[int] | tuple[int, int, int] + The number of points along each edge + spinstate: int + The spin-channel to use either 1 or 2 + kpoint: int + The k-point to use (the index of the list printed from `output k_point_list`) + filename: str + The filename to use + format: str + The format to output the cube file in: cube, gOpenMol, or xsf + elf_type: int + The type of electron localization function to use (see FHI-aims manual) + """ + + name: str = "AimsCube" + type: str = field(default_factory=str) + origin: Sequence[float] | tuple[float, float, float] = [0.0, 0.0, 0.0] + edges: Sequence[Sequence[float]] = [[0.1, 0.0, 0.0], [0.0, 0.1, 0.0], [0.0, 0.0, 0.1]] + points: Sequence[int] | tuple[int, int, int] = [0, 0, 0] + format: str = "cube" + spinstate: int | None = None + kpoint: int | None = None + filename: str | None = None + elf_type: int | None = None + + def __post_init__(self): + """Check the inputted variables to make sure they are correct""" + split_type = self.type.split() + if split_type[0] in ALLOWED_AIMS_CUBE_TYPES: + if len(split_type) > 1: + msg = f"Cube of type {split_type[0]} can not have a state associated with it" + raise ValueError(msg) + elif split_type[0] in ALLOWED_AIMS_CUBE_TYPES_STATE: + if len(split_type) != 2: + msg = f"Cube of type {split_type[0]} must have a state associated with it" + raise ValueError(msg) + else: + raise ValueError("Cube type undefined") + + if self.format not in ALLOWED_AIMS_CUBE_FORMATS: + raise ValueError("Cube file must have a format of cube, gOpenMol, or xsf") + + if self.spinstate is not None and (self.spinstate not in [1, 2]): + raise ValueError("Spin state must be 1 or 2") + + if len(self.origin) != 3: + raise ValueError("The cube origin must have 3 components") + + if len(self.points) != 3: + raise ValueError("The number of points per edge must have 3 components") + + if len(self.edges) != 3: + raise ValueError("Only three cube edges can be passed") + + for edge in self.edges: + if len(edge) != 3: + raise ValueError("Each cube edge must have 3 components") + + if self.elf_type is not None and self.type != "elf": + raise ValueError("elf_type only used when the cube type is elf") + + @property + def control_block(self): + cb = f"output cube {self.type}\n" + cb += f" cube origin {self.origin}\n" + for ii in range(3): + cb += f" cube edge {self.points[ii]} " + cb += f"{self.edges[ii][0]: .12e} " + cb += f"{self.edges[ii][1]: .12e} " + cb += f"{self.edges[ii][2]: .12e}\n" + cb += f" cube format {self.format}\n" + if self.spinstate is not None: + cb += f" cube spinstate {self.spinstate}\n" + if self.kpoint is not None: + cb += f" cube kpoint {self.kpoint}\n" + if self.filename is not None: + cb += f" cube filename {self.filename}\n" + if self.elf_type is not None: + cb += f" cube elf_type {self.elf_type}\n" + + return cb + + +@dataclass +class AimsControlIn(MSONable): + """Class representing and FHI-aims control.in file""" + + _parameters: dict[str, Any] = field(default_factory=dict) + + def __postinit__(self): + if "output" not in self._parameters: + self._parameters["output"] = [] + + def __getitem__(self, key: str) -> Any: + """Get an attribute of the class""" + if key not in self._parameters: + raise AttributeError(f"{key} not set in AimsControlIn") + return self._parameters[key] + + def __setitem__(self, key: str, value: Any): + """set an attribute of the class""" + if key == "output": + if isinstance(value, str): + value = [value] + self._parameters[key] += value + else: + self._parameters[key] = value + + @property + def parameters(self): + return self._parameters + + @parameters.setter + def parameters(self, parameters: dict[str, Any]): + """reload a control.in inputs from a parameters dictionary""" + self._parameters = parameters + + def get_aims_control_parameter_str(self, key, value, format): + return f"{key :35s}" + (format % value) + "\n" + + def write_file( + self, + structure: Structure, + directory: str | Path | None = None, + verbose_header: bool = False, + overwrite: bool = False, + ): + """Writes the geometry.in file + + Parameters + ---------- + structure: Structure + The structure to write the input file for + directory: str or Path + The directory to write the geometry.in file + verbose_header: bool + If True print the input option dictionary + overwrite: bool + If True allow to overwrite existing files + """ + if directory is None: + directory = Path.cwd() + + if (Path(directory) / "control.in").exists() and not overwrite: + raise ValueError(f"control.in file already in {directory}") + + lim = "#" + "=" * 79 + + parameters = deepcopy(self._parameters) + + with open(f"{directory}/geometry.in", "w") as fd: + fd.write("#" + "=" * 72 + "\n") + fd.write(f"# FHI-aims geometry file: {directory}/geometry.in\n") + fd.write("# File generated from pymatgen\n") + fd.write(f"# {time.asctime()}\n") + fd.write(self.content) + + if parameters["xc"] == "LDA": + parameters["xc"] = "pw-lda" + + cubes = parameters.pop("cubes", None) + + if verbose_header: + fd.write("# \n# List of parameters used to initialize the calculator:") + for p, v in parameters.items(): + s = f"# {p}:{v}\n" + fd.write(s) + fd.write(lim + "\n") + + assert not ("smearing" in parameters and "occupation_type" in parameters) + + for key, value in parameters.items(): + if key in ["species_dir", "plus_u"]: + continue + if key == "smearing": + name = parameters["smearing"][0].lower() + if name == "fermi-dirac": + name = "fermi" + width = parameters["smearing"][1] + if name == "methfessel-paxton": + order = parameters["smearing"][2] + order = " %d" % order + else: + order = "" + + fd.write(self.get_aims_control_parameter_str("occupation_type", (name, width, order), "%s %f%s")) + elif key == "output": + for output_type in value: + fd.write(self.get_aims_control_parameter_str(key, output_type, "%s")) + elif key == "vdw_correction_hirshfeld" and value: + fd.write(self.get_aims_control_parameter_str(key, "", "%s")) + elif isinstance(value, bool): + fd.write(self.get_aims_control_parameter_str(key, str(value).lower(), ".%s.")) + elif isinstance(value, (tuple, list)): + fd.write(self.get_aims_control_parameter_str(key, " ".join([str(x) for x in value]), "%s")) + elif isinstance(value, str): + fd.write(self.get_aims_control_parameter_str(key, value, "%s")) + else: + fd.write(self.get_aims_control_parameter_str(key, value, "%r")) + + if cubes: + for cube in cubes: + fd.write(cube.control_block) + + fd.write(lim + "\n\n") + fd.write(self.get_species_block(structure, self._parameters["species_dir"])) + + def get_species_block(self, structure, species_dir): + """Get the basis set information for a structure""" + sb = "" + species = np.unique(structure.species) + for sp in species: + filename = f"{species_dir}/{sp.Z:02d}_{sp.symbol}_default" + with open(filename) as sf: + sb += "\n".join(sf.readlines()) + return sb diff --git a/pymatgen/io/aims/aims_output.py b/pymatgen/io/aims/output.py similarity index 100% rename from pymatgen/io/aims/aims_output.py rename to pymatgen/io/aims/output.py From e3d1daa40f36e8991db09b227648ee14b8ba8f97 Mon Sep 17 00:00:00 2001 From: Thomas Purcell Date: Fri, 27 Oct 2023 16:09:34 +0200 Subject: [PATCH 03/30] Add test for the aims parsers Adjusted from ASE parser tests --- pymatgen/io/aims/parsers.py | 199 +++-- tests/io/aims/test_aims_parsers.py | 1157 ++++++++++++++++++++++++++++ 2 files changed, 1286 insertions(+), 70 deletions(-) create mode 100644 tests/io/aims/test_aims_parsers.py diff --git a/pymatgen/io/aims/parsers.py b/pymatgen/io/aims/parsers.py index 8480a73c010..6ed25ca5c44 100644 --- a/pymatgen/io/aims/parsers.py +++ b/pymatgen/io/aims/parsers.py @@ -272,7 +272,14 @@ def initial_structure(self): site_properties["magmoms"] = self.initial_magnetic_moments if lattice: - return Structure(lattice, species, coords, np.sum(self.initial_charges), site_properties=site_properties) + return Structure( + lattice, + species, + coords, + np.sum(self.initial_charges), + coords_are_cartesian=True, + site_properties=site_properties, + ) return Molecule(species, coords, np.sum(self.initial_charges), site_properties=site_properties) @@ -325,19 +332,25 @@ def _parse_k_points(self): """Get the list of k-points used in the calculation.""" n_kpts = self.parse_scalar("n_kpts") if n_kpts is None: - return { - "k_points": None, - "k_point_weights": None, - } + self._cache.update( + { + "k_points": None, + "k_point_weights": None, + } + ) + return n_kpts = int(n_kpts) line_start = self.reverse_search_for(["| K-points in task"]) line_end = self.reverse_search_for(["| k-point:"]) if (line_start == LINE_NOT_FOUND) or (line_end == LINE_NOT_FOUND) or (line_end - line_start != n_kpts): - return { - "k_points": None, - "k_point_weights": None, - } + self._cache.update( + { + "k_points": None, + "k_point_weights": None, + } + ) + return k_points = np.zeros((n_kpts, 3)) k_point_weights = np.zeros(n_kpts) @@ -351,7 +364,7 @@ def _parse_k_points(self): "k_point_weights": k_point_weights, } ) - return None + return @property def n_atoms(self) -> int: @@ -486,10 +499,7 @@ def _parse_structure(self): For the given section of the aims output file generate the calculated structure. """ - lattice = self.lattice - velocities = self.velocities - species = self.species - coords = self.coords + species, coords, velocities, lattice = self._parse_lattice_atom_pos() site_properties = dict() if len(velocities) > 0: @@ -512,10 +522,16 @@ def _parse_structure(self): site_properties = None if lattice is not None: - return Structure(lattice, species, coords, site_properties=site_properties, properties=properties) + return Structure( + lattice, + species, + coords, + site_properties=site_properties, + properties=properties, + coords_are_cartesian=True, + ) return Molecule(species, coords, site_properties=site_properties, properties=properties) - @property def _parse_lattice_atom_pos(self) -> tuple[list[str], list[Vector3D], list[Vector3D], Lattice | None]: """Get the lattice of the structure @@ -531,9 +547,9 @@ def _parse_lattice_atom_pos(self) -> tuple[list[str], list[Vector3D], list[Vecto The lattice of the system """ lattice_vectors = [] - velocities = [] - species = [] - coords = [] + velocities: list[Vector3D] = [] + species: list[str] = [] + coords: list[Vector3D] = [] start_keys = [ "Atomic structure (and velocities) as used in the preceding time step", @@ -542,7 +558,12 @@ def _parse_lattice_atom_pos(self) -> tuple[list[str], list[Vector3D], list[Vecto ] line_start = self.reverse_search_for(start_keys) if line_start == LINE_NOT_FOUND: - return self.initial_structure + species = [sp.symbol for sp in self.initial_structure.species] + coords = self.initial_structure.cart_coords.tolist() + velocities = list(self.initial_structure.site_properties.get("velocity", [])) + lattice = self.initial_lattice + + return (species, coords, velocities, lattice) line_start += 1 @@ -560,30 +581,51 @@ def _parse_lattice_atom_pos(self) -> tuple[list[str], list[Vector3D], list[Vecto elif "velocity " in line: velocities.append([float(inp) for inp in line.split()[1:]]) - return species, coords, velocities, Lattice(lattice_vectors) + lattice = Lattice(lattice_vectors) if len(lattice_vectors) == 3 else None + return species, coords, velocities, lattice @property def species(self): if "species" not in self._cache: - self._cache.update(self._parse_lattice_atom_pos()) + ( + self._cache["species"], + self._cache["coords"], + self._cache["velocities"], + self._cache["lattice"], + ) = self._parse_lattice_atom_pos() return self._cache["species"] @property def coords(self): if "coords" not in self._cache: - self._cache.update(self._parse_lattice_atom_pos()) + ( + self._cache["species"], + self._cache["coords"], + self._cache["velocities"], + self._cache["lattice"], + ) = self._parse_lattice_atom_pos() return self._cache["coords"] @property def velocities(self): if "velocities" not in self._cache: - self._cache.update(self._parse_lattice_atom_pos()) + ( + self._cache["species"], + self._cache["coords"], + self._cache["velocities"], + self._cache["lattice"], + ) = self._parse_lattice_atom_pos() return self._cache["velocities"] @property def lattice(self): if "lattice" not in self._cache: - self._cache.update(self._parse_lattice_atom_pos()) + ( + self._cache["species"], + self._cache["coords"], + self._cache["velocities"], + self._cache["lattice"], + ) = self._parse_lattice_atom_pos() return self._cache["lattice"] @property @@ -782,12 +824,12 @@ def results(self): # Properties from the aims.out header @property - def initial_structure(self): + def initial_structure(self) -> Structure | Molecule: """Return the initial structure of the calculation.""" return self._header["initial_structure"] @property - def initial_lattice(self): + def initial_lattice(self) -> Lattice | None: """Return the initial lattice vectors for the structure.""" return self._header["initial_lattice"] @@ -877,7 +919,7 @@ def hirshfeld_volumes(self): @property def hirshfeld_dipole(self): """Return the Hirshfeld systematic dipole moment for the chunk.""" - if self.lattice is not None: + if self.lattice is None: return self._parse_hirshfeld()["dipole"] return None @@ -903,30 +945,39 @@ def direct_gap(self): return self._parse_homo_lumo()["direct_gap"] -def get_header_chunk(fd): +def get_lines(content: str) -> list[str]: + """Get a list of lines from a str or file of content""" + if isinstance(content, str): + return [line.strip() for line in content.split("\n")] + return [line.strip() for line in content.readlines()] + + +def get_header_chunk(content: str) -> AimsOutHeaderChunk: """Return the header information from the aims.out file.""" + lines = get_lines(content) header = [] - line = "" + stopped = False # Stop the header once the first SCF cycle begins - while ( - "Convergence: q app. | density | eigen (eV) | Etot (eV)" not in line - and "Begin self-consistency iteration #" not in line - ): - try: - line = next(fd).strip() # Raises StopIteration on empty file - except StopIteration: - raise ParseError("No SCF steps present, calculation failed at setup.") from None - + for line in lines: header.append(line) + if ( + "Convergence: q app. | density | eigen (eV) | Etot (eV)" not in line + and "Begin self-consistency iteration #" not in line + ): + stopped = True + break + + if not stopped: + raise ParseError("No SCF steps present, calculation failed at setup.") + return AimsOutHeaderChunk(header) -def get_aims_out_chunks(fd, header_chunk): +def get_aims_out_chunks(content, header_chunk): """Yield unprocessed chunks (header, lines) for each AimsOutChunk image.""" - try: - line = next(fd).strip() # Raises StopIteration on empty file - except StopIteration: + lines = filter(lambda x: x not in header_chunk.lines, get_lines(content)) + if len(lines) == 0: return # If the calculation is relaxation the updated structural information @@ -939,15 +990,16 @@ def get_aims_out_chunks(fd, header_chunk): # If SCF is not converged then do not treat the next chunk_end_line as a # new chunk until after the SCF is re-initialized ignore_chunk_end_line = False + line_iter = lines.__iter__() while True: try: - line = next(fd).strip() # Raises StopIteration on empty file + line = next(line_iter).strip() # Raises StopIteration on empty file except StopIteration: break - lines = [] + chunk_lines = [] while chunk_end_line not in line or ignore_chunk_end_line: - lines.append(line) + chunk_lines.append(line) # If SCF cycle not converged or numerical stresses are requested, # don't end chunk on next Re-initialization patterns = [ @@ -964,10 +1016,10 @@ def get_aims_out_chunks(fd, header_chunk): ignore_chunk_end_line = False try: - line = next(fd).strip() + line = next(line_iter).strip() except StopIteration: break - yield AimsOutCalcChunk(lines, header_chunk) + yield AimsOutCalcChunk(chunk_lines, header_chunk) def check_convergence(chunks: list[AimsOutCalcChunk], non_convergence_ok: bool = False) -> bool: @@ -990,6 +1042,11 @@ def check_convergence(chunks: list[AimsOutCalcChunk], non_convergence_ok: bool = return True +def read_aims_header_info_from_content(content: str) -> tuple[dict[str, str], dict[str, Any]]: + header_chunk = get_header_chunk(content) + return header_chunk.metadata_summary, header_chunk.header_summary + + def read_aims_header_info( filename: str | Path, ) -> tuple[dict[str, str], dict[str, Any]]: @@ -1004,23 +1061,34 @@ def read_aims_header_info( ------- The calculation metadata and the system summary """ - header_chunk = None + content = None for path in [Path(filename), Path(f"{filename}.gz")]: if not path.exists(): continue if path.suffix == ".gz": with gzip.open(filename, "rt") as fd: - header_chunk = get_header_chunk(fd) + content = fd.read() else: with open(filename) as fd: - header_chunk = get_header_chunk(fd) + content = fd.read() - if header_chunk is None: + if content is None: raise FileNotFoundError(f"The requested output file {filename} does not exist.") - system_summary = header_chunk.header_summary - metadata = header_chunk.metadata_summary - return metadata, system_summary + return read_aims_header_info_from_content(content) + + +def read_aims_output_from_content( + content: str, index: int | slice = -1, non_convergence_ok: bool = False +) -> SiteCollection | Sequence[SiteCollection]: + """Read and aims output file from the content of a file""" + header_chunk = get_header_chunk(content) + chunks = list(get_aims_out_chunks(content, header_chunk)) + + check_convergence(chunks, non_convergence_ok) + # Relaxations have an additional footer chunk due to how it is split + images = [chunk.atoms for chunk in chunks[:-1]] if header_chunk.is_relaxation else [chunk.atoms for chunk in chunks] + return images[index] def read_aims_output( @@ -1043,29 +1111,20 @@ def read_aims_output( Returns ------- - The selected Structure objects + The selected atoms """ - chunks = None + content = None for path in [Path(filename), Path(f"{filename}.gz")]: if not path.exists(): continue if path.suffix == ".gz": with gzip.open(path, "rt") as fd: - header_chunk = get_header_chunk(fd) - chunks = list(get_aims_out_chunks(fd, header_chunk)) + content = fd.read() else: with open(path) as fd: - header_chunk = get_header_chunk(fd) - chunks = list(get_aims_out_chunks(fd, header_chunk)) + content = fd.read() - if chunks is None: + if content is None: raise FileNotFoundError(f"The requested output file {filename} does not exist.") - check_convergence(chunks, non_convergence_ok) - - # Relaxations have an additional footer chunk due to how it is split - if header_chunk.is_relaxation: - images = [chunk.structure for chunk in chunks[:-1]] - else: - images = [chunk.structure for chunk in chunks] - return images[index] + return read_aims_output_from_content(content, index, non_convergence_ok) diff --git a/tests/io/aims/test_aims_parsers.py b/tests/io/aims/test_aims_parsers.py new file mode 100644 index 00000000000..a192c614cb0 --- /dev/null +++ b/tests/io/aims/test_aims_parsers.py @@ -0,0 +1,1157 @@ +# flake8: noqa +import numpy as np +from ase.io import read +from pymatgen.io.aims.parsers import ( + AimsParseError, + AimsOutChunk, + AimsOutHeaderChunk, + AimsOutCalcChunk, + EV_PER_A3_TO_KBAR, + LINE_NOT_FOUND, +) + +from ase.stress import full_3x3_to_voigt_6_stress + +from numpy.linalg import norm + +import pytest + +eps_hp = 1e-15 # The espsilon value used to compare numbers that are high-precision +eps_lp = 1e-7 # The espsilon value used to compare numbers that are low-precision + + +@pytest.fixture +def default_chunk(): + lines = ["TEST", "A", "TEST", "| Number of atoms: 200 atoms"] + return AimsOutChunk(lines) + + +def test_reverse_search_for(default_chunk): + assert default_chunk.reverse_search_for(["TEST"]) == 2 + assert default_chunk.reverse_search_for(["TEST"], 1) == 2 + + assert default_chunk.reverse_search_for(["TEST A"]) == LINE_NOT_FOUND + + assert default_chunk.reverse_search_for(["A"]) == 1 + assert default_chunk.reverse_search_for(["A"], 2) == LINE_NOT_FOUND + + +def test_search_for_all(default_chunk): + assert default_chunk.search_for_all("TEST") == [0, 2] + assert default_chunk.search_for_all("TEST", 0, 1) == [0] + assert default_chunk.search_for_all("TEST", 1, -1) == [2] + + +def test_search_parse_scalar(default_chunk): + assert default_chunk.parse_scalar("n_atoms") == 200 + assert default_chunk.parse_scalar("n_electrons") is None + + +@pytest.fixture +def empty_header_chunk(): + return AimsOutHeaderChunk([]) + + +@pytest.mark.parametrize( + "attrname", + [ + "n_atoms", + "n_bands", + "n_electrons", + "n_spins", + "initial_structure", + ], +) +def test_missing_parameter(attrname, empty_header_chunk): + with pytest.raises(AimsParseError, match="No information about"): + getattr(empty_header_chunk, attrname) + + +def test_default_header_electronic_temperature(empty_header_chunk): + assert empty_header_chunk.electronic_temperature == 0.1 + + +# def test_default_header_constraints(empty_header_chunk): +# assert empty_header_chunk.constraints == [] + + +def test_default_header_initial_lattice(empty_header_chunk): + assert empty_header_chunk.initial_lattice is None + + +def test_default_header_is_md(empty_header_chunk): + assert not empty_header_chunk.is_md + + +def test_default_header_is_relaxation(empty_header_chunk): + assert not empty_header_chunk.is_relaxation + + +def test_default_header_n_k_points(empty_header_chunk): + assert empty_header_chunk.n_k_points is None + + +def test_default_header_k_points(empty_header_chunk): + assert empty_header_chunk.k_points is None + + +def test_default_header_k_point_weights(empty_header_chunk): + assert empty_header_chunk.k_point_weights is None + + +@pytest.fixture +def initial_lattice(): + return np.array( + [ + [1.00000000, 2.70300000, 3.70300000], + [4.70300000, 2.00000000, 6.70300000], + [8.70300000, 7.70300000, 3.00000000], + ] + ) + + +@pytest.fixture +def initial_positions(): + return (np.array([[0.000, 1.000, 2.000], [2.703, 3.703, 4.703]]),) + + +@pytest.fixture +def header_chunk(): + lines = """ + | Number of atoms : 2 + | Number of Kohn-Sham states (occupied + empty): 3 + The structure contains 2 atoms, and a total of 28.000 electrons. + | Number of spin channels : 2 + Occupation type: Gaussian broadening, width = 0.500000E-01 eV. + Found relaxation constraint for atom 1: x coordinate fixed. + Found relaxation constraint for atom 1: y coordinate fixed. + Found relaxation constraint for atom 2: All coordinates fixed. + Input geometry: + | Unit cell: + | 1.00000000 2.70300000 3.70300000 + | 4.70300000 2.00000000 6.70300000 + | 8.70300000 7.70300000 3.00000000 + | Atomic structure: + | Atom x [A] y [A] z [A] + | 1: Species Na 0.00000000 1.00000000 2.00000000 + | 2: Species Cl 2.70300000 3.70300000 4.70300000 + Initializing the k-points + Using symmetry for reducing the k-points + | k-points reduced from: 8 to 8 + | Number of k-points : 8 + The eigenvectors in the calculations are REAL. + | K-points in task 0: 2 + | K-points in task 1: 2 + | K-points in task 2: 2 + | K-points in task 3: 2 + | k-point: 1 at 0.000000 0.000000 0.000000 , weight: 0.12500000 + | k-point: 2 at 0.000000 0.000000 0.500000 , weight: 0.12500000 + | k-point: 3 at 0.000000 0.500000 0.000000 , weight: 0.12500000 + | k-point: 4 at 0.000000 0.500000 0.500000 , weight: 0.12500000 + | k-point: 5 at 0.500000 0.000000 0.000000 , weight: 0.12500000 + | k-point: 6 at 0.500000 0.000000 0.500000 , weight: 0.12500000 + | k-point: 7 at 0.500000 0.500000 0.000000 , weight: 0.12500000 + | k-point: 8 at 0.500000 0.500000 0.500000 , weight: 0.12500000 + Geometry relaxation: A file "geometry.in.next_step" is written out by default after each step. + Complete information for previous time-step: + """ + lines = lines.splitlines() + for ll, line in enumerate(lines): + lines[ll] = line.strip() + + return AimsOutHeaderChunk(lines) + + +def test_header_n_atoms(header_chunk): + assert header_chunk.n_atoms == 2 + + +def test_header_n_bands(header_chunk): + assert header_chunk.n_bands == 3 + + +def test_header_n_electrons(header_chunk): + assert header_chunk.n_electrons == 28 + + +def test_header_n_spins(header_chunk): + assert header_chunk.n_spins == 2 + + +def test_header_initial_structure(header_chunk, initial_lattice, initial_positions): + assert len(header_chunk.initial_structure) == 2 + assert np.allclose( + header_chunk.initial_structure.lattice.matrix, + initial_lattice, + ) + assert np.allclose(header_chunk.initial_structure.cart_coords, initial_positions) + assert np.all(["Na", "Cl"] == [sp.symbol for sp in header_chunk.initial_structure.species]) + + +def test_header_initial_lattice(header_chunk, initial_lattice): + assert np.allclose(header_chunk.initial_lattice.matrix, initial_lattice) + + +def test_header_electronic_temperature(header_chunk): + assert header_chunk.electronic_temperature == 0.05 + + +def test_header_is_md(header_chunk): + assert header_chunk.is_md + + +def test_header_is_relaxation(header_chunk): + assert header_chunk.is_relaxation + + +def test_header_n_k_points(header_chunk): + assert header_chunk.n_k_points == 8 + + +@pytest.fixture +def k_points(): + return np.array( + [ + [0.000, 0.000, 0.000], + [0.000, 0.000, 0.500], + [0.000, 0.500, 0.000], + [0.000, 0.500, 0.500], + [0.500, 0.000, 0.000], + [0.500, 0.000, 0.500], + [0.500, 0.500, 0.000], + [0.500, 0.500, 0.500], + ] + ) + + +@pytest.fixture +def k_point_weights(): + return np.full((8), 0.125) + + +def test_header_k_point_weights(header_chunk, k_point_weights): + assert np.allclose(header_chunk.k_point_weights, k_point_weights) + + +def test_header_k_points(header_chunk, k_points): + assert np.allclose(header_chunk.k_points, k_points) + + +def test_header_header_summary(header_chunk, k_points, k_point_weights): + header_summary = { + "initial_structure": header_chunk.initial_structure, + "initial_lattice": header_chunk.initial_lattice, + # "constraints": header_chunk.constraints, + "is_relaxation": True, + "is_md": True, + "n_atoms": 2, + "n_bands": 3, + "n_electrons": 28, + "n_spins": 2, + "electronic_temperature": 0.05, + "n_k_points": 8, + "k_points": k_points, + "k_point_weights": k_point_weights, + } + for key, val in header_chunk.header_summary.items(): + # if key == "constraints": + # continue + if isinstance(val, np.ndarray): + assert np.allclose(val, header_summary[key]) + else: + assert val == header_summary[key] + + +@pytest.fixture +def empty_calc_chunk(header_chunk): + return AimsOutCalcChunk([], header_chunk) + + +def test_header_transfer_n_atoms(empty_calc_chunk): + assert empty_calc_chunk.n_atoms == 2 + + +def test_header_transfer_n_bands(empty_calc_chunk): + assert empty_calc_chunk.n_bands == 3 + + +def test_header_transfer_n_electrons(empty_calc_chunk): + assert empty_calc_chunk.n_electrons == 28 + + +def test_header_transfer_n_spins(empty_calc_chunk): + assert empty_calc_chunk.n_spins == 2 + + +def test_header_transfer_initial_lattice(empty_calc_chunk, initial_lattice): + assert np.allclose(empty_calc_chunk.initial_lattice.matrix, initial_lattice) + + +def test_header_transfer_initial_structure(empty_calc_chunk, initial_lattice, initial_positions): + assert np.allclose(empty_calc_chunk.initial_structure.lattice.matrix, empty_calc_chunk.initial_lattice.matrix) + assert len(empty_calc_chunk.initial_structure) == 2 + assert np.allclose(empty_calc_chunk.initial_structure.lattice.matrix, initial_lattice) + assert np.allclose(empty_calc_chunk.initial_structure.cart_coords, initial_positions) + assert np.all(["Na", "Cl"] == [sp.symbol for sp in empty_calc_chunk.initial_structure.species]) + + +def test_header_transfer_electronic_temperature(empty_calc_chunk): + assert empty_calc_chunk.electronic_temperature == 0.05 + + +def test_header_transfer_n_k_points(empty_calc_chunk): + assert empty_calc_chunk.n_k_points == 8 + + +def test_header_transfer_k_point_weights(empty_calc_chunk, k_point_weights): + assert np.allclose(empty_calc_chunk.k_point_weights, k_point_weights) + + +def test_header_transfer_k_points(empty_calc_chunk, k_points): + assert np.allclose(empty_calc_chunk.k_points, k_points) + + +def test_default_calc_energy_raises_error(empty_calc_chunk): + with pytest.raises(AimsParseError, match="No energy is associated with the structure."): + getattr(empty_calc_chunk, "energy") + + +@pytest.mark.parametrize( + "attrname", + [ + "forces", + "stresses", + "stress", + "free_energy", + "n_iter", + "magmom", + "E_f", + "dipole", + "hirshfeld_charges", + "hirshfeld_volumes", + "hirshfeld_atomic_dipoles", + "hirshfeld_dipole", + ], +) +def test_chunk_defaults_none(attrname, empty_calc_chunk): + assert getattr(empty_calc_chunk, attrname) is None + + +def test_default_calc_is_metallic(empty_calc_chunk): + assert not empty_calc_chunk.is_metallic + + +def test_default_calc_converged(empty_calc_chunk): + assert not empty_calc_chunk.converged + + +@pytest.fixture +def calc_chunk(header_chunk): + lines = """ + | Number of self-consistency cycles : 58 + | N = N_up - N_down (sum over all k points): 0.00000 + | Chemical potential (Fermi level): -8.24271207 eV + Total atomic forces (unitary forces were cleaned, then relaxation constraints were applied) [eV/Ang]: + | 1 1.000000000000000E+00 2.000000000000000E+00 3.000000000000000E+00 + | 2 6.000000000000000E+00 5.000000000000000E+00 4.000000000000000E+00 + - Per atom stress (eV) used for heat flux calculation: + Atom | Stress components (1,1), (2,2), (3,3), (1,2), (1,3), (2,3) + ------------------------------------------------------------------- + 1 | -1.0000000000E+01 -2.0000000000E+01 -3.0000000000E+01 -4.0000000000E+01 -5.0000000000E+01 -6.0000000000E+01 + 2 | 1.0000000000E+01 2.0000000000E+01 3.0000000000E+01 4.0000000000E+01 5.0000000000E+01 6.0000000000E+01 + ------------------------------------------------------------------- + +-------------------------------------------------------------------+ + | Analytical stress tensor - Symmetrized | + | Cartesian components [eV/A**3] | + +-------------------------------------------------------------------+ + | x y z | + | | + | x 1.00000000 2.00000000 3.00000000 | + | y 2.00000000 5.00000000 6.00000000 | + | z 3.00000000 6.00000000 7.00000000 | + | | + | Pressure: 0.00383825 [eV/A**3] | + | | + +-------------------------------------------------------------------+ + Energy and forces in a compact form: + | Total energy uncorrected : -0.169503986610555E+05 eV + | Total energy corrected : -2.169503986610555E+05 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -3.169503986610555E+05 eV + Performing Hirshfeld analysis of fragment charges and moments. + ---------------------------------------------------------------------- + | Atom 1: Na + | Hirshfeld charge : 0.20898543 + | Free atom volume : 82.26734086 + | Hirshfeld volume : 73.39467444 + | Hirshfeld spin moment : 0.00000000 + | Hirshfeld dipole vector : 0.00000000 0.00000000 -0.00000000 + | Hirshfeld dipole moment : 0.00000000 + | Hirshfeld second moments: 0.19955428 0.00000002 0.00000002 + | 0.00000002 0.19955473 -0.00000005 + | 0.00000002 -0.00000005 0.19955473 + ---------------------------------------------------------------------- + | Atom 2: Cl + | Hirshfeld charge : -0.20840994 + | Free atom volume : 65.62593663 + | Hirshfeld volume : 62.86011074 + | Hirshfeld spin moment : 0.00000000 + | Hirshfeld dipole vector : 0.00000000 0.00000000 0.00000000 + | Hirshfeld dipole moment : 0.00000000 + | Hirshfeld second moments: 0.01482616 -0.00000001 -0.00000001 + | -0.00000001 0.01482641 0.00000001 + | -0.00000001 0.00000001 0.01482641 + ---------------------------------------------------------------------- + Writing Kohn-Sham eigenvalues. + + Spin-up eigenvalues: + K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + + State Occupation Eigenvalue [Ha] Eigenvalue [eV] + 1 1 0.036749 1.000000 + 2 1 0.183747 5.000000 + 3 0 0.330744 9.000000 + + Spin-down eigenvalues: + K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + + State Occupation Eigenvalue [Ha] Eigenvalue [eV] + 1 1 0.110248 3.000000 + 2 1 0.257245 7.000000 + 3 0 0.404243 11.000000 + + + Spin-up eigenvalues: + K-point: 2 at 0.000000 0.000000 0.500000 (in units of recip. lattice) + + State Occupation Eigenvalue [Ha] Eigenvalue [eV] + 1 1 0.477741 13.000000 + 2 1 0.624739 17.000000 + 3 0 0.771736 21.000000 + + Spin-down eigenvalues: + K-point: 2 at 0.000000 0.000000 0.500000 (in units of recip. lattice) + + State Occupation Eigenvalue [Ha] Eigenvalue [eV] + 1 1 0.551240 15.000000 + 2 1 0.698237 19.000000 + 3 0 0.845234 23.000000 + + + Spin-up eigenvalues: + K-point: 3 at 0.000000 0.500000 0.000000 (in units of recip. lattice) + + State Occupation Eigenvalue [Ha] Eigenvalue [eV] + 1 1 0.918733 25.000000 + 2 1 1.065730 29.000000 + 3 0 1.212728 33.000000 + + Spin-down eigenvalues: + K-point: 3 at 0.000000 0.500000 0.000000 (in units of recip. lattice) + + State Occupation Eigenvalue [Ha] Eigenvalue [eV] + 1 1 0.992232 27.000000 + 2 1 1.139229 31.000000 + 3 0 1.286226 35.000000 + + + Spin-up eigenvalues: + K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) + + State Occupation Eigenvalue [Ha] Eigenvalue [eV] + 1 1 1.359725 37.000000 + 2 1 1.506722 41.000000 + 3 0 1.653720 45.000000 + + Spin-down eigenvalues: + K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) + + State Occupation Eigenvalue [Ha] Eigenvalue [eV] + 1 1 1.433224 39.000000 + 2 1 1.580221 43.000000 + 3 0 1.727218 47.000000 + + + Spin-up eigenvalues: + K-point: 5 at 0.500000 0.000000 0.000000 (in units of recip. lattice) + + State Occupation Eigenvalue [Ha] Eigenvalue [eV] + 1 1 1.800717 49.000000 + 2 1 1.947714 53.000000 + 3 0 2.094711 57.000000 + + Spin-down eigenvalues: + K-point: 5 at 0.500000 0.000000 0.000000 (in units of recip. lattice) + + State Occupation Eigenvalue [Ha] Eigenvalue [eV] + 1 1 1.874216 51.000000 + 2 1 2.021213 55.000000 + 3 0 2.168210 59.000000 + + + Spin-up eigenvalues: + K-point: 6 at 0.500000 0.000000 0.500000 (in units of recip. lattice) + + State Occupation Eigenvalue [Ha] Eigenvalue [eV] + 1 1 2.241709 61.000000 + 2 1 2.388706 65.000000 + 3 0 2.535703 69.000000 + + Spin-down eigenvalues: + K-point: 6 at 0.500000 0.000000 0.500000 (in units of recip. lattice) + + State Occupation Eigenvalue [Ha] Eigenvalue [eV] + 1 1 2.315207 63.000000 + 2 1 2.462205 67.000000 + 3 0 2.609202 71.000000 + + + Spin-up eigenvalues: + K-point: 7 at 0.500000 0.500000 0.000000 (in units of recip. lattice) + + State Occupation Eigenvalue [Ha] Eigenvalue [eV] + 1 1 2.682701 73.000000 + 2 1 2.829698 77.000000 + 3 0 2.976695 81.000000 + + Spin-down eigenvalues: + K-point: 7 at 0.500000 0.500000 0.000000 (in units of recip. lattice) + + State Occupation Eigenvalue [Ha] Eigenvalue [eV] + 1 1 2.756199 75.000000 + 2 1 2.903197 79.000000 + 3 0 3.050194 83.000000 + + + Spin-up eigenvalues: + K-point: 8 at 0.500000 0.500000 0.500000 (in units of recip. lattice) + + State Occupation Eigenvalue [Ha] Eigenvalue [eV] + 1 1 3.123693 85.000000 + 2 1 3.270690 89.000000 + 3 0 3.417687 93.000000 + + Spin-down eigenvalues: + K-point: 8 at 0.500000 0.500000 0.500000 (in units of recip. lattice) + + State Occupation Eigenvalue [Ha] Eigenvalue [eV] + 1 1 3.197191 87.000000 + 2 1 3.344189 91.000000 + 3 0 3.491186 95.000000 + + Current spin moment of the entire structure : + | N = N_up - N_down (sum over all k points): 0.00000 + | S (sum over all k points) : 0.00000 + + What follows are estimated values for band gap, HOMO, LUMO, etc. + | They are estimated on a discrete k-point grid and not necessarily exact. + | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. + + Highest occupied state (VBM) at -8.19345940 eV (relative to internal zero) + | Occupation number: 1.00000000 + | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + | Spin channel: 1 + + Lowest unoccupied state (CBM) at -3.62542909 eV (relative to internal zero) + | Occupation number: 0.00000000 + | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + | Spin channel: 1 + + ESTIMATED overall HOMO-LUMO gap: 4.56803031 eV between HOMO at k-point 1 and LUMO at k-point 1 + | This appears to be a direct band gap. + The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid + this system is most likely an insulator or a semiconductor. + | Chemical Potential : -7.44914181 eV + + Self-consistency cycle converged. + material is metallic within the approximate finite broadening function (occupation_type) + Have a nice day. + ------------------------------------------------------------ + """ + lines = lines.splitlines() + for ll, line in enumerate(lines): + lines[ll] = line.strip() + return AimsOutCalcChunk(lines, header_chunk) + + +@pytest.fixture +def numerical_stress_chunk(header_chunk): + lines = """ + | Number of self-consistency cycles : 58 + | N = N_up - N_down (sum over all k points): 0.00000 + | Chemical potential (Fermi level): -8.24271207 eV + Total atomic forces (unitary forces were cleaned, then relaxation constraints were applied) [eV/Ang]: + | 1 1.000000000000000E+00 2.000000000000000E+00 3.000000000000000E+00 + | 2 6.000000000000000E+00 5.000000000000000E+00 4.000000000000000E+00 + - Per atom stress (eV) used for heat flux calculation: + Atom | Stress components (1,1), (2,2), (3,3), (1,2), (1,3), (2,3) + ------------------------------------------------------------------- + 1 | -1.0000000000E+01 -2.0000000000E+01 -3.0000000000E+01 -4.0000000000E+01 -5.0000000000E+01 -6.0000000000E+01 + 2 | 1.0000000000E+01 2.0000000000E+01 3.0000000000E+01 4.0000000000E+01 5.0000000000E+01 6.0000000000E+01 + ------------------------------------------------------------------- + +-------------------------------------------------------------------+ + | Numerical stress tensor | + | Cartesian components [eV/A**3] | + +-------------------------------------------------------------------+ + | x y z | + | | + | x 1.00000000 2.00000000 3.00000000 | + | y 2.00000000 5.00000000 6.00000000 | + | z 3.00000000 6.00000000 7.00000000 | + | | + | Pressure: 0.00383825 [eV/A**3] | + | | + +-------------------------------------------------------------------+ + Energy and forces in a compact form: + | Total energy uncorrected : -0.169503986610555E+05 eV + | Total energy corrected : -2.169503986610555E+05 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -3.169503986610555E+05 eV + + Writing Kohn-Sham eigenvalues. + + Spin-up eigenvalues: + K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + + State Occupation Eigenvalue [Ha] Eigenvalue [eV] + 1 1 0.036749 1.000000 + 2 1 0.183747 5.000000 + 3 0 0.330744 9.000000 + + Spin-down eigenvalues: + K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + + State Occupation Eigenvalue [Ha] Eigenvalue [eV] + 1 1 0.110248 3.000000 + 2 1 0.257245 7.000000 + 3 0 0.404243 11.000000 + + + Spin-up eigenvalues: + K-point: 2 at 0.000000 0.000000 0.500000 (in units of recip. lattice) + + State Occupation Eigenvalue [Ha] Eigenvalue [eV] + 1 1 0.477741 13.000000 + 2 1 0.624739 17.000000 + 3 0 0.771736 21.000000 + + Spin-down eigenvalues: + K-point: 2 at 0.000000 0.000000 0.500000 (in units of recip. lattice) + + State Occupation Eigenvalue [Ha] Eigenvalue [eV] + 1 1 0.551240 15.000000 + 2 1 0.698237 19.000000 + 3 0 0.845234 23.000000 + + + Spin-up eigenvalues: + K-point: 3 at 0.000000 0.500000 0.000000 (in units of recip. lattice) + + State Occupation Eigenvalue [Ha] Eigenvalue [eV] + 1 1 0.918733 25.000000 + 2 1 1.065730 29.000000 + 3 0 1.212728 33.000000 + + Spin-down eigenvalues: + K-point: 3 at 0.000000 0.500000 0.000000 (in units of recip. lattice) + + State Occupation Eigenvalue [Ha] Eigenvalue [eV] + 1 1 0.992232 27.000000 + 2 1 1.139229 31.000000 + 3 0 1.286226 35.000000 + + + Spin-up eigenvalues: + K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) + + State Occupation Eigenvalue [Ha] Eigenvalue [eV] + 1 1 1.359725 37.000000 + 2 1 1.506722 41.000000 + 3 0 1.653720 45.000000 + + Spin-down eigenvalues: + K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) + + State Occupation Eigenvalue [Ha] Eigenvalue [eV] + 1 1 1.433224 39.000000 + 2 1 1.580221 43.000000 + 3 0 1.727218 47.000000 + + + Spin-up eigenvalues: + K-point: 5 at 0.500000 0.000000 0.000000 (in units of recip. lattice) + + State Occupation Eigenvalue [Ha] Eigenvalue [eV] + 1 1 1.800717 49.000000 + 2 1 1.947714 53.000000 + 3 0 2.094711 57.000000 + + Spin-down eigenvalues: + K-point: 5 at 0.500000 0.000000 0.000000 (in units of recip. lattice) + + State Occupation Eigenvalue [Ha] Eigenvalue [eV] + 1 1 1.874216 51.000000 + 2 1 2.021213 55.000000 + 3 0 2.168210 59.000000 + + + Spin-up eigenvalues: + K-point: 6 at 0.500000 0.000000 0.500000 (in units of recip. lattice) + + State Occupation Eigenvalue [Ha] Eigenvalue [eV] + 1 1 2.241709 61.000000 + 2 1 2.388706 65.000000 + 3 0 2.535703 69.000000 + + Spin-down eigenvalues: + K-point: 6 at 0.500000 0.000000 0.500000 (in units of recip. lattice) + + State Occupation Eigenvalue [Ha] Eigenvalue [eV] + 1 1 2.315207 63.000000 + 2 1 2.462205 67.000000 + 3 0 2.609202 71.000000 + + + Spin-up eigenvalues: + K-point: 7 at 0.500000 0.500000 0.000000 (in units of recip. lattice) + + State Occupation Eigenvalue [Ha] Eigenvalue [eV] + 1 1 2.682701 73.000000 + 2 1 2.829698 77.000000 + 3 0 2.976695 81.000000 + + Spin-down eigenvalues: + K-point: 7 at 0.500000 0.500000 0.000000 (in units of recip. lattice) + + State Occupation Eigenvalue [Ha] Eigenvalue [eV] + 1 1 2.756199 75.000000 + 2 1 2.903197 79.000000 + 3 0 3.050194 83.000000 + + + Spin-up eigenvalues: + K-point: 8 at 0.500000 0.500000 0.500000 (in units of recip. lattice) + + State Occupation Eigenvalue [Ha] Eigenvalue [eV] + 1 1 3.123693 85.000000 + 2 1 3.270690 89.000000 + 3 0 3.417687 93.000000 + + Spin-down eigenvalues: + K-point: 8 at 0.500000 0.500000 0.500000 (in units of recip. lattice) + + State Occupation Eigenvalue [Ha] Eigenvalue [eV] + 1 1 3.197191 87.000000 + 2 1 3.344189 91.000000 + 3 0 3.491186 95.000000 + + Current spin moment of the entire structure : + | N = N_up - N_down (sum over all k points): 0.00000 + | S (sum over all k points) : 0.00000 + + What follows are estimated values for band gap, HOMO, LUMO, etc. + | They are estimated on a discrete k-point grid and not necessarily exact. + | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. + + Highest occupied state (VBM) at -8.19345940 eV (relative to internal zero) + | Occupation number: 1.00000000 + | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + | Spin channel: 1 + + Lowest unoccupied state (CBM) at -3.62542909 eV (relative to internal zero) + | Occupation number: 0.00000000 + | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + | Spin channel: 1 + + ESTIMATED overall HOMO-LUMO gap: 4.56803031 eV between HOMO at k-point 1 and LUMO at k-point 1 + | This appears to be a direct band gap. + The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid + this system is most likely an insulator or a semiconductor. + | Chemical Potential : -7.44914181 eV + + Self-consistency cycle converged. + material is metallic within the approximate finite broadening function (occupation_type) + Have a nice day. + ------------------------------------------------------------ + """ + lines = lines.splitlines() + for ll, line in enumerate(lines): + lines[ll] = line.strip() + return AimsOutCalcChunk(lines, header_chunk) + + +def test_calc_structure(calc_chunk, initial_lattice, initial_positions): + assert len(calc_chunk.structure.species) == 2 + assert np.allclose(calc_chunk.structure.lattice.matrix, initial_lattice) + assert np.allclose(calc_chunk.structure.cart_coords, initial_positions) + assert np.all(["Na", "Cl"] == [sp.symbol for sp in calc_chunk.structure.species]) + + +def test_calc_forces(calc_chunk): + forces = np.array([[1.0, 2.0, 3.0], [6.0, 5.0, 4.0]]) + assert np.allclose(calc_chunk.forces, forces) + + # Different because of the constraints + assert np.allclose(calc_chunk.structure.site_properties["force"], forces) + assert np.allclose(calc_chunk.results["forces"], forces) + + +def test_calc_stresses(calc_chunk): + stresses = EV_PER_A3_TO_KBAR * np.array( + [ + [-10.0, -20.0, -30.0, -60.0, -50.0, -40.0], + [10.0, 20.0, 30.0, 60.0, 50.0, 40.0], + ] + ) + assert np.allclose(calc_chunk.stresses, stresses) + assert np.allclose(calc_chunk.structure.site_properties["atomic_virial_stress"], stresses) + assert np.allclose(calc_chunk.results["stresses"], stresses) + + +def test_calc_stress(calc_chunk): + stress = EV_PER_A3_TO_KBAR * full_3x3_to_voigt_6_stress( + np.array( + [ + [1.00000000, 2.00000000, 3.00000000], + [2.00000000, 5.00000000, 6.00000000], + [3.00000000, 6.00000000, 7.00000000], + ] + ) + ) + assert np.allclose(calc_chunk.stress, stress) + assert np.allclose(calc_chunk.structure.properties["stress"], stress) + assert np.allclose(calc_chunk.results["stress"], stress) + + +def test_calc_num_stress(numerical_stress_chunk): + stress = EV_PER_A3_TO_KBAR * full_3x3_to_voigt_6_stress( + np.array( + [ + [1.00000000, 2.00000000, 3.00000000], + [2.00000000, 5.00000000, 6.00000000], + [3.00000000, 6.00000000, 7.00000000], + ] + ) + ) + assert np.allclose(numerical_stress_chunk.stress, stress) + assert np.allclose(numerical_stress_chunk.structure.properties["stress"], stress) + assert np.allclose(numerical_stress_chunk.results["stress"], stress) + + +def test_calc_free_energy(calc_chunk): + free_energy = -3.169503986610555e05 + assert np.abs(calc_chunk.free_energy - free_energy) < eps_hp + assert np.abs(calc_chunk.structure.properties["free_energy"] - free_energy) < eps_hp + assert np.abs(calc_chunk.results["free_energy"] - free_energy) < eps_hp + + +def test_calc_energy(calc_chunk): + energy = -2.169503986610555e05 + assert np.abs(calc_chunk.energy - energy) < eps_hp + assert np.abs(calc_chunk.structure.properties["energy"] - energy) < eps_hp + assert np.abs(calc_chunk.results["energy"] - energy) < eps_hp + + +def test_calc_magnetic_moment(calc_chunk): + magmom = 0 + assert calc_chunk.magmom == magmom + assert calc_chunk.structure.properties["magmom"] == magmom + assert calc_chunk.results["magmom"] == magmom + + +def test_calc_n_iter(calc_chunk): + n_iter = 58 + assert calc_chunk.n_iter == n_iter + assert calc_chunk.results["n_iter"] == n_iter + + +def test_calc_fermi_energy(calc_chunk): + Ef = -8.24271207 + assert np.abs(calc_chunk.E_f - Ef) < eps_lp + assert np.abs(calc_chunk.results["fermi_energy"] - Ef) < eps_lp + + +def test_calc_dipole(calc_chunk): + assert calc_chunk.dipole is None + + +def test_calc_is_metallic(calc_chunk): + assert calc_chunk.is_metallic + + +def test_calc_converged(calc_chunk): + assert calc_chunk.converged + + +def test_calc_hirshfeld_charges(calc_chunk): + hirshfeld_charges = [0.20898543, -0.20840994] + assert np.allclose(calc_chunk.hirshfeld_charges, hirshfeld_charges) + assert np.allclose(calc_chunk.results["hirshfeld_charges"], hirshfeld_charges) + + +def test_calc_hirshfeld_volumes(calc_chunk): + hirshfeld_volumes = [73.39467444, 62.86011074] + assert np.allclose(calc_chunk.hirshfeld_volumes, hirshfeld_volumes) + assert np.allclose(calc_chunk.results["hirshfeld_volumes"], hirshfeld_volumes) + + +def test_calc_hirshfeld_atomic_dipoles(calc_chunk): + hirshfeld_atomic_dipoles = np.zeros((2, 3)) + assert np.allclose(calc_chunk.hirshfeld_atomic_dipoles, hirshfeld_atomic_dipoles) + assert np.allclose(calc_chunk.results["hirshfeld_atomic_dipoles"], hirshfeld_atomic_dipoles) + + +def test_calc_hirshfeld_dipole(calc_chunk): + assert calc_chunk.hirshfeld_dipole is None + + +@pytest.fixture +def molecular_header_chunk(): + lines = """ + | Number of atoms : 3 + | Number of spin channels : 1 + The structure contains 3 atoms and a total of 10.000 electrons. + Input geometry: + | Atomic structure: + | Atom x [A] y [A] z [A] + | 1: Species O 0.00000000 0.00000000 0.00000000 + | 2: Species H 0.95840000 0.00000000 0.00000000 + | 3: Species H -0.24000000 0.92790000 0.00000000 + 'Geometry relaxation: A file geometry.in.next_step is written out by default after each step.' + | Maximum number of basis functions : 7 + | Number of Kohn-Sham states (occupied + empty): 11 + Reducing total number of Kohn-Sham states to 7. + """ + + lines = lines.splitlines() + for ll, line in enumerate(lines): + lines[ll] = line.strip() + + return AimsOutHeaderChunk(lines) + + +@pytest.mark.parametrize( + "attrname", + [ + "k_points", + "k_point_weights", + "initial_lattice", + "n_k_points", + ], +) +def test_chunk_molecular_header_defaults_none(attrname, molecular_header_chunk): + assert getattr(molecular_header_chunk, attrname) is None + + +def test_molecular_header_n_bands(molecular_header_chunk): + assert molecular_header_chunk.n_bands == 7 + + +def test_molecular_header_initial_structure(molecular_header_chunk, molecular_positions): + assert len(molecular_header_chunk.initial_structure) == 3 + assert np.all(["O", "H", "H"] == [sp.symbol for sp in molecular_header_chunk.initial_structure.species]) + assert np.allclose( + molecular_header_chunk.initial_structure.cart_coords, + np.array( + [ + [0.00000000, 0.00000000, 0.00000000], + [0.95840000, 0.00000000, 0.00000000], + [-0.24000000, 0.92790000, 0.00000000], + ] + ), + ) + + +@pytest.fixture +def molecular_calc_chunk(molecular_header_chunk): + lines = """ + | Number of self-consistency cycles : 7 + | Chemical Potential : -0.61315483 eV + Updated atomic structure: + x [A] y [A] z [A] + atom -0.00191785 -0.00243279 0.00000000 O + atom 0.97071531 -0.00756333 0.00000000 H + atom -0.25039746 0.93789612 -0.00000000 H + | Total dipole moment [eAng] : 0.260286493869765E+00 0.336152447755231E+00 0.470003778119121E-15 + Energy and forces in a compact form: + | Total energy uncorrected : -0.206778551123339E+04 eV + | Total energy corrected : -5.206778551123339E+04 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -2.206778551123339E+04 eV + Total atomic forces (unitary forces cleaned) [eV/Ang]: + | 1 0.502371357164392E-03 0.518627676606471E-03 0.000000000000000E+00 + | 2 -0.108826758257187E-03 -0.408128912334209E-03 -0.649037698626122E-27 + | 3 -0.393544598907207E-03 -0.110498764272267E-03 -0.973556547939183E-27 + Performing Hirshfeld analysis of fragment charges and moments. + ---------------------------------------------------------------------- + | Atom 1: O + | Hirshfeld charge : -0.32053200 + | Free atom volume : 23.59848617 + | Hirshfeld volume : 21.83060659 + | Hirshfeld dipole vector : 0.04249319 0.05486053 0.00000000 + | Hirshfeld dipole moment : 0.06939271 + | Hirshfeld second moments: 0.04964380 -0.04453278 -0.00000000 + | -0.04453278 0.02659295 0.00000000 + | -0.00000000 0.00000000 -0.05608173 + ---------------------------------------------------------------------- + | Atom 2: H + | Hirshfeld charge : 0.16022630 + | Free atom volume : 10.48483941 + | Hirshfeld volume : 6.07674041 + | Hirshfeld dipole vector : 0.13710134 -0.00105126 0.00000000 + | Hirshfeld dipole moment : 0.13710537 + | Hirshfeld second moments: 0.12058896 -0.01198026 -0.00000000 + | -0.01198026 0.14550360 0.00000000 + | -0.00000000 0.00000000 0.10836357 + ---------------------------------------------------------------------- + | Atom 3: H + | Hirshfeld charge : 0.16020375 + | Free atom volume : 10.48483941 + | Hirshfeld volume : 6.07684447 + | Hirshfeld dipole vector : -0.03534982 0.13248706 0.00000000 + | Hirshfeld dipole moment : 0.13712195 + | Hirshfeld second moments: 0.14974686 -0.00443579 -0.00000000 + | -0.00443579 0.11633028 -0.00000000 + | -0.00000000 -0.00000000 0.10836209 + ---------------- + Writing Kohn-Sham eigenvalues. + + State Occupation Eigenvalue [Ha] Eigenvalue [eV] + 1 2.00000 -18.640915 -507.24511 + 2 2.00000 -0.918449 -24.99226 + 3 2.00000 -0.482216 -13.12175 + 4 2.00000 -0.338691 -9.21626 + 5 2.00000 -0.264427 -7.19543 + 6 0.00000 -0.000414 -0.01127 + 7 0.00000 0.095040 2.58616 + + Highest occupied state (VBM) at -7.19542820 eV + | Occupation number: 2.00000000 + + Lowest unoccupied state (CBM) at -0.01126981 eV + | Occupation number: 0.00000000 + + Overall HOMO-LUMO gap: 7.18415839 eV. + | Chemical Potential : -0.61315483 eV + + Self-consistency cycle converged. + Have a nice day. + ------------------------------------------------------------ + + """ + lines = lines.splitlines() + for ll, line in enumerate(lines): + lines[ll] = line.strip() + return AimsOutCalcChunk(lines, molecular_header_chunk) + + +@pytest.fixture +def molecular_positions(): + return np.array( + [ + [-0.00191785, -0.00243279, 0.00000000], + [0.97071531, -0.00756333, 0.00000000], + [-0.25039746, 0.93789612, 0.00000000], + ] + ) + + +def test_molecular_calc_atoms(molecular_calc_chunk, molecular_positions): + assert len(molecular_calc_chunk.structure.species) == 3 + assert np.allclose(molecular_calc_chunk.structure.cart_coords, molecular_positions) + assert np.all(["O", "H", "H"] == [sp.symbol for sp in molecular_calc_chunk.structure.species]) + + +def test_molecular_calc_forces(molecular_calc_chunk): + forces = np.array( + [ + [0.502371357164392e-03, 0.518627676606471e-03, 0.000000000000000e00], + [-0.108826758257187e-03, -0.408128912334209e-03, -0.649037698626122e-27], + [-0.393544598907207e-03, -0.110498764272267e-03, -0.973556547939183e-27], + ] + ) + assert np.allclose(molecular_calc_chunk.forces, forces) + assert np.allclose(molecular_calc_chunk.structure.site_properties["force"], forces) + assert np.allclose(molecular_calc_chunk.results["forces"], forces) + + +@pytest.mark.parametrize( + "attrname", + [ + "stresses", + "stress", + "magmom", + "E_f", + ], +) +def test_chunk_molecular_defaults_none(attrname, molecular_calc_chunk): + assert getattr(molecular_calc_chunk, attrname) is None + + +def test_molecular_calc_free_energy(molecular_calc_chunk): + free_energy = -2.206778551123339e04 + assert np.abs(molecular_calc_chunk.free_energy - free_energy) < eps_hp + assert np.abs(molecular_calc_chunk.results["free_energy"] - free_energy) < eps_hp + assert np.abs(molecular_calc_chunk.structure.properties["free_energy"] - free_energy) < eps_hp + + +def test_molecular_calc_energy(molecular_calc_chunk): + energy = -0.206778551123339e04 + assert np.abs(molecular_calc_chunk.energy - energy) < eps_hp + assert np.abs(molecular_calc_chunk.structure.properties["energy"] - energy) < eps_hp + assert np.abs(molecular_calc_chunk.results["energy"] - energy) < eps_hp + + +def test_molecular_calc_n_iter(molecular_calc_chunk): + n_iter = 7 + assert molecular_calc_chunk.n_iter == n_iter + assert molecular_calc_chunk.results["n_iter"] == n_iter + + +def test_molecular_calc_dipole(molecular_calc_chunk): + dipole = [0.260286493869765, 0.336152447755231, 0.470003778119121e-15] + assert np.allclose(molecular_calc_chunk.dipole, dipole) + assert np.allclose(molecular_calc_chunk.structure.properties["dipole"], dipole) + assert np.allclose(molecular_calc_chunk.results["dipole"], dipole) + + +def test_molecular_calc_is_metallic(molecular_calc_chunk): + assert not molecular_calc_chunk.is_metallic + + +def test_molecular_calc_converged(molecular_calc_chunk): + assert molecular_calc_chunk.converged + + +@pytest.fixture +def molecular_hirshfeld_charges(): + return np.array([-0.32053200, 0.16022630, 0.16020375]) + + +def test_molecular_calc_hirshfeld_charges(molecular_calc_chunk, molecular_hirshfeld_charges): + assert np.allclose(molecular_calc_chunk.hirshfeld_charges, molecular_hirshfeld_charges) + assert np.allclose(molecular_calc_chunk.results["hirshfeld_charges"], molecular_hirshfeld_charges) + + +def test_molecular_calc_hirshfeld_volumes(molecular_calc_chunk): + hirshfeld_volumes = np.array([21.83060659, 6.07674041, 6.07684447]) + assert np.allclose(molecular_calc_chunk.hirshfeld_volumes, hirshfeld_volumes) + assert np.allclose(molecular_calc_chunk.results["hirshfeld_volumes"], hirshfeld_volumes) + + +def test_molecular_calc_hirshfeld_atomic_dipoles(molecular_calc_chunk): + hirshfeld_atomic_dipoles = np.array( + [ + [0.04249319, 0.05486053, 0.00000000], + [0.13710134, -0.00105126, 0.00000000], + [-0.03534982, 0.13248706, 0.00000000], + ] + ) + assert np.allclose(molecular_calc_chunk.hirshfeld_atomic_dipoles, hirshfeld_atomic_dipoles) + assert np.allclose( + molecular_calc_chunk.results["hirshfeld_atomic_dipoles"], + hirshfeld_atomic_dipoles, + ) + + +def test_molecular_calc_hirshfeld_dipole(molecular_calc_chunk, molecular_hirshfeld_charges, molecular_positions): + hirshfeld_dipole = np.sum(molecular_hirshfeld_charges.reshape((-1, 1)) * molecular_positions, axis=1) + assert np.allclose(molecular_calc_chunk.hirshfeld_dipole, hirshfeld_dipole) + assert np.allclose(molecular_calc_chunk.results["hirshfeld_dipole"], hirshfeld_dipole) From b311ac4b1f9624fe282cd2628f0fc77d5aef636a Mon Sep 17 00:00:00 2001 From: Thomas Purcell Date: Mon, 30 Oct 2023 09:38:18 +0100 Subject: [PATCH 04/30] Add tests for AimsOutputs 1) How to handle stress in properties? --- pymatgen/io/aims/output.py | 27 ++++++++- pymatgen/io/aims/parsers.py | 20 +++---- tests/io/aims/test_aims_outputs.py | 88 ++++++++++++++++++++++++++++++ 3 files changed, 123 insertions(+), 12 deletions(-) create mode 100644 tests/io/aims/test_aims_outputs.py diff --git a/pymatgen/io/aims/output.py b/pymatgen/io/aims/output.py index 9975834ddf3..b5c802a3d2a 100644 --- a/pymatgen/io/aims/output.py +++ b/pymatgen/io/aims/output.py @@ -4,9 +4,15 @@ from typing import TYPE_CHECKING, Any import numpy as np -from atomate2.aims.io.parsers import read_aims_header_info, read_aims_output from monty.json import MontyDecoder, MSONable +from pymatgen.io.aims.parsers import ( + read_aims_header_info, + read_aims_header_info_from_content, + read_aims_output, + read_aims_output_from_content, +) + if TYPE_CHECKING: from collections.abc import Sequence from pathlib import Path @@ -21,7 +27,7 @@ class AimsOutput(MSONable): def __init__( self, - results: Sequence[Molecule | Structure], + results: Molecule | Structure | Sequence[Molecule | Structure], metadata: dict[str, Any], structure_summary: dict[str, Any], ): @@ -66,6 +72,20 @@ def from_outfile(cls, outfile: str | Path): return cls(results, metadata, structure_summary) + @classmethod + def from_str(cls, content: str): + """Construct an AimsOutput from an output file. + + Parameters + ---------- + outfile: str + The content of the aims.out file + """ + metadata, structure_summary = read_aims_header_info_from_content(content) + results = read_aims_output_from_content(content, index=slice(0, None)) + + return cls(results, metadata, structure_summary) + @classmethod def from_dict(cls, d: dict[str, Any]): """Construct an AimsOutput from a dictionary. @@ -76,6 +96,9 @@ def from_dict(cls, d: dict[str, Any]): The dictionary used to create AimsOutput """ decoded = {k: MontyDecoder().process_decoded(v) for k, v in d.items() if not k.startswith("@")} + for struct in decoded["results"]: + struct.properties = {k: MontyDecoder().process_decoded(v) for k, v in struct.properties.items()} + return cls(decoded["results"], decoded["metadata"], decoded["structure_summary"]) def get_results_for_image(self, image_ind: int) -> Structure | Molecule: diff --git a/pymatgen/io/aims/parsers.py b/pymatgen/io/aims/parsers.py index 6ed25ca5c44..b33ca1d51ef 100644 --- a/pymatgen/io/aims/parsers.py +++ b/pymatgen/io/aims/parsers.py @@ -15,7 +15,6 @@ from emmet.core.math import Vector3D - from pymatgen.core.structure import SiteCollection # TARP: Originally an object, but type hinting needs this to be an int LINE_NOT_FOUND = -1000 @@ -945,25 +944,24 @@ def direct_gap(self): return self._parse_homo_lumo()["direct_gap"] -def get_lines(content: str) -> list[str]: +def get_lines(content) -> list[str]: """Get a list of lines from a str or file of content""" if isinstance(content, str): return [line.strip() for line in content.split("\n")] return [line.strip() for line in content.readlines()] -def get_header_chunk(content: str) -> AimsOutHeaderChunk: +def get_header_chunk(content) -> AimsOutHeaderChunk: """Return the header information from the aims.out file.""" lines = get_lines(content) header = [] - stopped = False # Stop the header once the first SCF cycle begins for line in lines: header.append(line) if ( - "Convergence: q app. | density | eigen (eV) | Etot (eV)" not in line - and "Begin self-consistency iteration #" not in line + "Convergence: q app. | density | eigen (eV) | Etot (eV)" in line + or "Begin self-consistency iteration #" in line ): stopped = True break @@ -976,7 +974,7 @@ def get_header_chunk(content: str) -> AimsOutHeaderChunk: def get_aims_out_chunks(content, header_chunk): """Yield unprocessed chunks (header, lines) for each AimsOutChunk image.""" - lines = filter(lambda x: x not in header_chunk.lines, get_lines(content)) + lines = list(filter(lambda x: x not in header_chunk.lines, get_lines(content))) if len(lines) == 0: return @@ -1080,14 +1078,16 @@ def read_aims_header_info( def read_aims_output_from_content( content: str, index: int | slice = -1, non_convergence_ok: bool = False -) -> SiteCollection | Sequence[SiteCollection]: +) -> Structure | Molecule | Sequence[Structure | Molecule]: """Read and aims output file from the content of a file""" header_chunk = get_header_chunk(content) chunks = list(get_aims_out_chunks(content, header_chunk)) check_convergence(chunks, non_convergence_ok) # Relaxations have an additional footer chunk due to how it is split - images = [chunk.atoms for chunk in chunks[:-1]] if header_chunk.is_relaxation else [chunk.atoms for chunk in chunks] + images = ( + [chunk.structure for chunk in chunks[:-1]] if header_chunk.is_relaxation else [chunk.atoms for chunk in chunks] + ) return images[index] @@ -1095,7 +1095,7 @@ def read_aims_output( filename: str | Path, index: int | slice = -1, non_convergence_ok: bool = False, -) -> SiteCollection | Sequence[SiteCollection]: +) -> Structure | Molecule | Sequence[Structure | Molecule]: """Import FHI-aims output files with all data available. Includes all structures for relaxations and MD runs with FHI-aims diff --git a/tests/io/aims/test_aims_outputs.py b/tests/io/aims/test_aims_outputs.py new file mode 100644 index 00000000000..5def0b57960 --- /dev/null +++ b/tests/io/aims/test_aims_outputs.py @@ -0,0 +1,88 @@ +from __future__ import annotations + +import json +from pathlib import Path + +import numpy as np +from monty.json import MontyDecoder, MontyEncoder + +from pymatgen.core import Structure +from pymatgen.io.aims.output import AimsOutput + +outfile_dir = Path(__file__).parent / "aims_output_files" + + +def comp_images(test, ref): + assert test.species == ref.species + if isinstance(test, Structure): + assert np.allclose(test.lattice.matrix, ref.lattice.matrix) + assert np.allclose(test.cart_coords, ref.cart_coords) + + for key, val in test.site_properties.items(): + assert np.allclose(val, ref.site_properties[key]) + + for key, val in test.properties.items(): + assert np.allclose(val, ref.properties[key]) + + +def test_aims_output_si(): + si = AimsOutput.from_outfile(f"{outfile_dir}/si.out") + with open(f"{outfile_dir}/si_ref.json") as ref_file: + si_ref = json.load(ref_file, cls=MontyDecoder) + + assert si_ref.metadata == si.metadata + assert si_ref.structure_summary == si.structure_summary + + assert si_ref.n_images == si.n_images + for ii in range(si.n_images): + comp_images(si.get_results_for_image(ii), si_ref.get_results_for_image(ii)) + + assert json.dumps(si.as_dict(), cls=MontyEncoder) == json.dumps(si_ref.as_dict(), cls=MontyEncoder) + + +def test_aims_output_h2o(): + h2o = AimsOutput.from_outfile(f"{outfile_dir}/h2o.out") + with open(f"{outfile_dir}/h2o_ref.json") as ref_file: + h2o_ref = json.load(ref_file, cls=MontyDecoder) + + assert h2o_ref.metadata == h2o.metadata + assert h2o_ref.structure_summary == h2o.structure_summary + + assert h2o_ref.n_images == h2o.n_images + for ii in range(h2o.n_images): + comp_images(h2o.get_results_for_image(ii), h2o_ref.get_results_for_image(ii)) + + assert json.dumps(h2o.as_dict(), cls=MontyEncoder) == json.dumps(h2o_ref.as_dict(), cls=MontyEncoder) + + +def test_aims_output_si_str(): + with open(f"{outfile_dir}/si.out") as si_out: + si = AimsOutput.from_str(si_out.read()) + with open(f"{outfile_dir}/si_ref.json") as ref_file: + si_ref = json.load(ref_file, cls=MontyDecoder) + + assert si_ref.metadata == si.metadata + assert si_ref.structure_summary == si.structure_summary + + assert si_ref.n_images == si.n_images + for ii in range(si.n_images): + comp_images(si.get_results_for_image(ii), si_ref.get_results_for_image(ii)) + + assert json.dumps(si.as_dict(), cls=MontyEncoder) == json.dumps(si_ref.as_dict(), cls=MontyEncoder) + + +def test_aims_output_h2o_str(): + with open(f"{outfile_dir}/h2o.out") as h2o_out: + h2o = AimsOutput.from_str(h2o_out.read()) + + with open(f"{outfile_dir}/h2o_ref.json") as ref_file: + h2o_ref = json.load(ref_file, cls=MontyDecoder) + + assert h2o_ref.metadata == h2o.metadata + assert h2o_ref.structure_summary == h2o.structure_summary + + assert h2o_ref.n_images == h2o.n_images + for ii in range(h2o.n_images): + comp_images(h2o.get_results_for_image(ii), h2o_ref.get_results_for_image(ii)) + + assert json.dumps(h2o.as_dict(), cls=MontyEncoder) == json.dumps(h2o_ref.as_dict(), cls=MontyEncoder) From 2088fc81f563f20fdc915bdf21c4286072257ebd Mon Sep 17 00:00:00 2001 From: Thomas Purcell Date: Mon, 30 Oct 2023 10:45:37 +0100 Subject: [PATCH 05/30] Add aims output refrence files For aims outputs checks --- tests/io/aims/aims_output_files/h2o.out | 4244 +++++++++ tests/io/aims/aims_output_files/h2o_ref.json | 403 + tests/io/aims/aims_output_files/si.out | 8198 ++++++++++++++++++ tests/io/aims/aims_output_files/si_ref.json | 767 ++ 4 files changed, 13612 insertions(+) create mode 100644 tests/io/aims/aims_output_files/h2o.out create mode 100644 tests/io/aims/aims_output_files/h2o_ref.json create mode 100644 tests/io/aims/aims_output_files/si.out create mode 100644 tests/io/aims/aims_output_files/si_ref.json diff --git a/tests/io/aims/aims_output_files/h2o.out b/tests/io/aims/aims_output_files/h2o.out new file mode 100644 index 00000000000..cbcf8b1f574 --- /dev/null +++ b/tests/io/aims/aims_output_files/h2o.out @@ -0,0 +1,4244 @@ +------------------------------------------------------------ + Invoking FHI-aims ... + + When using FHI-aims, please cite the following reference: + + Volker Blum, Ralf Gehrke, Felix Hanke, Paula Havu, + Ville Havu, Xinguo Ren, Karsten Reuter, and Matthias Scheffler, + 'Ab Initio Molecular Simulations with Numeric Atom-Centered Orbitals', + Computer Physics Communications 180, 2175-2196 (2009) + + In addition, many other developments in FHI-aims are likely important for + your particular application. A partial list of references is given at the end of + this file. Thank you for giving credit to the authors of these developments. + + For any questions about FHI-aims, please visit our slack channel at + + https://fhi-aims.slack.com + + and our main development and support site at + + https://aims-git.rz-berlin.mpg.de . + + The latter site, in particular, has a wiki to collect information, as well + as an issue tracker to log discussions, suggest improvements, and report issues + or bugs. https://aims-git.rz-berlin.mpg.de is also the main development site + of the project and all new and updated code versions can be obtained there. + Please send an email to aims-coordinators@fhi-berlin.mpg.de and we will add + you to these sites. They are for you and everyone is welcome there. + +------------------------------------------------------------ + + + + Date : 20230628, Time : 095500.899 + Time zero on CPU 1 : 0.163200300000000E+01 s. + Internal wall clock time zero : 457178100.899 s. + + FHI-aims created a unique identifier for this run for later identification + aims_uuid : 099AC112-61D8-44F8-AB69-102154672282 + + Build configuration of the current instance of FHI-aims + ------------------------------------------------------- + FHI-aims version : 220309 + Commit number : 232d594a3 + CMake host system : Linux-5.4.0-146-generic + CMake version : 3.26.3 + Fortran compiler : /home/tpurcell/intel/oneapi/mpi/2021.6.0/bin/mpiifort (Intel) version 2021.6.0.20220226 + Fortran compiler flags: -O3 -ip -fp-model precise + C compiler : /home/tpurcell/intel/oneapi/compiler/2022.1.0/linux/bin/intel64/icc (Intel) version 2021.6.0.20220226 + C compiler flags : -m64 -O3 -ip -fp-model precise -std=gnu99 + Using MPI + Using ScaLAPACK + Using LibXC + Using i-PI + Using RLSY + Linking against: /home/tpurcell/intel/oneapi/mkl/2022.1.0/lib/intel64/libmkl_scalapack_lp64.so + /home/tpurcell/intel/oneapi/mkl/2022.1.0/lib/intel64/libmkl_blacs_intelmpi_lp64.so + /home/tpurcell/intel/oneapi/mkl/2022.1.0/lib/intel64/libmkl_intel_lp64.so + /home/tpurcell/intel/oneapi/mkl/2022.1.0/lib/intel64/libmkl_sequential.so + /home/tpurcell/intel/oneapi/mkl/2022.1.0/lib/intel64/libmkl_core.so + + Using 1 parallel tasks. + Task 0 on host nomadbook-7 reporting. + + Performing system and environment tests: + *** Environment variable OMP_NUM_THREADS is set to + 2 + *** For performance reasons you might want to set it to 1 + | Checking for ScaLAPACK... + | Testing pdtran()... + | All pdtran() tests passed. + + Obtaining array dimensions for all initial allocations: + + ----------------------------------------------------------------------- + Parsing control.in (first pass over file, find array dimensions only). + The contents of control.in will be repeated verbatim below + unless switched off by setting 'verbatim_writeout .false.' . + in the first line of control.in . + ----------------------------------------------------------------------- + + #=============================================================================== + # Created using the Atomic Simulation Environment (ASE) + + # Tue Jun 27 18:06:33 2023 + + #=============================================================================== + xc pbe + relativistic atomic_zora scalar + relax_geometry trm 1e-3 + #=============================================================================== + + ################################################################################ + # + # FHI-aims code project + # VB, Fritz-Haber Institut, 2009 + # + # Suggested "light" defaults for O atom (to be pasted into control.in file) + # Be sure to double-check any results obtained with these settings for post-processing, + # e.g., with the "tight" defaults and larger basis sets. + # + ################################################################################ + species O + # global species definitions + nucleus 8 + mass 15.9994 + # + l_hartree 4 + # + cut_pot 3.5 1.5 1.0 + basis_dep_cutoff 1e-4 + # + radial_base 36 5.0 + radial_multiplier 1 + angular_grids specified + division 0.2659 50 + division 0.4451 110 + division 0.6052 194 + division 0.7543 302 + # division 0.8014 434 + # division 0.8507 590 + # division 0.8762 770 + # division 0.9023 974 + # division 1.2339 1202 + # outer_grid 974 + outer_grid 302 + ################################################################################ + # + # Definition of "minimal" basis + # + ################################################################################ + # valence basis states + valence 2 s 2. + valence 2 p 4. + # ion occupancy + ion_occ 2 s 1. + ion_occ 2 p 3. + ################################################################################ + # + # Suggested additional basis functions. For production calculations, + # uncomment them one after another (the most important basis functions are + # listed first). + # + # Constructed for dimers: 1.0 A, 1.208 A, 1.5 A, 2.0 A, 3.0 A + # + ################################################################################ + # "First tier" - improvements: -699.05 meV to -159.38 meV + hydro 2 p 1.8 + hydro 3 d 7.6 + hydro 3 s 6.4 + # "Second tier" - improvements: -49.91 meV to -5.39 meV + # hydro 4 f 11.6 + # hydro 3 p 6.2 + # hydro 3 d 5.6 + # hydro 5 g 17.6 + # hydro 1 s 0.75 + # "Third tier" - improvements: -2.83 meV to -0.50 meV + # ionic 2 p auto + # hydro 4 f 10.8 + # hydro 4 d 4.7 + # hydro 2 s 6.8 + # "Fourth tier" - improvements: -0.40 meV to -0.12 meV + # hydro 3 p 5 + # hydro 3 s 3.3 + # hydro 5 g 15.6 + # hydro 4 f 17.6 + # hydro 4 d 14 + # Further basis functions - -0.08 meV and below + # hydro 3 s 2.1 + # hydro 4 d 11.6 + # hydro 3 p 16 + # hydro 2 s 17.2 + ################################################################################ + # + # FHI-aims code project + # VB, Fritz-Haber Institut, 2009 + # + # Suggested "light" defaults for H atom (to be pasted into control.in file) + # Be sure to double-check any results obtained with these settings for post-processing, + # e.g., with the "tight" defaults and larger basis sets. + # + ################################################################################ + species H + # global species definitions + nucleus 1 + mass 1.00794 + # + l_hartree 4 + # + cut_pot 3.5 1.5 1.0 + basis_dep_cutoff 1e-4 + # + radial_base 24 5.0 + radial_multiplier 1 + angular_grids specified + division 0.2421 50 + division 0.3822 110 + division 0.4799 194 + division 0.5341 302 + # division 0.5626 434 + # division 0.5922 590 + # division 0.6542 770 + # division 0.6868 1202 + # outer_grid 770 + outer_grid 302 + ################################################################################ + # + # Definition of "minimal" basis + # + ################################################################################ + # valence basis states + valence 1 s 1. + # ion occupancy + ion_occ 1 s 0.5 + ################################################################################ + # + # Suggested additional basis functions. For production calculations, + # uncomment them one after another (the most important basis functions are + # listed first). + # + # Basis constructed for dimers: 0.5 A, 0.7 A, 1.0 A, 1.5 A, 2.5 A + # + ################################################################################ + # "First tier" - improvements: -1014.90 meV to -62.69 meV + hydro 2 s 2.1 + hydro 2 p 3.5 + # "Second tier" - improvements: -12.89 meV to -1.83 meV + # hydro 1 s 0.85 + # hydro 2 p 3.7 + # hydro 2 s 1.2 + # hydro 3 d 7 + # "Third tier" - improvements: -0.25 meV to -0.12 meV + # hydro 4 f 11.2 + # hydro 3 p 4.8 + # hydro 4 d 9 + # hydro 3 s 3.2 + + ----------------------------------------------------------------------- + Completed first pass over input file control.in . + ----------------------------------------------------------------------- + + + ----------------------------------------------------------------------- + Parsing geometry.in (first pass over file, find array dimensions only). + The contents of geometry.in will be repeated verbatim below + unless switched off by setting 'verbatim_writeout .false.' . + in the first line of geometry.in . + ----------------------------------------------------------------------- + + #=============================================================================== + # Created using the Atomic Simulation Environment (ASE) + + # Tue Jun 27 18:06:33 2023 + + #======================================================= + atom 0.0000000000000000 0.0000000000000000 0.1192620000000000 O + atom 0.0000000000000000 0.7632390000000000 -0.4770470000000000 H + atom 0.0000000000000000 -0.7632390000000000 -0.4770470000000000 H + + ----------------------------------------------------------------------- + Completed first pass over input file geometry.in . + ----------------------------------------------------------------------- + + + Basic array size parameters: + | Number of species : 2 + | Number of atoms : 3 + | Max. basis fn. angular momentum : 2 + | Max. atomic/ionic basis occupied n: 2 + | Max. number of basis fn. types : 2 + | Max. radial fns per species/type : 3 + | Max. logarithmic grid size : 1301 + | Max. radial integration grid size : 36 + | Max. angular integration grid size: 302 + | Max. angular grid division number : 8 + | Radial grid for Hartree potential : 1301 + | Number of spin channels : 1 + +------------------------------------------------------------ + Reading file control.in. +------------------------------------------------------------ + XC: Using PBE gradient-corrected functionals. + Scalar relativistic treatment of kinetic energy: on-site free-atom approximation to ZORA. + Geometry relaxation: Modified BFGS - TRM (trust radius method) for lattice optimization. + Convergence accuracy for geometry relaxation: Maximum force < 0.100000E-02 eV/A. + + Reading configuration options for species O . + | Found nuclear charge : 8.0000 + | Found atomic mass : 15.9994000000000 amu + | Found l_max for Hartree potential : 4 + | Found cutoff potl. onset [A], width [A], scale factor : 3.50000 1.50000 1.00000 + | Threshold for basis-dependent cutoff potential is 0.100000E-03 + | Found data for basic radial integration grid : 36 points, outermost radius = 5.000 A + | Found multiplier for basic radial grid : 1 + | Found angular grid specification: user-specified. + | Specified grid contains 5 separate shells. + | Check grid settings after all constraints further below. + | Found free-atom valence shell : 2 s 2.000 + | Found free-atom valence shell : 2 p 4.000 + | No ionic wave fns used. Skipping ion_occ. + | No ionic wave fns used. Skipping ion_occ. + | Found hydrogenic basis function : 2 p 1.800 + | Found hydrogenic basis function : 3 d 7.600 + | Found hydrogenic basis function : 3 s 6.400 + Species O : Missing cutoff potential type. + Defaulting to exp(1/x)/(1-x)^2 type cutoff potential. + Species O : No 'logarithmic' tag. Using default grid for free atom: + | Default logarithmic grid data [bohr] : 0.1000E-03 0.1000E+03 0.1012E+01 + Species O : On-site basis accuracy parameter (for Gram-Schmidt orthonormalisation) not specified. + Using default value basis_acc = 0.1000000E-03. + Species O : Using default innermost maximum threshold i_radial= 2 for radial functions. + Species O : Default cutoff onset for free atom density etc. : 0.35000000E+01 AA. + Species O : Basic radial grid will be enhanced according to radial_multiplier = 1, to contain 36 grid points. + + Reading configuration options for species H . + | Found nuclear charge : 1.0000 + | Found atomic mass : 1.00794000000000 amu + | Found l_max for Hartree potential : 4 + | Found cutoff potl. onset [A], width [A], scale factor : 3.50000 1.50000 1.00000 + | Threshold for basis-dependent cutoff potential is 0.100000E-03 + | Found data for basic radial integration grid : 24 points, outermost radius = 5.000 A + | Found multiplier for basic radial grid : 1 + | Found angular grid specification: user-specified. + | Specified grid contains 5 separate shells. + | Check grid settings after all constraints further below. + | Found free-atom valence shell : 1 s 1.000 + | No ionic wave fns used. Skipping ion_occ. + | Found hydrogenic basis function : 2 s 2.100 + | Found hydrogenic basis function : 2 p 3.500 + Species H : Missing cutoff potential type. + Defaulting to exp(1/x)/(1-x)^2 type cutoff potential. + Species H : No 'logarithmic' tag. Using default grid for free atom: + | Default logarithmic grid data [bohr] : 0.1000E-03 0.1000E+03 0.1012E+01 + Species H : On-site basis accuracy parameter (for Gram-Schmidt orthonormalisation) not specified. + Using default value basis_acc = 0.1000000E-03. + Species H : Using default innermost maximum threshold i_radial= 2 for radial functions. + Species H : Default cutoff onset for free atom density etc. : 0.35000000E+01 AA. + Species H : Basic radial grid will be enhanced according to radial_multiplier = 1, to contain 24 grid points. + + Finished reading input file 'control.in'. + +------------------------------------------------------------ + + +------------------------------------------------------------ + Reading geometry description geometry.in. +------------------------------------------------------------ + | The smallest distance between any two atoms is 0.96856502 AA. + | The first atom of this pair is atom number 1 . + | The second atom of this pair is atom number 2 . + Input structure read successfully. + The structure contains 3 atoms, and a total of 10.000 electrons. + + Input geometry: + | No unit cell requested. + | Atomic structure: + | Atom x [A] y [A] z [A] + | 1: Species O 0.00000000 0.00000000 0.11926200 + | 2: Species H 0.00000000 0.76323900 -0.47704700 + | 3: Species H 0.00000000 -0.76323900 -0.47704700 + + + Finished reading input file 'control.in'. + + +------------------------------------------------------------ + Reading geometry description geometry.in. +------------------------------------------------------------ + + Consistency checks for stacksize environment parameter are next. + + | Maximum stacksize for task 0: unlimited + | Current stacksize for task 0: unlimited + + Consistency checks for the contents of control.in are next. + + MPI_IN_PLACE appears to work with this MPI implementation. + | Keeping use_mpi_in_place .true. (see manual). + Target number of points in a grid batch is not set. Defaulting to 100 + Method for grid partitioning is not set. Defaulting to parallel hash+maxmin partitioning. + Batch size limit is not set. Defaulting to 200 + By default, will store active basis functions for each batch. + If in need of memory, prune_basis_once .false. can be used to disable this option. + communication_type for Hartree potential was not specified. + Defaulting to calc_hartree . + Defaulting to Pulay charge density mixer. + Pulay mixer: Number of relevant iterations not set. + Defaulting to 8 iterations. + Pulay mixer: Number of initial linear mixing iterations not set. + Defaulting to 0 iterations. + Work space size for distributed Hartree potential not set. + Defaulting to 0.200000E+03 MB. + Mixing parameter for charge density mixing has not been set. + Using default: charge_mix_param = 0.0500. + The mixing parameter will be adjusted in iteration number 2 of the first full s.c.f. cycle only. + Algorithm-dependent basis array size parameters: + | n_max_pulay : 8 + Maximum number of self-consistency iterations not provided. + Presetting 1000 iterations. + Presetting 1001 iterations before the initial mixing cycle + is restarted anyway using the sc_init_iter criterion / keyword. + Presetting a factor 1.000 between actual scf density residual + and density convergence criterion sc_accuracy_rho below which sc_init_iter + takes no effect. + * No s.c.f. convergence criteria (sc_accuracy_*) were provided in control.in. + * The run will proceed with a reasonable default guess, but please check whether. + * the s.c.f. cycles seem to take too much or too little time. + No maximum number of relaxation steps, defaulting to 1000 + Default initial Hessian is Lindh matrix (thres = 15.00) plus 0.200000E+01 eV/A^2 times unity. + No maximum energy tolerance for TRM/BFGS moves, defaulting to 0.100000E-02 + Maximum energy tolerance by which TRM/BFGS trajectory may increase over multiple steps: 0.300000E-02 + No harmonic length scale. Defaulting to 0.250000E-01 A. + No trust radius initializer. Defaulting to 0.200000E+00 A. + Forces evaluation will include force correction term due to incomplete self-consistency (default). + * Notice: The s.c.f. convergence criterion sc_accuracy_rho was not provided. + * We used to stop in this case, and ask the user to provide reasonable + * scf convergence criteria. However, this led some users to employ criteria + * that led to extremely long run times, e.g., for simple relaxation. + * We now preset a default value for sc_accuracy_rho if it is not set. + * You may still wish to check if this setting is too tight or too loose for your needs. + * Based on n_atoms and forces and force-correction status, FHI-aims chose sc_accuracy_rho = 0.266667E-05 . + Force calculation: scf convergence accuracy of forces not set. + Defaulting to 'sc_accuracy_forces not_checked'. + Handling of forces: Unphysical translation and rotation will be removed from forces. + No accuracy limit for integral partition fn. given. Defaulting to 0.1000E-14. + No threshold value for u(r) in integrations given. Defaulting to 0.1000E-05. + No occupation type (smearing scheme) given. Defaulting to Gaussian broadening, width = 0.1000E-01 eV. + The width will be adjusted in iteration number 2 of the first full s.c.f. cycle only. + S.C.F. convergence parameters will be adjusted in iteration number 2 of the first full s.c.f. cycle only. + No accuracy for occupation numbers given. Defaulting to 0.1000E-12. + No threshold value for occupation numbers given. Defaulting to 0.0000E+00. + No accuracy for fermi level given. Defaulting to 0.1000E-19. + Maximum # of iterations to find E_F not set. Defaulting to 200. + Preferred method for the eigenvalue solver ('KS_method') not specified in 'control.in'. + Defaulting to serial version LAPACK (via ELSI). + Will not use alltoall communication since running on < 1024 CPUs. + Threshold for basis singularities not set. + Default threshold for basis singularities: 0.1000E-04 + partition_type (choice of integration weights) for integrals was not specified. + | Using a version of the partition function of Stratmann and coworkers ('stratmann_sparse'). + | At each grid point, the set of atoms used to build the partition table is smoothly restricted to + | only those atoms whose free-atom density would be non-zero at that grid point. + Partitioning for Hartree potential was not defined. Using partition_type for integrals. + | Adjusted default value of keyword multip_moments_threshold to: 0.10000000E-11 + | This value may affect high angular momentum components of the Hartree potential in periodic systems. + Spin handling was not defined in control.in. Defaulting to unpolarized case. + No q(lm)/r^(l+1) cutoff set for long-range Hartree potential. + | Using default value of 0.100000E-09 . + | Verify using the multipole_threshold keyword. + Defaulting to new monopole extrapolation. + Density update method: automatic selection selected. + Geometry relaxation: A file "geometry.in.next_step" is written out by default after each step. + | This file contains the geometry of the current relaxation step as well as + | the current Hessian matrix needed to restart the relaxation algorithm. + | If you do not want part or all of this information, use the keywords + | "write_restart_geometry" or "hessian_to_restart_geometry" to switch the output off. + Charge integration errors on the 3D integration grid will be compensated + by explicit normalization and distribution of residual charges. + Use the "compensate_multipole_errors" flag to change this behaviour. + Set 'collect_eigenvectors' to be '.true.' for all serial calculations. This is mandatory. + Set 'collect_eigenvectors' to be '.true.' for use_density_matrix .false. + Set 'collect_eigenvectors' to be '.true.' for KS_method lapack_fast and serial. + + Consistency checks for the contents of geometry.in are next. + + Number of empty states per atom not set in control.in - providing a guess from actual geometry. + | Total number of empty states used during s.c.f. cycle: 6 + If you use a very high smearing, use empty_states (per atom!) in control.in to increase this value. + + Structure-dependent array size parameters: + | Maximum number of distinct radial functions : 9 + | Maximum number of basis functions : 24 + | Number of Kohn-Sham states (occupied + empty): 11 +------------------------------------------------------------ + +------------------------------------------------------------ + Preparing all fixed parts of the calculation. +------------------------------------------------------------ + Determining machine precision: + 2.225073858507201E-308 + Setting up grids for atomic and cluster calculations. + + Creating wave function, potential, and density for free atoms. + Runtime choices for atomic solver: + | atomic solver xc : PBE + | compute density gradient: 1 + | compute kinetic density : F + + Species: O + + List of occupied orbitals and eigenvalues: + n l occ energy [Ha] energy [eV] + 1 0 2.0000 -18.926989 -515.0296 + 2 0 2.0000 -0.880247 -23.9527 + 2 1 4.0000 -0.331514 -9.0210 + + + Species: H + + List of occupied orbitals and eigenvalues: + n l occ energy [Ha] energy [eV] + 1 0 1.0000 -0.237593 -6.4652 + + + Adding cutoff potential to free-atom effective potential. + Creating fixed part of basis set: Ionic, confined, hydrogenic. + + O hydrogenic: + + List of hydrogenic basis orbitals: + n l effective z eigenvalue [eV] inner max. [A] outer max. [A] outer radius [A] + 2 1 1.800000 -10.9749 1.164242 1.164242 4.578029 + 3 2 7.600000 -87.3180 0.624125 0.624125 3.251020 + 3 0 6.400000 -61.9207 0.061167 1.081902 4.001998 + + + H hydrogenic: + + List of hydrogenic basis orbitals: + n l effective z eigenvalue [eV] inner max. [A] outer max. [A] outer radius [A] + 2 0 2.100000 -14.9728 0.193243 1.317208 4.583499 + 2 1 3.500000 -41.6669 0.602369 0.602369 3.723403 + + Creating atomic-like basis functions for current effective potential. + + Species O : + + List of atomic basis orbitals and eigenvalues: + n l energy [Ha] energy [eV] outer radius [A] + 1 0 -18.926989 -515.0296 1.415765 + 2 0 -0.880247 -23.9527 4.413171 + 2 1 -0.331514 -9.0210 4.522403 + + + Species H : + + List of atomic basis orbitals and eigenvalues: + n l energy [Ha] energy [eV] outer radius [A] + 1 0 -0.237593 -6.4652 4.527807 + + Assembling full basis from fixed parts. + | Species O : atomic orbital 1 s accepted. + | Species O : hydro orbital 3 s accepted. + | Species O : atomic orbital 2 s accepted. + | Species O : atomic orbital 2 p accepted. + | Species O : hydro orbital 2 p accepted. + | Species O : hydro orbital 3 d accepted. + | Species H : atomic orbital 1 s accepted. + | Species H : hydro orbital 2 s accepted. + | Species H : hydro orbital 2 p accepted. + + Basis size parameters after reduction: + | Total number of radial functions: 9 + | Total number of basis functions : 24 + + Per-task memory consumption for arrays in subroutine allocate_ext: + | 2.998708MB. + Testing on-site integration grid accuracy. + | Species Function (log., in eV) (rad., in eV) + 1 1 -515.0295626295 -515.0294562738 + 1 2 15.1698434419 15.1699322204 + 1 3 -21.6038822678 -21.6039118105 + 1 4 -9.0211123393 -9.0212703513 + 1 5 8.3047696391 8.2854840999 + 1 6 45.8428042125 45.8427461222 + 2 7 -6.4664147733 -6.4652229287 + 2 8 13.7099062243 13.7158503352 + 2 9 25.2661739479 25.2663166526 + + Preparing densities etc. for the partition functions (integrals / Hartree potential). + + Preparations completed. + max(cpu_time) : 0.064 s. + Wall clock time (cpu1) : 0.064 s. +------------------------------------------------------------ + +------------------------------------------------------------ + Begin self-consistency loop: Initialization. + + Date : 20230628, Time : 095500.973 +------------------------------------------------------------ + + Initializing index lists of integration centers etc. from given atomic structure: + | Number of centers in hartree potential : 3 + | Number of centers in hartree multipole : 3 + | Number of centers in electron density summation: 3 + | Number of centers in basis integrals : 3 + | Number of centers in integrals : 3 + | Number of centers in hamiltonian : 3 + + Initializing relaxation algorithms. + Finished initialization of distributed Hessian storage. + | Global dimension: 9 + | BLACS block size: 9 + | Number of workers: 1 + + Partitioning the integration grid into batches with parallel hashing+maxmin method. + | Number of batches: 256 + | Maximal batch size: 67 + | Minimal batch size: 58 + | Average batch size: 62.203 + | Standard deviation of batch sizes: 2.500 + + Integration load balanced across 1 MPI tasks. + Work distribution over tasks is as follows: + Task 0 has 15924 integration points. + Initializing partition tables, free-atom densities, potentials, etc. across the integration grid (initialize_grid_storage). + | initialize_grid_storage: Actual outermost partition radius vs. multipole_radius_free + | (-- VB: in principle, multipole_radius_free should be larger, hence this output) + | Species 1: Confinement radius = 4.999999999999999 AA, multipole_radius_free = 5.048384829883283 AA. + | Species 1: outer_partition_radius set to 5.048384829883283 AA . + | Species 2: Confinement radius = 4.999999999999999 AA, multipole_radius_free = 5.054417573612229 AA. + | Species 2: outer_partition_radius set to 5.054417573612229 AA . + | The sparse table of interatomic distances needs 0.09 kbyte instead of 0.07 kbyte of memory. + | Using the partition_type stratmann_smoother will reduce your memory usage. + | Net number of integration points: 15924 + | of which are non-zero points : 14536 + Renormalizing the initial density to the exact electron count on the 3D integration grid. + | Initial density: Formal number of electrons (from input files) : 10.0000000000 + | Integrated number of electrons on 3D grid : 9.9999431549 + | Charge integration error : -0.0000568451 + | Normalization factor for density and gradient : 1.0000056845 + Renormalizing the free-atom superposition density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 10.0000000000 + | Integrated number of electrons on 3D grid : 9.9999431549 + | Charge integration error : -0.0000568451 + | Normalization factor for density and gradient : 1.0000056845 + Obtaining max. number of non-zero basis functions in each batch (get_n_compute_maxes). + | Maximal number of non-zero basis functions: 24 in task 0 + Selecting the method for density update. + Loop over occupied states selected for charge density update. + Allocating 0.002 MB for KS_eigenvector + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.021 s, elapsed 0.021 s + Integrating overlap matrix. + Time summed over all CPUs for integration: real work 0.006 s, elapsed 0.006 s + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Overlap matrix is not singular + | Lowest and highest eigenvalues : 0.1639E-01, 0.2709E+01 + Finished singularity check of overlap matrix + | Time : 0.000 s + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.000 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -2.79227000 eV + Writing Kohn-Sham eigenvalues. + + State Occupation Eigenvalue [Ha] Eigenvalue [eV] + 1 2.00000 -19.032811 -517.90915 + 2 2.00000 -1.096687 -29.84238 + 3 2.00000 -0.625757 -17.02772 + 4 2.00000 -0.509068 -13.85246 + 5 2.00000 -0.435914 -11.86183 + 6 0.00000 -0.049192 -1.33858 + 7 0.00000 0.033225 0.90409 + 8 0.00000 0.215393 5.86114 + 9 0.00000 0.249072 6.77760 + 10 0.00000 0.301761 8.21135 + 11 0.00000 0.508037 13.82440 + + Highest occupied state (VBM) at -11.86182706 eV + | Occupation number: 2.00000000 + + Lowest unoccupied state (CBM) at -1.33858062 eV + | Occupation number: 0.00000000 + + Overall HOMO-LUMO gap: 10.52324644 eV. + Calculating total energy contributions from superposition of free atom densities. + + Total energy components: + | Sum of eigenvalues : -43.40047679 Ha -1180.98706138 eV + | XC energy correction : -9.02427629 Ha -245.56305186 eV + | XC potential correction : 11.60300934 Ha 315.73394853 eV + | Free-atom electrostatic energy: -35.72127400 Ha -972.02532155 eV + | Hartree energy correction : 0.00000000 Ha 0.00000000 eV + | Entropy correction : 0.00000000 Ha 0.00000000 eV + | --------------------------- + | Total energy : -76.54301773 Ha -2082.84148626 eV + | Total energy, T -> 0 : -76.54301773 Ha -2082.84148626 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -76.54301773 Ha -2082.84148626 eV + + Derived energy quantities: + | Kinetic energy : 75.72371465 Ha 2060.54711517 eV + | Electrostatic energy : -143.24245610 Ha -3897.82554957 eV + | Energy correction for multipole + | error in Hartree potential : 0.00000000 Ha 0.00000000 eV + | Sum of eigenvalues per atom : -393.66235379 eV + | Total energy (T->0) per atom : -694.28049542 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -694.28049542 eV + Initialize hartree_potential_storage + Max. number of atoms included in rho_multipole: 3 + + End scf initialization - timings : max(cpu_time) wall_clock(cpu1) + | Time for scf. initialization : 0.058 s 0.058 s + | Boundary condition initialization : 0.000 s 0.000 s + | Relaxation initialization : 0.000 s 0.000 s + | Integration : 0.028 s 0.027 s + | Solution of K.-S. eqns. : 0.000 s 0.001 s + | Grid partitioning : 0.012 s 0.012 s + | Preloading free-atom quantities on grid : 0.009 s 0.009 s + | Free-atom superposition energy : 0.008 s 0.008 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 0.009 MB (on task 0) + | Maximum: 0.009 MB (on task 0) + | Average: 0.009 MB + | Peak value for overall tracked memory usage: + | Minimum: 0.549 MB (on task 0 after allocating grid_partition) + | Maximum: 0.549 MB (on task 0 after allocating grid_partition) + | Average: 0.549 MB + | Largest tracked array allocation so far: + | Minimum: 0.364 MB (all_coords on task 0) + | Maximum: 0.364 MB (all_coords on task 0) + | Average: 0.364 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + Evaluating new KS density. + Integration grid: deviation in total charge ( - N_e) = -8.881784E-15 + + Time for density update prior : max(cpu_time) wall_clock(cpu1) + | self-consistency iterative process : 0.014 s 0.013 s + +------------------------------------------------------------ + Begin self-consistency iteration # 1 + + Date : 20230628, Time : 095501.044 +------------------------------------------------------------ + Pulay mixing of updated and previous charge densities. + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 10.0000000000 + | Integrated number of electrons on 3D grid : 10.0000000000 + | Charge integration error : 0.0000000000 + | Normalization factor for density and gradient : 1.0000000000 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = 0.480609E-13 + | Sum of charges compensated after spline to logarithmic grids = 0.121981E-04 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = 0.479102E-13 + Summing up the Hartree potential. + Time summed over all CPUs for potential: real work 0.008 s, elapsed 0.008 s + | RMS charge density error from multipole expansion : 0.353198E-03 + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.021 s, elapsed 0.021 s + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.000 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -2.61100247 eV + Writing Kohn-Sham eigenvalues. + + State Occupation Eigenvalue [Ha] Eigenvalue [eV] + 1 2.00000 -18.993769 -516.84676 + 2 2.00000 -1.077613 -29.32333 + 3 2.00000 -0.609308 -16.58011 + 4 2.00000 -0.489541 -13.32110 + 5 2.00000 -0.415574 -11.30835 + 6 0.00000 -0.044601 -1.21365 + 7 0.00000 0.039616 1.07801 + 8 0.00000 0.223818 6.09038 + 9 0.00000 0.257915 7.01823 + 10 0.00000 0.307769 8.37482 + 11 0.00000 0.513654 13.97725 + + Highest occupied state (VBM) at -11.30835240 eV + | Occupation number: 2.00000000 + + Lowest unoccupied state (CBM) at -1.21365069 eV + | Occupation number: 0.00000000 + + Overall HOMO-LUMO gap: 10.09470171 eV. + + Total energy components: + | Sum of eigenvalues : -43.17161059 Ha -1174.75929518 eV + | XC energy correction : -9.04989993 Ha -246.26030676 eV + | XC potential correction : 11.63658499 Ha 316.64758837 eV + | Free-atom electrostatic energy: -35.72127400 Ha -972.02532155 eV + | Hartree energy correction : -0.21960533 Ha -5.97576519 eV + | Entropy correction : 0.00000000 Ha 0.00000000 eV + | --------------------------- + | Total energy : -76.52580486 Ha -2082.37310032 eV + | Total energy, T -> 0 : -76.52580486 Ha -2082.37310032 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -76.52580486 Ha -2082.37310032 eV + + Derived energy quantities: + | Kinetic energy : 75.87943483 Ha 2064.78447672 eV + | Electrostatic energy : -143.35533976 Ha -3900.89727028 eV + | Energy correction for multipole + | error in Hartree potential : 0.00010724 Ha 0.00291817 eV + | Sum of eigenvalues per atom : -391.58643173 eV + | Total energy (T->0) per atom : -694.12436677 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -694.12436677 eV + Evaluating new KS density. + Integration grid: deviation in total charge ( - N_e) = -2.664535E-14 + + Self-consistency convergence accuracy: + | Change of charge density : 0.3070E+00 + | Change of sum of eigenvalues : 0.6228E+01 eV + | Change of total energy : 0.4684E+00 eV + + +------------------------------------------------------------ + End self-consistency iteration # 1 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 0.045 s 0.046 s + | Charge density update : 0.013 s 0.013 s + | Density mixing : 0.001 s 0.001 s + | Hartree multipole update : 0.002 s 0.002 s + | Hartree multipole summation : 0.008 s 0.008 s + | Integration : 0.022 s 0.021 s + | Solution of K.-S. eqns. : 0.000 s 0.001 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 0.009 MB (on task 0) + | Maximum: 0.009 MB (on task 0) + | Average: 0.009 MB + | Peak value for overall tracked memory usage: + | Minimum: 0.549 MB (on task 0 after allocating grid_partition) + | Maximum: 0.549 MB (on task 0 after allocating grid_partition) + | Average: 0.549 MB + | Largest tracked array allocation so far: + | Minimum: 0.364 MB (all_coords on task 0) + | Maximum: 0.364 MB (all_coords on task 0) + | Average: 0.364 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + +------------------------------------------------------------ + Begin self-consistency iteration # 2 + + Date : 20230628, Time : 095501.090 +------------------------------------------------------------ + Pulay mixing of updated and previous charge densities. + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 10.0000000000 + | Integrated number of electrons on 3D grid : 10.0000000000 + | Charge integration error : -0.0000000000 + | Normalization factor for density and gradient : 1.0000000000 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = -0.272912E-13 + | Sum of charges compensated after spline to logarithmic grids = 0.868881E-04 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = -0.276848E-13 + Summing up the Hartree potential. + Time summed over all CPUs for potential: real work 0.008 s, elapsed 0.008 s + | RMS charge density error from multipole expansion : 0.249403E-02 + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.021 s, elapsed 0.021 s + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.001 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -1.50966676 eV + Highest occupied state (VBM) at -8.17692053 eV + | Occupation number: 2.00000000 + + Lowest unoccupied state (CBM) at -0.44769917 eV + | Occupation number: 0.00000000 + + Overall HOMO-LUMO gap: 7.72922136 eV. + + Checking to see if s.c.f. parameters should be adjusted. + The system likely has a gap. Increased the default Pulay mixing parameter (charge_mix_param). Value: 0.200000 . + Kept the default occupation width. Value: 0.010000 eV. + + Total energy components: + | Sum of eigenvalues : -41.86980201 Ha -1139.33528147 eV + | XC energy correction : -9.20277869 Ha -250.42034953 eV + | XC potential correction : 11.83691214 Ha 322.09876756 eV + | Free-atom electrostatic energy: -35.72127400 Ha -972.02532155 eV + | Hartree energy correction : -1.51668467 Ha -41.27108979 eV + | Entropy correction : 0.00000000 Ha 0.00000000 eV + | --------------------------- + | Total energy : -76.47362723 Ha -2080.95327478 eV + | Total energy, T -> 0 : -76.47362723 Ha -2080.95327478 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -76.47362723 Ha -2080.95327478 eV + + Derived energy quantities: + | Kinetic energy : 76.68903147 Ha 2086.81472232 eV + | Electrostatic energy : -143.95988001 Ha -3917.34764757 eV + | Energy correction for multipole + | error in Hartree potential : 0.00051820 Ha 0.01410099 eV + | Sum of eigenvalues per atom : -379.77842716 eV + | Total energy (T->0) per atom : -693.65109159 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -693.65109159 eV + Evaluating new KS density. + Integration grid: deviation in total charge ( - N_e) = 3.730349E-14 + + Self-consistency convergence accuracy: + | Change of charge density : 0.2694E+00 + | Change of sum of eigenvalues : 0.3542E+02 eV + | Change of total energy : 0.1420E+01 eV + + +------------------------------------------------------------ + End self-consistency iteration # 2 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 0.045 s 0.045 s + | Charge density update : 0.013 s 0.013 s + | Density mixing : 0.001 s 0.001 s + | Hartree multipole update : 0.002 s 0.002 s + | Hartree multipole summation : 0.008 s 0.008 s + | Integration : 0.021 s 0.020 s + | Solution of K.-S. eqns. : 0.000 s 0.001 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 0.009 MB (on task 0) + | Maximum: 0.009 MB (on task 0) + | Average: 0.009 MB + | Peak value for overall tracked memory usage: + | Minimum: 0.549 MB (on task 0 after allocating grid_partition) + | Maximum: 0.549 MB (on task 0 after allocating grid_partition) + | Average: 0.549 MB + | Largest tracked array allocation so far: + | Minimum: 0.364 MB (all_coords on task 0) + | Maximum: 0.364 MB (all_coords on task 0) + | Average: 0.364 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + +------------------------------------------------------------ + Begin self-consistency iteration # 3 + + Date : 20230628, Time : 095501.135 +------------------------------------------------------------ + Pulay mixing of updated and previous charge densities. + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 10.0000000000 + | Integrated number of electrons on 3D grid : 10.0000000000 + | Charge integration error : -0.0000000000 + | Normalization factor for density and gradient : 1.0000000000 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = -0.358512E-13 + | Sum of charges compensated after spline to logarithmic grids = 0.608613E-04 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = -0.356667E-13 + Summing up the Hartree potential. + Time summed over all CPUs for potential: real work 0.008 s, elapsed 0.008 s + | RMS charge density error from multipole expansion : 0.373864E-02 + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.021 s, elapsed 0.021 s + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.000 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -1.83276307 eV + Highest occupied state (VBM) at -9.47939984 eV + | Occupation number: 2.00000000 + + Lowest unoccupied state (CBM) at -0.67075811 eV + | Occupation number: 0.00000000 + + Overall HOMO-LUMO gap: 8.80864173 eV. + + Total energy components: + | Sum of eigenvalues : -42.51834920 Ha -1156.98314838 eV + | XC energy correction : -9.12444892 Ha -248.28888805 eV + | XC potential correction : 11.73383120 Ha 319.29379235 eV + | Free-atom electrostatic energy: -35.72127400 Ha -972.02532155 eV + | Hartree energy correction : -0.85867394 Ha -23.36570686 eV + | Entropy correction : 0.00000000 Ha 0.00000000 eV + | --------------------------- + | Total energy : -76.48891487 Ha -2081.36927249 eV + | Total energy, T -> 0 : -76.48891487 Ha -2081.36927249 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -76.48891487 Ha -2081.36927249 eV + + Derived energy quantities: + | Kinetic energy : 75.97577172 Ha 2067.40593692 eV + | Electrostatic energy : -143.34023766 Ha -3900.48632136 eV + | Energy correction for multipole + | error in Hartree potential : -0.00170401 Ha -0.04636857 eV + | Sum of eigenvalues per atom : -385.66104946 eV + | Total energy (T->0) per atom : -693.78975750 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -693.78975750 eV + Evaluating new KS density. + Integration grid: deviation in total charge ( - N_e) = 0.000000E+00 + + Self-consistency convergence accuracy: + | Change of charge density : 0.1194E+00 + | Change of sum of eigenvalues : -0.1765E+02 eV + | Change of total energy : -0.4160E+00 eV + + +------------------------------------------------------------ + End self-consistency iteration # 3 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 0.046 s 0.045 s + | Charge density update : 0.013 s 0.013 s + | Density mixing : 0.002 s 0.001 s + | Hartree multipole update : 0.002 s 0.002 s + | Hartree multipole summation : 0.008 s 0.008 s + | Integration : 0.021 s 0.021 s + | Solution of K.-S. eqns. : 0.000 s 0.000 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 0.009 MB (on task 0) + | Maximum: 0.009 MB (on task 0) + | Average: 0.009 MB + | Peak value for overall tracked memory usage: + | Minimum: 0.549 MB (on task 0 after allocating grid_partition) + | Maximum: 0.549 MB (on task 0 after allocating grid_partition) + | Average: 0.549 MB + | Largest tracked array allocation so far: + | Minimum: 0.364 MB (all_coords on task 0) + | Maximum: 0.364 MB (all_coords on task 0) + | Average: 0.364 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + +------------------------------------------------------------ + Begin self-consistency iteration # 4 + + Date : 20230628, Time : 095501.181 +------------------------------------------------------------ + Pulay mixing of updated and previous charge densities. + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 10.0000000000 + | Integrated number of electrons on 3D grid : 10.0000000000 + | Charge integration error : -0.0000000000 + | Normalization factor for density and gradient : 1.0000000000 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = 0.447679E-13 + | Sum of charges compensated after spline to logarithmic grids = 0.117137E-03 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = 0.456534E-13 + Summing up the Hartree potential. + Time summed over all CPUs for potential: real work 0.008 s, elapsed 0.008 s + | RMS charge density error from multipole expansion : 0.612177E-02 + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.021 s, elapsed 0.021 s + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.001 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -1.00486968 eV + Highest occupied state (VBM) at -7.58224787 eV + | Occupation number: 2.00000000 + + Lowest unoccupied state (CBM) at -0.09841615 eV + | Occupation number: 0.00000000 + + Overall HOMO-LUMO gap: 7.48383172 eV. + + Total energy components: + | Sum of eigenvalues : -41.78332068 Ha -1136.98200470 eV + | XC energy correction : -9.21749844 Ha -250.82089418 eV + | XC potential correction : 11.85563613 Ha 322.60827311 eV + | Free-atom electrostatic energy: -35.72127400 Ha -972.02532155 eV + | Hartree energy correction : -1.60353532 Ha -43.63441626 eV + | Entropy correction : 0.00000000 Ha 0.00000000 eV + | --------------------------- + | Total energy : -76.46999231 Ha -2080.85436358 eV + | Total energy, T -> 0 : -76.46999231 Ha -2080.85436358 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -76.46999231 Ha -2080.85436358 eV + + Derived energy quantities: + | Kinetic energy : 76.23184146 Ha 2074.37394903 eV + | Electrostatic energy : -143.48433533 Ha -3904.40741844 eV + | Energy correction for multipole + | error in Hartree potential : -0.00273119 Ha -0.07431933 eV + | Sum of eigenvalues per atom : -378.99400157 eV + | Total energy (T->0) per atom : -693.61812119 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -693.61812119 eV + Evaluating new KS density. + Integration grid: deviation in total charge ( - N_e) = 1.065814E-14 + + Self-consistency convergence accuracy: + | Change of charge density : 0.1621E+00 + | Change of sum of eigenvalues : 0.2000E+02 eV + | Change of total energy : 0.5149E+00 eV + + +------------------------------------------------------------ + End self-consistency iteration # 4 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 0.047 s 0.046 s + | Charge density update : 0.013 s 0.012 s + | Density mixing : 0.003 s 0.002 s + | Hartree multipole update : 0.002 s 0.002 s + | Hartree multipole summation : 0.008 s 0.008 s + | Integration : 0.021 s 0.021 s + | Solution of K.-S. eqns. : 0.000 s 0.001 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 0.009 MB (on task 0) + | Maximum: 0.009 MB (on task 0) + | Average: 0.009 MB + | Peak value for overall tracked memory usage: + | Minimum: 0.549 MB (on task 0 after allocating grid_partition) + | Maximum: 0.549 MB (on task 0 after allocating grid_partition) + | Average: 0.549 MB + | Largest tracked array allocation so far: + | Minimum: 0.364 MB (all_coords on task 0) + | Maximum: 0.364 MB (all_coords on task 0) + | Average: 0.364 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + +------------------------------------------------------------ + Begin self-consistency iteration # 5 + + Date : 20230628, Time : 095501.228 +------------------------------------------------------------ + Pulay mixing of updated and previous charge densities. + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 10.0000000000 + | Integrated number of electrons on 3D grid : 10.0000000000 + | Charge integration error : 0.0000000000 + | Normalization factor for density and gradient : 1.0000000000 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = 0.930286E-13 + | Sum of charges compensated after spline to logarithmic grids = 0.120298E-03 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = 0.929549E-13 + Summing up the Hartree potential. + Time summed over all CPUs for potential: real work 0.008 s, elapsed 0.008 s + | RMS charge density error from multipole expansion : 0.613785E-02 + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.022 s, elapsed 0.022 s + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.000 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -0.98598576 eV + Highest occupied state (VBM) at -7.54693784 eV + | Occupation number: 2.00000000 + + Lowest unoccupied state (CBM) at -0.08558240 eV + | Occupation number: 0.00000000 + + Overall HOMO-LUMO gap: 7.46135544 eV. + + Total energy components: + | Sum of eigenvalues : -41.76913271 Ha -1136.59593031 eV + | XC energy correction : -9.21934311 Ha -250.87109021 eV + | XC potential correction : 11.85806416 Ha 322.67434318 eV + | Free-atom electrostatic energy: -35.72127400 Ha -972.02532155 eV + | Hartree energy correction : -1.61818974 Ha -44.03318308 eV + | Entropy correction : 0.00000000 Ha 0.00000000 eV + | --------------------------- + | Total energy : -76.46987539 Ha -2080.85118197 eV + | Total energy, T -> 0 : -76.46987539 Ha -2080.85118197 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -76.46987539 Ha -2080.85118197 eV + + Derived energy quantities: + | Kinetic energy : 76.23723292 Ha 2074.52065823 eV + | Electrostatic energy : -143.48776520 Ha -3904.50074999 eV + | Energy correction for multipole + | error in Hartree potential : -0.00277183 Ha -0.07542532 eV + | Sum of eigenvalues per atom : -378.86531010 eV + | Total energy (T->0) per atom : -693.61706066 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -693.61706066 eV + Evaluating new KS density. + Integration grid: deviation in total charge ( - N_e) = -2.486900E-14 + + Self-consistency convergence accuracy: + | Change of charge density : 0.3224E-01 + | Change of sum of eigenvalues : 0.3861E+00 eV + | Change of total energy : 0.3182E-02 eV + + +------------------------------------------------------------ + End self-consistency iteration # 5 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 0.047 s 0.047 s + | Charge density update : 0.013 s 0.013 s + | Density mixing : 0.003 s 0.002 s + | Hartree multipole update : 0.002 s 0.002 s + | Hartree multipole summation : 0.008 s 0.008 s + | Integration : 0.022 s 0.022 s + | Solution of K.-S. eqns. : 0.000 s 0.000 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 0.009 MB (on task 0) + | Maximum: 0.009 MB (on task 0) + | Average: 0.009 MB + | Peak value for overall tracked memory usage: + | Minimum: 0.549 MB (on task 0 after allocating grid_partition) + | Maximum: 0.549 MB (on task 0 after allocating grid_partition) + | Average: 0.549 MB + | Largest tracked array allocation so far: + | Minimum: 0.364 MB (all_coords on task 0) + | Maximum: 0.364 MB (all_coords on task 0) + | Average: 0.364 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + +------------------------------------------------------------ + Begin self-consistency iteration # 6 + + Date : 20230628, Time : 095501.275 +------------------------------------------------------------ + Pulay mixing of updated and previous charge densities. + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 10.0000000000 + | Integrated number of electrons on 3D grid : 10.0000000000 + | Charge integration error : -0.0000000000 + | Normalization factor for density and gradient : 1.0000000000 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = 0.237368E-13 + | Sum of charges compensated after spline to logarithmic grids = 0.145012E-03 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = 0.237860E-13 + Summing up the Hartree potential. + Time summed over all CPUs for potential: real work 0.008 s, elapsed 0.008 s + | RMS charge density error from multipole expansion : 0.636222E-02 + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.021 s, elapsed 0.021 s + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.000 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -0.83114754 eV + Highest occupied state (VBM) at -7.26694753 eV + | Occupation number: 2.00000000 + + Lowest unoccupied state (CBM) at 0.02109373 eV + | Occupation number: 0.00000000 + + Overall HOMO-LUMO gap: 7.28804126 eV. + + Total energy components: + | Sum of eigenvalues : -41.66008202 Ha -1133.62851024 eV + | XC energy correction : -9.23378999 Ha -251.26420986 eV + | XC potential correction : 11.87707254 Ha 323.19158760 eV + | Free-atom electrostatic energy: -35.72127400 Ha -972.02532155 eV + | Hartree energy correction : -1.73119749 Ha -47.10828065 eV + | Entropy correction : 0.00000000 Ha 0.00000000 eV + | --------------------------- + | Total energy : -76.46927097 Ha -2080.83473471 eV + | Total energy, T -> 0 : -76.46927097 Ha -2080.83473471 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -76.46927097 Ha -2080.83473471 eV + + Derived energy quantities: + | Kinetic energy : 76.26661039 Ha 2075.32005989 eV + | Electrostatic energy : -143.50209137 Ha -3904.89058474 eV + | Energy correction for multipole + | error in Hartree potential : -0.00315687 Ha -0.08590286 eV + | Sum of eigenvalues per atom : -377.87617008 eV + | Total energy (T->0) per atom : -693.61157824 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -693.61157824 eV + Evaluating new KS density. + Integration grid: deviation in total charge ( - N_e) = -1.953993E-14 + + Self-consistency convergence accuracy: + | Change of charge density : 0.2988E-01 + | Change of sum of eigenvalues : 0.2967E+01 eV + | Change of total energy : 0.1645E-01 eV + + +------------------------------------------------------------ + End self-consistency iteration # 6 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 0.051 s 0.051 s + | Charge density update : 0.013 s 0.013 s + | Density mixing : 0.006 s 0.006 s + | Hartree multipole update : 0.002 s 0.002 s + | Hartree multipole summation : 0.008 s 0.008 s + | Integration : 0.022 s 0.022 s + | Solution of K.-S. eqns. : 0.000 s 0.000 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 0.009 MB (on task 0) + | Maximum: 0.009 MB (on task 0) + | Average: 0.009 MB + | Peak value for overall tracked memory usage: + | Minimum: 0.549 MB (on task 0 after allocating grid_partition) + | Maximum: 0.549 MB (on task 0 after allocating grid_partition) + | Average: 0.549 MB + | Largest tracked array allocation so far: + | Minimum: 0.364 MB (all_coords on task 0) + | Maximum: 0.364 MB (all_coords on task 0) + | Average: 0.364 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + +------------------------------------------------------------ + Begin self-consistency iteration # 7 + + Date : 20230628, Time : 095501.326 +------------------------------------------------------------ + Pulay mixing of updated and previous charge densities. + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 10.0000000000 + | Integrated number of electrons on 3D grid : 10.0000000000 + | Charge integration error : 0.0000000000 + | Normalization factor for density and gradient : 1.0000000000 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = 0.350518E-13 + | Sum of charges compensated after spline to logarithmic grids = 0.161509E-03 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = 0.354207E-13 + Summing up the Hartree potential. + Time summed over all CPUs for potential: real work 0.008 s, elapsed 0.008 s + | RMS charge density error from multipole expansion : 0.647720E-02 + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.021 s, elapsed 0.021 s + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.000 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -0.74168939 eV + Highest occupied state (VBM) at -7.09752919 eV + | Occupation number: 2.00000000 + + Lowest unoccupied state (CBM) at 0.08405329 eV + | Occupation number: 0.00000000 + + Overall HOMO-LUMO gap: 7.18158248 eV. + + Total energy components: + | Sum of eigenvalues : -41.59374938 Ha -1131.82350724 eV + | XC energy correction : -9.24249280 Ha -251.50102532 eV + | XC potential correction : 11.88854091 Ha 323.50365794 eV + | Free-atom electrostatic energy: -35.72127400 Ha -972.02532155 eV + | Hartree energy correction : -1.80017602 Ha -48.98528182 eV + | Entropy correction : 0.00000000 Ha 0.00000000 eV + | --------------------------- + | Total energy : -76.46915128 Ha -2080.83147799 eV + | Total energy, T -> 0 : -76.46915128 Ha -2080.83147799 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -76.46915128 Ha -2080.83147799 eV + + Derived energy quantities: + | Kinetic energy : 76.28493278 Ha 2075.81863733 eV + | Electrostatic energy : -143.51159126 Ha -3905.14909000 eV + | Energy correction for multipole + | error in Hartree potential : -0.00340166 Ha -0.09256383 eV + | Sum of eigenvalues per atom : -377.27450241 eV + | Total energy (T->0) per atom : -693.61049266 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -693.61049266 eV + Evaluating new KS density. + Integration grid: deviation in total charge ( - N_e) = 2.842171E-14 + + Self-consistency convergence accuracy: + | Change of charge density : 0.1231E-01 + | Change of sum of eigenvalues : 0.1805E+01 eV + | Change of total energy : 0.3257E-02 eV + + +------------------------------------------------------------ + End self-consistency iteration # 7 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 0.049 s 0.049 s + | Charge density update : 0.013 s 0.013 s + | Density mixing : 0.004 s 0.004 s + | Hartree multipole update : 0.002 s 0.002 s + | Hartree multipole summation : 0.008 s 0.008 s + | Integration : 0.022 s 0.022 s + | Solution of K.-S. eqns. : 0.000 s 0.000 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 0.009 MB (on task 0) + | Maximum: 0.009 MB (on task 0) + | Average: 0.009 MB + | Peak value for overall tracked memory usage: + | Minimum: 0.549 MB (on task 0 after allocating grid_partition) + | Maximum: 0.549 MB (on task 0 after allocating grid_partition) + | Average: 0.549 MB + | Largest tracked array allocation so far: + | Minimum: 0.364 MB (all_coords on task 0) + | Maximum: 0.364 MB (all_coords on task 0) + | Average: 0.364 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + +------------------------------------------------------------ + Begin self-consistency iteration # 8 + + Date : 20230628, Time : 095501.375 +------------------------------------------------------------ + Pulay mixing of updated and previous charge densities. + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 10.0000000000 + | Integrated number of electrons on 3D grid : 10.0000000000 + | Charge integration error : 0.0000000000 + | Normalization factor for density and gradient : 1.0000000000 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = 0.404879E-13 + | Sum of charges compensated after spline to logarithmic grids = 0.164296E-03 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = 0.404879E-13 + Summing up the Hartree potential. + Time summed over all CPUs for potential: real work 0.008 s, elapsed 0.008 s + | RMS charge density error from multipole expansion : 0.650047E-02 + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.022 s, elapsed 0.022 s + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.000 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -0.72702459 eV + Highest occupied state (VBM) at -7.07120848 eV + | Occupation number: 2.00000000 + + Lowest unoccupied state (CBM) at 0.09449783 eV + | Occupation number: 0.00000000 + + Overall HOMO-LUMO gap: 7.16570631 eV. + + Total energy components: + | Sum of eigenvalues : -41.58376611 Ha -1131.55184853 eV + | XC energy correction : -9.24381832 Ha -251.53709447 eV + | XC potential correction : 11.89028876 Ha 323.55121924 eV + | Free-atom electrostatic energy: -35.72127400 Ha -972.02532155 eV + | Hartree energy correction : -1.81058075 Ha -49.26840907 eV + | Entropy correction : 0.00000000 Ha 0.00000000 eV + | --------------------------- + | Total energy : -76.46915042 Ha -2080.83145438 eV + | Total energy, T -> 0 : -76.46915042 Ha -2080.83145438 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -76.46915042 Ha -2080.83145438 eV + + Derived energy quantities: + | Kinetic energy : 76.28672331 Ha 2075.86736033 eV + | Electrostatic energy : -143.51205541 Ha -3905.16172024 eV + | Energy correction for multipole + | error in Hartree potential : -0.00344832 Ha -0.09383351 eV + | Sum of eigenvalues per atom : -377.18394951 eV + | Total energy (T->0) per atom : -693.61048479 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -693.61048479 eV + Evaluating new KS density. + Integration grid: deviation in total charge ( - N_e) = 3.552714E-14 + + Self-consistency convergence accuracy: + | Change of charge density : 0.1250E-02 + | Change of sum of eigenvalues : 0.2717E+00 eV + | Change of total energy : 0.2361E-04 eV + + +------------------------------------------------------------ + End self-consistency iteration # 8 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 0.048 s 0.048 s + | Charge density update : 0.013 s 0.013 s + | Density mixing : 0.003 s 0.003 s + | Hartree multipole update : 0.002 s 0.002 s + | Hartree multipole summation : 0.008 s 0.008 s + | Integration : 0.022 s 0.022 s + | Solution of K.-S. eqns. : 0.000 s 0.000 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 0.009 MB (on task 0) + | Maximum: 0.009 MB (on task 0) + | Average: 0.009 MB + | Peak value for overall tracked memory usage: + | Minimum: 0.549 MB (on task 0 after allocating grid_partition) + | Maximum: 0.549 MB (on task 0 after allocating grid_partition) + | Average: 0.549 MB + | Largest tracked array allocation so far: + | Minimum: 0.364 MB (all_coords on task 0) + | Maximum: 0.364 MB (all_coords on task 0) + | Average: 0.364 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + +------------------------------------------------------------ + Begin self-consistency iteration # 9 + + Date : 20230628, Time : 095501.423 +------------------------------------------------------------ + Pulay mixing of updated and previous charge densities. + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 10.0000000000 + | Integrated number of electrons on 3D grid : 10.0000000000 + | Charge integration error : 0.0000000000 + | Normalization factor for density and gradient : 1.0000000000 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = 0.123087E-12 + | Sum of charges compensated after spline to logarithmic grids = 0.163432E-03 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = 0.124711E-12 + Summing up the Hartree potential. + Time summed over all CPUs for potential: real work 0.008 s, elapsed 0.008 s + | RMS charge density error from multipole expansion : 0.649308E-02 + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.021 s, elapsed 0.021 s + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.000 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -0.73150611 eV + Highest occupied state (VBM) at -7.07781963 eV + | Occupation number: 2.00000000 + + Lowest unoccupied state (CBM) at 0.09138305 eV + | Occupation number: 0.00000000 + + Overall HOMO-LUMO gap: 7.16920268 eV. + + Total energy components: + | Sum of eigenvalues : -41.58620402 Ha -1131.61818755 eV + | XC energy correction : -9.24347846 Ha -251.52784639 eV + | XC potential correction : 11.88984104 Ha 323.53903622 eV + | Free-atom electrostatic energy: -35.72127400 Ha -972.02532155 eV + | Hartree energy correction : -1.80803473 Ha -49.19912835 eV + | Entropy correction : 0.00000000 Ha 0.00000000 eV + | --------------------------- + | Total energy : -76.46915017 Ha -2080.83144762 eV + | Total energy, T -> 0 : -76.46915017 Ha -2080.83144762 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -76.46915017 Ha -2080.83144762 eV + + Derived energy quantities: + | Kinetic energy : 76.28677355 Ha 2075.86872736 eV + | Electrostatic energy : -143.51244526 Ha -3905.17232859 eV + | Energy correction for multipole + | error in Hartree potential : -0.00343219 Ha -0.09339472 eV + | Sum of eigenvalues per atom : -377.20606252 eV + | Total energy (T->0) per atom : -693.61048254 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -693.61048254 eV + Evaluating new KS density. + Integration grid: deviation in total charge ( - N_e) = 1.776357E-15 + + Self-consistency convergence accuracy: + | Change of charge density : 0.3854E-03 + | Change of sum of eigenvalues : -0.6634E-01 eV + | Change of total energy : 0.6755E-05 eV + + +------------------------------------------------------------ + End self-consistency iteration # 9 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 0.047 s 0.047 s + | Charge density update : 0.013 s 0.013 s + | Density mixing : 0.003 s 0.003 s + | Hartree multipole update : 0.002 s 0.002 s + | Hartree multipole summation : 0.008 s 0.008 s + | Integration : 0.021 s 0.021 s + | Solution of K.-S. eqns. : 0.000 s 0.000 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 0.010 MB (on task 0) + | Maximum: 0.010 MB (on task 0) + | Average: 0.010 MB + | Peak value for overall tracked memory usage: + | Minimum: 0.549 MB (on task 0 after allocating grid_partition) + | Maximum: 0.549 MB (on task 0 after allocating grid_partition) + | Average: 0.549 MB + | Largest tracked array allocation so far: + | Minimum: 0.364 MB (all_coords on task 0) + | Maximum: 0.364 MB (all_coords on task 0) + | Average: 0.364 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + +------------------------------------------------------------ + Begin self-consistency iteration # 10 + + Date : 20230628, Time : 095501.470 +------------------------------------------------------------ + Pulay mixing of updated and previous charge densities. + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 10.0000000000 + | Integrated number of electrons on 3D grid : 10.0000000000 + | Charge integration error : 0.0000000000 + | Normalization factor for density and gradient : 1.0000000000 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = 0.434642E-13 + | Sum of charges compensated after spline to logarithmic grids = 0.163336E-03 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = 0.436118E-13 + Summing up the Hartree potential. + Time summed over all CPUs for potential: real work 0.008 s, elapsed 0.008 s + | RMS charge density error from multipole expansion : 0.649266E-02 + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.021 s, elapsed 0.021 s + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.000 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -0.73194815 eV + Highest occupied state (VBM) at -7.07878555 eV + | Occupation number: 2.00000000 + + Lowest unoccupied state (CBM) at 0.09105437 eV + | Occupation number: 0.00000000 + + Overall HOMO-LUMO gap: 7.16983991 eV. + + Total energy components: + | Sum of eigenvalues : -41.58658022 Ha -1131.62842454 eV + | XC energy correction : -9.24343119 Ha -251.52656013 eV + | XC potential correction : 11.88977861 Ha 323.53733745 eV + | Free-atom electrostatic energy: -35.72127400 Ha -972.02532155 eV + | Hartree energy correction : -1.80764338 Ha -49.18847899 eV + | Entropy correction : 0.00000000 Ha 0.00000000 eV + | --------------------------- + | Total energy : -76.46915017 Ha -2080.83144776 eV + | Total energy, T -> 0 : -76.46915017 Ha -2080.83144776 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -76.46915017 Ha -2080.83144776 eV + + Derived energy quantities: + | Kinetic energy : 76.28667075 Ha 2075.86592990 eV + | Electrostatic energy : -143.51238973 Ha -3905.17081753 eV + | Energy correction for multipole + | error in Hartree potential : -0.00343077 Ha -0.09335597 eV + | Sum of eigenvalues per atom : -377.20947485 eV + | Total energy (T->0) per atom : -693.61048259 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -693.61048259 eV + Evaluating new KS density. + Integration grid: deviation in total charge ( - N_e) = -2.486900E-14 + + Self-consistency convergence accuracy: + | Change of charge density : 0.4204E-04 + | Change of sum of eigenvalues : -0.1024E-01 eV + | Change of total energy : -0.1338E-06 eV + + +------------------------------------------------------------ + End self-consistency iteration # 10 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 0.047 s 0.047 s + | Charge density update : 0.013 s 0.013 s + | Density mixing : 0.003 s 0.003 s + | Hartree multipole update : 0.002 s 0.002 s + | Hartree multipole summation : 0.008 s 0.007 s + | Integration : 0.021 s 0.022 s + | Solution of K.-S. eqns. : 0.000 s 0.000 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 0.010 MB (on task 0) + | Maximum: 0.010 MB (on task 0) + | Average: 0.010 MB + | Peak value for overall tracked memory usage: + | Minimum: 0.549 MB (on task 0 after allocating grid_partition) + | Maximum: 0.549 MB (on task 0 after allocating grid_partition) + | Average: 0.549 MB + | Largest tracked array allocation so far: + | Minimum: 0.364 MB (all_coords on task 0) + | Maximum: 0.364 MB (all_coords on task 0) + | Average: 0.364 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + +------------------------------------------------------------ + Begin self-consistency iteration # 11 + + Date : 20230628, Time : 095501.517 +------------------------------------------------------------ + Pulay mixing of updated and previous charge densities. + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 10.0000000000 + | Integrated number of electrons on 3D grid : 10.0000000000 + | Charge integration error : -0.0000000000 + | Normalization factor for density and gradient : 1.0000000000 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = 0.382003E-13 + | Sum of charges compensated after spline to logarithmic grids = 0.163377E-03 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = 0.378313E-13 + Summing up the Hartree potential. + Time summed over all CPUs for potential: real work 0.009 s, elapsed 0.009 s + | RMS charge density error from multipole expansion : 0.649286E-02 + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.021 s, elapsed 0.021 s + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.000 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -0.73176936 eV + Highest occupied state (VBM) at -7.07842135 eV + | Occupation number: 2.00000000 + + Lowest unoccupied state (CBM) at 0.09118270 eV + | Occupation number: 0.00000000 + + Overall HOMO-LUMO gap: 7.16960405 eV. + + Total energy components: + | Sum of eigenvalues : -41.58643672 Ha -1131.62451950 eV + | XC energy correction : -9.24344966 Ha -251.52706278 eV + | XC potential correction : 11.88980299 Ha 323.53800085 eV + | Free-atom electrostatic energy: -35.72127400 Ha -972.02532155 eV + | Hartree energy correction : -1.80779279 Ha -49.19254463 eV + | Entropy correction : 0.00000000 Ha 0.00000000 eV + | --------------------------- + | Total energy : -76.46915017 Ha -2080.83144761 eV + | Total energy, T -> 0 : -76.46915017 Ha -2080.83144761 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -76.46915017 Ha -2080.83144761 eV + + Derived energy quantities: + | Kinetic energy : 76.28671545 Ha 2075.86714629 eV + | Electrostatic energy : -143.51241596 Ha -3905.17153112 eV + | Energy correction for multipole + | error in Hartree potential : -0.00343129 Ha -0.09337004 eV + | Sum of eigenvalues per atom : -377.20817317 eV + | Total energy (T->0) per atom : -693.61048254 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -693.61048254 eV + Evaluating new KS density. + Integration grid: deviation in total charge ( - N_e) = 1.598721E-14 + + Self-consistency convergence accuracy: + | Change of charge density : 0.2545E-04 + | Change of sum of eigenvalues : 0.3905E-02 eV + | Change of total energy : 0.1444E-06 eV + + +------------------------------------------------------------ + End self-consistency iteration # 11 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 0.048 s 0.048 s + | Charge density update : 0.013 s 0.014 s + | Density mixing : 0.003 s 0.003 s + | Hartree multipole update : 0.002 s 0.001 s + | Hartree multipole summation : 0.009 s 0.009 s + | Integration : 0.021 s 0.021 s + | Solution of K.-S. eqns. : 0.000 s 0.000 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 0.010 MB (on task 0) + | Maximum: 0.010 MB (on task 0) + | Average: 0.010 MB + | Peak value for overall tracked memory usage: + | Minimum: 0.549 MB (on task 0 after allocating grid_partition) + | Maximum: 0.549 MB (on task 0 after allocating grid_partition) + | Average: 0.549 MB + | Largest tracked array allocation so far: + | Minimum: 0.364 MB (all_coords on task 0) + | Maximum: 0.364 MB (all_coords on task 0) + | Average: 0.364 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + +------------------------------------------------------------ + Begin self-consistency iteration # 12 + + Date : 20230628, Time : 095501.565 +------------------------------------------------------------ + Pulay mixing of updated and previous charge densities. + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 10.0000000000 + | Integrated number of electrons on 3D grid : 10.0000000000 + | Charge integration error : 0.0000000000 + | Normalization factor for density and gradient : 1.0000000000 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = 0.373394E-13 + | Sum of charges compensated after spline to logarithmic grids = 0.163375E-03 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = 0.380035E-13 + Summing up the Hartree potential. + Time summed over all CPUs for potential: real work 0.007 s, elapsed 0.007 s + | RMS charge density error from multipole expansion : 0.649285E-02 + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.021 s, elapsed 0.021 s + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.000 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -0.73177804 eV + Highest occupied state (VBM) at -7.07842907 eV + | Occupation number: 2.00000000 + + Lowest unoccupied state (CBM) at 0.09117707 eV + | Occupation number: 0.00000000 + + Overall HOMO-LUMO gap: 7.16960614 eV. + + Total energy components: + | Sum of eigenvalues : -41.58643930 Ha -1131.62458986 eV + | XC energy correction : -9.24344918 Ha -251.52704966 eV + | XC potential correction : 11.88980236 Ha 323.53798377 eV + | Free-atom electrostatic energy: -35.72127400 Ha -972.02532155 eV + | Hartree energy correction : -1.80779006 Ha -49.19247030 eV + | Entropy correction : 0.00000000 Ha 0.00000000 eV + | --------------------------- + | Total energy : -76.46915017 Ha -2080.83144760 eV + | Total energy, T -> 0 : -76.46915017 Ha -2080.83144760 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -76.46915017 Ha -2080.83144760 eV + + Derived energy quantities: + | Kinetic energy : 76.28671580 Ha 2075.86715580 eV + | Electrostatic energy : -143.51241679 Ha -3905.17155374 eV + | Energy correction for multipole + | error in Hartree potential : -0.00343126 Ha -0.09336937 eV + | Sum of eigenvalues per atom : -377.20819662 eV + | Total energy (T->0) per atom : -693.61048253 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -693.61048253 eV + Evaluating new KS density. + Integration grid: deviation in total charge ( - N_e) = 1.421085E-14 + + Self-consistency convergence accuracy: + | Change of charge density : 0.6725E-06 + | Change of sum of eigenvalues : -0.7036E-04 eV + | Change of total energy : 0.1583E-07 eV + + Electronic self-consistency reached - switching on the force computation. + + +------------------------------------------------------------ + End self-consistency iteration # 12 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 0.047 s 0.046 s + | Charge density & force component update : 0.013 s 0.013 s + | Density mixing : 0.003 s 0.003 s + | Hartree multipole update : 0.002 s 0.001 s + | Hartree multipole summation : 0.008 s 0.008 s + | Hartree pot. SCF incomplete forces : 0.000 s 0.000 s + | Integration : 0.021 s 0.021 s + | Solution of K.-S. eqns. : 0.000 s 0.000 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 0.010 MB (on task 0) + | Maximum: 0.010 MB (on task 0) + | Average: 0.010 MB + | Peak value for overall tracked memory usage: + | Minimum: 0.549 MB (on task 0 after allocating grid_partition) + | Maximum: 0.549 MB (on task 0 after allocating grid_partition) + | Average: 0.549 MB + | Largest tracked array allocation so far: + | Minimum: 0.364 MB (all_coords on task 0) + | Maximum: 0.364 MB (all_coords on task 0) + | Average: 0.364 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + +------------------------------------------------------------ + Begin self-consistency iteration # 13 + + Date : 20230628, Time : 095501.612 +------------------------------------------------------------ + Pulay mixing of updated and previous charge densities. + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 10.0000000000 + | Integrated number of electrons on 3D grid : 10.0000000000 + | Charge integration error : -0.0000000000 + | Normalization factor for density and gradient : 1.0000000000 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = -0.312391E-14 + | Sum of charges compensated after spline to logarithmic grids = 0.163375E-03 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = -0.209081E-14 + Summing up the Hartree potential. + Time summed over all CPUs for potential: real work 0.024 s, elapsed 0.024 s + | RMS charge density error from multipole expansion : 0.649285E-02 + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.021 s, elapsed 0.021 s + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.000 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -0.73177723 eV + Highest occupied state (VBM) at -7.07842768 eV + | Occupation number: 2.00000000 + + Lowest unoccupied state (CBM) at 0.09117765 eV + | Occupation number: 0.00000000 + + Overall HOMO-LUMO gap: 7.16960533 eV. + + Total energy components: + | Sum of eigenvalues : -41.58643878 Ha -1131.62457563 eV + | XC energy correction : -9.24344925 Ha -251.52705153 eV + | XC potential correction : 11.88980246 Ha 323.53798624 eV + | Free-atom electrostatic energy: -35.72127400 Ha -972.02532155 eV + | Hartree energy correction : -1.80779060 Ha -49.19248513 eV + | Entropy correction : 0.00000000 Ha 0.00000000 eV + | --------------------------- + | Total energy : -76.46915017 Ha -2080.83144760 eV + | Total energy, T -> 0 : -76.46915017 Ha -2080.83144760 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -76.46915017 Ha -2080.83144760 eV + + Derived energy quantities: + | Kinetic energy : 76.28671582 Ha 2075.86715635 eV + | Electrostatic energy : -143.51241674 Ha -3905.17155242 eV + | Energy correction for multipole + | error in Hartree potential : -0.00343126 Ha -0.09336945 eV + | Sum of eigenvalues per atom : -377.20819188 eV + | Total energy (T->0) per atom : -693.61048253 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -693.61048253 eV + Evaluating new KS density and force components. + Integration grid: deviation in total charge ( - N_e) = 2.486900E-14 + + atomic forces [eV/Ang]: + ----------------------- + atom # 1 + Hellmann-Feynman : -0.329545E-12 -0.107615E-11 0.176407E+02 + Ionic forces : 0.000000E+00 0.000000E+00 0.000000E+00 + Multipole : 0.168077E-12 -0.141368E-12 -0.897884E-01 + Hartree pot. SCF incomplete : 0.144342E-12 0.296708E-12 -0.390350E-06 + Pulay + GGA : 0.981201E-12 -0.399171E-11 -0.173658E+02 + ---------------------------------------------------------------- + Total forces( 1) : 0.964076E-12 -0.491252E-11 0.185135E+00 + atom # 2 + Hellmann-Feynman : -0.252432E-14 0.468977E+00 -0.413666E+00 + Ionic forces : 0.000000E+00 0.000000E+00 0.000000E+00 + Multipole : -0.626561E-15 -0.448375E-02 -0.317610E-01 + Hartree pot. SCF incomplete : 0.259584E-14 -0.130223E-06 -0.879668E-07 + Pulay + GGA : -0.145540E-13 -0.293948E+00 0.341633E+00 + ---------------------------------------------------------------- + Total forces( 2) : -0.151091E-13 0.170545E+00 -0.103795E+00 + atom # 3 + Hellmann-Feynman : 0.890643E-15 -0.468977E+00 -0.413666E+00 + Ionic forces : 0.000000E+00 0.000000E+00 0.000000E+00 + Multipole : -0.224484E-15 0.448375E-02 -0.317610E-01 + Hartree pot. SCF incomplete : -0.330869E-14 0.130223E-06 -0.879668E-07 + Pulay + GGA : 0.245841E-13 0.293948E+00 0.341633E+00 + ---------------------------------------------------------------- + Total forces( 3) : 0.219416E-13 -0.170545E+00 -0.103795E+00 + + + Self-consistency convergence accuracy: + | Change of charge density : 0.8667E-07 + | Change of sum of eigenvalues : 0.1423E-04 eV + | Change of total energy : -0.2718E-09 eV + | Change of forces : 0.4057E+00 eV/A + + Writing Kohn-Sham eigenvalues. + + State Occupation Eigenvalue [Ha] Eigenvalue [eV] + 1 2.00000 -18.788144 -511.25140 + 2 2.00000 -0.926801 -25.21953 + 3 2.00000 -0.479271 -13.04164 + 4 2.00000 -0.338876 -9.22128 + 5 2.00000 -0.260127 -7.07843 + 6 0.00000 0.003351 0.09118 + 7 0.00000 0.101965 2.77460 + 8 0.00000 0.297791 8.10331 + 9 0.00000 0.334106 9.09149 + 10 0.00000 0.368731 10.03368 + 11 0.00000 0.578309 15.73660 + + Highest occupied state (VBM) at -7.07842768 eV + | Occupation number: 2.00000000 + + Lowest unoccupied state (CBM) at 0.09117765 eV + | Occupation number: 0.00000000 + + Overall HOMO-LUMO gap: 7.16960533 eV. + | Chemical Potential : -0.73177723 eV + + Self-consistency cycle converged. + + +------------------------------------------------------------ + End self-consistency iteration # 13 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 0.121 s 0.120 s + | Charge density & force component update : 0.054 s 0.054 s + | Density mixing : 0.004 s 0.004 s + | Hartree multipole update : 0.002 s 0.002 s + | Hartree multipole summation : 0.024 s 0.024 s + | Hartree pot. SCF incomplete forces : 0.015 s 0.015 s + | Integration : 0.021 s 0.021 s + | Solution of K.-S. eqns. : 0.000 s 0.000 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 0.010 MB (on task 0) + | Maximum: 0.010 MB (on task 0) + | Average: 0.010 MB + | Peak value for overall tracked memory usage: + | Minimum: 0.549 MB (on task 0 after allocating grid_partition) + | Maximum: 0.549 MB (on task 0 after allocating grid_partition) + | Average: 0.549 MB + | Largest tracked array allocation so far: + | Minimum: 0.364 MB (all_coords on task 0) + | Maximum: 0.364 MB (all_coords on task 0) + | Average: 0.364 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + Removing unitary transformations (pure translations, rotations) from forces on atoms. + Atomic forces before filtering: + | Net force on center of mass : 0.970908E-12 -0.489462E-11 -0.224546E-01 eV/A + | Net torque on center of mass: 0.196541E-11 0.381900E-12 0.282785E-13 eV + Atomic forces after filtering: + | Net force on center of mass : -0.365084E-27 0.223008E-16 -0.223008E-16 eV/A + | Net torque on center of mass: 0.118011E-16 -0.241892E-28 0.309607E-28 eV + + Energy and forces in a compact form: + | Total energy uncorrected : -0.208083144759841E+04 eV + | Total energy corrected : -0.208083144759841E+04 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -0.208083144759841E+04 eV + Total atomic forces (unitary forces cleaned) [eV/Ang]: + | 1 -0.162259424656531E-27 -0.272372884812723E-11 0.192619418545703E+00 + | 2 -0.121694568492398E-27 0.170544629723911E+00 -0.963097092739153E-01 + | 3 -0.811297123282653E-28 -0.170544629721187E+00 -0.963097092717873E-01 + + ------------------------------------ + Start decomposition of the XC Energy + ------------------------------------ + X and C from original XC functional choice + Hartree-Fock Energy : 0.000000000 Ha 0.000000000 eV + X Energy : -8.918299910 Ha -242.679287946 eV + C Energy : -0.325149335 Ha -8.847763582 eV + XC Energy w/o HF : -9.243449246 Ha -251.527051528 eV + Total XC Energy : -9.243449246 Ha -251.527051528 eV + ------------------------------------ + LDA X and C from self-consistent density + X Energy LDA : -8.102145071 Ha -220.470584797 eV + C Energy LDA : -0.659545176 Ha -17.947137392 eV + ------------------------------------ + End decomposition of the XC Energy + ------------------------------------ + +------------------------------------------------------------ + Relaxation / MD: End force evaluation. : max(cpu_time) wall_clock(cpu1) + | Time for this force evaluation : 0.768 s 0.768 s + +------------------------------------------------------------ + Geometry optimization: Attempting to predict improved coordinates. + + Removing unitary transformations (pure translations, rotations) from forces on atoms. + Atomic forces before filtering: + | Net force on center of mass : -0.365084E-27 0.223008E-16 -0.223008E-16 eV/A + | Net torque on center of mass: 0.118011E-16 -0.241892E-28 0.309607E-28 eV + Atomic forces after filtering: + | Net force on center of mass : 0.108086E-42 0.223008E-16 -0.223008E-16 eV/A + | Net torque on center of mass: -0.118011E-16 0.211671E-59 0.000000E+00 eV + Net remaining forces (excluding translations, rotations) in present geometry: + || Forces on atoms || = 0.192619E+00 eV/A. + Maximum force component is 0.192619E+00 eV/A. + Present geometry is not yet converged. + + Relaxation step number 1: Predicting new coordinates. + + Advancing geometry using trust radius method. + Allocating 0.002 MB for stored_KS_eigenvector + | Hessian has 0 negative and 6 zero eigenvalues. + | Positive eigenvalues (eV/A^2): 3.26E+01 ... 1.51E+02 + | Use Quasi-Newton step of length |H^-1 F| = 4.31E-03 A. + Finished advancing geometry + | Time : 0.001 s + Updated atomic structure: + x [A] y [A] z [A] + atom -0.00000000 -0.00000000 0.11975785 O + atom 0.00000000 0.76625386 -0.47729492 H + atom -0.00000000 -0.76625386 -0.47729492 H +------------------------------------------------------------ + Writing the current geometry to file "geometry.in.next_step". + Writing estimated Hessian matrix to file 'hessian.aims' + +------------------------------------------------------------ + Begin self-consistency loop: Re-initialization. + + Date : 20230628, Time : 095501.742 +------------------------------------------------------------ + + Initializing index lists of integration centers etc. from given atomic structure: + | Number of centers in hartree potential : 3 + | Number of centers in hartree multipole : 3 + | Number of centers in electron density summation: 3 + | Number of centers in basis integrals : 3 + | Number of centers in integrals : 3 + | Number of centers in hamiltonian : 3 + Partitioning the integration grid into batches with parallel hashing+maxmin method. + | Number of batches: 256 + | Maximal batch size: 65 + | Minimal batch size: 60 + | Average batch size: 62.203 + | Standard deviation of batch sizes: 1.470 + + Integration load balanced across 1 MPI tasks. + Work distribution over tasks is as follows: + Initializing partition tables, free-atom densities, potentials, etc. across the integration grid (initialize_grid_storage). + | Species 1: outer_partition_radius set to 5.048384829883283 AA . + | Species 2: outer_partition_radius set to 5.054417573612229 AA . + | The sparse table of interatomic distances needs 0.09 kbyte instead of 0.07 kbyte of memory. + | Using the partition_type stratmann_smoother will reduce your memory usage. + | Net number of integration points: 15924 + | of which are non-zero points : 14544 + Renormalizing the initial density to the exact electron count on the 3D integration grid. + | Initial density: Formal number of electrons (from input files) : 10.0000000000 + | Integrated number of electrons on 3D grid : 9.9999452850 + | Charge integration error : -0.0000547150 + | Normalization factor for density and gradient : 1.0000054715 + Renormalizing the free-atom superposition density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 10.0000000000 + | Integrated number of electrons on 3D grid : 9.9999452850 + | Charge integration error : -0.0000547150 + | Normalization factor for density and gradient : 1.0000054715 + Obtaining max. number of non-zero basis functions in each batch (get_n_compute_maxes). + Calculating total energy contributions from superposition of free atom densities. + Initialize hartree_potential_storage + Integrating overlap matrix. + Time summed over all CPUs for integration: real work 0.006 s, elapsed 0.006 s + Orthonormalizing eigenvectors + + End scf reinitialization - timings : max(cpu_time) wall_clock(cpu1) + | Time for scf. reinitialization : 0.034 s 0.035 s + | Boundary condition initialization : 0.000 s 0.000 s + | Integration : 0.006 s 0.006 s + | Grid partitioning : 0.012 s 0.012 s + | Preloading free-atom quantities on grid : 0.008 s 0.008 s + | Free-atom superposition energy : 0.008 s 0.008 s + | K.-S. eigenvector reorthonormalization : 0.000 s 0.000 s +------------------------------------------------------------ + Evaluating new KS density. + Integration grid: deviation in total charge ( - N_e) = 3.197442E-14 + + Time for density update prior : max(cpu_time) wall_clock(cpu1) + | self-consistency iterative process : 0.013 s 0.013 s + +------------------------------------------------------------ + Begin self-consistency iteration # 1 + + Date : 20230628, Time : 095501.790 +------------------------------------------------------------ + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 10.0000000000 + | Integrated number of electrons on 3D grid : 10.0000000000 + | Charge integration error : -0.0000000000 + | Normalization factor for density and gradient : 1.0000000000 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = -0.275495E-13 + | Sum of charges compensated after spline to logarithmic grids = 0.163522E-03 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = -0.263688E-13 + Summing up the Hartree potential. + Time summed over all CPUs for potential: real work 0.007 s, elapsed 0.007 s + | RMS charge density error from multipole expansion : 0.648259E-02 + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.021 s, elapsed 0.021 s + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.000 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -0.78602879 eV + Writing Kohn-Sham eigenvalues. + + State Occupation Eigenvalue [Ha] Eigenvalue [eV] + 1 2.00000 -18.786961 -511.21921 + 2 2.00000 -0.924744 -25.16357 + 3 2.00000 -0.477899 -13.00430 + 4 2.00000 -0.337826 -9.19272 + 5 2.00000 -0.259220 -7.05374 + 6 0.00000 0.002973 0.08091 + 7 0.00000 0.101163 2.75279 + 8 0.00000 0.298452 8.12129 + 9 0.00000 0.334566 9.10401 + 10 0.00000 0.369686 10.05966 + 11 0.00000 0.576213 15.67956 + + Highest occupied state (VBM) at -7.05373863 eV + | Occupation number: 2.00000000 + + Lowest unoccupied state (CBM) at 0.08091291 eV + | Occupation number: 0.00000000 + + Overall HOMO-LUMO gap: 7.13465154 eV. + + Total energy components: + | Sum of eigenvalues : -41.57330097 Ha -1131.26707776 eV + | XC energy correction : -9.24195258 Ha -251.48632509 eV + | XC potential correction : 11.88782558 Ha 323.48419268 eV + | Free-atom electrostatic energy: -35.73400870 Ha -972.37185039 eV + | Hartree energy correction : -1.80774296 Ha -49.19118864 eV + | Entropy correction : 0.00000000 Ha 0.00000000 eV + | --------------------------- + | Total energy : -76.46917963 Ha -2080.83224920 eV + | Total energy, T -> 0 : -76.46917963 Ha -2080.83224920 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -76.46917963 Ha -2080.83224920 eV + + Derived energy quantities: + | Kinetic energy : 76.28290527 Ha 2075.76346597 eV + | Electrostatic energy : -143.51013232 Ha -3905.10939008 eV + | Energy correction for multipole + | error in Hartree potential : -0.00337689 Ha -0.09188981 eV + | Sum of eigenvalues per atom : -377.08902592 eV + | Total energy (T->0) per atom : -693.61074973 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -693.61074973 eV + Evaluating new KS density. + Integration grid: deviation in total charge ( - N_e) = -1.065814E-14 + + Self-consistency convergence accuracy: + | Change of charge density : 0.1749E+00 + | Change of sum of eigenvalues : -0.1131E+04 eV + | Change of total energy : -0.2081E+04 eV + + +------------------------------------------------------------ + End self-consistency iteration # 1 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 0.045 s 0.044 s + | Charge density update : 0.013 s 0.013 s + | Density mixing : 0.000 s 0.000 s + | Hartree multipole update : 0.002 s 0.002 s + | Hartree multipole summation : 0.008 s 0.007 s + | Integration : 0.021 s 0.022 s + | Solution of K.-S. eqns. : 0.000 s 0.000 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 0.012 MB (on task 0) + | Maximum: 0.012 MB (on task 0) + | Average: 0.012 MB + | Peak value for overall tracked memory usage: + | Minimum: 0.558 MB (on task 0 after allocating grid_partition) + | Maximum: 0.558 MB (on task 0 after allocating grid_partition) + | Average: 0.558 MB + | Largest tracked array allocation so far: + | Minimum: 0.364 MB (all_coords on task 0) + | Maximum: 0.364 MB (all_coords on task 0) + | Average: 0.364 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + +------------------------------------------------------------ + Begin self-consistency iteration # 2 + + Date : 20230628, Time : 095501.835 +------------------------------------------------------------ + Pulay mixing of updated and previous charge densities. + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 10.0000000000 + | Integrated number of electrons on 3D grid : 10.0000000000 + | Charge integration error : 0.0000000000 + | Normalization factor for density and gradient : 1.0000000000 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = -0.597725E-14 + | Sum of charges compensated after spline to logarithmic grids = 0.163328E-03 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = -0.619863E-14 + Summing up the Hartree potential. + Time summed over all CPUs for potential: real work 0.008 s, elapsed 0.008 s + | RMS charge density error from multipole expansion : 0.648262E-02 + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.021 s, elapsed 0.021 s + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.000 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -0.79074788 eV + Highest occupied state (VBM) at -7.06351364 eV + | Occupation number: 2.00000000 + + Lowest unoccupied state (CBM) at 0.07777841 eV + | Occupation number: 0.00000000 + + Overall HOMO-LUMO gap: 7.14129205 eV. + + Total energy components: + | Sum of eigenvalues : -41.57785097 Ha -1131.39088942 eV + | XC energy correction : -9.24136553 Ha -251.47035076 eV + | XC potential correction : 11.88705618 Ha 323.46325637 eV + | Free-atom electrostatic energy: -35.73400870 Ha -972.37185039 eV + | Hartree energy correction : -1.80300942 Ha -49.06238254 eV + | Entropy correction : 0.00000000 Ha 0.00000000 eV + | --------------------------- + | Total energy : -76.46917843 Ha -2080.83221673 eV + | Total energy, T -> 0 : -76.46917843 Ha -2080.83221673 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -76.46917843 Ha -2080.83221673 eV + + Derived energy quantities: + | Kinetic energy : 76.27940659 Ha 2075.66826204 eV + | Electrostatic energy : -143.50721949 Ha -3905.03012801 eV + | Energy correction for multipole + | error in Hartree potential : -0.00338681 Ha -0.09215988 eV + | Sum of eigenvalues per atom : -377.13029647 eV + | Total energy (T->0) per atom : -693.61073891 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -693.61073891 eV + Evaluating new KS density. + Integration grid: deviation in total charge ( - N_e) = 3.730349E-14 + + Self-consistency convergence accuracy: + | Change of charge density : 0.1768E-02 + | Change of sum of eigenvalues : -0.1238E+00 eV + | Change of total energy : 0.3246E-04 eV + + +------------------------------------------------------------ + End self-consistency iteration # 2 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 0.045 s 0.044 s + | Charge density update : 0.013 s 0.013 s + | Density mixing : 0.001 s 0.000 s + | Hartree multipole update : 0.002 s 0.002 s + | Hartree multipole summation : 0.008 s 0.008 s + | Integration : 0.021 s 0.021 s + | Solution of K.-S. eqns. : 0.000 s 0.000 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 0.012 MB (on task 0) + | Maximum: 0.012 MB (on task 0) + | Average: 0.012 MB + | Peak value for overall tracked memory usage: + | Minimum: 0.558 MB (on task 0 after allocating grid_partition) + | Maximum: 0.558 MB (on task 0 after allocating grid_partition) + | Average: 0.558 MB + | Largest tracked array allocation so far: + | Minimum: 0.364 MB (all_coords on task 0) + | Maximum: 0.364 MB (all_coords on task 0) + | Average: 0.364 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + +------------------------------------------------------------ + Begin self-consistency iteration # 3 + + Date : 20230628, Time : 095501.879 +------------------------------------------------------------ + Pulay mixing of updated and previous charge densities. + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 10.0000000000 + | Integrated number of electrons on 3D grid : 10.0000000000 + | Charge integration error : -0.0000000000 + | Normalization factor for density and gradient : 1.0000000000 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = -0.102179E-12 + | Sum of charges compensated after spline to logarithmic grids = 0.163184E-03 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = -0.102671E-12 + Summing up the Hartree potential. + Time summed over all CPUs for potential: real work 0.008 s, elapsed 0.008 s + | RMS charge density error from multipole expansion : 0.648125E-02 + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.021 s, elapsed 0.021 s + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.000 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -0.79492051 eV + Highest occupied state (VBM) at -7.07052261 eV + | Occupation number: 2.00000000 + + Lowest unoccupied state (CBM) at 0.07510135 eV + | Occupation number: 0.00000000 + + Overall HOMO-LUMO gap: 7.14562396 eV. + + Total energy components: + | Sum of eigenvalues : -41.58115491 Ha -1131.48079421 eV + | XC energy correction : -9.24092567 Ha -251.45838141 eV + | XC potential correction : 11.88648080 Ha 323.44759935 eV + | Free-atom electrostatic energy: -35.73400870 Ha -972.37185039 eV + | Hartree energy correction : -1.79956965 Ha -48.96878163 eV + | Entropy correction : 0.00000000 Ha 0.00000000 eV + | --------------------------- + | Total energy : -76.46917812 Ha -2080.83220829 eV + | Total energy, T -> 0 : -76.46917812 Ha -2080.83220829 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -76.46917812 Ha -2080.83220829 eV + + Derived energy quantities: + | Kinetic energy : 76.27702007 Ha 2075.60332155 eV + | Electrostatic energy : -143.50527252 Ha -3904.97714843 eV + | Energy correction for multipole + | error in Hartree potential : -0.00339473 Ha -0.09237528 eV + | Sum of eigenvalues per atom : -377.16026474 eV + | Total energy (T->0) per atom : -693.61073610 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -693.61073610 eV + Evaluating new KS density. + Integration grid: deviation in total charge ( - N_e) = 2.842171E-14 + + Self-consistency convergence accuracy: + | Change of charge density : 0.8560E-03 + | Change of sum of eigenvalues : -0.8990E-01 eV + | Change of total energy : 0.8441E-05 eV + + +------------------------------------------------------------ + End self-consistency iteration # 3 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 0.046 s 0.046 s + | Charge density update : 0.013 s 0.013 s + | Density mixing : 0.002 s 0.002 s + | Hartree multipole update : 0.002 s 0.002 s + | Hartree multipole summation : 0.008 s 0.008 s + | Integration : 0.021 s 0.021 s + | Solution of K.-S. eqns. : 0.000 s 0.000 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 0.012 MB (on task 0) + | Maximum: 0.012 MB (on task 0) + | Average: 0.012 MB + | Peak value for overall tracked memory usage: + | Minimum: 0.558 MB (on task 0 after allocating grid_partition) + | Maximum: 0.558 MB (on task 0 after allocating grid_partition) + | Average: 0.558 MB + | Largest tracked array allocation so far: + | Minimum: 0.364 MB (all_coords on task 0) + | Maximum: 0.364 MB (all_coords on task 0) + | Average: 0.364 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + +------------------------------------------------------------ + Begin self-consistency iteration # 4 + + Date : 20230628, Time : 095501.925 +------------------------------------------------------------ + Pulay mixing of updated and previous charge densities. + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 10.0000000000 + | Integrated number of electrons on 3D grid : 10.0000000000 + | Charge integration error : -0.0000000000 + | Normalization factor for density and gradient : 1.0000000000 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = -0.100851E-13 + | Sum of charges compensated after spline to logarithmic grids = 0.163145E-03 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = -0.956852E-14 + Summing up the Hartree potential. + Time summed over all CPUs for potential: real work 0.008 s, elapsed 0.008 s + | RMS charge density error from multipole expansion : 0.647691E-02 + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.021 s, elapsed 0.021 s + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.000 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -0.79780277 eV + Highest occupied state (VBM) at -7.07168466 eV + | Occupation number: 2.00000000 + + Lowest unoccupied state (CBM) at 0.07346652 eV + | Occupation number: 0.00000000 + + Overall HOMO-LUMO gap: 7.14515119 eV. + + Total energy components: + | Sum of eigenvalues : -41.58182615 Ha -1131.49905950 eV + | XC energy correction : -9.24079857 Ha -251.45492285 eV + | XC potential correction : 11.88631758 Ha 323.44315793 eV + | Free-atom electrostatic energy: -35.73400870 Ha -972.37185039 eV + | Hartree energy correction : -1.79886203 Ha -48.94952637 eV + | Entropy correction : 0.00000000 Ha 0.00000000 eV + | --------------------------- + | Total energy : -76.46917786 Ha -2080.83220117 eV + | Total energy, T -> 0 : -76.46917786 Ha -2080.83220117 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -76.46917786 Ha -2080.83220117 eV + + Derived energy quantities: + | Kinetic energy : 76.27701160 Ha 2075.60309121 eV + | Electrostatic energy : -143.50539090 Ha -3904.98036954 eV + | Energy correction for multipole + | error in Hartree potential : -0.00339850 Ha -0.09247781 eV + | Sum of eigenvalues per atom : -377.16635317 eV + | Total energy (T->0) per atom : -693.61073372 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -693.61073372 eV + Evaluating new KS density. + Integration grid: deviation in total charge ( - N_e) = 1.776357E-14 + + Self-consistency convergence accuracy: + | Change of charge density : 0.3853E-03 + | Change of sum of eigenvalues : -0.1827E-01 eV + | Change of total energy : 0.7116E-05 eV + + +------------------------------------------------------------ + End self-consistency iteration # 4 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 0.047 s 0.048 s + | Charge density update : 0.013 s 0.014 s + | Density mixing : 0.002 s 0.003 s + | Hartree multipole update : 0.002 s 0.002 s + | Hartree multipole summation : 0.008 s 0.008 s + | Integration : 0.021 s 0.021 s + | Solution of K.-S. eqns. : 0.000 s 0.000 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 0.012 MB (on task 0) + | Maximum: 0.012 MB (on task 0) + | Average: 0.012 MB + | Peak value for overall tracked memory usage: + | Minimum: 0.558 MB (on task 0 after allocating grid_partition) + | Maximum: 0.558 MB (on task 0 after allocating grid_partition) + | Average: 0.558 MB + | Largest tracked array allocation so far: + | Minimum: 0.364 MB (all_coords on task 0) + | Maximum: 0.364 MB (all_coords on task 0) + | Average: 0.364 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + +------------------------------------------------------------ + Begin self-consistency iteration # 5 + + Date : 20230628, Time : 095501.973 +------------------------------------------------------------ + Pulay mixing of updated and previous charge densities. + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 10.0000000000 + | Integrated number of electrons on 3D grid : 10.0000000000 + | Charge integration error : 0.0000000000 + | Normalization factor for density and gradient : 1.0000000000 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = 0.734734E-13 + | Sum of charges compensated after spline to logarithmic grids = 0.163149E-03 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = 0.722190E-13 + Summing up the Hartree potential. + Time summed over all CPUs for potential: real work 0.008 s, elapsed 0.008 s + | RMS charge density error from multipole expansion : 0.647648E-02 + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.021 s, elapsed 0.021 s + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.000 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -0.79766159 eV + Highest occupied state (VBM) at -7.07161384 eV + | Occupation number: 2.00000000 + + Lowest unoccupied state (CBM) at 0.07355349 eV + | Occupation number: 0.00000000 + + Overall HOMO-LUMO gap: 7.14516733 eV. + + Total energy components: + | Sum of eigenvalues : -41.58180799 Ha -1131.49856536 eV + | XC energy correction : -9.24080192 Ha -251.45501412 eV + | XC potential correction : 11.88632210 Ha 323.44328082 eV + | Free-atom electrostatic energy: -35.73400870 Ha -972.37185039 eV + | Hartree energy correction : -1.79888135 Ha -48.95005198 eV + | Entropy correction : 0.00000000 Ha 0.00000000 eV + | --------------------------- + | Total energy : -76.46917786 Ha -2080.83220103 eV + | Total energy, T -> 0 : -76.46917786 Ha -2080.83220103 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -76.46917786 Ha -2080.83220103 eV + + Derived energy quantities: + | Kinetic energy : 76.27714979 Ha 2075.60685147 eV + | Electrostatic energy : -143.50552573 Ha -3904.98403838 eV + | Energy correction for multipole + | error in Hartree potential : -0.00339898 Ha -0.09249098 eV + | Sum of eigenvalues per atom : -377.16618845 eV + | Total energy (T->0) per atom : -693.61073368 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -693.61073368 eV + Evaluating new KS density. + Integration grid: deviation in total charge ( - N_e) = 1.065814E-14 + + Self-consistency convergence accuracy: + | Change of charge density : 0.5809E-04 + | Change of sum of eigenvalues : 0.4941E-03 eV + | Change of total energy : 0.1457E-06 eV + + +------------------------------------------------------------ + End self-consistency iteration # 5 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 0.045 s 0.045 s + | Charge density update : 0.013 s 0.013 s + | Density mixing : 0.002 s 0.002 s + | Hartree multipole update : 0.002 s 0.001 s + | Hartree multipole summation : 0.008 s 0.008 s + | Integration : 0.021 s 0.021 s + | Solution of K.-S. eqns. : 0.000 s 0.000 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 0.012 MB (on task 0) + | Maximum: 0.012 MB (on task 0) + | Average: 0.012 MB + | Peak value for overall tracked memory usage: + | Minimum: 0.558 MB (on task 0 after allocating grid_partition) + | Maximum: 0.558 MB (on task 0 after allocating grid_partition) + | Average: 0.558 MB + | Largest tracked array allocation so far: + | Minimum: 0.364 MB (all_coords on task 0) + | Maximum: 0.364 MB (all_coords on task 0) + | Average: 0.364 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + +------------------------------------------------------------ + Begin self-consistency iteration # 6 + + Date : 20230628, Time : 095502.018 +------------------------------------------------------------ + Pulay mixing of updated and previous charge densities. + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 10.0000000000 + | Integrated number of electrons on 3D grid : 10.0000000000 + | Charge integration error : -0.0000000000 + | Normalization factor for density and gradient : 1.0000000000 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = -0.293451E-13 + | Sum of charges compensated after spline to logarithmic grids = 0.163149E-03 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = -0.294189E-13 + Summing up the Hartree potential. + Time summed over all CPUs for potential: real work 0.008 s, elapsed 0.008 s + | RMS charge density error from multipole expansion : 0.647651E-02 + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.021 s, elapsed 0.021 s + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.000 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -0.79766462 eV + Highest occupied state (VBM) at -7.07163976 eV + | Occupation number: 2.00000000 + + Lowest unoccupied state (CBM) at 0.07354940 eV + | Occupation number: 0.00000000 + + Overall HOMO-LUMO gap: 7.14518917 eV. + + Total energy components: + | Sum of eigenvalues : -41.58181936 Ha -1131.49887469 eV + | XC energy correction : -9.24080079 Ha -251.45498348 eV + | XC potential correction : 11.88632061 Ha 323.44324034 eV + | Free-atom electrostatic energy: -35.73400870 Ha -972.37185039 eV + | Hartree energy correction : -1.79886962 Ha -48.94973278 eV + | Entropy correction : 0.00000000 Ha 0.00000000 eV + | --------------------------- + | Total energy : -76.46917785 Ha -2080.83220101 eV + | Total energy, T -> 0 : -76.46917785 Ha -2080.83220101 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -76.46917785 Ha -2080.83220101 eV + + Derived energy quantities: + | Kinetic energy : 76.27714255 Ha 2075.60665457 eV + | Electrostatic energy : -143.50551961 Ha -3904.98387210 eV + | Energy correction for multipole + | error in Hartree potential : -0.00339903 Ha -0.09249230 eV + | Sum of eigenvalues per atom : -377.16629156 eV + | Total energy (T->0) per atom : -693.61073367 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -693.61073367 eV + Evaluating new KS density. + Integration grid: deviation in total charge ( - N_e) = -1.598721E-14 + + Self-consistency convergence accuracy: + | Change of charge density : 0.3640E-05 + | Change of sum of eigenvalues : -0.3093E-03 eV + | Change of total energy : 0.2309E-07 eV + + +------------------------------------------------------------ + End self-consistency iteration # 6 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 0.046 s 0.046 s + | Charge density update : 0.013 s 0.013 s + | Density mixing : 0.002 s 0.002 s + | Hartree multipole update : 0.002 s 0.002 s + | Hartree multipole summation : 0.008 s 0.008 s + | Integration : 0.021 s 0.021 s + | Solution of K.-S. eqns. : 0.000 s 0.000 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 0.012 MB (on task 0) + | Maximum: 0.012 MB (on task 0) + | Average: 0.012 MB + | Peak value for overall tracked memory usage: + | Minimum: 0.558 MB (on task 0 after allocating grid_partition) + | Maximum: 0.558 MB (on task 0 after allocating grid_partition) + | Average: 0.558 MB + | Largest tracked array allocation so far: + | Minimum: 0.364 MB (all_coords on task 0) + | Maximum: 0.364 MB (all_coords on task 0) + | Average: 0.364 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + +------------------------------------------------------------ + Begin self-consistency iteration # 7 + + Date : 20230628, Time : 095502.065 +------------------------------------------------------------ + Pulay mixing of updated and previous charge densities. + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 10.0000000000 + | Integrated number of electrons on 3D grid : 10.0000000000 + | Charge integration error : 0.0000000000 + | Normalization factor for density and gradient : 1.0000000000 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = 0.478672E-13 + | Sum of charges compensated after spline to logarithmic grids = 0.163150E-03 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = 0.480148E-13 + Summing up the Hartree potential. + Time summed over all CPUs for potential: real work 0.007 s, elapsed 0.007 s + | RMS charge density error from multipole expansion : 0.647652E-02 + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.022 s, elapsed 0.022 s + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.000 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -0.79764716 eV + Highest occupied state (VBM) at -7.07161517 eV + | Occupation number: 2.00000000 + + Lowest unoccupied state (CBM) at 0.07355967 eV + | Occupation number: 0.00000000 + + Overall HOMO-LUMO gap: 7.14517483 eV. + + Total energy components: + | Sum of eigenvalues : -41.58180747 Ha -1131.49855116 eV + | XC energy correction : -9.24080255 Ha -251.45503119 eV + | XC potential correction : 11.88632290 Ha 323.44330269 eV + | Free-atom electrostatic energy: -35.73400870 Ha -972.37185039 eV + | Hartree energy correction : -1.79888204 Ha -48.95007091 eV + | Entropy correction : 0.00000000 Ha 0.00000000 eV + | --------------------------- + | Total energy : -76.46917785 Ha -2080.83220096 eV + | Total energy, T -> 0 : -76.46917785 Ha -2080.83220096 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -76.46917785 Ha -2080.83220096 eV + + Derived energy quantities: + | Kinetic energy : 76.27715281 Ha 2075.60693365 eV + | Electrostatic energy : -143.50552812 Ha -3904.98410342 eV + | Energy correction for multipole + | error in Hartree potential : -0.00339902 Ha -0.09249210 eV + | Sum of eigenvalues per atom : -377.16618372 eV + | Total energy (T->0) per atom : -693.61073365 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -693.61073365 eV + Evaluating new KS density. + Integration grid: deviation in total charge ( - N_e) = -1.776357E-14 + + Self-consistency convergence accuracy: + | Change of charge density : 0.2447E-05 + | Change of sum of eigenvalues : 0.3235E-03 eV + | Change of total energy : 0.4341E-07 eV + + Electronic self-consistency reached - switching on the force computation. + + +------------------------------------------------------------ + End self-consistency iteration # 7 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 0.047 s 0.046 s + | Charge density & force component update : 0.013 s 0.012 s + | Density mixing : 0.003 s 0.003 s + | Hartree multipole update : 0.002 s 0.001 s + | Hartree multipole summation : 0.008 s 0.008 s + | Hartree pot. SCF incomplete forces : 0.015 s 0.015 s + | Integration : 0.022 s 0.021 s + | Solution of K.-S. eqns. : 0.000 s 0.000 s + | Total energy evaluation : 0.000 s 0.001 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 0.012 MB (on task 0) + | Maximum: 0.012 MB (on task 0) + | Average: 0.012 MB + | Peak value for overall tracked memory usage: + | Minimum: 0.558 MB (on task 0 after allocating grid_partition) + | Maximum: 0.558 MB (on task 0 after allocating grid_partition) + | Average: 0.558 MB + | Largest tracked array allocation so far: + | Minimum: 0.364 MB (all_coords on task 0) + | Maximum: 0.364 MB (all_coords on task 0) + | Average: 0.364 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + +------------------------------------------------------------ + Begin self-consistency iteration # 8 + + Date : 20230628, Time : 095502.112 +------------------------------------------------------------ + Pulay mixing of updated and previous charge densities. + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 10.0000000000 + | Integrated number of electrons on 3D grid : 10.0000000000 + | Charge integration error : -0.0000000000 + | Normalization factor for density and gradient : 1.0000000000 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = 0.154966E-14 + | Sum of charges compensated after spline to logarithmic grids = 0.163150E-03 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = 0.491955E-15 + Summing up the Hartree potential. + Time summed over all CPUs for potential: real work 0.024 s, elapsed 0.024 s + | RMS charge density error from multipole expansion : 0.647652E-02 + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.022 s, elapsed 0.022 s + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.000 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -0.79764888 eV + Highest occupied state (VBM) at -7.07161657 eV + | Occupation number: 2.00000000 + + Lowest unoccupied state (CBM) at 0.07355876 eV + | Occupation number: 0.00000000 + + Overall HOMO-LUMO gap: 7.14517533 eV. + + Total energy components: + | Sum of eigenvalues : -41.58180820 Ha -1131.49857114 eV + | XC energy correction : -9.24080241 Ha -251.45502746 eV + | XC potential correction : 11.88632272 Ha 323.44329787 eV + | Free-atom electrostatic energy: -35.73400870 Ha -972.37185039 eV + | Hartree energy correction : -1.79888127 Ha -48.95004984 eV + | Entropy correction : 0.00000000 Ha 0.00000000 eV + | --------------------------- + | Total energy : -76.46917785 Ha -2080.83220096 eV + | Total energy, T -> 0 : -76.46917785 Ha -2080.83220096 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -76.46917785 Ha -2080.83220096 eV + + Derived energy quantities: + | Kinetic energy : 76.27715179 Ha 2075.60690600 eV + | Electrostatic energy : -143.50552724 Ha -3904.98407951 eV + | Energy correction for multipole + | error in Hartree potential : -0.00339903 Ha -0.09249223 eV + | Sum of eigenvalues per atom : -377.16619038 eV + | Total energy (T->0) per atom : -693.61073365 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -693.61073365 eV + Evaluating new KS density and force components. + Integration grid: deviation in total charge ( - N_e) = 2.309264E-14 + + atomic forces [eV/Ang]: + ----------------------- + atom # 1 + Hellmann-Feynman : 0.201844E-12 0.174695E-11 0.175356E+02 + Ionic forces : 0.000000E+00 0.000000E+00 0.000000E+00 + Multipole : 0.327274E-14 -0.151196E-12 -0.901744E-01 + Hartree pot. SCF incomplete : -0.268758E-12 -0.585313E-12 0.126175E-06 + Pulay + GGA : -0.376705E-11 -0.965991E-11 -0.174065E+02 + ---------------------------------------------------------------- + Total forces( 1) : -0.383069E-11 -0.864947E-11 0.389048E-01 + atom # 2 + Hellmann-Feynman : 0.222344E-14 0.338393E+00 -0.336427E+00 + Ionic forces : 0.000000E+00 0.000000E+00 0.000000E+00 + Multipole : 0.388560E-15 -0.450322E-02 -0.316752E-01 + Hartree pot. SCF incomplete : -0.186922E-13 -0.193470E-06 0.484390E-06 + Pulay + GGA : 0.205836E-13 -0.291714E+00 0.338461E+00 + ---------------------------------------------------------------- + Total forces( 2) : 0.450345E-14 0.421758E-01 -0.296398E-01 + atom # 3 + Hellmann-Feynman : 0.186135E-13 -0.338393E+00 -0.336427E+00 + Ionic forces : 0.000000E+00 0.000000E+00 0.000000E+00 + Multipole : 0.587569E-16 0.450322E-02 -0.316752E-01 + Hartree pot. SCF incomplete : -0.201227E-14 0.193470E-06 0.484390E-06 + Pulay + GGA : -0.338477E-13 0.291714E+00 0.338461E+00 + ---------------------------------------------------------------- + Total forces( 3) : -0.171877E-13 -0.421758E-01 -0.296398E-01 + + + Self-consistency convergence accuracy: + | Change of charge density : 0.2123E-06 + | Change of sum of eigenvalues : -0.1998E-04 eV + | Change of total energy : 0.1053E-08 eV + | Change of forces : 0.4504E+00 eV/A + + Writing Kohn-Sham eigenvalues. + + State Occupation Eigenvalue [Ha] Eigenvalue [eV] + 1 2.00000 -18.788449 -511.25972 + 2 2.00000 -0.925547 -25.18540 + 3 2.00000 -0.478591 -13.02311 + 4 2.00000 -0.338440 -9.20943 + 5 2.00000 -0.259877 -7.07162 + 6 0.00000 0.002703 0.07356 + 7 0.00000 0.100819 2.74341 + 8 0.00000 0.298122 8.11233 + 9 0.00000 0.334207 9.09425 + 10 0.00000 0.369442 10.05302 + 11 0.00000 0.575820 15.66887 + + Highest occupied state (VBM) at -7.07161657 eV + | Occupation number: 2.00000000 + + Lowest unoccupied state (CBM) at 0.07355876 eV + | Occupation number: 0.00000000 + + Overall HOMO-LUMO gap: 7.14517533 eV. + | Chemical Potential : -0.79764888 eV + + Self-consistency cycle converged. + + +------------------------------------------------------------ + End self-consistency iteration # 8 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 0.118 s 0.118 s + | Charge density & force component update : 0.054 s 0.054 s + | Density mixing : 0.002 s 0.002 s + | Hartree multipole update : 0.002 s 0.001 s + | Hartree multipole summation : 0.024 s 0.024 s + | Hartree pot. SCF incomplete forces : 0.015 s 0.015 s + | Integration : 0.022 s 0.022 s + | Solution of K.-S. eqns. : 0.000 s 0.000 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 0.012 MB (on task 0) + | Maximum: 0.012 MB (on task 0) + | Average: 0.012 MB + | Peak value for overall tracked memory usage: + | Minimum: 0.558 MB (on task 0 after allocating grid_partition) + | Maximum: 0.558 MB (on task 0 after allocating grid_partition) + | Average: 0.558 MB + | Largest tracked array allocation so far: + | Minimum: 0.364 MB (all_coords on task 0) + | Maximum: 0.364 MB (all_coords on task 0) + | Average: 0.364 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + Removing unitary transformations (pure translations, rotations) from forces on atoms. + Atomic forces before filtering: + | Net force on center of mass : -0.384337E-11 -0.107254E-10 -0.203748E-01 eV/A + | Net torque on center of mass: 0.424425E-11 -0.152222E-11 -0.166209E-13 eV + Atomic forces after filtering: + | Net force on center of mass : 0.811297E-27 0.000000E+00 0.000000E+00 eV/A + | Net torque on center of mass: -0.590053E-17 -0.645850E-28 0.644757E-35 eV + + Energy and forces in a compact form: + | Total energy uncorrected : -0.208083220096086E+04 eV + | Total energy corrected : -0.208083220096086E+04 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -0.208083220096086E+04 eV + Total atomic forces (unitary forces cleaned) [eV/Ang]: + | 1 0.162259424656531E-27 -0.387786774244967E-11 0.456963966289359E-01 + | 2 0.324518849313061E-27 0.421757890961139E-01 -0.228481983159783E-01 + | 3 0.324518849313061E-27 -0.421757890922361E-01 -0.228481983129576E-01 + + ------------------------------------ + Start decomposition of the XC Energy + ------------------------------------ + X and C from original XC functional choice + Hartree-Fock Energy : 0.000000000 Ha 0.000000000 eV + X Energy : -8.915793610 Ha -242.611088036 eV + C Energy : -0.325008800 Ha -8.843939422 eV + XC Energy w/o HF : -9.240802410 Ha -251.455027457 eV + Total XC Energy : -9.240802410 Ha -251.455027457 eV + ------------------------------------ + LDA X and C from self-consistent density + X Energy LDA : -8.099651011 Ha -220.402717964 eV + C Energy LDA : -0.659406655 Ha -17.943368043 eV + ------------------------------------ + End decomposition of the XC Energy + ------------------------------------ + +------------------------------------------------------------ + Relaxation / MD: End force evaluation. : max(cpu_time) wall_clock(cpu1) + | Time for this force evaluation : 0.496 s 0.497 s + +------------------------------------------------------------ + Geometry optimization: Attempting to predict improved coordinates. + + Removing unitary transformations (pure translations, rotations) from forces on atoms. + Atomic forces before filtering: + | Net force on center of mass : 0.811297E-27 0.000000E+00 0.000000E+00 eV/A + | Net torque on center of mass: -0.590053E-17 -0.645850E-28 0.644757E-35 eV + Atomic forces after filtering: + | Net force on center of mass : -0.324259E-42 0.000000E+00 0.000000E+00 eV/A + | Net torque on center of mass: 0.000000E+00 0.790178E-39 0.209879E-38 eV + Net remaining forces (excluding translations, rotations) in present geometry: + || Forces on atoms || = 0.456964E-01 eV/A. + Maximum force component is 0.456964E-01 eV/A. + Present geometry is not yet converged. + + Relaxation step number 2: Predicting new coordinates. + + Advancing geometry using trust radius method. + | True / expected gain: -7.53E-04 eV / -5.86E-04 eV = 1.2860 + | Harmonic / expected gain: -7.30E-04 eV / -5.86E-04 eV = 1.2461 + | Using harmonic gain instead of DE to judge step. + | Hessian has 0 negative and 6 zero eigenvalues. + | Positive eigenvalues (eV/A^2): 2.88E+01 ... 1.51E+02 + | Use Quasi-Newton step of length |H^-1 F| = 1.44E-03 A. + Finished advancing geometry + | Time : 0.000 s + Updated atomic structure: + x [A] y [A] z [A] + atom 0.00000000 -0.00000000 0.11989040 O + atom 0.00000000 0.76726299 -0.47736120 H + atom -0.00000000 -0.76726299 -0.47736120 H +------------------------------------------------------------ + Writing the current geometry to file "geometry.in.next_step". + Writing estimated Hessian matrix to file 'hessian.aims' + +------------------------------------------------------------ + Begin self-consistency loop: Re-initialization. + + Date : 20230628, Time : 095502.239 +------------------------------------------------------------ + + Initializing index lists of integration centers etc. from given atomic structure: + | Number of centers in hartree potential : 3 + | Number of centers in hartree multipole : 3 + | Number of centers in electron density summation: 3 + | Number of centers in basis integrals : 3 + | Number of centers in integrals : 3 + | Number of centers in hamiltonian : 3 + Partitioning the integration grid into batches with parallel hashing+maxmin method. + | Number of batches: 256 + | Maximal batch size: 65 + | Minimal batch size: 60 + | Average batch size: 62.203 + | Standard deviation of batch sizes: 1.470 + + Integration load balanced across 1 MPI tasks. + Work distribution over tasks is as follows: + Initializing partition tables, free-atom densities, potentials, etc. across the integration grid (initialize_grid_storage). + | Species 1: outer_partition_radius set to 5.048384829883283 AA . + | Species 2: outer_partition_radius set to 5.054417573612229 AA . + | The sparse table of interatomic distances needs 0.09 kbyte instead of 0.07 kbyte of memory. + | Using the partition_type stratmann_smoother will reduce your memory usage. + | Net number of integration points: 15924 + | of which are non-zero points : 14544 + Renormalizing the initial density to the exact electron count on the 3D integration grid. + | Initial density: Formal number of electrons (from input files) : 10.0000000000 + | Integrated number of electrons on 3D grid : 9.9999460462 + | Charge integration error : -0.0000539538 + | Normalization factor for density and gradient : 1.0000053954 + Renormalizing the free-atom superposition density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 10.0000000000 + | Integrated number of electrons on 3D grid : 9.9999460462 + | Charge integration error : -0.0000539538 + | Normalization factor for density and gradient : 1.0000053954 + Obtaining max. number of non-zero basis functions in each batch (get_n_compute_maxes). + Calculating total energy contributions from superposition of free atom densities. + Initialize hartree_potential_storage + Integrating overlap matrix. + Time summed over all CPUs for integration: real work 0.006 s, elapsed 0.006 s + Orthonormalizing eigenvectors + + End scf reinitialization - timings : max(cpu_time) wall_clock(cpu1) + | Time for scf. reinitialization : 0.034 s 0.034 s + | Boundary condition initialization : 0.000 s 0.000 s + | Integration : 0.006 s 0.006 s + | Grid partitioning : 0.012 s 0.012 s + | Preloading free-atom quantities on grid : 0.008 s 0.008 s + | Free-atom superposition energy : 0.008 s 0.008 s + | K.-S. eigenvector reorthonormalization : 0.000 s 0.000 s +------------------------------------------------------------ + Evaluating new KS density. + Integration grid: deviation in total charge ( - N_e) = 1.776357E-15 + + Time for density update prior : max(cpu_time) wall_clock(cpu1) + | self-consistency iterative process : 0.013 s 0.014 s + +------------------------------------------------------------ + Begin self-consistency iteration # 1 + + Date : 20230628, Time : 095502.287 +------------------------------------------------------------ + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 10.0000000000 + | Integrated number of electrons on 3D grid : 10.0000000000 + | Charge integration error : -0.0000000000 + | Normalization factor for density and gradient : 1.0000000000 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = -0.126678E-13 + | Sum of charges compensated after spline to logarithmic grids = 0.163201E-03 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = -0.129138E-13 + Summing up the Hartree potential. + Time summed over all CPUs for potential: real work 0.008 s, elapsed 0.008 s + | RMS charge density error from multipole expansion : 0.647320E-02 + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.021 s, elapsed 0.021 s + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.000 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -0.81584664 eV + Writing Kohn-Sham eigenvalues. + + State Occupation Eigenvalue [Ha] Eigenvalue [eV] + 1 2.00000 -18.788066 -511.24929 + 2 2.00000 -0.924879 -25.16724 + 3 2.00000 -0.478157 -13.01133 + 4 2.00000 -0.338091 -9.19992 + 5 2.00000 -0.259583 -7.06362 + 6 0.00000 0.002580 0.07021 + 7 0.00000 0.100559 2.73636 + 8 0.00000 0.298340 8.11825 + 9 0.00000 0.334356 9.09828 + 10 0.00000 0.369759 10.06166 + 11 0.00000 0.575118 15.64975 + + Highest occupied state (VBM) at -7.06361568 eV + | Occupation number: 2.00000000 + + Lowest unoccupied state (CBM) at 0.07021039 eV + | Occupation number: 0.00000000 + + Overall HOMO-LUMO gap: 7.13382606 eV. + + Total energy components: + | Sum of eigenvalues : -41.57755222 Ha -1131.38275999 eV + | XC energy correction : -9.24031874 Ha -251.44186625 eV + | XC potential correction : 11.88568386 Ha 323.42591349 eV + | Free-atom electrostatic energy: -35.73811056 Ha -972.48346788 eV + | Hartree energy correction : -1.79888236 Ha -48.95007960 eV + | Entropy correction : 0.00000000 Ha 0.00000000 eV + | --------------------------- + | Total energy : -76.46918003 Ha -2080.83226023 eV + | Total energy, T -> 0 : -76.46918003 Ha -2080.83226023 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -76.46918003 Ha -2080.83226023 eV + + Derived energy quantities: + | Kinetic energy : 76.27592956 Ha 2075.57364729 eV + | Electrostatic energy : -143.50479084 Ha -3904.96404126 eV + | Energy correction for multipole + | error in Hartree potential : -0.00338139 Ha -0.09201220 eV + | Sum of eigenvalues per atom : -377.12758666 eV + | Total energy (T->0) per atom : -693.61075341 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -693.61075341 eV + Evaluating new KS density. + Integration grid: deviation in total charge ( - N_e) = 5.329071E-15 + + Self-consistency convergence accuracy: + | Change of charge density : 0.1747E+00 + | Change of sum of eigenvalues : -0.1131E+04 eV + | Change of total energy : -0.2081E+04 eV + + +------------------------------------------------------------ + End self-consistency iteration # 1 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 0.044 s 0.043 s + | Charge density update : 0.013 s 0.013 s + | Density mixing : 0.000 s 0.000 s + | Hartree multipole update : 0.002 s 0.002 s + | Hartree multipole summation : 0.008 s 0.007 s + | Integration : 0.021 s 0.021 s + | Solution of K.-S. eqns. : 0.000 s 0.000 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 0.012 MB (on task 0) + | Maximum: 0.012 MB (on task 0) + | Average: 0.012 MB + | Peak value for overall tracked memory usage: + | Minimum: 0.558 MB (on task 0 after allocating grid_partition) + | Maximum: 0.558 MB (on task 0 after allocating grid_partition) + | Average: 0.558 MB + | Largest tracked array allocation so far: + | Minimum: 0.364 MB (all_coords on task 0) + | Maximum: 0.364 MB (all_coords on task 0) + | Average: 0.364 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + +------------------------------------------------------------ + Begin self-consistency iteration # 2 + + Date : 20230628, Time : 095502.330 +------------------------------------------------------------ + Pulay mixing of updated and previous charge densities. + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 10.0000000000 + | Integrated number of electrons on 3D grid : 10.0000000000 + | Charge integration error : 0.0000000000 + | Normalization factor for density and gradient : 1.0000000000 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = 0.718254E-14 + | Sum of charges compensated after spline to logarithmic grids = 0.163136E-03 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = 0.755151E-14 + Summing up the Hartree potential. + Time summed over all CPUs for potential: real work 0.008 s, elapsed 0.008 s + | RMS charge density error from multipole expansion : 0.647322E-02 + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.021 s, elapsed 0.021 s + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.000 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -0.81737047 eV + Highest occupied state (VBM) at -7.06676776 eV + | Occupation number: 2.00000000 + + Lowest unoccupied state (CBM) at 0.06919607 eV + | Occupation number: 0.00000000 + + Overall HOMO-LUMO gap: 7.13596383 eV. + + Total energy components: + | Sum of eigenvalues : -41.57901894 Ha -1131.42267146 eV + | XC energy correction : -9.24012938 Ha -251.43671332 eV + | XC potential correction : 11.88543568 Ha 323.41916031 eV + | Free-atom electrostatic energy: -35.73811056 Ha -972.48346788 eV + | Hartree energy correction : -1.79735675 Ha -48.90856569 eV + | Entropy correction : 0.00000000 Ha 0.00000000 eV + | --------------------------- + | Total energy : -76.46917995 Ha -2080.83225804 eV + | Total energy, T -> 0 : -76.46917995 Ha -2080.83225804 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -76.46917995 Ha -2080.83225804 eV + + Derived energy quantities: + | Kinetic energy : 76.27479953 Ha 2075.54289761 eV + | Electrostatic energy : -143.50385010 Ha -3904.93844233 eV + | Energy correction for multipole + | error in Hartree potential : -0.00338459 Ha -0.09209942 eV + | Sum of eigenvalues per atom : -377.14089049 eV + | Total energy (T->0) per atom : -693.61075268 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -693.61075268 eV + Evaluating new KS density. + Integration grid: deviation in total charge ( - N_e) = -3.375078E-14 + + Self-consistency convergence accuracy: + | Change of charge density : 0.5698E-03 + | Change of sum of eigenvalues : -0.3991E-01 eV + | Change of total energy : 0.2186E-05 eV + + +------------------------------------------------------------ + End self-consistency iteration # 2 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 0.045 s 0.045 s + | Charge density update : 0.013 s 0.013 s + | Density mixing : 0.001 s 0.001 s + | Hartree multipole update : 0.002 s 0.002 s + | Hartree multipole summation : 0.008 s 0.007 s + | Integration : 0.021 s 0.022 s + | Solution of K.-S. eqns. : 0.000 s 0.000 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 0.012 MB (on task 0) + | Maximum: 0.012 MB (on task 0) + | Average: 0.012 MB + | Peak value for overall tracked memory usage: + | Minimum: 0.558 MB (on task 0 after allocating grid_partition) + | Maximum: 0.558 MB (on task 0 after allocating grid_partition) + | Average: 0.558 MB + | Largest tracked array allocation so far: + | Minimum: 0.364 MB (all_coords on task 0) + | Maximum: 0.364 MB (all_coords on task 0) + | Average: 0.364 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + +------------------------------------------------------------ + Begin self-consistency iteration # 3 + + Date : 20230628, Time : 095502.375 +------------------------------------------------------------ + Pulay mixing of updated and previous charge densities. + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 10.0000000000 + | Integrated number of electrons on 3D grid : 10.0000000000 + | Charge integration error : 0.0000000000 + | Normalization factor for density and gradient : 1.0000000000 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = 0.342155E-13 + | Sum of charges compensated after spline to logarithmic grids = 0.163089E-03 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = 0.350026E-13 + Summing up the Hartree potential. + Time summed over all CPUs for potential: real work 0.008 s, elapsed 0.008 s + | RMS charge density error from multipole expansion : 0.647279E-02 + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.021 s, elapsed 0.021 s + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.000 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -0.81872111 eV + Highest occupied state (VBM) at -7.06902905 eV + | Occupation number: 2.00000000 + + Lowest unoccupied state (CBM) at 0.06832818 eV + | Occupation number: 0.00000000 + + Overall HOMO-LUMO gap: 7.13735724 eV. + + Total energy components: + | Sum of eigenvalues : -41.58008451 Ha -1131.45166724 eV + | XC energy correction : -9.23998730 Ha -251.43284728 eV + | XC potential correction : 11.88524985 Ha 323.41410357 eV + | Free-atom electrostatic energy: -35.73811056 Ha -972.48346788 eV + | Hartree energy correction : -1.79624740 Ha -48.87837868 eV + | Entropy correction : 0.00000000 Ha 0.00000000 eV + | --------------------------- + | Total energy : -76.46917993 Ha -2080.83225751 eV + | Total energy, T -> 0 : -76.46917993 Ha -2080.83225751 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -76.46917993 Ha -2080.83225751 eV + + Derived energy quantities: + | Kinetic energy : 76.27402717 Ha 2075.52188073 eV + | Electrostatic energy : -143.50321980 Ha -3904.92129097 eV + | Energy correction for multipole + | error in Hartree potential : -0.00338715 Ha -0.09216904 eV + | Sum of eigenvalues per atom : -377.15055575 eV + | Total energy (T->0) per atom : -693.61075250 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -693.61075250 eV + Evaluating new KS density. + Integration grid: deviation in total charge ( - N_e) = 7.105427E-15 + + Self-consistency convergence accuracy: + | Change of charge density : 0.2761E-03 + | Change of sum of eigenvalues : -0.2900E-01 eV + | Change of total energy : 0.5288E-06 eV + + +------------------------------------------------------------ + End self-consistency iteration # 3 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 0.047 s 0.047 s + | Charge density update : 0.013 s 0.013 s + | Density mixing : 0.002 s 0.002 s + | Hartree multipole update : 0.002 s 0.002 s + | Hartree multipole summation : 0.008 s 0.009 s + | Integration : 0.021 s 0.021 s + | Solution of K.-S. eqns. : 0.000 s 0.000 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 0.012 MB (on task 0) + | Maximum: 0.012 MB (on task 0) + | Average: 0.012 MB + | Peak value for overall tracked memory usage: + | Minimum: 0.558 MB (on task 0 after allocating grid_partition) + | Maximum: 0.558 MB (on task 0 after allocating grid_partition) + | Average: 0.558 MB + | Largest tracked array allocation so far: + | Minimum: 0.364 MB (all_coords on task 0) + | Maximum: 0.364 MB (all_coords on task 0) + | Average: 0.364 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + +------------------------------------------------------------ + Begin self-consistency iteration # 4 + + Date : 20230628, Time : 095502.422 +------------------------------------------------------------ + Pulay mixing of updated and previous charge densities. + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 10.0000000000 + | Integrated number of electrons on 3D grid : 10.0000000000 + | Charge integration error : -0.0000000000 + | Normalization factor for density and gradient : 1.0000000000 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = -0.440300E-13 + | Sum of charges compensated after spline to logarithmic grids = 0.163076E-03 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = -0.448417E-13 + Summing up the Hartree potential. + Time summed over all CPUs for potential: real work 0.008 s, elapsed 0.008 s + | RMS charge density error from multipole expansion : 0.647142E-02 + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.021 s, elapsed 0.021 s + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.000 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -0.81965761 eV + Highest occupied state (VBM) at -7.06940695 eV + | Occupation number: 2.00000000 + + Lowest unoccupied state (CBM) at 0.06779685 eV + | Occupation number: 0.00000000 + + Overall HOMO-LUMO gap: 7.13720380 eV. + + Total energy components: + | Sum of eigenvalues : -41.58030203 Ha -1131.45758603 eV + | XC energy correction : -9.23994587 Ha -251.43171988 eV + | XC potential correction : 11.88519665 Ha 323.41265594 eV + | Free-atom electrostatic energy: -35.73811056 Ha -972.48346788 eV + | Hartree energy correction : -1.79601805 Ha -48.87213773 eV + | Entropy correction : 0.00000000 Ha 0.00000000 eV + | --------------------------- + | Total energy : -76.46917986 Ha -2080.83225557 eV + | Total energy, T -> 0 : -76.46917986 Ha -2080.83225557 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -76.46917986 Ha -2080.83225557 eV + + Derived energy quantities: + | Kinetic energy : 76.27401887 Ha 2075.52165471 eV + | Electrostatic energy : -143.50325285 Ha -3904.92219040 eV + | Energy correction for multipole + | error in Hartree potential : -0.00338837 Ha -0.09220225 eV + | Sum of eigenvalues per atom : -377.15252868 eV + | Total energy (T->0) per atom : -693.61075186 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -693.61075186 eV + Evaluating new KS density. + Integration grid: deviation in total charge ( - N_e) = 7.105427E-15 + + Self-consistency convergence accuracy: + | Change of charge density : 0.1243E-03 + | Change of sum of eigenvalues : -0.5919E-02 eV + | Change of total energy : 0.1944E-05 eV + + +------------------------------------------------------------ + End self-consistency iteration # 4 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 0.046 s 0.046 s + | Charge density update : 0.013 s 0.013 s + | Density mixing : 0.001 s 0.002 s + | Hartree multipole update : 0.002 s 0.001 s + | Hartree multipole summation : 0.008 s 0.008 s + | Integration : 0.021 s 0.022 s + | Solution of K.-S. eqns. : 0.000 s 0.000 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 0.012 MB (on task 0) + | Maximum: 0.012 MB (on task 0) + | Average: 0.012 MB + | Peak value for overall tracked memory usage: + | Minimum: 0.558 MB (on task 0 after allocating grid_partition) + | Maximum: 0.558 MB (on task 0 after allocating grid_partition) + | Average: 0.558 MB + | Largest tracked array allocation so far: + | Minimum: 0.364 MB (all_coords on task 0) + | Maximum: 0.364 MB (all_coords on task 0) + | Average: 0.364 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + +------------------------------------------------------------ + Begin self-consistency iteration # 5 + + Date : 20230628, Time : 095502.468 +------------------------------------------------------------ + Pulay mixing of updated and previous charge densities. + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 10.0000000000 + | Integrated number of electrons on 3D grid : 10.0000000000 + | Charge integration error : -0.0000000000 + | Normalization factor for density and gradient : 1.0000000000 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = -0.172430E-13 + | Sum of charges compensated after spline to logarithmic grids = 0.163077E-03 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = -0.169724E-13 + Summing up the Hartree potential. + Time summed over all CPUs for potential: real work 0.008 s, elapsed 0.008 s + | RMS charge density error from multipole expansion : 0.647128E-02 + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.021 s, elapsed 0.021 s + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.000 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -0.81961572 eV + Highest occupied state (VBM) at -7.06938908 eV + | Occupation number: 2.00000000 + + Lowest unoccupied state (CBM) at 0.06782280 eV + | Occupation number: 0.00000000 + + Overall HOMO-LUMO gap: 7.13721189 eV. + + Total energy components: + | Sum of eigenvalues : -41.58029853 Ha -1131.45749082 eV + | XC energy correction : -9.23994659 Ha -251.43173953 eV + | XC potential correction : 11.88519764 Ha 323.41268286 eV + | Free-atom electrostatic energy: -35.73811056 Ha -972.48346788 eV + | Hartree energy correction : -1.79602181 Ha -48.87224016 eV + | Entropy correction : 0.00000000 Ha 0.00000000 eV + | --------------------------- + | Total energy : -76.46917986 Ha -2080.83225553 eV + | Total energy, T -> 0 : -76.46917986 Ha -2080.83225553 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -76.46917986 Ha -2080.83225553 eV + + Derived energy quantities: + | Kinetic energy : 76.27406155 Ha 2075.52281628 eV + | Electrostatic energy : -143.50329482 Ha -3904.92333228 eV + | Energy correction for multipole + | error in Hartree potential : -0.00338853 Ha -0.09220664 eV + | Sum of eigenvalues per atom : -377.15249694 eV + | Total energy (T->0) per atom : -693.61075184 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -693.61075184 eV + Evaluating new KS density. + Integration grid: deviation in total charge ( - N_e) = -3.019807E-14 + + Self-consistency convergence accuracy: + | Change of charge density : 0.1883E-04 + | Change of sum of eigenvalues : 0.9521E-04 eV + | Change of total energy : 0.3472E-07 eV + + +------------------------------------------------------------ + End self-consistency iteration # 5 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 0.046 s 0.047 s + | Charge density update : 0.013 s 0.014 s + | Density mixing : 0.002 s 0.002 s + | Hartree multipole update : 0.002 s 0.002 s + | Hartree multipole summation : 0.008 s 0.008 s + | Integration : 0.021 s 0.021 s + | Solution of K.-S. eqns. : 0.000 s 0.000 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 0.012 MB (on task 0) + | Maximum: 0.012 MB (on task 0) + | Average: 0.012 MB + | Peak value for overall tracked memory usage: + | Minimum: 0.558 MB (on task 0 after allocating grid_partition) + | Maximum: 0.558 MB (on task 0 after allocating grid_partition) + | Average: 0.558 MB + | Largest tracked array allocation so far: + | Minimum: 0.364 MB (all_coords on task 0) + | Maximum: 0.364 MB (all_coords on task 0) + | Average: 0.364 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + +------------------------------------------------------------ + Begin self-consistency iteration # 6 + + Date : 20230628, Time : 095502.515 +------------------------------------------------------------ + Pulay mixing of updated and previous charge densities. + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 10.0000000000 + | Integrated number of electrons on 3D grid : 10.0000000000 + | Charge integration error : -0.0000000000 + | Normalization factor for density and gradient : 1.0000000000 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = 0.122989E-14 + | Sum of charges compensated after spline to logarithmic grids = 0.163077E-03 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = 0.393564E-15 + Summing up the Hartree potential. + Time summed over all CPUs for potential: real work 0.007 s, elapsed 0.008 s + | RMS charge density error from multipole expansion : 0.647129E-02 + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.021 s, elapsed 0.021 s + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.000 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -0.81961221 eV + Highest occupied state (VBM) at -7.06939046 eV + | Occupation number: 2.00000000 + + Lowest unoccupied state (CBM) at 0.06782418 eV + | Occupation number: 0.00000000 + + Overall HOMO-LUMO gap: 7.13721465 eV. + + Total energy components: + | Sum of eigenvalues : -41.58029885 Ha -1131.45749970 eV + | XC energy correction : -9.23994671 Ha -251.43174263 eV + | XC potential correction : 11.88519778 Ha 323.41268677 eV + | Free-atom electrostatic energy: -35.73811056 Ha -972.48346788 eV + | Hartree energy correction : -1.79602152 Ha -48.87223208 eV + | Entropy correction : 0.00000000 Ha 0.00000000 eV + | --------------------------- + | Total energy : -76.46917986 Ha -2080.83225552 eV + | Total energy, T -> 0 : -76.46917986 Ha -2080.83225552 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -76.46917986 Ha -2080.83225552 eV + + Derived energy quantities: + | Kinetic energy : 76.27406201 Ha 2075.52282880 eV + | Electrostatic energy : -143.50329516 Ha -3904.92334169 eV + | Energy correction for multipole + | error in Hartree potential : -0.00338854 Ha -0.09220694 eV + | Sum of eigenvalues per atom : -377.15249990 eV + | Total energy (T->0) per atom : -693.61075184 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -693.61075184 eV + Evaluating new KS density. + Integration grid: deviation in total charge ( - N_e) = -4.618528E-14 + + Self-consistency convergence accuracy: + | Change of charge density : 0.1111E-05 + | Change of sum of eigenvalues : -0.8881E-05 eV + | Change of total energy : 0.1723E-07 eV + + Electronic self-consistency reached - switching on the force computation. + + +------------------------------------------------------------ + End self-consistency iteration # 6 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 0.046 s 0.046 s + | Charge density & force component update : 0.013 s 0.013 s + | Density mixing : 0.003 s 0.002 s + | Hartree multipole update : 0.002 s 0.002 s + | Hartree multipole summation : 0.008 s 0.008 s + | Hartree pot. SCF incomplete forces : 0.015 s 0.015 s + | Integration : 0.021 s 0.021 s + | Solution of K.-S. eqns. : 0.000 s 0.000 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 0.012 MB (on task 0) + | Maximum: 0.012 MB (on task 0) + | Average: 0.012 MB + | Peak value for overall tracked memory usage: + | Minimum: 0.558 MB (on task 0 after allocating grid_partition) + | Maximum: 0.558 MB (on task 0 after allocating grid_partition) + | Average: 0.558 MB + | Largest tracked array allocation so far: + | Minimum: 0.364 MB (all_coords on task 0) + | Maximum: 0.364 MB (all_coords on task 0) + | Average: 0.364 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + +------------------------------------------------------------ + Begin self-consistency iteration # 7 + + Date : 20230628, Time : 095502.561 +------------------------------------------------------------ + Pulay mixing of updated and previous charge densities. + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 10.0000000000 + | Integrated number of electrons on 3D grid : 10.0000000000 + | Charge integration error : 0.0000000000 + | Normalization factor for density and gradient : 1.0000000000 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = 0.228513E-13 + | Sum of charges compensated after spline to logarithmic grids = 0.163077E-03 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = 0.225807E-13 + Summing up the Hartree potential. + Time summed over all CPUs for potential: real work 0.024 s, elapsed 0.024 s + | RMS charge density error from multipole expansion : 0.647129E-02 + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.021 s, elapsed 0.021 s + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.000 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -0.81960980 eV + Highest occupied state (VBM) at -7.06938675 eV + | Occupation number: 2.00000000 + + Lowest unoccupied state (CBM) at 0.06782564 eV + | Occupation number: 0.00000000 + + Overall HOMO-LUMO gap: 7.13721240 eV. + + Total energy components: + | Sum of eigenvalues : -41.58029708 Ha -1131.45745146 eV + | XC energy correction : -9.23994696 Ha -251.43174949 eV + | XC potential correction : 11.88519811 Ha 323.41269575 eV + | Free-atom electrostatic energy: -35.73811056 Ha -972.48346788 eV + | Hartree energy correction : -1.79602337 Ha -48.87228244 eV + | Entropy correction : 0.00000000 Ha 0.00000000 eV + | --------------------------- + | Total energy : -76.46917986 Ha -2080.83225551 eV + | Total energy, T -> 0 : -76.46917986 Ha -2080.83225551 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -76.46917986 Ha -2080.83225551 eV + + Derived energy quantities: + | Kinetic energy : 76.27406348 Ha 2075.52286864 eV + | Electrostatic energy : -143.50329637 Ha -3904.92337465 eV + | Energy correction for multipole + | error in Hartree potential : -0.00338854 Ha -0.09220690 eV + | Sum of eigenvalues per atom : -377.15248382 eV + | Total energy (T->0) per atom : -693.61075184 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -693.61075184 eV + Evaluating new KS density and force components. + Integration grid: deviation in total charge ( - N_e) = 3.375078E-14 + + atomic forces [eV/Ang]: + ----------------------- + atom # 1 + Hellmann-Feynman : -0.748664E-13 0.595448E-11 0.175027E+02 + Ionic forces : 0.000000E+00 0.000000E+00 0.000000E+00 + Multipole : 0.290398E-13 -0.721957E-14 -0.902990E-01 + Hartree pot. SCF incomplete : -0.278847E-12 0.302588E-12 0.116426E-04 + Pulay + GGA : 0.107576E-11 -0.100303E-10 -0.174195E+02 + ---------------------------------------------------------------- + Total forces( 1) : 0.751090E-12 -0.378045E-11 -0.710329E-02 + atom # 2 + Hellmann-Feynman : -0.105808E-13 0.296175E+00 -0.312050E+00 + Ionic forces : 0.000000E+00 0.000000E+00 0.000000E+00 + Multipole : 0.402699E-15 -0.451209E-02 -0.316561E-01 + Hartree pot. SCF incomplete : 0.868541E-14 0.890914E-06 0.188241E-05 + Pulay + GGA : 0.851889E-14 -0.291007E+00 0.337412E+00 + ---------------------------------------------------------------- + Total forces( 2) : 0.702617E-14 0.657031E-03 -0.629131E-02 + atom # 3 + Hellmann-Feynman : -0.319427E-14 -0.296175E+00 -0.312050E+00 + Ionic forces : 0.000000E+00 0.000000E+00 0.000000E+00 + Multipole : -0.783889E-16 0.451209E-02 -0.316561E-01 + Hartree pot. SCF incomplete : 0.781889E-14 -0.890914E-06 0.188241E-05 + Pulay + GGA : -0.101225E-13 0.291007E+00 0.337412E+00 + ---------------------------------------------------------------- + Total forces( 3) : -0.557627E-14 -0.657031E-03 -0.629131E-02 + + + Self-consistency convergence accuracy: + | Change of charge density : 0.3543E-06 + | Change of sum of eigenvalues : 0.4825E-04 eV + | Change of total energy : 0.5599E-08 eV + | Change of forces : 0.4731E+00 eV/A + + Writing Kohn-Sham eigenvalues. + + State Occupation Eigenvalue [Ha] Eigenvalue [eV] + 1 2.00000 -18.788546 -511.26235 + 2 2.00000 -0.925138 -25.17429 + 3 2.00000 -0.478381 -13.01741 + 4 2.00000 -0.338288 -9.20530 + 5 2.00000 -0.259795 -7.06939 + 6 0.00000 0.002493 0.06783 + 7 0.00000 0.100448 2.73333 + 8 0.00000 0.298234 8.11536 + 9 0.00000 0.334240 9.09513 + 10 0.00000 0.369680 10.05951 + 11 0.00000 0.574990 15.64628 + + Highest occupied state (VBM) at -7.06938675 eV + | Occupation number: 2.00000000 + + Lowest unoccupied state (CBM) at 0.06782564 eV + | Occupation number: 0.00000000 + + Overall HOMO-LUMO gap: 7.13721240 eV. + | Chemical Potential : -0.81960980 eV + + Self-consistency cycle converged. + + +------------------------------------------------------------ + End self-consistency iteration # 7 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 0.118 s 0.119 s + | Charge density & force component update : 0.054 s 0.054 s + | Density mixing : 0.003 s 0.003 s + | Hartree multipole update : 0.002 s 0.002 s + | Hartree multipole summation : 0.024 s 0.024 s + | Hartree pot. SCF incomplete forces : 0.015 s 0.015 s + | Integration : 0.021 s 0.021 s + | Solution of K.-S. eqns. : 0.000 s 0.000 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 0.012 MB (on task 0) + | Maximum: 0.012 MB (on task 0) + | Average: 0.012 MB + | Peak value for overall tracked memory usage: + | Minimum: 0.558 MB (on task 0 after allocating grid_partition) + | Maximum: 0.558 MB (on task 0 after allocating grid_partition) + | Average: 0.558 MB + | Largest tracked array allocation so far: + | Minimum: 0.364 MB (all_coords on task 0) + | Maximum: 0.364 MB (all_coords on task 0) + | Average: 0.364 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + Removing unitary transformations (pure translations, rotations) from forces on atoms. + Atomic forces before filtering: + | Net force on center of mass : 0.752540E-12 -0.972825E-11 -0.196859E-01 eV/A + | Net torque on center of mass: 0.387025E-11 0.298771E-12 -0.966938E-14 eV + Atomic forces after filtering: + | Net force on center of mass : -0.202824E-27 0.000000E+00 0.696899E-17 eV/A + | Net torque on center of mass: 0.103720E-17 0.646065E-28 0.133932E-36 eV + + Energy and forces in a compact form: + | Total energy uncorrected : -0.208083225551071E+04 eV + | Total energy corrected : -0.208083225551071E+04 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -0.208083225551071E+04 eV + Total atomic forces (unitary forces cleaned) [eV/Ang]: + | 1 0.405648561641326E-28 0.551198801267693E-12 -0.541321794005289E-03 + | 2 -0.121694568492398E-27 0.657031192731074E-03 0.270660897217135E-03 + | 3 -0.121694568492398E-27 -0.657031193282273E-03 0.270660896788161E-03 + + ------------------------------------ + Start decomposition of the XC Energy + ------------------------------------ + X and C from original XC functional choice + Hartree-Fock Energy : 0.000000000 Ha 0.000000000 eV + X Energy : -8.914983781 Ha -242.589051486 eV + C Energy : -0.324963179 Ha -8.842698008 eV + XC Energy w/o HF : -9.239946960 Ha -251.431749494 eV + Total XC Energy : -9.239946960 Ha -251.431749494 eV + ------------------------------------ + LDA X and C from self-consistent density + X Energy LDA : -8.098845171 Ha -220.380789948 eV + C Energy LDA : -0.659361820 Ha -17.942148003 eV + ------------------------------------ + End decomposition of the XC Energy + ------------------------------------ + +------------------------------------------------------------ + Relaxation / MD: End force evaluation. : max(cpu_time) wall_clock(cpu1) + | Time for this force evaluation : 0.449 s 0.449 s + +------------------------------------------------------------ + Geometry optimization: Attempting to predict improved coordinates. + + Removing unitary transformations (pure translations, rotations) from forces on atoms. + Atomic forces before filtering: + | Net force on center of mass : -0.202824E-27 0.000000E+00 0.696899E-17 eV/A + | Net torque on center of mass: 0.103720E-17 0.646065E-28 0.133932E-36 eV + Atomic forces after filtering: + | Net force on center of mass : 0.540432E-43 -0.871124E-19 0.000000E+00 eV/A + | Net torque on center of mass: -0.691468E-19 0.215273E-39 0.746290E-44 eV + Net remaining forces (excluding translations, rotations) in present geometry: + || Forces on atoms || = 0.657031E-03 eV/A. + Maximum force component is 0.657031E-03 eV/A. + Present geometry is converged. + +------------------------------------------------------------ + Final atomic structure: + x [A] y [A] z [A] + atom 0.00000000 -0.00000000 0.11989040 O + atom 0.00000000 0.76726299 -0.47736120 H + atom -0.00000000 -0.76726299 -0.47736120 H +------------------------------------------------------------ + +------------------------------------------------------------------------------ + Final output of selected total energy values: + + The following output summarizes some interesting total energy values + at the end of a run (AFTER all relaxation, molecular dynamics, etc.). + + | Total energy of the DFT / Hartree-Fock s.c.f. calculation : -2080.832255511 eV + | Final zero-broadening corrected energy (caution - metals only) : -2080.832255511 eV + | For reference only, the value of 1 Hartree used in FHI-aims is : 27.211384500 eV + + Before relying on these values, please be sure to understand exactly which + total energy value is referred to by a given number. Different objects may + all carry the same name 'total energy'. Definitions: + + Total energy of the DFT / Hartree-Fock s.c.f. calculation: + | Note that this energy does not include ANY quantities calculated after the + | s.c.f. cycle, in particular not ANY RPA, MP2, etc. many-body perturbation terms. + + Final zero-broadening corrected energy: + | For metallic systems only, a broadening of the occupation numbers at the Fermi + | level can be extrapolated back to zero broadening by an electron-gas inspired + | formula. For all systems that are not real metals, this value can be + | meaningless and should be avoided. + +------------------------------------------------------------------------------ + Methods described in the following list of references were used in this FHI-aims run. + If you publish the results, please make sure to cite these reference if they apply. + FHI-aims is an academic code, and for our developers (often, Ph.D. students + and postdocs), scientific credit in the community is essential. + Thank you for helping us! + + For any use of FHI-aims, please cite: + + Volker Blum, Ralf Gehrke, Felix Hanke, Paula Havu, Ville Havu, + Xinguo Ren, Karsten Reuter, and Matthias Scheffler + 'Ab initio molecular simulations with numeric atom-centered orbitals' + Computer Physics Communications 180, 2175-2196 (2009) + http://doi.org/10.1016/j.cpc.2009.06.022 + + + The ELSI infrastructure was used in your run to solve the Kohn-Sham electronic structure. + Please check out http://elsi-interchange.org to learn more. + If scalability is important for your project, please acknowledge ELSI by citing: + + V. W-z. Yu, F. Corsetti, A. Garcia, W. P. Huhn, M. Jacquelin, W. Jia, + B. Lange, L. Lin, J. Lu, W. Mi, A. Seifitokaldani, A. Vazquez-Mayagoitia, + C. Yang, H. Yang, and V. Blum + 'ELSI: A unified software interface for Kohn-Sham electronic structure solvers' + Computer Physics Communications 222, 267-285 (2018). + http://doi.org/10.1016/j.cpc.2017.09.007 + + + For the real-space grid partitioning and parallelization used in this calculation, please cite: + + Ville Havu, Volker Blum, Paula Havu, and Matthias Scheffler, + 'Efficient O(N) integration for all-electron electronic structure calculation' + 'using numerically tabulated basis functions' + Journal of Computational Physics 228, 8367-8379 (2009). + http://doi.org/10.1016/j.jcp.2009.08.008 + + Of course, there are many other important community references, e.g., those cited in the + above references. Our list is limited to references that describe implementations in the + FHI-aims code. The reason is purely practical (length of this list) - please credit others as well. + +------------------------------------------------------------ + Leaving FHI-aims. + Date : 20230628, Time : 095502.689 + + Computational steps: + | Number of self-consistency cycles : 28 + | Number of SCF (re)initializations : 3 + | Number of relaxation steps : 2 + + Detailed time accounting : max(cpu_time) wall_clock(cpu1) + | Total time : 1.789 s 1.790 s + | Preparation time : 0.064 s 0.064 s + | Boundary condition initialization : 0.000 s 0.000 s + | Grid partitioning : 0.035 s 0.036 s + | Preloading free-atom quantities on grid : 0.026 s 0.025 s + | Free-atom superposition energy : 0.024 s 0.024 s + | Total time for integrations : 0.636 s 0.635 s + | Total time for solution of K.-S. equations : 0.006 s 0.004 s + | Total time for EV reorthonormalization : 0.000 s 0.000 s + | Total time for density & force components : 0.528 s 0.528 s + | Total time for mixing : 0.064 s 0.062 s + | Total time for Hartree multipole update : 0.047 s 0.050 s + | Total time for Hartree multipole sum : 0.268 s 0.270 s + | Total time for total energy evaluation : 0.001 s 0.001 s + | Total time NSC force correction : 0.045 s 0.045 s + | Total time for scaled ZORA corrections : 0.000 s 0.000 s + + Partial memory accounting: + | Residual value for overall tracked memory usage across tasks: 0.000000 MB (should be 0.000000 MB) + | Peak values for overall tracked memory usage: + | Minimum: 0.558 MB (on task 0 after allocating grid_partition) + | Maximum: 0.558 MB (on task 0 after allocating grid_partition) + | Average: 0.558 MB + | Largest tracked array allocation: + | Minimum: 0.364 MB (all_coords on task 0) + | Maximum: 0.364 MB (all_coords on task 0) + | Average: 0.364 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. + + Have a nice day. +------------------------------------------------------------ diff --git a/tests/io/aims/aims_output_files/h2o_ref.json b/tests/io/aims/aims_output_files/h2o_ref.json new file mode 100644 index 00000000000..de1a49375eb --- /dev/null +++ b/tests/io/aims/aims_output_files/h2o_ref.json @@ -0,0 +1,403 @@ +{ + "@module": "pymatgen.io.aims.output", + "@class": "AimsOutput", + "results": [ + { + "@module": "pymatgen.core.structure", + "@class": "Molecule", + "charge": 0.0, + "spin_multiplicity": 1, + "sites": [ + { + "name": "O", + "species": [ + { + "element": "O", + "occu": 1 + } + ], + "xyz": [ + 0.0, + 0.0, + 0.119262 + ], + "properties": { + "force": { + "@module": "numpy", + "@class": "array", + "dtype": "float64", + "data": [ + -1.62259424656531e-28, + -2.72372884812723e-12, + 0.192619418545703 + ] + } + }, + "label": "O" + }, + { + "name": "H", + "species": [ + { + "element": "H", + "occu": 1 + } + ], + "xyz": [ + 0.0, + 0.763239, + -0.477047 + ], + "properties": { + "force": { + "@module": "numpy", + "@class": "array", + "dtype": "float64", + "data": [ + 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"force": { + "@module": "numpy", + "@class": "array", + "dtype": "float64", + "data": [ + -1.21694568492398e-28, + -0.000657031193282273, + 0.000270660896788161 + ] + } + }, + "label": "H" + } + ], + "properties": { + "energy": -2080.83225551071, + "free_energy": -2080.83225551071, + "fermi_energy": -0.8196098, + "vbm": -7.06938675, + "cbm": 0.06782564, + "gap": 7.1372124, + "direct_gap": 7.1372124 + }, + "@version": null + } + ], + "metadata": { + "commit_hash": "232d594a3", + "aims_uuid": "099AC112-61D8-44F8-AB69-102154672282", + "version_number": "220309", + "fortran_compiler": "mpiifort (Intel) version 2021.6.0.20220226", + "c_compiler": "icc (Intel) version 2021.6.0.20220226", + "fortran_compiler_flags": "-O3 -ip -fp-model precise", + "c_compiler_flags": "-m64 -O3 -ip -fp-model precise -std=gnu99", + "build_type": [ + "MPI", + "ScaLAPACK", + "LibXC", + "i-PI", + "RLSY" + ], + "linked_against": [ + "/home/tpurcell/intel/oneapi/mkl/2022.1.0/lib/intel64/libmkl_scalapack_lp64.so", + "/home/tpurcell/intel/oneapi/mkl/2022.1.0/lib/intel64/libmkl_blacs_intelmpi_lp64.so", + "/home/tpurcell/intel/oneapi/mkl/2022.1.0/lib/intel64/libmkl_intel_lp64.so", + "/home/tpurcell/intel/oneapi/mkl/2022.1.0/lib/intel64/libmkl_sequential.so", + "/home/tpurcell/intel/oneapi/mkl/2022.1.0/lib/intel64/libmkl_core.so" + ] + }, + "structure_summary": { + "initial_structure": { + "@module": "pymatgen.core.structure", + "@class": "Molecule", + "charge": 0.0, + "spin_multiplicity": 1, + "sites": [ + { + "name": "O", + "species": [ + { + "element": "O", + "occu": 1 + } + ], + "xyz": [ + 0.0, + 0.0, + 0.119262 + ], + "properties": { + "charge": 0.0 + }, + "label": "O" + }, + { + "name": "H", + "species": [ + { + "element": "H", + "occu": 1 + } + ], + "xyz": [ + 0.0, + 0.763239, + -0.477047 + ], + "properties": { + "charge": 0.0 + }, + "label": "H" + }, + { + "name": "H", + "species": [ + { + "element": "H", + "occu": 1 + } + ], + "xyz": [ + 0.0, + -0.763239, + -0.477047 + ], + "properties": { + "charge": 0.0 + }, + "label": "H" + } + ], + "properties": {}, + "@version": null + }, + "initial_lattice": null, + "is_relaxation": true, + "is_md": false, + "n_atoms": 3, + "n_bands": 11, + "n_electrons": 10, + "n_spins": 1, + "electronic_temperature": 0.1, + "n_k_points": null, + "k_points": null, + "k_point_weights": null + } +} diff --git a/tests/io/aims/aims_output_files/si.out b/tests/io/aims/aims_output_files/si.out new file mode 100644 index 00000000000..f2698b20cd1 --- /dev/null +++ b/tests/io/aims/aims_output_files/si.out @@ -0,0 +1,8198 @@ +------------------------------------------------------------ + Invoking FHI-aims ... + + When using FHI-aims, please cite the following reference: + + Volker Blum, Ralf Gehrke, Felix Hanke, Paula Havu, + Ville Havu, Xinguo Ren, Karsten Reuter, and Matthias Scheffler, + 'Ab Initio Molecular Simulations with Numeric Atom-Centered Orbitals', + Computer Physics Communications 180, 2175-2196 (2009) + + In addition, many other developments in FHI-aims are likely important for + your particular application. A partial list of references is given at the end of + this file. Thank you for giving credit to the authors of these developments. + + For any questions about FHI-aims, please visit our slack channel at + + https://fhi-aims.slack.com + + and our main development and support site at + + https://aims-git.rz-berlin.mpg.de . + + The latter site, in particular, has a wiki to collect information, as well + as an issue tracker to log discussions, suggest improvements, and report issues + or bugs. https://aims-git.rz-berlin.mpg.de is also the main development site + of the project and all new and updated code versions can be obtained there. + Please send an email to aims-coordinators@fhi-berlin.mpg.de and we will add + you to these sites. They are for you and everyone is welcome there. + +------------------------------------------------------------ + + + + Date : 20230628, Time : 104123.048 + Time zero on CPU 1 : 0.162197700000000E+01 s. + Internal wall clock time zero : 457180883.048 s. + + FHI-aims created a unique identifier for this run for later identification + aims_uuid : 7F959EC8-A7E1-43AC-A4DA-9302788CF7F6 + + Build configuration of the current instance of FHI-aims + ------------------------------------------------------- + FHI-aims version : 220309 + Commit number : 232d594a3 + CMake host system : Linux-5.4.0-146-generic + CMake version : 3.26.3 + Fortran compiler : /home/tpurcell/intel/oneapi/mpi/2021.6.0/bin/mpiifort (Intel) version 2021.6.0.20220226 + Fortran compiler flags: -O3 -ip -fp-model precise + C compiler : /home/tpurcell/intel/oneapi/compiler/2022.1.0/linux/bin/intel64/icc (Intel) version 2021.6.0.20220226 + C compiler flags : -m64 -O3 -ip -fp-model precise -std=gnu99 + Using MPI + Using ScaLAPACK + Using LibXC + Using i-PI + Using RLSY + Linking against: /home/tpurcell/intel/oneapi/mkl/2022.1.0/lib/intel64/libmkl_scalapack_lp64.so + /home/tpurcell/intel/oneapi/mkl/2022.1.0/lib/intel64/libmkl_blacs_intelmpi_lp64.so + /home/tpurcell/intel/oneapi/mkl/2022.1.0/lib/intel64/libmkl_intel_lp64.so + /home/tpurcell/intel/oneapi/mkl/2022.1.0/lib/intel64/libmkl_sequential.so + /home/tpurcell/intel/oneapi/mkl/2022.1.0/lib/intel64/libmkl_core.so + + Using 1 parallel tasks. + Task 0 on host nomadbook-7 reporting. + + Performing system and environment tests: + *** Environment variable OMP_NUM_THREADS is set to + 2 + *** For performance reasons you might want to set it to 1 + | Checking for ScaLAPACK... + | Testing pdtran()... + | All pdtran() tests passed. + + Obtaining array dimensions for all initial allocations: + + ----------------------------------------------------------------------- + Parsing control.in (first pass over file, find array dimensions only). + The contents of control.in will be repeated verbatim below + unless switched off by setting 'verbatim_writeout .false.' . + in the first line of control.in . + ----------------------------------------------------------------------- + + #=============================================================================== + # Created using the Atomic Simulation Environment (ASE) + + # Tue Jun 27 18:06:33 2023 + + #=============================================================================== + xc pbe + relativistic atomic_zora scalar + relax_geometry trm 1e-3 + relax_unit_cell full + k_grid 2 2 2 + #=============================================================================== + + ################################################################################ + # + # FHI-aims code project + # VB, Fritz-Haber Institut, 2009 + # + # Suggested "light" defaults for Si atom (to be pasted into control.in file) + # Be sure to double-check any results obtained with these settings for post-processing, + # e.g., with the "tight" defaults and larger basis sets. + # + # 2020/09/08 Added f function to "light" after reinspection of Delta test outcomes. + # This was done for all of Al-Cl and is a tricky decision since it makes + # "light" calculations measurably more expensive for these elements. + # Nevertheless, outcomes for P, S, Cl (and to some extent, Si) appear + # to justify this choice. + # + ################################################################################ + species Si + # global species definitions + nucleus 14 + mass 28.0855 + # + l_hartree 4 + # + cut_pot 3.5 1.5 1.0 + basis_dep_cutoff 1e-4 + # + radial_base 42 5.0 + radial_multiplier 1 + angular_grids specified + division 0.5866 50 + division 0.9616 110 + division 1.2249 194 + division 1.3795 302 + # division 1.4810 434 + # division 1.5529 590 + # division 1.6284 770 + # division 1.7077 974 + # division 2.4068 1202 + # outer_grid 974 + outer_grid 302 + ################################################################################ + # + # Definition of "minimal" basis + # + ################################################################################ + # valence basis states + valence 3 s 2. + valence 3 p 2. + # ion occupancy + ion_occ 3 s 1. + ion_occ 3 p 1. + ################################################################################ + # + # Suggested additional basis functions. For production calculations, + # uncomment them one after another (the most important basis functions are + # listed first). + # + # Constructed for dimers: 1.75 A, 2.0 A, 2.25 A, 2.75 A, 3.75 A + # + ################################################################################ + # "First tier" - improvements: -571.96 meV to -37.03 meV + hydro 3 d 4.2 + hydro 2 p 1.4 + hydro 4 f 6.2 + ionic 3 s auto + # "Second tier" - improvements: -16.76 meV to -3.03 meV + # hydro 3 d 9 + # hydro 5 g 9.4 + # hydro 4 p 4 + # hydro 1 s 0.65 + # "Third tier" - improvements: -3.89 meV to -0.60 meV + # ionic 3 d auto + # hydro 3 s 2.6 + # hydro 4 f 8.4 + # hydro 3 d 3.4 + # hydro 3 p 7.8 + # "Fourth tier" - improvements: -0.33 meV to -0.11 meV + # hydro 2 p 1.6 + # hydro 5 g 10.8 + # hydro 5 f 11.2 + # hydro 3 d 1 + # hydro 4 s 4.5 + # Further basis functions that fell out of the optimization - noise + # level... < -0.08 meV + # hydro 4 d 6.6 + # hydro 5 g 16.4 + # hydro 4 d 9 + + ----------------------------------------------------------------------- + Completed first pass over input file control.in . + ----------------------------------------------------------------------- + + + ----------------------------------------------------------------------- + Parsing geometry.in (first pass over file, find array dimensions only). + The contents of geometry.in will be repeated verbatim below + unless switched off by setting 'verbatim_writeout .false.' . + in the first line of geometry.in . + ----------------------------------------------------------------------- + + #=============================================================================== + # Created using the Atomic Simulation Environment (ASE) + + # Tue Jun 27 18:06:33 2023 + + #======================================================= + lattice_vector 0.0000000000000000 2.7549999999999999 2.7549999999999999 + lattice_vector 2.7549999999999999 0.0000000000000000 2.7549999999999999 + lattice_vector 2.7549999999999999 2.7549999999999999 0.0000000000000000 + atom_frac 0.0000000000000000 0.0000000000000000 -0.0000000000000000 Si + atom_frac 0.2500000000000000 0.2500000000000000 0.2500000000000000 Si + + ----------------------------------------------------------------------- + Completed first pass over input file geometry.in . + ----------------------------------------------------------------------- + + + Basic array size parameters: + | Number of species : 1 + | Number of atoms : 2 + | Number of lattice vectors : 3 + | Max. basis fn. angular momentum : 3 + | Max. atomic/ionic basis occupied n: 3 + | Max. number of basis fn. types : 3 + | Max. radial fns per species/type : 5 + | Max. logarithmic grid size : 1346 + | Max. radial integration grid size : 42 + | Max. angular integration grid size: 302 + | Max. angular grid division number : 8 + | Radial grid for Hartree potential : 1346 + | Number of spin channels : 1 + +------------------------------------------------------------ + Reading file control.in. +------------------------------------------------------------ + XC: Using PBE gradient-corrected functionals. + Scalar relativistic treatment of kinetic energy: on-site free-atom approximation to ZORA. + Geometry relaxation: Modified BFGS - TRM (trust radius method) for lattice optimization. + Convergence accuracy for geometry relaxation: Maximum force < 0.100000E-02 eV/A. + Found k-point grid: 2 2 2 + + Reading configuration options for species Si . + | Found nuclear charge : 14.0000 + | Found atomic mass : 28.0855000000000 amu + | Found l_max for Hartree potential : 4 + | Found cutoff potl. onset [A], width [A], scale factor : 3.50000 1.50000 1.00000 + | Threshold for basis-dependent cutoff potential is 0.100000E-03 + | Found data for basic radial integration grid : 42 points, outermost radius = 5.000 A + | Found multiplier for basic radial grid : 1 + | Found angular grid specification: user-specified. + | Specified grid contains 5 separate shells. + | Check grid settings after all constraints further below. + | Found free-atom valence shell : 3 s 2.000 + | Found free-atom valence shell : 3 p 2.000 + | Found free-ion valence shell : 3 s 1.000 + | Found free-ion valence shell : 3 p 1.000 + | Found hydrogenic basis function : 3 d 4.200 + | Found hydrogenic basis function : 2 p 1.400 + | Found hydrogenic basis function : 4 f 6.200 + | Found ionic basis function : 3 s , default cutoff radius. + Species Si : Missing cutoff potential type. + Defaulting to exp(1/x)/(1-x)^2 type cutoff potential. + Species Si: No 'logarithmic' tag. Using default grid for free atom: + | Default logarithmic grid data [bohr] : 0.1000E-03 0.1000E+03 0.1012E+01 + | Will include ionic basis functions of 2.0-fold positive Si ion. + Species Si: On-site basis accuracy parameter (for Gram-Schmidt orthonormalisation) not specified. + Using default value basis_acc = 0.1000000E-03. + Species Si : Using default innermost maximum threshold i_radial= 2 for radial functions. + Species Si : Default cutoff onset for free atom density etc. : 0.35000000E+01 AA. + Species Si : Basic radial grid will be enhanced according to radial_multiplier = 1, to contain 42 grid points. + + Finished reading input file 'control.in'. + +------------------------------------------------------------ + + +------------------------------------------------------------ + Reading geometry description geometry.in. +------------------------------------------------------------ + | The smallest distance between any two atoms is 2.38589999 AA. + | The first atom of this pair is atom number 1 . + | The second atom of this pair is atom number 2 . + | Wigner-Seitz cell of the first atom image 0 1 0 . + | (The Wigner-Seitz cell of the second atom is 0 0 0 by definition.) + + Symmetry information by spglib: + | Precision set to 0.1E-04 + | Number of Operations : 48 + | Space group : 227 + | International : Fd-3m + | Schoenflies : Oh^7 + Input structure read successfully. + The structure contains 2 atoms, and a total of 28.000 electrons. + + Input geometry: + | Unit cell: + | 0.00000000 2.75500000 2.75500000 + | 2.75500000 0.00000000 2.75500000 + | 2.75500000 2.75500000 0.00000000 + | Atomic structure: + | Atom x [A] y [A] z [A] + | 1: Species Si 0.00000000 0.00000000 0.00000000 + | 2: Species Si 1.37750000 1.37750000 1.37750000 + + Lattice parameters for 3D lattice (in Angstroms) : 3.896158 3.896158 3.896158 + Angle(s) between unit vectors (in degrees) : 60.000000 60.000000 60.000000 + + + Quantities derived from the lattice vectors: + | Reciprocal lattice vector 1: -1.140324 1.140324 1.140324 + | Reciprocal lattice vector 2: 1.140324 -1.140324 1.140324 + | Reciprocal lattice vector 3: 1.140324 1.140324 -1.140324 + | Unit cell volume : 0.418210E+02 A^3 + + Fractional coordinates: + L1 L2 L3 + atom_frac 0.00000000 0.00000000 0.00000000 Si + atom_frac 0.25000000 0.25000000 0.25000000 Si + + + Finished reading input file 'control.in'. + + +------------------------------------------------------------ + Reading geometry description geometry.in. +------------------------------------------------------------ + + Consistency checks for stacksize environment parameter are next. + + | Maximum stacksize for task 0: unlimited + | Current stacksize for task 0: unlimited + + Consistency checks for the contents of control.in are next. + + MPI_IN_PLACE appears to work with this MPI implementation. + | Keeping use_mpi_in_place .true. (see manual). + Target number of points in a grid batch is not set. Defaulting to 100 + Method for grid partitioning is not set. Defaulting to parallel hash+maxmin partitioning. + Batch size limit is not set. Defaulting to 200 + By default, will store active basis functions for each batch. + If in need of memory, prune_basis_once .false. can be used to disable this option. + communication_type for Hartree potential was not specified. + Defaulting to calc_hartree . + Defaulting to Pulay charge density mixer. + Pulay mixer: Number of relevant iterations not set. + Defaulting to 8 iterations. + Pulay mixer: Number of initial linear mixing iterations not set. + Defaulting to 0 iterations. + Work space size for distributed Hartree potential not set. + Defaulting to 0.200000E+03 MB. + Mixing parameter for charge density mixing has not been set. + Using default: charge_mix_param = 0.0500. + The mixing parameter will be adjusted in iteration number 2 of the first full s.c.f. cycle only. + Algorithm-dependent basis array size parameters: + | n_max_pulay : 8 + Maximum number of self-consistency iterations not provided. + Presetting 1000 iterations. + Presetting 1001 iterations before the initial mixing cycle + is restarted anyway using the sc_init_iter criterion / keyword. + Presetting a factor 1.000 between actual scf density residual + and density convergence criterion sc_accuracy_rho below which sc_init_iter + takes no effect. + * No s.c.f. convergence criteria (sc_accuracy_*) were provided in control.in. + * The run will proceed with a reasonable default guess, but please check whether. + * the s.c.f. cycles seem to take too much or too little time. + No maximum number of relaxation steps, defaulting to 1000 + Default initial Hessian is Lindh matrix (thres = 15.00) plus 0.200000E+01 eV/A^2 times unity. + No maximum energy tolerance for TRM/BFGS moves, defaulting to 0.100000E-02 + Maximum energy tolerance by which TRM/BFGS trajectory may increase over multiple steps: 0.300000E-02 + No harmonic length scale. Defaulting to 0.250000E-01 A. + No trust radius initializer. Defaulting to 0.200000E+00 A. + Unit cell relaxation: Unit cell will be relaxed fully. + Unit cell relaxation: Analytical stress will be used. + Analytical stress will be computed. + Analytical stress calculation: Only the upper triangle is calculated. + Final output is symmetrized. + Analytical stress calculation: scf convergence accuracy of stress not set. + Analytical stress self-consistency will not be checked explicitly. + Be sure to set other criteria like sc_accuracy_rho tight enough. + Forces evaluation will include force correction term due to incomplete self-consistency (default). + * Notice: The s.c.f. convergence criterion sc_accuracy_rho was not provided. + * We used to stop in this case, and ask the user to provide reasonable + * scf convergence criteria. However, this led some users to employ criteria + * that led to extremely long run times, e.g., for simple relaxation. + * We now preset a default value for sc_accuracy_rho if it is not set. + * You may still wish to check if this setting is too tight or too loose for your needs. + * Based on n_atoms and forces and force-correction status, FHI-aims chose sc_accuracy_rho = 0.500000E-06 . + Force calculation: scf convergence accuracy of forces not set. + Defaulting to 'sc_accuracy_forces not_checked'. + Handling of forces: Unphysical translation and rotation will be removed from forces. + No accuracy limit for integral partition fn. given. Defaulting to 0.1000E-14. + No threshold value for u(r) in integrations given. Defaulting to 0.1000E-05. + No occupation type (smearing scheme) given. Defaulting to Gaussian broadening, width = 0.1000E-01 eV. + The width will be adjusted in iteration number 2 of the first full s.c.f. cycle only. + S.C.F. convergence parameters will be adjusted in iteration number 2 of the first full s.c.f. cycle only. + No accuracy for occupation numbers given. Defaulting to 0.1000E-12. + No threshold value for occupation numbers given. Defaulting to 0.0000E+00. + No accuracy for fermi level given. Defaulting to 0.1000E-19. + Maximum # of iterations to find E_F not set. Defaulting to 200. + Preferred method for the eigenvalue solver ('KS_method') not specified in 'control.in'. + Defaulting to serial version LAPACK (via ELSI). + Will not use alltoall communication since running on < 1024 CPUs. + Threshold for basis singularities not set. + Default threshold for basis singularities: 0.1000E-04 + partition_type (choice of integration weights) for integrals was not specified. + | Using a version of the partition function of Stratmann and coworkers ('stratmann_sparse'). + | At each grid point, the set of atoms used to build the partition table is smoothly restricted to + | only those atoms whose free-atom density would be non-zero at that grid point. + Partitioning for Hartree potential was not defined. Using partition_type for integrals. + | Adjusted default value of keyword multip_moments_threshold to: 0.10000000E-11 + | This value may affect high angular momentum components of the Hartree potential in periodic systems. + Spin handling was not defined in control.in. Defaulting to unpolarized case. + Angular momentum expansion for Kerker preconditioner not set explicitly. + | Using default value of 0 + No explicit requirement for turning off preconditioner. + | By default, it will be turned off when the charge convergence reaches + | sc_accuracy_rho = 0.500000E-06 + No special mixing parameter while Kerker preconditioner is on. + Using default: charge_mix_param = 0.0500. + No q(lm)/r^(l+1) cutoff set for long-range Hartree potential. + | Using default value of 0.100000E-09 . + | Verify using the multipole_threshold keyword. + Defaulting to new monopole extrapolation. + Density update method: automatic selection selected. + Using density matrix based charge density update. + Using density matrix based charge density update. + Using packed matrix style: index . + Geometry relaxation: A file "geometry.in.next_step" is written out by default after each step. + | This file contains the geometry of the current relaxation step as well as + | the current Hessian matrix needed to restart the relaxation algorithm. + | If you do not want part or all of this information, use the keywords + | "write_restart_geometry" or "hessian_to_restart_geometry" to switch the output off. + Defaulting to use time-reversal symmetry for k-point grid. + Charge integration errors on the 3D integration grid will be compensated + by explicit normalization and distribution of residual charges. + Use the "compensate_multipole_errors" flag to change this behaviour. + Set 'collect_eigenvectors' to be '.true.' for all serial calculations. This is mandatory. + Set 'collect_eigenvectors' to be '.true.' for KS_method lapack_fast and serial. + + Consistency checks for the contents of geometry.in are next. + + + Range separation radius for Ewald summation (hartree_convergence_parameter): 3.95124372 bohr. + Number of empty states per atom not set in control.in - providing a guess from actual geometry. + | Total number of empty states used during s.c.f. cycle: 6 + If you use a very high smearing, use empty_states (per atom!) in control.in to increase this value. + + Structure-dependent array size parameters: + | Maximum number of distinct radial functions : 9 + | Maximum number of basis functions : 50 + | Number of Kohn-Sham states (occupied + empty): 20 +------------------------------------------------------------ + +------------------------------------------------------------ + Preparing all fixed parts of the calculation. +------------------------------------------------------------ + Determining machine precision: + 2.225073858507201E-308 + Setting up grids for atomic and cluster calculations. + + Creating wave function, potential, and density for free atoms. + Runtime choices for atomic solver: + | atomic solver xc : PBE + | compute density gradient: 1 + | compute kinetic density : F + + Species: Si + + List of occupied orbitals and eigenvalues: + n l occ energy [Ha] energy [eV] + 1 0 2.0000 -65.767597 -1789.6274 + 2 0 2.0000 -5.115610 -139.2028 + 3 0 2.0000 -0.388877 -10.5819 + 2 1 6.0000 -3.500197 -95.2452 + 3 1 2.0000 -0.140803 -3.8315 + + + Adding cutoff potential to free-atom effective potential. + Creating fixed part of basis set: Ionic, confined, hydrogenic. + + Si ion: + + List of free ionic orbitals and eigenvalues: + n l energy [Ha] energy [eV] + 1 0 -66.641157 -1813.3982 + 2 0 -5.964274 -162.2962 + 3 0 -1.073878 -29.2217 + 2 1 -4.350005 -118.3697 + 3 1 -0.776571 -21.1316 + + + List of ionic basis orbitals and eigenvalues: + n l energy [Ha] energy [eV] outer radius [A] + 3 0 -1.073857 -29.2211 4.214062 + + + Si hydrogenic: + + List of hydrogenic basis orbitals: + n l effective z eigenvalue [eV] inner max. [A] outer max. [A] outer radius [A] + 3 2 4.200000 -26.6624 1.139231 1.139231 4.534782 + 2 1 1.400000 -6.4613 1.472672 1.472672 4.590560 + 4 3 6.200000 -32.6778 1.368518 1.368518 4.534782 + + Creating atomic-like basis functions for current effective potential. + + Species Si : + + List of atomic basis orbitals and eigenvalues: + n l energy [Ha] energy [eV] outer radius [A] + 1 0 -65.767597 -1789.6274 0.789468 + 2 0 -5.115610 -139.2028 2.815114 + 3 0 -0.388877 -10.5819 4.534782 + 2 1 -3.500197 -95.2452 3.259919 + 3 1 -0.140803 -3.8315 4.590560 + + Assembling full basis from fixed parts. + | Species Si : atomic orbital 1 s accepted. + | Species Si : atomic orbital 2 s accepted. + | Species Si : ionic orbital 3 s accepted. + | Species Si : atomic orbital 3 s accepted. + | Species Si : atomic orbital 2 p accepted. + | Species Si : atomic orbital 3 p accepted. + | Species Si : hydro orbital 2 p accepted. + | Species Si : hydro orbital 3 d accepted. + | Species Si : hydro orbital 4 f accepted. + + Basis size parameters after reduction: + | Total number of radial functions: 9 + | Total number of basis functions : 50 + + Per-task memory consumption for arrays in subroutine allocate_ext: + | 3.102808MB. + Testing on-site integration grid accuracy. + | Species Function (log., in eV) (rad., in eV) + 1 1 -1789.6273740966 -1789.6266345813 + 1 2 -139.2028173376 -139.2028132357 + 1 3 -10.2237226190 -10.2235219160 + 1 4 5.6355365073 5.5558633521 *** + 1 5 -95.2452114632 -95.2452114537 + 1 6 -3.8413965043 -3.8571292824 + 1 7 6.4035522332 6.2277973139 *** + 1 8 6.3860095444 6.3839142324 + 1 9 19.3722793793 19.3677446767 + * Note: Onsite integrals marked "***" above are less accurate than + * onsite_accuracy_threshold = 0.03000 eV. Usually, this is harmless. + * When in doubt, tighten the "radial" and/or "radial_multiplier" flags to check. + + Preparing densities etc. for the partition functions (integrals / Hartree potential). + + Preparations completed. + max(cpu_time) : 0.110 s. + Wall clock time (cpu1) : 0.111 s. +------------------------------------------------------------ + +------------------------------------------------------------ + Begin self-consistency loop: Initialization. + + Date : 20230628, Time : 104123.175 +------------------------------------------------------------ + + Initializing index lists of integration centers etc. from given atomic structure: + Mapping all atomic coordinates to central unit cell. + + Initializing the k-points + Using symmetry for reducing the k-points + | k-points reduced from: 8 to 8 + | Number of k-points : 8 + The eigenvectors in the calculations are REAL. + | K-points in task 0: 8 + | Number of basis functions in the Hamiltonian integrals : 2161 + | Number of basis functions in a single unit cell : 50 + | Number of centers in hartree potential : 708 + | Number of centers in hartree multipole : 318 + | Number of centers in electron density summation: 190 + | Number of centers in basis integrals : 198 + | Number of centers in integrals : 101 + | Number of centers in hamiltonian : 190 + | Consuming 14 KiB for k_phase. + | Number of super-cells (origin) [n_cells] : 2197 + | Number of super-cells (after PM_index) [n_cells] : 112 + | Number of super-cells in hamiltonian [n_cells_in_hamiltonian]: 112 + | Size of matrix packed + index [n_hamiltonian_matrix_size] : 86003 + + Initializing relaxation algorithms. + Finished initialization of distributed Hessian storage. + | Global dimension: 15 + | BLACS block size: 15 + | Number of workers: 1 + + | Estimated reciprocal-space cutoff momentum G_max: 2.36080402 bohr^-1 . + | Reciprocal lattice points for long-range Hartree potential: 58 + Partitioning the integration grid into batches with parallel hashing+maxmin method. + | Number of batches: 128 + | Maximal batch size: 90 + | Minimal batch size: 85 + | Average batch size: 87.562 + | Standard deviation of batch sizes: 1.493 + + Integration load balanced across 1 MPI tasks. + Work distribution over tasks is as follows: + Task 0 has 11208 integration points. + Initializing partition tables, free-atom densities, potentials, etc. across the integration grid (initialize_grid_storage). + | initialize_grid_storage: Actual outermost partition radius vs. multipole_radius_free + | (-- VB: in principle, multipole_radius_free should be larger, hence this output) + | Species 1: Confinement radius = 4.999999999999999 AA, multipole_radius_free = 5.000694715736543 AA. + | Species 1: outer_partition_radius set to 5.000694715736543 AA . + | The sparse table of interatomic distances needs 212.76 kbyte instead of 313.63 kbyte of memory. + | Net number of integration points: 11208 + | of which are non-zero points : 9844 + | Numerical average free-atom electrostatic potential : -12.56983149 eV + Renormalizing the initial density to the exact electron count on the 3D integration grid. + | Initial density: Formal number of electrons (from input files) : 28.0000000000 + | Integrated number of electrons on 3D grid : 28.0044890464 + | Charge integration error : 0.0044890464 + | Normalization factor for density and gradient : 0.9998397026 + Renormalizing the free-atom superposition density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 28.0000000000 + | Integrated number of electrons on 3D grid : 28.0044890464 + | Charge integration error : 0.0044890464 + | Normalization factor for density and gradient : 0.9998397026 + Obtaining max. number of non-zero basis functions in each batch (get_n_compute_maxes). + | Maximal number of non-zero basis functions: 673 in task 0 + Allocating 0.061 MB for KS_eigenvector + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.435 s, elapsed 0.435 s + Integrating overlap matrix. + Time summed over all CPUs for integration: real work 0.286 s, elapsed 0.286 s + Decreasing sparse matrix size: + | Tolerance: 0.1000E-12 + Hamiltonian matrix + | Array has 76538 nonzero elements out of 86003 elements + | Sparsity factor is 0.110 + Overlap matrix + | Array has 69730 nonzero elements out of 86003 elements + | Sparsity factor is 0.189 + New size of hamiltonian matrix: 77039 + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Singularity check in k-point 1, task 0 (analysis for other k-points/tasks may follow below): + Overlap matrix is not singular + | Lowest and highest eigenvalues : 0.9901E-03, 0.6283E+01 + Finished singularity check of overlap matrix + | Time : 0.000 s + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.000 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -5.54754229 eV + Writing Kohn-Sham eigenvalues. + K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + + State Occupation Eigenvalue [Ha] Eigenvalue [eV] + 1 2.00000 -65.786672 -1790.14643 + 2 2.00000 -65.786672 -1790.14643 + 3 2.00000 -5.138850 -139.83522 + 4 2.00000 -5.138620 -139.82897 + 5 2.00000 -3.523444 -95.87778 + 6 2.00000 -3.523444 -95.87778 + 7 2.00000 -3.523444 -95.87778 + 8 2.00000 -3.522920 -95.86354 + 9 2.00000 -3.522920 -95.86354 + 10 2.00000 -3.522920 -95.86354 + 11 2.00000 -0.648513 -17.64694 + 12 2.00000 -0.222890 -6.06515 + 13 2.00000 -0.222890 -6.06515 + 14 2.00000 -0.222890 -6.06515 + 15 0.00000 -0.122072 -3.32176 + 16 0.00000 -0.122072 -3.32176 + 17 0.00000 -0.122072 -3.32176 + 18 0.00000 -0.117492 -3.19713 + 19 0.00000 0.074623 2.03061 + 20 0.00000 0.074623 2.03061 + + What follows are estimated values for band gap, HOMO, LUMO, etc. + | They are estimated on a discrete k-point grid and not necessarily exact. + | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. + + Highest occupied state (VBM) at -6.06515226 eV (relative to internal zero) + | Occupation number: 2.00000000 + | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + + Lowest unoccupied state (CBM) at -4.99146902 eV (relative to internal zero) + | Occupation number: 0.00000000 + | K-point: 6 at 0.500000 0.000000 0.500000 (in units of recip. lattice) + + ESTIMATED overall HOMO-LUMO gap: 1.07368323 eV between HOMO at k-point 1 and LUMO at k-point 6 + | This appears to be an indirect band gap. + | Smallest direct gap : 2.62680162 eV for k_point 3 at 0.000000 0.500000 0.000000 (in units of recip. lattice) + The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, + this system is most likely an insulator or a semiconductor. + Calculating total energy contributions from superposition of free atom densities. + + Total energy components: + | Sum of eigenvalues : -329.10882970 Ha -8955.50690722 eV + | XC energy correction : -41.70173345 Ha -1134.76190321 eV + | XC potential correction : 53.85472519 Ha 1465.46163427 eV + | Free-atom electrostatic energy: -263.69998542 Ha -7175.64169592 eV + | Hartree energy correction : 0.00000000 Ha 0.00000000 eV + | Entropy correction : 0.00000000 Ha 0.00000000 eV + | --------------------------- + | Total energy : -580.65582338 Ha -15800.44887208 eV + | Total energy, T -> 0 : -580.65582338 Ha -15800.44887208 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -580.65582338 Ha -15800.44887208 eV + + Derived energy quantities: + | Kinetic energy : 582.33599532 Ha 15846.16867687 eV + | Electrostatic energy : -1121.29008525 Ha -30511.85564573 eV + | Energy correction for multipole + | error in Hartree potential : 0.00000000 Ha 0.00000000 eV + | Sum of eigenvalues per atom : -4477.75345361 eV + | Total energy (T->0) per atom : -7900.22443604 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -7900.22443604 eV + Initialize hartree_potential_storage + Max. number of atoms included in rho_multipole: 2 + + End scf initialization - timings : max(cpu_time) wall_clock(cpu1) + | Time for scf. initialization : 1.052 s 1.052 s + | Boundary condition initialization : 0.062 s 0.061 s + | Relaxation initialization : 0.000 s 0.001 s + | Integration : 0.723 s 0.723 s + | Solution of K.-S. eqns. : 0.006 s 0.006 s + | Grid partitioning : 0.037 s 0.036 s + | Preloading free-atom quantities on grid : 0.196 s 0.197 s + | Free-atom superposition energy : 0.028 s 0.028 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 1.537 MB (on task 0) + | Maximum: 1.537 MB (on task 0) + | Average: 1.537 MB + | Peak value for overall tracked memory usage: + | Minimum: 6.565 MB (on task 0 after allocating wave) + | Maximum: 6.565 MB (on task 0 after allocating wave) + | Average: 6.565 MB + | Largest tracked array allocation so far: + | Minimum: 3.456 MB (hamiltonian_shell on task 0) + | Maximum: 3.456 MB (hamiltonian_shell on task 0) + | Average: 3.456 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + Evaluating new KS density using the density matrix + Evaluating density matrix + Time summed over all CPUs for getting density from density matrix: real work 0.918 s, elapsed 0.918 s + Integration grid: deviation in total charge ( - N_e) = -4.618528E-14 + + Time for density update prior : max(cpu_time) wall_clock(cpu1) + | self-consistency iterative process : 0.914 s 0.919 s + +------------------------------------------------------------ + Begin self-consistency iteration # 1 + + Date : 20230628, Time : 104125.146 +------------------------------------------------------------ + Pulay mixing of updated and previous charge densities. + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 28.0000000000 + | Integrated number of electrons on 3D grid : 27.9997706824 + | Charge integration error : -0.0002293176 + | Normalization factor for density and gradient : 1.0000081900 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = 0.174607E-12 + | Sum of charges compensated after spline to logarithmic grids = -0.539729E-05 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = 0.000000E+00 + Summing up the Hartree potential. + Time summed over all CPUs for potential: real work 0.329 s, elapsed 0.329 s + | RMS charge density error from multipole expansion : 0.688731E-03 + | Average real-space part of the electrostatic potential : 0.02728917 eV + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.432 s, elapsed 0.432 s + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.000 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -5.51709006 eV + Writing Kohn-Sham eigenvalues. + K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + + State Occupation Eigenvalue [Ha] Eigenvalue [eV] + 1 2.00000 -65.783258 -1790.05352 + 2 2.00000 -65.783258 -1790.05352 + 3 2.00000 -5.136258 -139.76468 + 4 2.00000 -5.136028 -139.75842 + 5 2.00000 -3.520781 -95.80534 + 6 2.00000 -3.520781 -95.80534 + 7 2.00000 -3.520781 -95.80534 + 8 2.00000 -3.520258 -95.79108 + 9 2.00000 -3.520258 -95.79108 + 10 2.00000 -3.520258 -95.79108 + 11 2.00000 -0.647408 -17.61686 + 12 2.00000 -0.221469 -6.02649 + 13 2.00000 -0.221469 -6.02649 + 14 2.00000 -0.221469 -6.02649 + 15 0.00000 -0.121223 -3.29865 + 16 0.00000 -0.121223 -3.29865 + 17 0.00000 -0.121223 -3.29865 + 18 0.00000 -0.115839 -3.15215 + 19 0.00000 0.075426 2.05244 + 20 0.00000 0.075426 2.05244 + + What follows are estimated values for band gap, HOMO, LUMO, etc. + | They are estimated on a discrete k-point grid and not necessarily exact. + | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. + + Highest occupied state (VBM) at -6.02649044 eV (relative to internal zero) + | Occupation number: 2.00000000 + | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + + Lowest unoccupied state (CBM) at -4.97745287 eV (relative to internal zero) + | Occupation number: 0.00000000 + | K-point: 6 at 0.500000 0.000000 0.500000 (in units of recip. lattice) + + ESTIMATED overall HOMO-LUMO gap: 1.04903757 eV between HOMO at k-point 1 and LUMO at k-point 6 + | This appears to be an indirect band gap. + | Smallest direct gap : 2.62049196 eV for k_point 3 at 0.000000 0.500000 0.000000 (in units of recip. lattice) + The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, + this system is most likely an insulator or a semiconductor. + + Total energy components: + | Sum of eigenvalues : -329.04311153 Ha -8953.71862494 eV + | XC energy correction : -41.70627212 Ha -1134.88540669 eV + | XC potential correction : 53.86059820 Ha 1465.62144695 eV + | Free-atom electrostatic energy: -263.69998542 Ha -7175.64169592 eV + | Hartree energy correction : -0.06595607 Ha -1.79475600 eV + | Entropy correction : 0.00000000 Ha 0.00000000 eV + | --------------------------- + | Total energy : -580.65472694 Ha -15800.41903659 eV + | Total energy, T -> 0 : -580.65472694 Ha -15800.41903659 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -580.65472694 Ha -15800.41903659 eV + + Derived energy quantities: + | Kinetic energy : 582.35664842 Ha 15846.73067623 eV + | Electrostatic energy : -1121.30510324 Ha -30512.26430613 eV + | Energy correction for multipole + | error in Hartree potential : 0.00092076 Ha 0.02505523 eV + | Sum of eigenvalues per atom : -4476.85931247 eV + | Total energy (T->0) per atom : -7900.20951830 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -7900.20951830 eV + Evaluating new KS density using the density matrix + Evaluating density matrix + Time summed over all CPUs for getting density from density matrix: real work 0.878 s, elapsed 0.878 s + Integration grid: deviation in total charge ( - N_e) = 5.684342E-14 + + Self-consistency convergence accuracy: + | Change of charge density : 0.1472E+00 + | Change of sum of eigenvalues : 0.1788E+01 eV + | Change of total energy : 0.2984E-01 eV + + +------------------------------------------------------------ + End self-consistency iteration # 1 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 1.820 s 1.831 s + | Charge density update : 0.873 s 0.879 s + | Density mixing & preconditioning : 0.180 s 0.181 s + | Hartree multipole update : 0.001 s 0.001 s + | Hartree multipole summation : 0.329 s 0.332 s + | Integration : 0.431 s 0.433 s + | Solution of K.-S. eqns. : 0.005 s 0.005 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 1.537 MB (on task 0) + | Maximum: 1.537 MB (on task 0) + | Average: 1.537 MB + | Peak value for overall tracked memory usage: + | Minimum: 7.765 MB (on task 0 after allocating gradient_basis_wave) + | Maximum: 7.765 MB (on task 0 after allocating gradient_basis_wave) + | Average: 7.765 MB + | Largest tracked array allocation so far: + | Minimum: 3.456 MB (hamiltonian_shell on task 0) + | Maximum: 3.456 MB (hamiltonian_shell on task 0) + | Average: 3.456 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + +------------------------------------------------------------ + Begin self-consistency iteration # 2 + + Date : 20230628, Time : 104126.977 +------------------------------------------------------------ + Pulay mixing of updated and previous charge densities. + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 28.0000000000 + | Integrated number of electrons on 3D grid : 27.9958223750 + | Charge integration error : -0.0041776250 + | Normalization factor for density and gradient : 1.0001492232 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = 0.248636E-12 + | Sum of charges compensated after spline to logarithmic grids = -0.103125E-03 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = 0.000000E+00 + Summing up the Hartree potential. + Time summed over all CPUs for potential: real work 0.392 s, elapsed 0.392 s + | RMS charge density error from multipole expansion : 0.131324E-01 + | Average real-space part of the electrostatic potential : 0.51574400 eV + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.432 s, elapsed 0.432 s + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.000 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -4.86564087 eV + What follows are estimated values for band gap, HOMO, LUMO, etc. + | They are estimated on a discrete k-point grid and not necessarily exact. + | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. + + Highest occupied state (VBM) at -5.26885362 eV (relative to internal zero) + | Occupation number: 2.00000000 + | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + + Lowest unoccupied state (CBM) at -4.61373730 eV (relative to internal zero) + | Occupation number: 0.00000000 + | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) + + ESTIMATED overall HOMO-LUMO gap: 0.65511632 eV between HOMO at k-point 1 and LUMO at k-point 4 + | This appears to be an indirect band gap. + | Smallest direct gap : 2.43194692 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, + this system is most likely an insulator or a semiconductor. + + Checking to see if s.c.f. parameters should be adjusted. + The system likely has a gap. Increased the default Pulay mixing parameter (charge_mix_param). Value: 0.200000 . + Kept the default occupation width. Value: 0.010000 eV. + + Total energy components: + | Sum of eigenvalues : -327.86163892 Ha -8921.56911953 eV + | XC energy correction : -41.81168620 Ha -1137.75386970 eV + | XC potential correction : 53.99474106 Ha 1469.27165986 eV + | Free-atom electrostatic energy: -263.69998542 Ha -7175.64169592 eV + | Hartree energy correction : -1.26787332 Ha -34.50058828 eV + | Entropy correction : -0.00000000 Ha -0.00000000 eV + | --------------------------- + | Total energy : -580.64644280 Ha -15800.19361357 eV + | Total energy, T -> 0 : -580.64644280 Ha -15800.19361357 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -580.64644280 Ha -15800.19361357 eV + + Derived energy quantities: + | Kinetic energy : 582.68623392 Ha 15855.69915398 eV + | Electrostatic energy : -1121.52099052 Ha -30518.13889784 eV + | Energy correction for multipole + | error in Hartree potential : 0.01752068 Ha 0.47676194 eV + | Sum of eigenvalues per atom : -4460.78455977 eV + | Total energy (T->0) per atom : -7900.09680678 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -7900.09680678 eV + Evaluating new KS density using the density matrix + Evaluating density matrix + Time summed over all CPUs for getting density from density matrix: real work 0.878 s, elapsed 0.878 s + Integration grid: deviation in total charge ( - N_e) = 1.065814E-13 + + Self-consistency convergence accuracy: + | Change of charge density : 0.1397E+00 + | Change of sum of eigenvalues : 0.3215E+02 eV + | Change of total energy : 0.2254E+00 eV + + +------------------------------------------------------------ + End self-consistency iteration # 2 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 1.879 s 1.891 s + | Charge density update : 0.874 s 0.880 s + | Density mixing & preconditioning : 0.178 s 0.179 s + | Hartree multipole update : 0.001 s 0.001 s + | Hartree multipole summation : 0.392 s 0.394 s + | Integration : 0.430 s 0.433 s + | Solution of K.-S. eqns. : 0.005 s 0.004 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 1.537 MB (on task 0) + | Maximum: 1.537 MB (on task 0) + | Average: 1.537 MB + | Peak value for overall tracked memory usage: + | Minimum: 7.766 MB (on task 0 after allocating gradient_basis_wave) + | Maximum: 7.766 MB (on task 0 after allocating gradient_basis_wave) + | Average: 7.766 MB + | Largest tracked array allocation so far: + | Minimum: 3.456 MB (hamiltonian_shell on task 0) + | Maximum: 3.456 MB (hamiltonian_shell on task 0) + | Average: 3.456 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + +------------------------------------------------------------ + Begin self-consistency iteration # 3 + + Date : 20230628, Time : 104128.868 +------------------------------------------------------------ + Pulay mixing of updated and previous charge densities. + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 28.0000000000 + | Integrated number of electrons on 3D grid : 27.9993663856 + | Charge integration error : -0.0006336144 + | Normalization factor for density and gradient : 1.0000226296 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = -0.386371E-13 + | Sum of charges compensated after spline to logarithmic grids = -0.111544E-03 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = 0.000000E+00 + Summing up the Hartree potential. + Time summed over all CPUs for potential: real work 0.392 s, elapsed 0.392 s + | RMS charge density error from multipole expansion : 0.138367E-01 + | Average real-space part of the electrostatic potential : 0.50527974 eV + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.432 s, elapsed 0.433 s + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.000 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -4.88620788 eV + What follows are estimated values for band gap, HOMO, LUMO, etc. + | They are estimated on a discrete k-point grid and not necessarily exact. + | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. + + Highest occupied state (VBM) at -5.29937334 eV (relative to internal zero) + | Occupation number: 2.00000000 + | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + + Lowest unoccupied state (CBM) at -4.61132158 eV (relative to internal zero) + | Occupation number: 0.00000000 + | K-point: 6 at 0.500000 0.000000 0.500000 (in units of recip. lattice) + + ESTIMATED overall HOMO-LUMO gap: 0.68805176 eV between HOMO at k-point 1 and LUMO at k-point 6 + | This appears to be an indirect band gap. + | Smallest direct gap : 2.43473574 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, + this system is most likely an insulator or a semiconductor. + + Total energy components: + | Sum of eigenvalues : -328.00561270 Ha -8925.48684534 eV + | XC energy correction : -41.79877840 Ha -1137.40263057 eV + | XC potential correction : 53.97806660 Ha 1468.81792492 eV + | Free-atom electrostatic energy: -263.69998542 Ha -7175.64169592 eV + | Hartree energy correction : -1.12001652 Ha -30.47720020 eV + | Entropy correction : 0.00000000 Ha 0.00000000 eV + | --------------------------- + | Total energy : -580.64632643 Ha -15800.19044711 eV + | Total energy, T -> 0 : -580.64632643 Ha -15800.19044711 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -580.64632643 Ha -15800.19044711 eV + + Derived energy quantities: + | Kinetic energy : 582.50125777 Ha 15850.66569691 eV + | Electrostatic energy : -1121.34880581 Ha -30513.45351345 eV + | Energy correction for multipole + | error in Hartree potential : 0.01868691 Ha 0.50849666 eV + | Sum of eigenvalues per atom : -4462.74342267 eV + | Total energy (T->0) per atom : -7900.09522355 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -7900.09522355 eV + Evaluating new KS density using the density matrix + Evaluating density matrix + Time summed over all CPUs for getting density from density matrix: real work 0.877 s, elapsed 0.877 s + Integration grid: deviation in total charge ( - N_e) = 2.842171E-14 + + Self-consistency convergence accuracy: + | Change of charge density : 0.2064E-01 + | Change of sum of eigenvalues : -0.3918E+01 eV + | Change of total energy : 0.3166E-02 eV + + +------------------------------------------------------------ + End self-consistency iteration # 3 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 1.881 s 1.893 s + | Charge density update : 0.872 s 0.879 s + | Density mixing & preconditioning : 0.181 s 0.181 s + | Hartree multipole update : 0.001 s 0.001 s + | Hartree multipole summation : 0.392 s 0.394 s + | Integration : 0.430 s 0.433 s + | Solution of K.-S. eqns. : 0.005 s 0.005 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 1.538 MB (on task 0) + | Maximum: 1.538 MB (on task 0) + | Average: 1.538 MB + | Peak value for overall tracked memory usage: + | Minimum: 7.766 MB (on task 0 after allocating gradient_basis_wave) + | Maximum: 7.766 MB (on task 0 after allocating gradient_basis_wave) + | Average: 7.766 MB + | Largest tracked array allocation so far: + | Minimum: 3.456 MB (hamiltonian_shell on task 0) + | Maximum: 3.456 MB (hamiltonian_shell on task 0) + | Average: 3.456 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + +------------------------------------------------------------ + Begin self-consistency iteration # 4 + + Date : 20230628, Time : 104130.761 +------------------------------------------------------------ + Pulay mixing of updated and previous charge densities. + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 28.0000000000 + | Integrated number of electrons on 3D grid : 27.9993017485 + | Charge integration error : -0.0006982515 + | Normalization factor for density and gradient : 1.0000249382 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = 0.127016E-12 + | Sum of charges compensated after spline to logarithmic grids = -0.124177E-03 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = 0.000000E+00 + Summing up the Hartree potential. + Time summed over all CPUs for potential: real work 0.394 s, elapsed 0.394 s + | RMS charge density error from multipole expansion : 0.151234E-01 + | Average real-space part of the electrostatic potential : 0.51490697 eV + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.432 s, elapsed 0.432 s + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.001 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.000 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -4.87204434 eV + What follows are estimated values for band gap, HOMO, LUMO, etc. + | They are estimated on a discrete k-point grid and not necessarily exact. + | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. + + Highest occupied state (VBM) at -5.29286016 eV (relative to internal zero) + | Occupation number: 2.00000000 + | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + + Lowest unoccupied state (CBM) at -4.58355519 eV (relative to internal zero) + | Occupation number: 0.00000000 + | K-point: 7 at 0.500000 0.500000 0.000000 (in units of recip. lattice) + + ESTIMATED overall HOMO-LUMO gap: 0.70930496 eV between HOMO at k-point 1 and LUMO at k-point 7 + | This appears to be an indirect band gap. + | Smallest direct gap : 2.42480865 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, + this system is most likely an insulator or a semiconductor. + + Total energy components: + | Sum of eigenvalues : -328.10105415 Ha -8928.08393921 eV + | XC energy correction : -41.79191602 Ha -1137.21589584 eV + | XC potential correction : 53.96893080 Ha 1468.56932705 eV + | Free-atom electrostatic energy: -263.69998542 Ha -7175.64169592 eV + | Hartree energy correction : -1.02214339 Ha -27.81393683 eV + | Entropy correction : 0.00000000 Ha 0.00000000 eV + | --------------------------- + | Total energy : -580.64616818 Ha -15800.18614075 eV + | Total energy, T -> 0 : -580.64616818 Ha -15800.18614075 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -580.64616818 Ha -15800.18614075 eV + + Derived energy quantities: + | Kinetic energy : 582.32598076 Ha 15845.89616684 eV + | Electrostatic energy : -1121.18023292 Ha -30508.86641175 eV + | Energy correction for multipole + | error in Hartree potential : 0.02061469 Ha 0.56095417 eV + | Sum of eigenvalues per atom : -4464.04196961 eV + | Total energy (T->0) per atom : -7900.09307038 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -7900.09307038 eV + Evaluating new KS density using the density matrix + Evaluating density matrix + Time summed over all CPUs for getting density from density matrix: real work 0.878 s, elapsed 0.878 s + Integration grid: deviation in total charge ( - N_e) = 5.684342E-14 + + Self-consistency convergence accuracy: + | Change of charge density : 0.1231E-01 + | Change of sum of eigenvalues : -0.2597E+01 eV + | Change of total energy : 0.4306E-02 eV + + +------------------------------------------------------------ + End self-consistency iteration # 4 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 1.881 s 1.892 s + | Charge density update : 0.874 s 0.879 s + | Density mixing & preconditioning : 0.178 s 0.179 s + | Hartree multipole update : 0.001 s 0.001 s + | Hartree multipole summation : 0.394 s 0.396 s + | Integration : 0.430 s 0.432 s + | Solution of K.-S. eqns. : 0.005 s 0.005 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 1.538 MB (on task 0) + | Maximum: 1.538 MB (on task 0) + | Average: 1.538 MB + | Peak value for overall tracked memory usage: + | Minimum: 7.766 MB (on task 0 after allocating gradient_basis_wave) + | Maximum: 7.766 MB (on task 0 after allocating gradient_basis_wave) + | Average: 7.766 MB + | Largest tracked array allocation so far: + | Minimum: 3.456 MB (hamiltonian_shell on task 0) + | Maximum: 3.456 MB (hamiltonian_shell on task 0) + | Average: 3.456 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + +------------------------------------------------------------ + Begin self-consistency iteration # 5 + + Date : 20230628, Time : 104132.653 +------------------------------------------------------------ + Pulay mixing of updated and previous charge densities. + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 28.0000000000 + | Integrated number of electrons on 3D grid : 28.0007654108 + | Charge integration error : 0.0007654108 + | Normalization factor for density and gradient : 0.9999726646 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = 0.113849E-12 + | Sum of charges compensated after spline to logarithmic grids = -0.121847E-03 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = 0.000000E+00 + Summing up the Hartree potential. + Time summed over all CPUs for potential: real work 0.392 s, elapsed 0.392 s + | RMS charge density error from multipole expansion : 0.150727E-01 + | Average real-space part of the electrostatic potential : 0.49589346 eV + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.432 s, elapsed 0.432 s + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.000 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -4.88328636 eV + What follows are estimated values for band gap, HOMO, LUMO, etc. + | They are estimated on a discrete k-point grid and not necessarily exact. + | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. + + Highest occupied state (VBM) at -5.30466705 eV (relative to internal zero) + | Occupation number: 2.00000000 + | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + + Lowest unoccupied state (CBM) at -4.59249490 eV (relative to internal zero) + | Occupation number: 0.00000000 + | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) + + ESTIMATED overall HOMO-LUMO gap: 0.71217215 eV between HOMO at k-point 1 and LUMO at k-point 4 + | This appears to be an indirect band gap. + | Smallest direct gap : 2.42925330 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, + this system is most likely an insulator or a semiconductor. + + Total energy components: + | Sum of eigenvalues : -328.15577741 Ha -8929.57303500 eV + | XC energy correction : -41.78965399 Ha -1137.15434277 eV + | XC potential correction : 53.96575153 Ha 1468.48281475 eV + | Free-atom electrostatic energy: -263.69998542 Ha -7175.64169592 eV + | Hartree energy correction : -0.96645644 Ha -26.29861771 eV + | Entropy correction : 0.00000000 Ha 0.00000000 eV + | --------------------------- + | Total energy : -580.64612172 Ha -15800.18487664 eV + | Total energy, T -> 0 : -580.64612172 Ha -15800.18487664 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -580.64612172 Ha -15800.18487664 eV + + Derived energy quantities: + | Kinetic energy : 582.29516914 Ha 15845.05773999 eV + | Electrostatic energy : -1121.15163688 Ha -30508.08827387 eV + | Energy correction for multipole + | error in Hartree potential : 0.02040284 Ha 0.55518946 eV + | Sum of eigenvalues per atom : -4464.78651750 eV + | Total energy (T->0) per atom : -7900.09243832 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -7900.09243832 eV + Evaluating new KS density using the density matrix + Evaluating density matrix + Time summed over all CPUs for getting density from density matrix: real work 0.878 s, elapsed 0.878 s + Integration grid: deviation in total charge ( - N_e) = 5.329071E-14 + + Self-consistency convergence accuracy: + | Change of charge density : 0.3697E-02 + | Change of sum of eigenvalues : -0.1489E+01 eV + | Change of total energy : 0.1264E-02 eV + + +------------------------------------------------------------ + End self-consistency iteration # 5 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 1.880 s 1.892 s + | Charge density update : 0.874 s 0.880 s + | Density mixing & preconditioning : 0.178 s 0.179 s + | Hartree multipole update : 0.001 s 0.001 s + | Hartree multipole summation : 0.393 s 0.395 s + | Integration : 0.430 s 0.432 s + | Solution of K.-S. eqns. : 0.005 s 0.005 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 1.538 MB (on task 0) + | Maximum: 1.538 MB (on task 0) + | Average: 1.538 MB + | Peak value for overall tracked memory usage: + | Minimum: 7.766 MB (on task 0 after allocating gradient_basis_wave) + | Maximum: 7.766 MB (on task 0 after allocating gradient_basis_wave) + | Average: 7.766 MB + | Largest tracked array allocation so far: + | Minimum: 3.456 MB (hamiltonian_shell on task 0) + | Maximum: 3.456 MB (hamiltonian_shell on task 0) + | Average: 3.456 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + +------------------------------------------------------------ + Begin self-consistency iteration # 6 + + Date : 20230628, Time : 104134.545 +------------------------------------------------------------ + Pulay mixing of updated and previous charge densities. + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 28.0000000000 + | Integrated number of electrons on 3D grid : 28.0001271580 + | Charge integration error : 0.0001271580 + | Normalization factor for density and gradient : 0.9999954587 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = 0.170005E-12 + | Sum of charges compensated after spline to logarithmic grids = -0.121146E-03 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = 0.000000E+00 + Summing up the Hartree potential. + Time summed over all CPUs for potential: real work 0.392 s, elapsed 0.392 s + | RMS charge density error from multipole expansion : 0.149973E-01 + | Average real-space part of the electrostatic potential : 0.48838703 eV + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.432 s, elapsed 0.432 s + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.001 s + Finished solving standard eigenproblem + | Time : 0.000 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -4.89304867 eV + What follows are estimated values for band gap, HOMO, LUMO, etc. + | They are estimated on a discrete k-point grid and not necessarily exact. + | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. + + Highest occupied state (VBM) at -5.31568837 eV (relative to internal zero) + | Occupation number: 2.00000000 + | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + + Lowest unoccupied state (CBM) at -4.59826078 eV (relative to internal zero) + | Occupation number: 0.00000000 + | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) + + ESTIMATED overall HOMO-LUMO gap: 0.71742759 eV between HOMO at k-point 1 and LUMO at k-point 4 + | This appears to be an indirect band gap. + | Smallest direct gap : 2.43284984 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, + this system is most likely an insulator or a semiconductor. + + Total energy components: + | Sum of eigenvalues : -328.17991453 Ha -8930.22983952 eV + | XC energy correction : -41.78779479 Ha -1137.10375136 eV + | XC potential correction : 53.96336410 Ha 1468.41784950 eV + | Free-atom electrostatic energy: -263.69998542 Ha -7175.64169592 eV + | Hartree energy correction : -0.94177100 Ha -25.62689267 eV + | Entropy correction : 0.00000000 Ha 0.00000000 eV + | --------------------------- + | Total energy : -580.64610163 Ha -15800.18432997 eV + | Total energy, T -> 0 : -580.64610163 Ha -15800.18432997 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -580.64610163 Ha -15800.18432997 eV + + Derived energy quantities: + | Kinetic energy : 582.28772081 Ha 15844.85506064 eV + | Electrostatic energy : -1121.14602766 Ha -30507.93563924 eV + | Energy correction for multipole + | error in Hartree potential : 0.02029783 Ha 0.55233193 eV + | Sum of eigenvalues per atom : -4465.11491976 eV + | Total energy (T->0) per atom : -7900.09216498 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -7900.09216498 eV + Evaluating new KS density using the density matrix + Evaluating density matrix + Time summed over all CPUs for getting density from density matrix: real work 0.878 s, elapsed 0.878 s + Integration grid: deviation in total charge ( - N_e) = -5.684342E-14 + + Self-consistency convergence accuracy: + | Change of charge density : 0.1082E-02 + | Change of sum of eigenvalues : -0.6568E+00 eV + | Change of total energy : 0.5467E-03 eV + + +------------------------------------------------------------ + End self-consistency iteration # 6 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 1.880 s 1.891 s + | Charge density update : 0.873 s 0.879 s + | Density mixing & preconditioning : 0.178 s 0.179 s + | Hartree multipole update : 0.001 s 0.001 s + | Hartree multipole summation : 0.392 s 0.394 s + | Integration : 0.430 s 0.433 s + | Solution of K.-S. eqns. : 0.005 s 0.005 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 1.538 MB (on task 0) + | Maximum: 1.538 MB (on task 0) + | Average: 1.538 MB + | Peak value for overall tracked memory usage: + | Minimum: 7.766 MB (on task 0 after allocating gradient_basis_wave) + | Maximum: 7.766 MB (on task 0 after allocating gradient_basis_wave) + | Average: 7.766 MB + | Largest tracked array allocation so far: + | Minimum: 3.456 MB (hamiltonian_shell on task 0) + | Maximum: 3.456 MB (hamiltonian_shell on task 0) + | Average: 3.456 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + +------------------------------------------------------------ + Begin self-consistency iteration # 7 + + Date : 20230628, Time : 104136.436 +------------------------------------------------------------ + Pulay mixing of updated and previous charge densities. + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 28.0000000000 + | Integrated number of electrons on 3D grid : 27.9999503327 + | Charge integration error : -0.0000496673 + | Normalization factor for density and gradient : 1.0000017738 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = 0.874785E-13 + | Sum of charges compensated after spline to logarithmic grids = -0.122079E-03 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = 0.000000E+00 + Summing up the Hartree potential. + Time summed over all CPUs for potential: real work 0.392 s, elapsed 0.392 s + | RMS charge density error from multipole expansion : 0.151009E-01 + | Average real-space part of the electrostatic potential : 0.49319331 eV + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.433 s, elapsed 0.433 s + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.000 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -4.88720335 eV + What follows are estimated values for band gap, HOMO, LUMO, etc. + | They are estimated on a discrete k-point grid and not necessarily exact. + | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. + + Highest occupied state (VBM) at -5.30957832 eV (relative to internal zero) + | Occupation number: 2.00000000 + | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + + Lowest unoccupied state (CBM) at -4.59363164 eV (relative to internal zero) + | Occupation number: 0.00000000 + | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) + + ESTIMATED overall HOMO-LUMO gap: 0.71594668 eV between HOMO at k-point 1 and LUMO at k-point 4 + | This appears to be an indirect band gap. + | Smallest direct gap : 2.43056833 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, + this system is most likely an insulator or a semiconductor. + + Total energy components: + | Sum of eigenvalues : -328.16539134 Ha -8929.83464325 eV + | XC energy correction : -41.78931786 Ha -1137.14519629 eV + | XC potential correction : 53.96533763 Ha 1468.47155192 eV + | Free-atom electrostatic energy: -263.69998542 Ha -7175.64169592 eV + | Hartree energy correction : -0.95674602 Ha -26.03438384 eV + | Entropy correction : 0.00000000 Ha 0.00000000 eV + | --------------------------- + | Total energy : -580.64610301 Ha -15800.18436738 eV + | Total energy, T -> 0 : -580.64610301 Ha -15800.18436738 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -580.64610301 Ha -15800.18436738 eV + + Derived energy quantities: + | Kinetic energy : 582.30449763 Ha 15845.31158105 eV + | Electrostatic energy : -1121.16128278 Ha -30508.35075214 eV + | Energy correction for multipole + | error in Hartree potential : 0.02045069 Ha 0.55649154 eV + | Sum of eigenvalues per atom : -4464.91732162 eV + | Total energy (T->0) per atom : -7900.09218369 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -7900.09218369 eV + Evaluating new KS density using the density matrix + Evaluating density matrix + Time summed over all CPUs for getting density from density matrix: real work 0.878 s, elapsed 0.878 s + Integration grid: deviation in total charge ( - N_e) = 0.000000E+00 + + Self-consistency convergence accuracy: + | Change of charge density : 0.9762E-03 + | Change of sum of eigenvalues : 0.3952E+00 eV + | Change of total energy : -0.3741E-04 eV + + +------------------------------------------------------------ + End self-consistency iteration # 7 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 1.881 s 1.893 s + | Charge density update : 0.874 s 0.880 s + | Density mixing & preconditioning : 0.178 s 0.179 s + | Hartree multipole update : 0.001 s 0.001 s + | Hartree multipole summation : 0.393 s 0.395 s + | Integration : 0.431 s 0.434 s + | Solution of K.-S. eqns. : 0.005 s 0.004 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 1.538 MB (on task 0) + | Maximum: 1.538 MB (on task 0) + | Average: 1.538 MB + | Peak value for overall tracked memory usage: + | Minimum: 7.766 MB (on task 0 after allocating gradient_basis_wave) + | Maximum: 7.766 MB (on task 0 after allocating gradient_basis_wave) + | Average: 7.766 MB + | Largest tracked array allocation so far: + | Minimum: 3.456 MB (hamiltonian_shell on task 0) + | Maximum: 3.456 MB (hamiltonian_shell on task 0) + | Average: 3.456 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + +------------------------------------------------------------ + Begin self-consistency iteration # 8 + + Date : 20230628, Time : 104138.329 +------------------------------------------------------------ + Pulay mixing of updated and previous charge densities. + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 28.0000000000 + | Integrated number of electrons on 3D grid : 27.9999822413 + | Charge integration error : -0.0000177587 + | Normalization factor for density and gradient : 1.0000006342 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = 0.311694E-12 + | Sum of charges compensated after spline to logarithmic grids = -0.122168E-03 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = 0.000000E+00 + Summing up the Hartree potential. + Time summed over all CPUs for potential: real work 0.393 s, elapsed 0.393 s + | RMS charge density error from multipole expansion : 0.151074E-01 + | Average real-space part of the electrostatic potential : 0.49358685 eV + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.432 s, elapsed 0.432 s + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.000 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -4.88678031 eV + What follows are estimated values for band gap, HOMO, LUMO, etc. + | They are estimated on a discrete k-point grid and not necessarily exact. + | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. + + Highest occupied state (VBM) at -5.30913777 eV (relative to internal zero) + | Occupation number: 2.00000000 + | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + + Lowest unoccupied state (CBM) at -4.59330002 eV (relative to internal zero) + | Occupation number: 0.00000000 + | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) + + ESTIMATED overall HOMO-LUMO gap: 0.71583774 eV between HOMO at k-point 1 and LUMO at k-point 4 + | This appears to be an indirect band gap. + | Smallest direct gap : 2.43040051 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, + this system is most likely an insulator or a semiconductor. + + Total energy components: + | Sum of eigenvalues : -328.16455080 Ha -8929.81177108 eV + | XC energy correction : -41.78939437 Ha -1137.14727826 eV + | XC potential correction : 53.96543501 Ha 1468.47420172 eV + | Free-atom electrostatic energy: -263.69998542 Ha -7175.64169592 eV + | Hartree energy correction : -0.95760741 Ha -26.05782341 eV + | Entropy correction : 0.00000000 Ha 0.00000000 eV + | --------------------------- + | Total energy : -580.64610299 Ha -15800.18436694 eV + | Total energy, T -> 0 : -580.64610299 Ha -15800.18436694 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -580.64610299 Ha -15800.18436694 eV + + Derived energy quantities: + | Kinetic energy : 582.30488896 Ha 15845.32222982 eV + | Electrostatic energy : -1121.16159758 Ha -30508.35931850 eV + | Energy correction for multipole + | error in Hartree potential : 0.02046340 Ha 0.55683750 eV + | Sum of eigenvalues per atom : -4464.90588554 eV + | Total energy (T->0) per atom : -7900.09218347 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -7900.09218347 eV + Evaluating new KS density using the density matrix + Evaluating density matrix + Time summed over all CPUs for getting density from density matrix: real work 0.881 s, elapsed 0.881 s + Integration grid: deviation in total charge ( - N_e) = -6.039613E-14 + + Self-consistency convergence accuracy: + | Change of charge density : 0.5217E-04 + | Change of sum of eigenvalues : 0.2287E-01 eV + | Change of total energy : 0.4390E-06 eV + + +------------------------------------------------------------ + End self-consistency iteration # 8 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 1.888 s 1.900 s + | Charge density update : 0.876 s 0.883 s + | Density mixing & preconditioning : 0.183 s 0.184 s + | Hartree multipole update : 0.001 s 0.001 s + | Hartree multipole summation : 0.393 s 0.395 s + | Integration : 0.430 s 0.433 s + | Solution of K.-S. eqns. : 0.005 s 0.004 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 1.538 MB (on task 0) + | Maximum: 1.538 MB (on task 0) + | Average: 1.538 MB + | Peak value for overall tracked memory usage: + | Minimum: 7.766 MB (on task 0 after allocating gradient_basis_wave) + | Maximum: 7.766 MB (on task 0 after allocating gradient_basis_wave) + | Average: 7.766 MB + | Largest tracked array allocation so far: + | Minimum: 3.456 MB (hamiltonian_shell on task 0) + | Maximum: 3.456 MB (hamiltonian_shell on task 0) + | Average: 3.456 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + +------------------------------------------------------------ + Begin self-consistency iteration # 9 + + Date : 20230628, Time : 104140.229 +------------------------------------------------------------ + Pulay mixing of updated and previous charge densities. + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 28.0000000000 + | Integrated number of electrons on 3D grid : 27.9999984129 + | Charge integration error : -0.0000015871 + | Normalization factor for density and gradient : 1.0000000567 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = 0.183238E-12 + | Sum of charges compensated after spline to logarithmic grids = -0.122152E-03 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = 0.000000E+00 + Summing up the Hartree potential. + Time summed over all CPUs for potential: real work 0.393 s, elapsed 0.393 s + | RMS charge density error from multipole expansion : 0.151052E-01 + | Average real-space part of the electrostatic potential : 0.49360086 eV + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.432 s, elapsed 0.432 s + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.000 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -4.88679696 eV + What follows are estimated values for band gap, HOMO, LUMO, etc. + | They are estimated on a discrete k-point grid and not necessarily exact. + | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. + + Highest occupied state (VBM) at -5.30914296 eV (relative to internal zero) + | Occupation number: 2.00000000 + | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + + Lowest unoccupied state (CBM) at -4.59333953 eV (relative to internal zero) + | Occupation number: 0.00000000 + | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) + + ESTIMATED overall HOMO-LUMO gap: 0.71580344 eV between HOMO at k-point 1 and LUMO at k-point 4 + | This appears to be an indirect band gap. + | Smallest direct gap : 2.43041245 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, + this system is most likely an insulator or a semiconductor. + + Total energy components: + | Sum of eigenvalues : -328.16438111 Ha -8929.80715350 eV + | XC energy correction : -41.78939735 Ha -1137.14735920 eV + | XC potential correction : 53.96543963 Ha 1468.47432741 eV + | Free-atom electrostatic energy: -263.69998542 Ha -7175.64169592 eV + | Hartree energy correction : -0.95777908 Ha -26.06249469 eV + | Entropy correction : 0.00000000 Ha 0.00000000 eV + | --------------------------- + | Total energy : -580.64610332 Ha -15800.18437589 eV + | Total energy, T -> 0 : -580.64610332 Ha -15800.18437589 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -580.64610332 Ha -15800.18437589 eV + + Derived energy quantities: + | Kinetic energy : 582.30500669 Ha 15845.32543330 eV + | Electrostatic energy : -1121.16171266 Ha -30508.36245000 eV + | Energy correction for multipole + | error in Hartree potential : 0.02046055 Ha 0.55675977 eV + | Sum of eigenvalues per atom : -4464.90357675 eV + | Total energy (T->0) per atom : -7900.09218795 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -7900.09218795 eV + Evaluating new KS density using the density matrix + Evaluating density matrix + Time summed over all CPUs for getting density from density matrix: real work 0.878 s, elapsed 0.878 s + Integration grid: deviation in total charge ( - N_e) = -4.263256E-14 + + Self-consistency convergence accuracy: + | Change of charge density : 0.2570E-04 + | Change of sum of eigenvalues : 0.4618E-02 eV + | Change of total energy : -0.8952E-05 eV + + +------------------------------------------------------------ + End self-consistency iteration # 9 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 1.880 s 1.891 s + | Charge density update : 0.873 s 0.879 s + | Density mixing & preconditioning : 0.178 s 0.178 s + | Hartree multipole update : 0.001 s 0.001 s + | Hartree multipole summation : 0.393 s 0.395 s + | Integration : 0.430 s 0.433 s + | Solution of K.-S. eqns. : 0.005 s 0.005 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 1.538 MB (on task 0) + | Maximum: 1.538 MB (on task 0) + | Average: 1.538 MB + | Peak value for overall tracked memory usage: + | Minimum: 7.766 MB (on task 0 after allocating gradient_basis_wave) + | Maximum: 7.766 MB (on task 0 after allocating gradient_basis_wave) + | Average: 7.766 MB + | Largest tracked array allocation so far: + | Minimum: 3.456 MB (hamiltonian_shell on task 0) + | Maximum: 3.456 MB (hamiltonian_shell on task 0) + | Average: 3.456 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + +------------------------------------------------------------ + Begin self-consistency iteration # 10 + + Date : 20230628, Time : 104142.120 +------------------------------------------------------------ + Pulay mixing of updated and previous charge densities. + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 28.0000000000 + | Integrated number of electrons on 3D grid : 27.9999978066 + | Charge integration error : -0.0000021934 + | Normalization factor for density and gradient : 1.0000000783 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = 0.194108E-12 + | Sum of charges compensated after spline to logarithmic grids = -0.122150E-03 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = 0.000000E+00 + Summing up the Hartree potential. + Time summed over all CPUs for potential: real work 0.393 s, elapsed 0.393 s + | RMS charge density error from multipole expansion : 0.151049E-01 + | Average real-space part of the electrostatic potential : 0.49364677 eV + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.432 s, elapsed 0.432 s + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.000 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -4.88676148 eV + What follows are estimated values for band gap, HOMO, LUMO, etc. + | They are estimated on a discrete k-point grid and not necessarily exact. + | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. + + Highest occupied state (VBM) at -5.30910305 eV (relative to internal zero) + | Occupation number: 2.00000000 + | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + + Lowest unoccupied state (CBM) at -4.59332232 eV (relative to internal zero) + | Occupation number: 0.00000000 + | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) + + ESTIMATED overall HOMO-LUMO gap: 0.71578073 eV between HOMO at k-point 1 and LUMO at k-point 4 + | This appears to be an indirect band gap. + | Smallest direct gap : 2.43040185 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, + this system is most likely an insulator or a semiconductor. + + Total energy components: + | Sum of eigenvalues : -328.16424229 Ha -8929.80337620 eV + | XC energy correction : -41.78940489 Ha -1137.14756448 eV + | XC potential correction : 53.96544959 Ha 1468.47459850 eV + | Free-atom electrostatic energy: -263.69998542 Ha -7175.64169592 eV + | Hartree energy correction : -0.95792043 Ha -26.06634104 eV + | Entropy correction : 0.00000000 Ha 0.00000000 eV + | --------------------------- + | Total energy : -580.64610344 Ha -15800.18437914 eV + | Total energy, T -> 0 : -580.64610344 Ha -15800.18437914 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -580.64610344 Ha -15800.18437914 eV + + Derived energy quantities: + | Kinetic energy : 582.30510406 Ha 15845.32808287 eV + | Electrostatic energy : -1121.16180261 Ha -30508.36489753 eV + | Energy correction for multipole + | error in Hartree potential : 0.02046059 Ha 0.55676111 eV + | Sum of eigenvalues per atom : -4464.90168810 eV + | Total energy (T->0) per atom : -7900.09218957 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -7900.09218957 eV + Evaluating new KS density using the density matrix + Evaluating density matrix + Time summed over all CPUs for getting density from density matrix: real work 0.879 s, elapsed 0.879 s + Integration grid: deviation in total charge ( - N_e) = -2.842171E-14 + + Self-consistency convergence accuracy: + | Change of charge density : 0.8655E-05 + | Change of sum of eigenvalues : 0.3777E-02 eV + | Change of total energy : -0.3241E-05 eV + + +------------------------------------------------------------ + End self-consistency iteration # 10 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 1.880 s 1.892 s + | Charge density update : 0.874 s 0.880 s + | Density mixing & preconditioning : 0.177 s 0.178 s + | Hartree multipole update : 0.001 s 0.002 s + | Hartree multipole summation : 0.393 s 0.394 s + | Integration : 0.430 s 0.432 s + | Solution of K.-S. eqns. : 0.005 s 0.004 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 1.538 MB (on task 0) + | Maximum: 1.538 MB (on task 0) + | Average: 1.538 MB + | Peak value for overall tracked memory usage: + | Minimum: 7.766 MB (on task 0 after allocating gradient_basis_wave) + | Maximum: 7.766 MB (on task 0 after allocating gradient_basis_wave) + | Average: 7.766 MB + | Largest tracked array allocation so far: + | Minimum: 3.456 MB (hamiltonian_shell on task 0) + | Maximum: 3.456 MB (hamiltonian_shell on task 0) + | Average: 3.456 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + +------------------------------------------------------------ + Begin self-consistency iteration # 11 + + Date : 20230628, Time : 104144.012 +------------------------------------------------------------ + Pulay mixing of updated and previous charge densities. + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 28.0000000000 + | Integrated number of electrons on 3D grid : 27.9999998400 + | Charge integration error : -0.0000001600 + | Normalization factor for density and gradient : 1.0000000057 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = 0.336367E-12 + | Sum of charges compensated after spline to logarithmic grids = -0.122151E-03 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = 0.000000E+00 + Summing up the Hartree potential. + Time summed over all CPUs for potential: real work 0.393 s, elapsed 0.393 s + | RMS charge density error from multipole expansion : 0.151050E-01 + | Average real-space part of the electrostatic potential : 0.49365281 eV + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.432 s, elapsed 0.432 s + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.000 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -4.88675747 eV + What follows are estimated values for band gap, HOMO, LUMO, etc. + | They are estimated on a discrete k-point grid and not necessarily exact. + | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. + + Highest occupied state (VBM) at -5.30909890 eV (relative to internal zero) + | Occupation number: 2.00000000 + | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + + Lowest unoccupied state (CBM) at -4.59331868 eV (relative to internal zero) + | Occupation number: 0.00000000 + | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) + + ESTIMATED overall HOMO-LUMO gap: 0.71578022 eV between HOMO at k-point 1 and LUMO at k-point 4 + | This appears to be an indirect band gap. + | Smallest direct gap : 2.43039979 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, + this system is most likely an insulator or a semiconductor. + + Total energy components: + | Sum of eigenvalues : -328.16422868 Ha -8929.80300586 eV + | XC energy correction : -41.78940590 Ha -1137.14759207 eV + | XC potential correction : 53.96545094 Ha 1468.47463513 eV + | Free-atom electrostatic energy: -263.69998542 Ha -7175.64169592 eV + | Hartree energy correction : -0.95793437 Ha -26.06672043 eV + | Entropy correction : 0.00000000 Ha 0.00000000 eV + | --------------------------- + | Total energy : -580.64610344 Ha -15800.18437915 eV + | Total energy, T -> 0 : -580.64610344 Ha -15800.18437915 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -580.64610344 Ha -15800.18437915 eV + + Derived energy quantities: + | Kinetic energy : 582.30511413 Ha 15845.32835703 eV + | Electrostatic energy : -1121.16181167 Ha -30508.36514411 eV + | Energy correction for multipole + | error in Hartree potential : 0.02046076 Ha 0.55676574 eV + | Sum of eigenvalues per atom : -4464.90150293 eV + | Total energy (T->0) per atom : -7900.09218958 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -7900.09218958 eV + Evaluating new KS density using the density matrix + Evaluating density matrix + Time summed over all CPUs for getting density from density matrix: real work 0.878 s, elapsed 0.878 s + Integration grid: deviation in total charge ( - N_e) = -3.552714E-14 + + Self-consistency convergence accuracy: + | Change of charge density : 0.6808E-06 + | Change of sum of eigenvalues : 0.3703E-03 eV + | Change of total energy : -0.1404E-07 eV + + +------------------------------------------------------------ + End self-consistency iteration # 11 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 1.881 s 1.892 s + | Charge density update : 0.874 s 0.880 s + | Density mixing & preconditioning : 0.177 s 0.178 s + | Hartree multipole update : 0.001 s 0.002 s + | Hartree multipole summation : 0.393 s 0.395 s + | Integration : 0.430 s 0.433 s + | Solution of K.-S. eqns. : 0.005 s 0.004 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 1.538 MB (on task 0) + | Maximum: 1.538 MB (on task 0) + | Average: 1.538 MB + | Peak value for overall tracked memory usage: + | Minimum: 7.766 MB (on task 0 after allocating gradient_basis_wave) + | Maximum: 7.766 MB (on task 0 after allocating gradient_basis_wave) + | Average: 7.766 MB + | Largest tracked array allocation so far: + | Minimum: 3.456 MB (hamiltonian_shell on task 0) + | Maximum: 3.456 MB (hamiltonian_shell on task 0) + | Average: 3.456 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + +------------------------------------------------------------ + Begin self-consistency iteration # 12 + + Date : 20230628, Time : 104145.904 +------------------------------------------------------------ + Pulay mixing of updated and previous charge densities. + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 28.0000000000 + | Integrated number of electrons on 3D grid : 28.0000000145 + | Charge integration error : 0.0000000145 + | Normalization factor for density and gradient : 0.9999999995 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = 0.273819E-12 + | Sum of charges compensated after spline to logarithmic grids = -0.122151E-03 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = 0.000000E+00 + Summing up the Hartree potential. + Time summed over all CPUs for potential: real work 0.393 s, elapsed 0.393 s + | RMS charge density error from multipole expansion : 0.151050E-01 + | Average real-space part of the electrostatic potential : 0.49365232 eV + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.432 s, elapsed 0.432 s + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.000 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -4.88675744 eV + What follows are estimated values for band gap, HOMO, LUMO, etc. + | They are estimated on a discrete k-point grid and not necessarily exact. + | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. + + Highest occupied state (VBM) at -5.30909879 eV (relative to internal zero) + | Occupation number: 2.00000000 + | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + + Lowest unoccupied state (CBM) at -4.59331890 eV (relative to internal zero) + | Occupation number: 0.00000000 + | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) + + ESTIMATED overall HOMO-LUMO gap: 0.71577988 eV between HOMO at k-point 1 and LUMO at k-point 4 + | This appears to be an indirect band gap. + | Smallest direct gap : 2.43039988 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, + this system is most likely an insulator or a semiconductor. + + Total energy components: + | Sum of eigenvalues : -328.16422901 Ha -8929.80301477 eV + | XC energy correction : -41.78940590 Ha -1137.14759207 eV + | XC potential correction : 53.96545093 Ha 1468.47463491 eV + | Free-atom electrostatic energy: -263.69998542 Ha -7175.64169592 eV + | Hartree energy correction : -0.95793403 Ha -26.06671134 eV + | Entropy correction : 0.00000000 Ha 0.00000000 eV + | --------------------------- + | Total energy : -580.64610344 Ha -15800.18437919 eV + | Total energy, T -> 0 : -580.64610344 Ha -15800.18437919 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -580.64610344 Ha -15800.18437919 eV + + Derived energy quantities: + | Kinetic energy : 582.30511376 Ha 15845.32834691 eV + | Electrostatic energy : -1121.16181130 Ha -30508.36513403 eV + | Energy correction for multipole + | error in Hartree potential : 0.02046074 Ha 0.55676512 eV + | Sum of eigenvalues per atom : -4464.90150738 eV + | Total energy (T->0) per atom : -7900.09218960 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -7900.09218960 eV + Preliminary charge convergence reached. Turning off preconditioner. + + Evaluating new KS density using the density matrix + Evaluating density matrix + Time summed over all CPUs for getting density from density matrix: real work 0.877 s, elapsed 0.877 s + Integration grid: deviation in total charge ( - N_e) = -1.350031E-13 + + Self-consistency convergence accuracy: + | Change of charge density : 0.1818E-06 + | Change of sum of eigenvalues : -0.8910E-05 eV + | Change of total energy : -0.4207E-07 eV + + Electronic self-consistency reached - switching on the force computation. + + Electronic self-consistency reached - switching on the analytical stress tensor computation. + + +------------------------------------------------------------ + End self-consistency iteration # 12 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 1.880 s 1.891 s + | Charge density & force component update : 0.873 s 0.879 s + | Density mixing : 0.178 s 0.178 s + | Hartree multipole update : 0.001 s 0.002 s + | Hartree multipole summation : 0.393 s 0.395 s + | Hartree pot. SCF incomplete forces : 0.000 s 0.000 s + | Integration : 0.430 s 0.432 s + | Solution of K.-S. eqns. : 0.005 s 0.005 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 1.538 MB (on task 0) + | Maximum: 1.538 MB (on task 0) + | Average: 1.538 MB + | Peak value for overall tracked memory usage: + | Minimum: 7.766 MB (on task 0 after allocating gradient_basis_wave) + | Maximum: 7.766 MB (on task 0 after allocating gradient_basis_wave) + | Average: 7.766 MB + | Largest tracked array allocation so far: + | Minimum: 3.456 MB (hamiltonian_shell on task 0) + | Maximum: 3.456 MB (hamiltonian_shell on task 0) + | Average: 3.456 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + +------------------------------------------------------------ + Begin self-consistency iteration # 13 + + Date : 20230628, Time : 104147.795 +------------------------------------------------------------ + Pulay mixing of updated and previous charge densities. + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 28.0000000000 + | Integrated number of electrons on 3D grid : 27.9999999788 + | Charge integration error : -0.0000000212 + | Normalization factor for density and gradient : 1.0000000008 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = 0.220709E-12 + | Sum of charges compensated after spline to logarithmic grids = -0.122151E-03 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = 0.000000E+00 + Summing up the Hartree potential. + Time summed over all CPUs for potential: real work 1.656 s, elapsed 1.656 s + | RMS charge density error from multipole expansion : 0.151050E-01 + | Average real-space part of the electrostatic potential : 0.49365270 eV + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.433 s, elapsed 0.433 s + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.000 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -4.88675710 eV + What follows are estimated values for band gap, HOMO, LUMO, etc. + | They are estimated on a discrete k-point grid and not necessarily exact. + | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. + + Highest occupied state (VBM) at -5.30909840 eV (relative to internal zero) + | Occupation number: 2.00000000 + | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + + Lowest unoccupied state (CBM) at -4.59331867 eV (relative to internal zero) + | Occupation number: 0.00000000 + | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) + + ESTIMATED overall HOMO-LUMO gap: 0.71577973 eV between HOMO at k-point 1 and LUMO at k-point 4 + | This appears to be an indirect band gap. + | Smallest direct gap : 2.43039973 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, + this system is most likely an insulator or a semiconductor. + + Total energy components: + | Sum of eigenvalues : -328.16422814 Ha -8929.80299115 eV + | XC energy correction : -41.78940596 Ha -1137.14759372 eV + | XC potential correction : 53.96545100 Ha 1468.47463700 eV + | Free-atom electrostatic energy: -263.69998542 Ha -7175.64169592 eV + | Hartree energy correction : -0.95793492 Ha -26.06673543 eV + | Entropy correction : 0.00000000 Ha 0.00000000 eV + | --------------------------- + | Total energy : -580.64610344 Ha -15800.18437921 eV + | Total energy, T -> 0 : -580.64610344 Ha -15800.18437921 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -580.64610344 Ha -15800.18437921 eV + + Derived energy quantities: + | Kinetic energy : 582.30511417 Ha 15845.32835809 eV + | Electrostatic energy : -1121.16181165 Ha -30508.36514358 eV + | Energy correction for multipole + | error in Hartree potential : 0.02046075 Ha 0.55676534 eV + | Sum of eigenvalues per atom : -4464.90149557 eV + | Total energy (T->0) per atom : -7900.09218960 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -7900.09218960 eV + Evaluating new KS density using the density matrix + Evaluating density matrix + Time summed over all CPUs for getting density from density matrix: real work 0.878 s, elapsed 0.878 s + Integration grid: deviation in total charge ( - N_e) = 8.526513E-14 + + atomic forces [eV/Ang]: + ----------------------- + atom # 1 + Hellmann-Feynman : -0.301813E-11 0.151709E-10 -0.597160E-11 + Ionic forces : 0.000000E+00 0.000000E+00 0.000000E+00 + Multipole : -0.429915E-12 0.408843E-12 0.330797E-12 + Hartree pot. SCF incomplete : 0.774785E-11 -0.164390E-11 0.271242E-11 + Pulay + GGA : 0.000000E+00 0.000000E+00 0.000000E+00 + ---------------------------------------------------------------- + Total forces( 1) : 0.429981E-11 0.139359E-10 -0.292838E-11 + atom # 2 + Hellmann-Feynman : -0.321159E-08 -0.323502E-08 -0.271578E-08 + Ionic forces : 0.000000E+00 0.000000E+00 0.000000E+00 + Multipole : -0.381397E-12 0.994567E-13 -0.178339E-12 + Hartree pot. SCF incomplete : -0.132766E-10 -0.328139E-11 -0.147250E-10 + Pulay + GGA : 0.000000E+00 0.000000E+00 0.000000E+00 + ---------------------------------------------------------------- + Total forces( 2) : -0.322524E-08 -0.323820E-08 -0.273068E-08 + + + Self-consistency convergence accuracy: + | Change of charge density : 0.4358E-07 + | Change of sum of eigenvalues : 0.2362E-04 eV + | Change of total energy : -0.1724E-07 eV + | Change of forces : 0.3752E-08 eV/A + + +------------------------------------------------------------ + End self-consistency iteration # 13 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 3.905 s 3.926 s + | Charge density & force component update : 0.874 s 0.880 s + | Density mixing : 0.002 s 0.002 s + | Hartree multipole update : 0.001 s 0.001 s + | Hartree multipole summation : 1.652 s 1.660 s + | Hartree pot. SCF incomplete forces : 0.941 s 0.946 s + | Integration : 0.430 s 0.433 s + | Solution of K.-S. eqns. : 0.005 s 0.004 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 1.538 MB (on task 0) + | Maximum: 1.538 MB (on task 0) + | Average: 1.538 MB + | Peak value for overall tracked memory usage: + | Minimum: 7.766 MB (on task 0 after allocating gradient_basis_wave) + | Maximum: 7.766 MB (on task 0 after allocating gradient_basis_wave) + | Average: 7.766 MB + | Largest tracked array allocation so far: + | Minimum: 3.456 MB (hamiltonian_shell on task 0) + | Maximum: 3.456 MB (hamiltonian_shell on task 0) + | Average: 3.456 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + +------------------------------------------------------------ + Begin self-consistency iteration # 14 + + Date : 20230628, Time : 104151.721 +------------------------------------------------------------ + Pulay mixing of updated and previous charge densities. + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 28.0000000000 + | Integrated number of electrons on 3D grid : 28.0000000000 + | Charge integration error : 0.0000000000 + | Normalization factor for density and gradient : 1.0000000000 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = 0.270874E-12 + | Sum of charges compensated after spline to logarithmic grids = -0.122151E-03 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = 0.000000E+00 + Summing up the Hartree potential. + Time summed over all CPUs for potential: real work 1.655 s, elapsed 1.655 s + | RMS charge density error from multipole expansion : 0.151050E-01 + | Average real-space part of the electrostatic potential : 0.49365270 eV + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.432 s, elapsed 0.432 s + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.000 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -4.88675710 eV + What follows are estimated values for band gap, HOMO, LUMO, etc. + | They are estimated on a discrete k-point grid and not necessarily exact. + | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. + + Highest occupied state (VBM) at -5.30909840 eV (relative to internal zero) + | Occupation number: 2.00000000 + | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + + Lowest unoccupied state (CBM) at -4.59331867 eV (relative to internal zero) + | Occupation number: 0.00000000 + | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) + + ESTIMATED overall HOMO-LUMO gap: 0.71577973 eV between HOMO at k-point 1 and LUMO at k-point 4 + | This appears to be an indirect band gap. + | Smallest direct gap : 2.43039973 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, + this system is most likely an insulator or a semiconductor. + + Total energy components: + | Sum of eigenvalues : -328.16422814 Ha -8929.80299120 eV + | XC energy correction : -41.78940596 Ha -1137.14759372 eV + | XC potential correction : 53.96545100 Ha 1468.47463700 eV + | Free-atom electrostatic energy: -263.69998542 Ha -7175.64169592 eV + | Hartree energy correction : -0.95793492 Ha -26.06673538 eV + | Entropy correction : 0.00000000 Ha 0.00000000 eV + | --------------------------- + | Total energy : -580.64610344 Ha -15800.18437921 eV + | Total energy, T -> 0 : -580.64610344 Ha -15800.18437921 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -580.64610344 Ha -15800.18437921 eV + + Derived energy quantities: + | Kinetic energy : 582.30511417 Ha 15845.32835807 eV + | Electrostatic energy : -1121.16181165 Ha -30508.36514356 eV + | Energy correction for multipole + | error in Hartree potential : 0.02046075 Ha 0.55676534 eV + | Sum of eigenvalues per atom : -4464.90149560 eV + | Total energy (T->0) per atom : -7900.09218960 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -7900.09218960 eV + Evaluating new KS density using the density matrix + Evaluating density matrix + Time summed over all CPUs for getting density from density matrix: real work 0.880 s, elapsed 0.880 s + + Evaluating density-matrix-based force terms: batch-based integration + Evaluating density matrix + Evaluating density matrix + Integration grid: deviation in total charge ( - N_e) = 5.684342E-14 + + atomic forces [eV/Ang]: + ----------------------- + atom # 1 + Hellmann-Feynman : -0.234213E-11 0.147179E-10 -0.562263E-11 + Ionic forces : 0.000000E+00 0.000000E+00 0.000000E+00 + Multipole : -0.426895E-12 -0.442928E-12 0.739783E-12 + Hartree pot. SCF incomplete : -0.617057E-13 -0.175337E-10 -0.164096E-11 + Pulay + GGA : -0.604955E-09 -0.281370E-08 -0.508452E-08 + ---------------------------------------------------------------- + Total forces( 1) : -0.607785E-09 -0.281696E-08 -0.509104E-08 + atom # 2 + Hellmann-Feynman : -0.321355E-08 -0.323494E-08 -0.271592E-08 + Ionic forces : 0.000000E+00 0.000000E+00 0.000000E+00 + Multipole : -0.158276E-11 -0.926307E-12 0.104550E-11 + Hartree pot. SCF incomplete : -0.148700E-10 -0.116788E-10 -0.446800E-11 + Pulay + GGA : 0.123613E-07 0.681601E-08 0.315313E-08 + ---------------------------------------------------------------- + Total forces( 2) : 0.913127E-08 0.356846E-08 0.433781E-09 + + + Analytical stress tensor components [eV] xx yy zz xy xz yz + ----------------------------------------------------------------------------------------------------------------------------------------------------------- + Nuclear Hellmann-Feynman : -0.1512290147E+02 -0.1512316362E+02 -0.1512316362E+02 -0.4495744872E-13 0.2437323406E-13 0.8556343749E-13 + Multipole Hellmann-Feynman : -0.3192783535E+02 -0.3192784615E+02 -0.3192784615E+02 0.5502862228E-12 0.1763303039E-11 0.9656615355E-13 + On-site Multipole corrections : -0.2831479611E+00 -0.2831479611E+00 -0.2831479611E+00 0.5397487875E-12 -0.1675883126E-12 -0.1160859080E-11 + Strain deriv. of the orbitals : 0.4588718671E+02 0.4588745791E+02 0.4588745791E+02 -0.9985870616E-10 0.5370060305E-10 0.5631374550E-10 + ----------------------------------------------------------------------------------------------------------------------------------------------------------- + Sum of all contributions : -0.1446698077E+01 -0.1446699812E+01 -0.1446699812E+01 -0.9881362860E-10 0.5532069101E-10 0.5533501601E-10 + + +-------------------------------------------------------------------+ + | Analytical stress tensor - Symmetrized | + | Cartesian components [eV/A**3] | + +-------------------------------------------------------------------+ + | x y z | + | | + | x -0.03459259 -0.00000000 0.00000000 | + | y -0.00000000 -0.03459263 0.00000000 | + | z 0.00000000 0.00000000 -0.03459263 | + | | + | Pressure: 0.03459262 [eV/A**3] | + | | + +-------------------------------------------------------------------+ + + + Self-consistency convergence accuracy: + | Change of charge density : 0.2433E-09 + | Change of sum of eigenvalues : -0.4863E-07 eV + | Change of total energy : 0.3094E-10 eV + | Change of forces : 0.2719E-11 eV/A + + Writing Kohn-Sham eigenvalues. + K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + + State Occupation Eigenvalue [Ha] Eigenvalue [eV] + 1 2.00000 -65.742465 -1788.94348 + 2 2.00000 -65.742465 -1788.94348 + 3 2.00000 -5.103523 -138.87393 + 4 2.00000 -5.103295 -138.86771 + 5 2.00000 -3.487125 -94.88950 + 6 2.00000 -3.487125 -94.88950 + 7 2.00000 -3.487125 -94.88950 + 8 2.00000 -3.486606 -94.87537 + 9 2.00000 -3.486606 -94.87537 + 10 2.00000 -3.486606 -94.87537 + 11 2.00000 -0.626307 -17.04268 + 12 2.00000 -0.195106 -5.30910 + 13 2.00000 -0.195106 -5.30910 + 14 2.00000 -0.195106 -5.30910 + 15 0.00000 -0.105790 -2.87870 + 16 0.00000 -0.105790 -2.87870 + 17 0.00000 -0.105790 -2.87870 + 18 0.00000 -0.087344 -2.37675 + 19 0.00000 0.089813 2.44394 + 20 0.00000 0.089813 2.44394 + + What follows are estimated values for band gap, HOMO, LUMO, etc. + | They are estimated on a discrete k-point grid and not necessarily exact. + | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. + + Highest occupied state (VBM) at -5.30909840 eV (relative to internal zero) + | Occupation number: 2.00000000 + | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + + Lowest unoccupied state (CBM) at -4.59331867 eV (relative to internal zero) + | Occupation number: 0.00000000 + | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) + + ESTIMATED overall HOMO-LUMO gap: 0.71577973 eV between HOMO at k-point 1 and LUMO at k-point 4 + | This appears to be an indirect band gap. + | Smallest direct gap : 2.43039973 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, + this system is most likely an insulator or a semiconductor. + | Chemical Potential : -4.88675710 eV + + Self-consistency cycle converged. + + +------------------------------------------------------------ + End self-consistency iteration # 14 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 20.526 s 20.662 s + | Charge density & force component update : 17.497 s 17.617 s + | Density mixing : 0.002 s 0.002 s + | Hartree multipole update : 0.001 s 0.001 s + | Hartree multipole summation : 1.650 s 1.658 s + | Hartree pot. SCF incomplete forces : 0.942 s 0.947 s + | Integration : 0.430 s 0.432 s + | Solution of K.-S. eqns. : 0.005 s 0.005 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 1.538 MB (on task 0) + | Maximum: 1.538 MB (on task 0) + | Average: 1.538 MB + | Peak value for overall tracked memory usage: + | Minimum: 14.236 MB (on task 0 after allocating d_wave) + | Maximum: 14.236 MB (on task 0 after allocating d_wave) + | Average: 14.236 MB + | Largest tracked array allocation so far: + | Minimum: 3.456 MB (hamiltonian_shell on task 0) + | Maximum: 3.456 MB (hamiltonian_shell on task 0) + | Average: 3.456 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + Removing unitary transformations (pure translations, rotations) from forces on atoms. + Atomic forces before filtering: + | Net force on center of mass : 0.852349E-08 0.751505E-09 -0.465726E-08 eV/A + Atomic forces after filtering: + | Net force on center of mass : 0.199384E-23 0.000000E+00 -0.132923E-23 eV/A + + Energy and forces in a compact form: + | Total energy uncorrected : -0.158001843792097E+05 eV + | Total energy corrected : -0.158001843792097E+05 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -0.158001843792097E+05 eV + Total atomic forces (unitary forces cleaned) [eV/Ang]: + | 1 -0.486952935970507E-08 -0.319270797951684E-08 -0.276241042439398E-08 + | 2 0.486952935970508E-08 0.319270797951684E-08 0.276241042439398E-08 + + ------------------------------------ + Start decomposition of the XC Energy + ------------------------------------ + X and C from original XC functional choice + Hartree-Fock Energy : 0.000000000 Ha 0.000000000 eV + X Energy : -40.702535223 Ha -1107.572336068 eV + C Energy : -1.086870742 Ha -29.575257650 eV + XC Energy w/o HF : -41.789405964 Ha -1137.147593718 eV + Total XC Energy : -41.789405964 Ha -1137.147593718 eV + ------------------------------------ + LDA X and C from self-consistent density + X Energy LDA : -37.637384307 Ha -1024.165335950 eV + C Energy LDA : -2.146804754 Ha -58.417529610 eV + ------------------------------------ + End decomposition of the XC Energy + ------------------------------------ + +------------------------------------------------------------ + Relaxation / MD: End force evaluation. : max(cpu_time) wall_clock(cpu1) + | Time for this force evaluation : 48.916 s 49.214 s + +------------------------------------------------------------ + Geometry optimization: Attempting to predict improved coordinates. + + +-------------------------------------------------------------------+ + | Generalized derivatives on lattice vectors [eV/A] | + +-------------------------------------------------------------------+ + |lattice_vector 0.26255863 -0.26255895 -0.26255895 | + |lattice_vector -0.26255863 0.26255895 -0.26255895 | + |lattice_vector -0.26255863 -0.26255895 0.26255895 | + +-------------------------------------------------------------------+ + | Forces on lattice vectors cleaned from atomic contributions [eV/A]| + +-------------------------------------------------------------------+ + |lattice_vector -0.26255863 0.26255895 0.26255895 | + |lattice_vector 0.26255863 -0.26255895 0.26255895 | + |lattice_vector 0.26255863 0.26255895 -0.26255895 | + +-------------------------------------------------------------------+ + Removing unitary transformations (pure translations, rotations) from forces on atoms. + Atomic forces before filtering: + | Net force on center of mass : 0.199384E-23 0.000000E+00 -0.132923E-23 eV/A + Atomic forces after filtering: + | Net force on center of mass : 0.664615E-24 0.000000E+00 0.000000E+00 eV/A + Net remaining forces (excluding translations, rotations) in present geometry: + || Forces on atoms || = 0.486953E-08 eV/A. + || Forces on lattice || = 0.262559E+00 eV/A^3. + Maximum force component is 0.262559E+00 eV/A. + Present geometry is not yet converged. + + Relaxation step number 1: Predicting new coordinates. + + Advancing geometry using trust radius method. + Allocating 0.061 MB for stored_KS_eigenvector + | Hessian has 0 negative and 3 zero eigenvalues. + | Positive eigenvalues (eV/A^2): 7.54E+00 ... 3.02E+01 + | Use Quasi-Newton step of length |H^-1 F| = 4.27E-02 A. + Finished advancing geometry + | Time : 0.001 s + Updated atomic structure: + x [A] y [A] z [A] + lattice_vector 0.00000002 2.77241620 2.77241620 + lattice_vector 2.77241617 -0.00000001 2.77241618 + lattice_vector 2.77241617 2.77241618 -0.00000001 + + atom -0.00000000 -0.00000000 -0.00000000 Si + atom 1.38620809 1.38620809 1.38620809 Si + + Fractional coordinates: + L1 L2 L3 + atom_frac -0.00000000 -0.00000000 -0.00000000 Si + atom_frac 0.25000000 0.25000000 0.25000000 Si +------------------------------------------------------------ + Writing the current geometry to file "geometry.in.next_step". + Writing estimated Hessian matrix to file 'hessian.aims' + + Quantities derived from the lattice vectors: + | Reciprocal lattice vector 1: -1.133161 1.133161 1.133161 + | Reciprocal lattice vector 2: 1.133161 -1.133161 1.133161 + | Reciprocal lattice vector 3: 1.133161 1.133161 -1.133161 + | Unit cell volume : 0.426192E+02 A^3 + + Range separation radius for Ewald summation (hartree_convergence_parameter): 3.97864235 bohr. + +------------------------------------------------------------ + Begin self-consistency loop: Re-initialization. + + Date : 20230628, Time : 104212.390 +------------------------------------------------------------ + + Initializing index lists of integration centers etc. from given atomic structure: + Mapping all atomic coordinates to central unit cell. + + Initializing the k-points + Using symmetry for reducing the k-points + | k-points reduced from: 8 to 8 + | Number of k-points : 8 + The eigenvectors in the calculations are REAL. + | K-points in task 0: 8 + | Number of basis functions in the Hamiltonian integrals : 2161 + | Number of basis functions in a single unit cell : 50 + | Number of centers in hartree potential : 708 + | Number of centers in hartree multipole : 318 + | Number of centers in electron density summation: 190 + | Number of centers in basis integrals : 198 + | Number of centers in integrals : 101 + | Number of centers in hamiltonian : 190 + | Consuming 14 KiB for k_phase. + | Number of super-cells (origin) [n_cells] : 2197 + | Number of super-cells (after PM_index) [n_cells] : 112 + | Number of super-cells in hamiltonian [n_cells_in_hamiltonian]: 112 + | Size of matrix packed + index [n_hamiltonian_matrix_size] : 85499 + Partitioning the integration grid into batches with parallel hashing+maxmin method. + | Number of batches: 128 + | Maximal batch size: 90 + | Minimal batch size: 85 + | Average batch size: 87.562 + | Standard deviation of batch sizes: 1.493 + + Integration load balanced across 1 MPI tasks. + Work distribution over tasks is as follows: + Initializing partition tables, free-atom densities, potentials, etc. across the integration grid (initialize_grid_storage). + | Species 1: outer_partition_radius set to 5.000694715736543 AA . + | The sparse table of interatomic distances needs 212.76 kbyte instead of 313.63 kbyte of memory. + | Net number of integration points: 11208 + | of which are non-zero points : 9852 + | Numerical average free-atom electrostatic potential : -12.33430044 eV + Renormalizing the initial density to the exact electron count on the 3D integration grid. + | Initial density: Formal number of electrons (from input files) : 28.0000000000 + | Integrated number of electrons on 3D grid : 28.0042648595 + | Charge integration error : 0.0042648595 + | Normalization factor for density and gradient : 0.9998477068 + Renormalizing the free-atom superposition density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 28.0000000000 + | Integrated number of electrons on 3D grid : 28.0042648595 + | Charge integration error : 0.0042648595 + | Normalization factor for density and gradient : 0.9998477068 + Obtaining max. number of non-zero basis functions in each batch (get_n_compute_maxes). + Calculating total energy contributions from superposition of free atom densities. + Initialize hartree_potential_storage + Integrating overlap matrix. + Time summed over all CPUs for integration: real work 0.265 s, elapsed 0.265 s + Orthonormalizing eigenvectors + + End scf reinitialization - timings : max(cpu_time) wall_clock(cpu1) + | Time for scf. reinitialization : 0.588 s 0.592 s + | Boundary condition initialization : 0.059 s 0.059 s + | Integration : 0.264 s 0.265 s + | Grid partitioning : 0.036 s 0.036 s + | Preloading free-atom quantities on grid : 0.189 s 0.190 s + | Free-atom superposition energy : 0.027 s 0.028 s + | K.-S. eigenvector reorthonormalization : 0.001 s 0.001 s +------------------------------------------------------------ + Evaluating new KS density using the density matrix + Evaluating density matrix + Time summed over all CPUs for getting density from density matrix: real work 0.842 s, elapsed 0.842 s + Integration grid: deviation in total charge ( - N_e) = -7.105427E-15 + + Time for density update prior : max(cpu_time) wall_clock(cpu1) + | self-consistency iterative process : 0.838 s 0.844 s + +------------------------------------------------------------ + Begin self-consistency iteration # 1 + + Date : 20230628, Time : 104213.826 +------------------------------------------------------------ + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 28.0000000000 + | Integrated number of electrons on 3D grid : 28.0000000000 + | Charge integration error : -0.0000000000 + | Normalization factor for density and gradient : 1.0000000000 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = -0.941446E-13 + | Sum of charges compensated after spline to logarithmic grids = -0.109990E-03 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = 0.000000E+00 + Summing up the Hartree potential. + | Estimated reciprocal-space cutoff momentum G_max: 2.34376572 bohr^-1 . + | Reciprocal lattice points for long-range Hartree potential: 58 + Time summed over all CPUs for potential: real work 0.392 s, elapsed 0.392 s + | RMS charge density error from multipole expansion : 0.147126E-01 + | Average real-space part of the electrostatic potential : 0.47611346 eV + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.414 s, elapsed 0.414 s + Decreasing sparse matrix size: + | Tolerance: 0.1000E-12 + Hamiltonian matrix + | Array has 78708 nonzero elements out of 85499 elements + | Sparsity factor is 0.079 + Overlap matrix + | Array has 70208 nonzero elements out of 85499 elements + | Sparsity factor is 0.179 + New size of hamiltonian matrix: 78735 + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Singularity check in k-point 1, task 0 (analysis for other k-points/tasks may follow below): + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.001 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -4.92413184 eV + Writing Kohn-Sham eigenvalues. + K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + + State Occupation Eigenvalue [Ha] Eigenvalue [eV] + 1 2.00000 -65.744985 -1789.01207 + 2 2.00000 -65.744985 -1789.01207 + 3 2.00000 -5.104589 -138.90292 + 4 2.00000 -5.104381 -138.89727 + 5 2.00000 -3.488273 -94.92075 + 6 2.00000 -3.488273 -94.92075 + 7 2.00000 -3.488273 -94.92075 + 8 2.00000 -3.487794 -94.90769 + 9 2.00000 -3.487794 -94.90769 + 10 2.00000 -3.487794 -94.90769 + 11 2.00000 -0.620837 -16.89383 + 12 2.00000 -0.194307 -5.28735 + 13 2.00000 -0.194307 -5.28735 + 14 2.00000 -0.194307 -5.28735 + 15 0.00000 -0.105227 -2.86338 + 16 0.00000 -0.105227 -2.86338 + 17 0.00000 -0.105227 -2.86338 + 18 0.00000 -0.094308 -2.56625 + 19 0.00000 0.090742 2.46922 + 20 0.00000 0.090742 2.46922 + + What follows are estimated values for band gap, HOMO, LUMO, etc. + | They are estimated on a discrete k-point grid and not necessarily exact. + | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. + + Highest occupied state (VBM) at -5.28735399 eV (relative to internal zero) + | Occupation number: 2.00000000 + | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + + Lowest unoccupied state (CBM) at -4.53451456 eV (relative to internal zero) + | Occupation number: 0.00000000 + | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) + + ESTIMATED overall HOMO-LUMO gap: 0.75283943 eV between HOMO at k-point 1 and LUMO at k-point 4 + | This appears to be an indirect band gap. + | Smallest direct gap : 2.42397618 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, + this system is most likely an insulator or a semiconductor. + + Total energy components: + | Sum of eigenvalues : -328.17151144 Ha -8930.00117985 eV + | XC energy correction : -41.77616004 Ha -1136.78715377 eV + | XC potential correction : 53.94777676 Ha 1467.99369627 eV + | Free-atom electrostatic energy: -263.74356637 Ha -7176.82759392 eV + | Hartree energy correction : -0.90343740 Ha -24.58378245 eV + | Entropy correction : 0.00000000 Ha 0.00000000 eV + | --------------------------- + | Total energy : -580.64689850 Ha -15800.20601371 eV + | Total energy, T -> 0 : -580.64689850 Ha -15800.20601371 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -580.64689850 Ha -15800.20601371 eV + + Derived energy quantities: + | Kinetic energy : 582.22497978 Ha 15843.14779022 eV + | Electrostatic energy : -1121.09571823 Ha -30506.56665016 eV + | Energy correction for multipole + | error in Hartree potential : 0.01980078 Ha 0.53880656 eV + | Sum of eigenvalues per atom : -4465.00058992 eV + | Total energy (T->0) per atom : -7900.10300686 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -7900.10300686 eV + Evaluating new KS density using the density matrix + Evaluating density matrix + Time summed over all CPUs for getting density from density matrix: real work 0.843 s, elapsed 0.843 s + Integration grid: deviation in total charge ( - N_e) = 9.592327E-14 + + Self-consistency convergence accuracy: + | Change of charge density : 0.1352E+00 + | Change of sum of eigenvalues : -0.8930E+04 eV + | Change of total energy : -0.1580E+05 eV + + +------------------------------------------------------------ + End self-consistency iteration # 1 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 1.649 s 1.659 s + | Charge density update : 0.838 s 0.844 s + | Density mixing & preconditioning : 0.000 s 0.000 s + | Hartree multipole update : 0.001 s 0.001 s + | Hartree multipole summation : 0.392 s 0.394 s + | Integration : 0.412 s 0.415 s + | Solution of K.-S. eqns. : 0.005 s 0.005 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 1.632 MB (on task 0) + | Maximum: 1.632 MB (on task 0) + | Average: 1.632 MB + | Peak value for overall tracked memory usage: + | Minimum: 14.236 MB (on task 0 after allocating d_wave) + | Maximum: 14.236 MB (on task 0 after allocating d_wave) + | Average: 14.236 MB + | Largest tracked array allocation so far: + | Minimum: 3.456 MB (hamiltonian_shell on task 0) + | Maximum: 3.456 MB (hamiltonian_shell on task 0) + | Average: 3.456 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + +------------------------------------------------------------ + Begin self-consistency iteration # 2 + + Date : 20230628, Time : 104215.485 +------------------------------------------------------------ + Pulay mixing of updated and previous charge densities. + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 28.0000000000 + | Integrated number of electrons on 3D grid : 27.9999681480 + | Charge integration error : -0.0000318520 + | Normalization factor for density and gradient : 1.0000011376 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = -0.224623E-12 + | Sum of charges compensated after spline to logarithmic grids = -0.109994E-03 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = 0.000000E+00 + Summing up the Hartree potential. + Time summed over all CPUs for potential: real work 0.392 s, elapsed 0.392 s + | RMS charge density error from multipole expansion : 0.147060E-01 + | Average real-space part of the electrostatic potential : 0.47622186 eV + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.418 s, elapsed 0.418 s + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.000 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -4.92436221 eV + What follows are estimated values for band gap, HOMO, LUMO, etc. + | They are estimated on a discrete k-point grid and not necessarily exact. + | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. + + Highest occupied state (VBM) at -5.28752711 eV (relative to internal zero) + | Occupation number: 2.00000000 + | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + + Lowest unoccupied state (CBM) at -4.53462713 eV (relative to internal zero) + | Occupation number: 0.00000000 + | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) + + ESTIMATED overall HOMO-LUMO gap: 0.75289998 eV between HOMO at k-point 1 and LUMO at k-point 4 + | This appears to be an indirect band gap. + | Smallest direct gap : 2.42401123 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, + this system is most likely an insulator or a semiconductor. + + Total energy components: + | Sum of eigenvalues : -328.16927255 Ha -8929.94025655 eV + | XC energy correction : -41.77644354 Ha -1136.79486832 eV + | XC potential correction : 53.94814771 Ha 1468.00379049 eV + | Free-atom electrostatic energy: -263.74356637 Ha -7176.82759392 eV + | Hartree energy correction : -0.90576420 Ha -24.64709786 eV + | Entropy correction : 0.00000000 Ha 0.00000000 eV + | --------------------------- + | Total energy : -580.64689895 Ha -15800.20602616 eV + | Total energy, T -> 0 : -580.64689895 Ha -15800.20602616 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -580.64689895 Ha -15800.20602616 eV + + Derived energy quantities: + | Kinetic energy : 582.23052760 Ha 15843.29875414 eV + | Electrostatic energy : -1121.10098301 Ha -30506.70991198 eV + | Energy correction for multipole + | error in Hartree potential : 0.01979779 Ha 0.53872539 eV + | Sum of eigenvalues per atom : -4464.97012828 eV + | Total energy (T->0) per atom : -7900.10301308 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -7900.10301308 eV + Evaluating new KS density using the density matrix + Evaluating density matrix + Time summed over all CPUs for getting density from density matrix: real work 0.843 s, elapsed 0.843 s + Integration grid: deviation in total charge ( - N_e) = -6.039613E-14 + + Self-consistency convergence accuracy: + | Change of charge density : 0.1080E-02 + | Change of sum of eigenvalues : 0.6092E-01 eV + | Change of total energy : -0.1245E-04 eV + + +------------------------------------------------------------ + End self-consistency iteration # 2 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 1.829 s 1.840 s + | Charge density update : 0.839 s 0.845 s + | Density mixing & preconditioning : 0.176 s 0.177 s + | Hartree multipole update : 0.001 s 0.001 s + | Hartree multipole summation : 0.392 s 0.394 s + | Integration : 0.416 s 0.419 s + | Solution of K.-S. eqns. : 0.005 s 0.004 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 1.632 MB (on task 0) + | Maximum: 1.632 MB (on task 0) + | Average: 1.632 MB + | Peak value for overall tracked memory usage: + | Minimum: 14.236 MB (on task 0 after allocating d_wave) + | Maximum: 14.236 MB (on task 0 after allocating d_wave) + | Average: 14.236 MB + | Largest tracked array allocation so far: + | Minimum: 3.456 MB (hamiltonian_shell on task 0) + | Maximum: 3.456 MB (hamiltonian_shell on task 0) + | Average: 3.456 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + +------------------------------------------------------------ + Begin self-consistency iteration # 3 + + Date : 20230628, Time : 104217.325 +------------------------------------------------------------ + Pulay mixing of updated and previous charge densities. + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 28.0000000000 + | Integrated number of electrons on 3D grid : 27.9998896082 + | Charge integration error : -0.0001103918 + | Normalization factor for density and gradient : 1.0000039426 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = -0.292231E-13 + | Sum of charges compensated after spline to logarithmic grids = -0.110006E-03 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = 0.000000E+00 + Summing up the Hartree potential. + Time summed over all CPUs for potential: real work 0.392 s, elapsed 0.392 s + | RMS charge density error from multipole expansion : 0.146846E-01 + | Average real-space part of the electrostatic potential : 0.47660009 eV + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.416 s, elapsed 0.416 s + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.000 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -4.92509627 eV + What follows are estimated values for band gap, HOMO, LUMO, etc. + | They are estimated on a discrete k-point grid and not necessarily exact. + | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. + + Highest occupied state (VBM) at -5.28807241 eV (relative to internal zero) + | Occupation number: 2.00000000 + | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + + Lowest unoccupied state (CBM) at -4.53498682 eV (relative to internal zero) + | Occupation number: 0.00000000 + | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) + + ESTIMATED overall HOMO-LUMO gap: 0.75308559 eV between HOMO at k-point 1 and LUMO at k-point 4 + | This appears to be an indirect band gap. + | Smallest direct gap : 2.42411875 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, + this system is most likely an insulator or a semiconductor. + + Total energy components: + | Sum of eigenvalues : -328.16210705 Ha -8929.74527316 eV + | XC energy correction : -41.77733114 Ha -1136.81902112 eV + | XC potential correction : 53.94931109 Ha 1468.03544747 eV + | Free-atom electrostatic energy: -263.74356637 Ha -7176.82759392 eV + | Hartree energy correction : -0.91320725 Ha -24.84963361 eV + | Entropy correction : 0.00000000 Ha 0.00000000 eV + | --------------------------- + | Total energy : -580.64690072 Ha -15800.20607434 eV + | Total energy, T -> 0 : -580.64690072 Ha -15800.20607434 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -580.64690072 Ha -15800.20607434 eV + + Derived energy quantities: + | Kinetic energy : 582.24779135 Ha 15843.76852458 eV + | Electrostatic energy : -1121.11736093 Ha -30507.15557780 eV + | Energy correction for multipole + | error in Hartree potential : 0.01978805 Ha 0.53846031 eV + | Sum of eigenvalues per atom : -4464.87263658 eV + | Total energy (T->0) per atom : -7900.10303717 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -7900.10303717 eV + Evaluating new KS density using the density matrix + Evaluating density matrix + Time summed over all CPUs for getting density from density matrix: real work 0.843 s, elapsed 0.843 s + Integration grid: deviation in total charge ( - N_e) = -3.552714E-15 + + Self-consistency convergence accuracy: + | Change of charge density : 0.8212E-03 + | Change of sum of eigenvalues : 0.1950E+00 eV + | Change of total energy : -0.4817E-04 eV + + +------------------------------------------------------------ + End self-consistency iteration # 3 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 1.829 s 1.840 s + | Charge density update : 0.839 s 0.845 s + | Density mixing & preconditioning : 0.177 s 0.178 s + | Hartree multipole update : 0.001 s 0.001 s + | Hartree multipole summation : 0.392 s 0.395 s + | Integration : 0.414 s 0.416 s + | Solution of K.-S. eqns. : 0.005 s 0.005 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 1.632 MB (on task 0) + | Maximum: 1.632 MB (on task 0) + | Average: 1.632 MB + | Peak value for overall tracked memory usage: + | Minimum: 14.236 MB (on task 0 after allocating d_wave) + | Maximum: 14.236 MB (on task 0 after allocating d_wave) + | Average: 14.236 MB + | Largest tracked array allocation so far: + | Minimum: 3.456 MB (hamiltonian_shell on task 0) + | Maximum: 3.456 MB (hamiltonian_shell on task 0) + | Average: 3.456 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + +------------------------------------------------------------ + Begin self-consistency iteration # 4 + + Date : 20230628, Time : 104219.165 +------------------------------------------------------------ + Pulay mixing of updated and previous charge densities. + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 28.0000000000 + | Integrated number of electrons on 3D grid : 27.9999408726 + | Charge integration error : -0.0000591274 + | Normalization factor for density and gradient : 1.0000021117 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = -0.172218E-12 + | Sum of charges compensated after spline to logarithmic grids = -0.110001E-03 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = 0.000000E+00 + Summing up the Hartree potential. + Time summed over all CPUs for potential: real work 0.391 s, elapsed 0.391 s + | RMS charge density error from multipole expansion : 0.146807E-01 + | Average real-space part of the electrostatic potential : 0.47680126 eV + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.416 s, elapsed 0.416 s + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.001 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -4.92516045 eV + What follows are estimated values for band gap, HOMO, LUMO, etc. + | They are estimated on a discrete k-point grid and not necessarily exact. + | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. + + Highest occupied state (VBM) at -5.28809015 eV (relative to internal zero) + | Occupation number: 2.00000000 + | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + + Lowest unoccupied state (CBM) at -4.53502662 eV (relative to internal zero) + | Occupation number: 0.00000000 + | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) + + ESTIMATED overall HOMO-LUMO gap: 0.75306353 eV between HOMO at k-point 1 and LUMO at k-point 4 + | This appears to be an indirect band gap. + | Smallest direct gap : 2.42410496 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, + this system is most likely an insulator or a semiconductor. + + Total energy components: + | Sum of eigenvalues : -328.16153795 Ha -8929.72978733 eV + | XC energy correction : -41.77728814 Ha -1136.81785082 eV + | XC potential correction : 53.94926632 Ha 1468.03422934 eV + | Free-atom electrostatic energy: -263.74356637 Ha -7176.82759392 eV + | Hartree energy correction : -0.91377546 Ha -24.86509528 eV + | Entropy correction : 0.00000000 Ha 0.00000000 eV + | --------------------------- + | Total energy : -580.64690159 Ha -15800.20609801 eV + | Total energy, T -> 0 : -580.64690159 Ha -15800.20609801 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -580.64690159 Ha -15800.20609801 eV + + Derived energy quantities: + | Kinetic energy : 582.24635446 Ha 15843.72942496 eV + | Electrostatic energy : -1121.11596792 Ha -30507.11767215 eV + | Energy correction for multipole + | error in Hartree potential : 0.01978597 Ha 0.53840359 eV + | Sum of eigenvalues per atom : -4464.86489366 eV + | Total energy (T->0) per atom : -7900.10304901 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -7900.10304901 eV + Evaluating new KS density using the density matrix + Evaluating density matrix + Time summed over all CPUs for getting density from density matrix: real work 0.843 s, elapsed 0.843 s + Integration grid: deviation in total charge ( - N_e) = 7.105427E-15 + + Self-consistency convergence accuracy: + | Change of charge density : 0.1212E-03 + | Change of sum of eigenvalues : 0.1549E-01 eV + | Change of total energy : -0.2367E-04 eV + + +------------------------------------------------------------ + End self-consistency iteration # 4 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 1.829 s 1.839 s + | Charge density update : 0.839 s 0.844 s + | Density mixing & preconditioning : 0.177 s 0.178 s + | Hartree multipole update : 0.001 s 0.001 s + | Hartree multipole summation : 0.392 s 0.394 s + | Integration : 0.414 s 0.416 s + | Solution of K.-S. eqns. : 0.005 s 0.005 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 1.632 MB (on task 0) + | Maximum: 1.632 MB (on task 0) + | Average: 1.632 MB + | Peak value for overall tracked memory usage: + | Minimum: 14.236 MB (on task 0 after allocating d_wave) + | Maximum: 14.236 MB (on task 0 after allocating d_wave) + | Average: 14.236 MB + | Largest tracked array allocation so far: + | Minimum: 3.456 MB (hamiltonian_shell on task 0) + | Maximum: 3.456 MB (hamiltonian_shell on task 0) + | Average: 3.456 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + +------------------------------------------------------------ + Begin self-consistency iteration # 5 + + Date : 20230628, Time : 104221.004 +------------------------------------------------------------ + Pulay mixing of updated and previous charge densities. + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 28.0000000000 + | Integrated number of electrons on 3D grid : 28.0000009518 + | Charge integration error : 0.0000009518 + | Normalization factor for density and gradient : 0.9999999660 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = -0.573319E-13 + | Sum of charges compensated after spline to logarithmic grids = -0.110000E-03 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = 0.000000E+00 + Summing up the Hartree potential. + Time summed over all CPUs for potential: real work 0.392 s, elapsed 0.392 s + | RMS charge density error from multipole expansion : 0.146804E-01 + | Average real-space part of the electrostatic potential : 0.47674538 eV + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.417 s, elapsed 0.417 s + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.000 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -4.92521506 eV + What follows are estimated values for band gap, HOMO, LUMO, etc. + | They are estimated on a discrete k-point grid and not necessarily exact. + | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. + + Highest occupied state (VBM) at -5.28815749 eV (relative to internal zero) + | Occupation number: 2.00000000 + | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + + Lowest unoccupied state (CBM) at -4.53505514 eV (relative to internal zero) + | Occupation number: 0.00000000 + | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) + + ESTIMATED overall HOMO-LUMO gap: 0.75310235 eV between HOMO at k-point 1 and LUMO at k-point 4 + | This appears to be an indirect band gap. + | Smallest direct gap : 2.42412689 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, + this system is most likely an insulator or a semiconductor. + + Total energy components: + | Sum of eigenvalues : -328.16171552 Ha -8929.73461922 eV + | XC energy correction : -41.77728120 Ha -1136.81766215 eV + | XC potential correction : 53.94925555 Ha 1468.03393614 eV + | Free-atom electrostatic energy: -263.74356637 Ha -7176.82759392 eV + | Hartree energy correction : -0.91359388 Ha -24.86015427 eV + | Entropy correction : 0.00000000 Ha 0.00000000 eV + | --------------------------- + | Total energy : -580.64690143 Ha -15800.20609342 eV + | Total energy, T -> 0 : -580.64690143 Ha -15800.20609342 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -580.64690143 Ha -15800.20609342 eV + + Derived energy quantities: + | Kinetic energy : 582.24622913 Ha 15843.72601460 eV + | Electrostatic energy : -1121.11584936 Ha -30507.11444587 eV + | Energy correction for multipole + | error in Hartree potential : 0.01978570 Ha 0.53839640 eV + | Sum of eigenvalues per atom : -4464.86730961 eV + | Total energy (T->0) per atom : -7900.10304671 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -7900.10304671 eV + Evaluating new KS density using the density matrix + Evaluating density matrix + Time summed over all CPUs for getting density from density matrix: real work 0.846 s, elapsed 0.846 s + Integration grid: deviation in total charge ( - N_e) = -2.131628E-14 + + Self-consistency convergence accuracy: + | Change of charge density : 0.1907E-04 + | Change of sum of eigenvalues : -0.4832E-02 eV + | Change of total energy : 0.4595E-05 eV + + +------------------------------------------------------------ + End self-consistency iteration # 5 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 1.831 s 1.843 s + | Charge density update : 0.841 s 0.847 s + | Density mixing & preconditioning : 0.177 s 0.178 s + | Hartree multipole update : 0.001 s 0.001 s + | Hartree multipole summation : 0.392 s 0.395 s + | Integration : 0.414 s 0.417 s + | Solution of K.-S. eqns. : 0.005 s 0.004 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 1.632 MB (on task 0) + | Maximum: 1.632 MB (on task 0) + | Average: 1.632 MB + | Peak value for overall tracked memory usage: + | Minimum: 14.236 MB (on task 0 after allocating d_wave) + | Maximum: 14.236 MB (on task 0 after allocating d_wave) + | Average: 14.236 MB + | Largest tracked array allocation so far: + | Minimum: 3.456 MB (hamiltonian_shell on task 0) + | Maximum: 3.456 MB (hamiltonian_shell on task 0) + | Average: 3.456 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + +------------------------------------------------------------ + Begin self-consistency iteration # 6 + + Date : 20230628, Time : 104222.847 +------------------------------------------------------------ + Pulay mixing of updated and previous charge densities. + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 28.0000000000 + | Integrated number of electrons on 3D grid : 28.0000003017 + | Charge integration error : 0.0000003017 + | Normalization factor for density and gradient : 0.9999999892 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = -0.979218E-13 + | Sum of charges compensated after spline to logarithmic grids = -0.110001E-03 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = 0.000000E+00 + Summing up the Hartree potential. + Time summed over all CPUs for potential: real work 0.392 s, elapsed 0.392 s + | RMS charge density error from multipole expansion : 0.146805E-01 + | Average real-space part of the electrostatic potential : 0.47675856 eV + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.416 s, elapsed 0.416 s + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.001 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -4.92519957 eV + What follows are estimated values for band gap, HOMO, LUMO, etc. + | They are estimated on a discrete k-point grid and not necessarily exact. + | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. + + Highest occupied state (VBM) at -5.28814004 eV (relative to internal zero) + | Occupation number: 2.00000000 + | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + + Lowest unoccupied state (CBM) at -4.53504651 eV (relative to internal zero) + | Occupation number: 0.00000000 + | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) + + ESTIMATED overall HOMO-LUMO gap: 0.75309352 eV between HOMO at k-point 1 and LUMO at k-point 4 + | This appears to be an indirect band gap. + | Smallest direct gap : 2.42412063 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, + this system is most likely an insulator or a semiconductor. + + Total energy components: + | Sum of eigenvalues : -328.16169163 Ha -8929.73396917 eV + | XC energy correction : -41.77728210 Ha -1136.81768649 eV + | XC potential correction : 53.94925665 Ha 1468.03396632 eV + | Free-atom electrostatic energy: -263.74356637 Ha -7176.82759392 eV + | Hartree energy correction : -0.91361801 Ha -24.86081093 eV + | Entropy correction : 0.00000000 Ha 0.00000000 eV + | --------------------------- + | Total energy : -580.64690145 Ha -15800.20609418 eV + | Total energy, T -> 0 : -580.64690145 Ha -15800.20609418 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -580.64690145 Ha -15800.20609418 eV + + Derived energy quantities: + | Kinetic energy : 582.24620850 Ha 15843.72545323 eV + | Electrostatic energy : -1121.11582786 Ha -30507.11386092 eV + | Energy correction for multipole + | error in Hartree potential : 0.01978591 Ha 0.53840207 eV + | Sum of eigenvalues per atom : -4464.86698458 eV + | Total energy (T->0) per atom : -7900.10304709 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -7900.10304709 eV + Evaluating new KS density using the density matrix + Evaluating density matrix + Time summed over all CPUs for getting density from density matrix: real work 0.846 s, elapsed 0.846 s + Integration grid: deviation in total charge ( - N_e) = -1.421085E-14 + + Self-consistency convergence accuracy: + | Change of charge density : 0.2242E-05 + | Change of sum of eigenvalues : 0.6500E-03 eV + | Change of total energy : -0.7676E-06 eV + + +------------------------------------------------------------ + End self-consistency iteration # 6 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 1.831 s 1.842 s + | Charge density update : 0.842 s 0.847 s + | Density mixing & preconditioning : 0.177 s 0.178 s + | Hartree multipole update : 0.001 s 0.001 s + | Hartree multipole summation : 0.392 s 0.394 s + | Integration : 0.414 s 0.417 s + | Solution of K.-S. eqns. : 0.005 s 0.005 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 1.632 MB (on task 0) + | Maximum: 1.632 MB (on task 0) + | Average: 1.632 MB + | Peak value for overall tracked memory usage: + | Minimum: 14.236 MB (on task 0 after allocating d_wave) + | Maximum: 14.236 MB (on task 0 after allocating d_wave) + | Average: 14.236 MB + | Largest tracked array allocation so far: + | Minimum: 3.456 MB (hamiltonian_shell on task 0) + | Maximum: 3.456 MB (hamiltonian_shell on task 0) + | Average: 3.456 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + +------------------------------------------------------------ + Begin self-consistency iteration # 7 + + Date : 20230628, Time : 104224.689 +------------------------------------------------------------ + Pulay mixing of updated and previous charge densities. + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 28.0000000000 + | Integrated number of electrons on 3D grid : 27.9999997341 + | Charge integration error : -0.0000002659 + | Normalization factor for density and gradient : 1.0000000095 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = -0.759542E-13 + | Sum of charges compensated after spline to logarithmic grids = -0.110001E-03 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = 0.000000E+00 + Summing up the Hartree potential. + Time summed over all CPUs for potential: real work 0.392 s, elapsed 0.392 s + | RMS charge density error from multipole expansion : 0.146805E-01 + | Average real-space part of the electrostatic potential : 0.47675972 eV + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.418 s, elapsed 0.418 s + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.000 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -4.92520057 eV + What follows are estimated values for band gap, HOMO, LUMO, etc. + | They are estimated on a discrete k-point grid and not necessarily exact. + | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. + + Highest occupied state (VBM) at -5.28814071 eV (relative to internal zero) + | Occupation number: 2.00000000 + | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + + Lowest unoccupied state (CBM) at -4.53504696 eV (relative to internal zero) + | Occupation number: 0.00000000 + | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) + + ESTIMATED overall HOMO-LUMO gap: 0.75309375 eV between HOMO at k-point 1 and LUMO at k-point 4 + | This appears to be an indirect band gap. + | Smallest direct gap : 2.42412065 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, + this system is most likely an insulator or a semiconductor. + + Total energy components: + | Sum of eigenvalues : -328.16168066 Ha -8929.73367061 eV + | XC energy correction : -41.77728329 Ha -1136.81771884 eV + | XC potential correction : 53.94925820 Ha 1468.03400849 eV + | Free-atom electrostatic energy: -263.74356637 Ha -7176.82759392 eV + | Hartree energy correction : -0.91362935 Ha -24.86111942 eV + | Entropy correction : 0.00000000 Ha 0.00000000 eV + | --------------------------- + | Total energy : -580.64690146 Ha -15800.20609430 eV + | Total energy, T -> 0 : -580.64690146 Ha -15800.20609430 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -580.64690146 Ha -15800.20609430 eV + + Derived energy quantities: + | Kinetic energy : 582.24622796 Ha 15843.72598272 eV + | Electrostatic energy : -1121.11584613 Ha -30507.11435818 eV + | Energy correction for multipole + | error in Hartree potential : 0.01978591 Ha 0.53840187 eV + | Sum of eigenvalues per atom : -4464.86683530 eV + | Total energy (T->0) per atom : -7900.10304715 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -7900.10304715 eV + Evaluating new KS density using the density matrix + Evaluating density matrix + Time summed over all CPUs for getting density from density matrix: real work 0.843 s, elapsed 0.843 s + Integration grid: deviation in total charge ( - N_e) = 2.842171E-14 + + Self-consistency convergence accuracy: + | Change of charge density : 0.1144E-05 + | Change of sum of eigenvalues : 0.2986E-03 eV + | Change of total energy : -0.1153E-06 eV + + +------------------------------------------------------------ + End self-consistency iteration # 7 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 1.831 s 1.842 s + | Charge density update : 0.839 s 0.845 s + | Density mixing & preconditioning : 0.178 s 0.179 s + | Hartree multipole update : 0.001 s 0.001 s + | Hartree multipole summation : 0.392 s 0.394 s + | Integration : 0.416 s 0.418 s + | Solution of K.-S. eqns. : 0.005 s 0.005 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 1.632 MB (on task 0) + | Maximum: 1.632 MB (on task 0) + | Average: 1.632 MB + | Peak value for overall tracked memory usage: + | Minimum: 14.236 MB (on task 0 after allocating d_wave) + | Maximum: 14.236 MB (on task 0 after allocating d_wave) + | Average: 14.236 MB + | Largest tracked array allocation so far: + | Minimum: 3.456 MB (hamiltonian_shell on task 0) + | Maximum: 3.456 MB (hamiltonian_shell on task 0) + | Average: 3.456 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + +------------------------------------------------------------ + Begin self-consistency iteration # 8 + + Date : 20230628, Time : 104226.531 +------------------------------------------------------------ + Pulay mixing of updated and previous charge densities. + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 28.0000000000 + | Integrated number of electrons on 3D grid : 28.0000000174 + | Charge integration error : 0.0000000174 + | Normalization factor for density and gradient : 0.9999999994 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = -0.172245E-12 + | Sum of charges compensated after spline to logarithmic grids = -0.110001E-03 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = 0.000000E+00 + Summing up the Hartree potential. + Time summed over all CPUs for potential: real work 0.391 s, elapsed 0.391 s + | RMS charge density error from multipole expansion : 0.146805E-01 + | Average real-space part of the electrostatic potential : 0.47675985 eV + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.417 s, elapsed 0.417 s + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.001 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -4.92520043 eV + What follows are estimated values for band gap, HOMO, LUMO, etc. + | They are estimated on a discrete k-point grid and not necessarily exact. + | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. + + Highest occupied state (VBM) at -5.28814063 eV (relative to internal zero) + | Occupation number: 2.00000000 + | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + + Lowest unoccupied state (CBM) at -4.53504686 eV (relative to internal zero) + | Occupation number: 0.00000000 + | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) + + ESTIMATED overall HOMO-LUMO gap: 0.75309377 eV between HOMO at k-point 1 and LUMO at k-point 4 + | This appears to be an indirect band gap. + | Smallest direct gap : 2.42412061 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, + this system is most likely an insulator or a semiconductor. + + Total energy components: + | Sum of eigenvalues : -328.16168179 Ha -8929.73370147 eV + | XC energy correction : -41.77728314 Ha -1136.81771479 eV + | XC potential correction : 53.94925800 Ha 1468.03400294 eV + | Free-atom electrostatic energy: -263.74356637 Ha -7176.82759392 eV + | Hartree energy correction : -0.91362816 Ha -24.86108705 eV + | Entropy correction : 0.00000000 Ha 0.00000000 eV + | --------------------------- + | Total energy : -580.64690146 Ha -15800.20609429 eV + | Total energy, T -> 0 : -580.64690146 Ha -15800.20609429 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -580.64690146 Ha -15800.20609429 eV + + Derived energy quantities: + | Kinetic energy : 582.24622659 Ha 15843.72594546 eV + | Electrostatic energy : -1121.11584491 Ha -30507.11432496 eV + | Energy correction for multipole + | error in Hartree potential : 0.01978591 Ha 0.53840201 eV + | Sum of eigenvalues per atom : -4464.86685073 eV + | Total energy (T->0) per atom : -7900.10304715 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -7900.10304715 eV + Preliminary charge convergence reached. Turning off preconditioner. + + Evaluating new KS density using the density matrix + Evaluating density matrix + Time summed over all CPUs for getting density from density matrix: real work 0.845 s, elapsed 0.845 s + Integration grid: deviation in total charge ( - N_e) = -2.131628E-14 + + Self-consistency convergence accuracy: + | Change of charge density : 0.1356E-06 + | Change of sum of eigenvalues : -0.3086E-04 eV + | Change of total energy : 0.7722E-08 eV + + Electronic self-consistency reached - switching on the force computation. + + Electronic self-consistency reached - switching on the analytical stress tensor computation. + + +------------------------------------------------------------ + End self-consistency iteration # 8 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 1.831 s 1.842 s + | Charge density & force component update : 0.841 s 0.846 s + | Density mixing : 0.178 s 0.179 s + | Hartree multipole update : 0.001 s 0.001 s + | Hartree multipole summation : 0.392 s 0.394 s + | Hartree pot. SCF incomplete forces : 0.942 s 0.947 s + | Integration : 0.414 s 0.417 s + | Solution of K.-S. eqns. : 0.005 s 0.005 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 1.632 MB (on task 0) + | Maximum: 1.632 MB (on task 0) + | Average: 1.632 MB + | Peak value for overall tracked memory usage: + | Minimum: 14.236 MB (on task 0 after allocating d_wave) + | Maximum: 14.236 MB (on task 0 after allocating d_wave) + | Average: 14.236 MB + | Largest tracked array allocation so far: + | Minimum: 3.456 MB (hamiltonian_shell on task 0) + | Maximum: 3.456 MB (hamiltonian_shell on task 0) + | Average: 3.456 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + +------------------------------------------------------------ + Begin self-consistency iteration # 9 + + Date : 20230628, Time : 104228.373 +------------------------------------------------------------ + Pulay mixing of updated and previous charge densities. + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 28.0000000000 + | Integrated number of electrons on 3D grid : 27.9999999992 + | Charge integration error : -0.0000000008 + | Normalization factor for density and gradient : 1.0000000000 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = -0.150379E-12 + | Sum of charges compensated after spline to logarithmic grids = -0.110001E-03 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = -0.150405E-12 + Summing up the Hartree potential. + Time summed over all CPUs for potential: real work 1.654 s, elapsed 1.654 s + | RMS charge density error from multipole expansion : 0.146805E-01 + | Average real-space part of the electrostatic potential : 0.47675985 eV + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.416 s, elapsed 0.416 s + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.000 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -4.92520044 eV + What follows are estimated values for band gap, HOMO, LUMO, etc. + | They are estimated on a discrete k-point grid and not necessarily exact. + | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. + + Highest occupied state (VBM) at -5.28814064 eV (relative to internal zero) + | Occupation number: 2.00000000 + | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + + Lowest unoccupied state (CBM) at -4.53504686 eV (relative to internal zero) + | Occupation number: 0.00000000 + | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) + + ESTIMATED overall HOMO-LUMO gap: 0.75309378 eV between HOMO at k-point 1 and LUMO at k-point 4 + | This appears to be an indirect band gap. + | Smallest direct gap : 2.42412061 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, + this system is most likely an insulator or a semiconductor. + + Total energy components: + | Sum of eigenvalues : -328.16168175 Ha -8929.73370032 eV + | XC energy correction : -41.77728314 Ha -1136.81771491 eV + | XC potential correction : 53.94925801 Ha 1468.03400310 eV + | Free-atom electrostatic energy: -263.74356637 Ha -7176.82759392 eV + | Hartree energy correction : -0.91362820 Ha -24.86108824 eV + | Entropy correction : 0.00000000 Ha 0.00000000 eV + | --------------------------- + | Total energy : -580.64690146 Ha -15800.20609429 eV + | Total energy, T -> 0 : -580.64690146 Ha -15800.20609429 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -580.64690146 Ha -15800.20609429 eV + + Derived energy quantities: + | Kinetic energy : 582.24622666 Ha 15843.72594733 eV + | Electrostatic energy : -1121.11584498 Ha -30507.11432671 eV + | Energy correction for multipole + | error in Hartree potential : 0.01978591 Ha 0.53840201 eV + | Sum of eigenvalues per atom : -4464.86685016 eV + | Total energy (T->0) per atom : -7900.10304715 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -7900.10304715 eV + Evaluating new KS density using the density matrix + Evaluating density matrix + Time summed over all CPUs for getting density from density matrix: real work 0.843 s, elapsed 0.843 s + Integration grid: deviation in total charge ( - N_e) = -7.460699E-14 + + atomic forces [eV/Ang]: + ----------------------- + atom # 1 + Hellmann-Feynman : -0.145696E-06 0.748304E-07 0.742362E-07 + Ionic forces : 0.000000E+00 0.000000E+00 0.000000E+00 + Multipole : 0.103356E-07 -0.366332E-08 -0.377652E-08 + Hartree pot. SCF incomplete : -0.454440E-09 0.155893E-09 0.272707E-09 + Pulay + GGA : 0.000000E+00 0.000000E+00 0.000000E+00 + ---------------------------------------------------------------- + Total forces( 1) : -0.135814E-06 0.713230E-07 0.707324E-07 + atom # 2 + Hellmann-Feynman : 0.145882E-06 -0.722275E-07 -0.731727E-07 + Ionic forces : 0.000000E+00 0.000000E+00 0.000000E+00 + Multipole : -0.103354E-07 0.366328E-08 0.377543E-08 + Hartree pot. SCF incomplete : 0.389921E-09 -0.232855E-09 -0.270420E-09 + Pulay + GGA : 0.000000E+00 0.000000E+00 0.000000E+00 + ---------------------------------------------------------------- + Total forces( 2) : 0.135936E-06 -0.687971E-07 -0.696677E-07 + + + Self-consistency convergence accuracy: + | Change of charge density : 0.4476E-08 + | Change of sum of eigenvalues : 0.1149E-05 eV + | Change of total energy : 0.1454E-09 eV + | Change of forces : 0.1677E-06 eV/A + + +------------------------------------------------------------ + End self-consistency iteration # 9 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 3.851 s 3.873 s + | Charge density & force component update : 0.839 s 0.845 s + | Density mixing : 0.002 s 0.002 s + | Hartree multipole update : 0.001 s 0.001 s + | Hartree multipole summation : 1.649 s 1.658 s + | Hartree pot. SCF incomplete forces : 0.941 s 0.946 s + | Integration : 0.414 s 0.416 s + | Solution of K.-S. eqns. : 0.005 s 0.005 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 1.632 MB (on task 0) + | Maximum: 1.632 MB (on task 0) + | Average: 1.632 MB + | Peak value for overall tracked memory usage: + | Minimum: 14.236 MB (on task 0 after allocating d_wave) + | Maximum: 14.236 MB (on task 0 after allocating d_wave) + | Average: 14.236 MB + | Largest tracked array allocation so far: + | Minimum: 3.456 MB (hamiltonian_shell on task 0) + | Maximum: 3.456 MB (hamiltonian_shell on task 0) + | Average: 3.456 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + +------------------------------------------------------------ + Begin self-consistency iteration # 10 + + Date : 20230628, Time : 104232.246 +------------------------------------------------------------ + Pulay mixing of updated and previous charge densities. + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 28.0000000000 + | Integrated number of electrons on 3D grid : 28.0000000000 + | Charge integration error : -0.0000000000 + | Normalization factor for density and gradient : 1.0000000000 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = -0.657781E-13 + | Sum of charges compensated after spline to logarithmic grids = -0.110001E-03 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = 0.000000E+00 + Summing up the Hartree potential. + Time summed over all CPUs for potential: real work 1.653 s, elapsed 1.653 s + | RMS charge density error from multipole expansion : 0.146805E-01 + | Average real-space part of the electrostatic potential : 0.47675985 eV + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.417 s, elapsed 0.417 s + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.000 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -4.92520044 eV + What follows are estimated values for band gap, HOMO, LUMO, etc. + | They are estimated on a discrete k-point grid and not necessarily exact. + | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. + + Highest occupied state (VBM) at -5.28814064 eV (relative to internal zero) + | Occupation number: 2.00000000 + | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + + Lowest unoccupied state (CBM) at -4.53504686 eV (relative to internal zero) + | Occupation number: 0.00000000 + | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) + + ESTIMATED overall HOMO-LUMO gap: 0.75309378 eV between HOMO at k-point 1 and LUMO at k-point 4 + | This appears to be an indirect band gap. + | Smallest direct gap : 2.42412061 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, + this system is most likely an insulator or a semiconductor. + + Total energy components: + | Sum of eigenvalues : -328.16168174 Ha -8929.73370007 eV + | XC energy correction : -41.77728314 Ha -1136.81771494 eV + | XC potential correction : 53.94925801 Ha 1468.03400314 eV + | Free-atom electrostatic energy: -263.74356637 Ha -7176.82759392 eV + | Hartree energy correction : -0.91362821 Ha -24.86108850 eV + | Entropy correction : 0.00000000 Ha 0.00000000 eV + | --------------------------- + | Total energy : -580.64690146 Ha -15800.20609429 eV + | Total energy, T -> 0 : -580.64690146 Ha -15800.20609429 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -580.64690146 Ha -15800.20609429 eV + + Derived energy quantities: + | Kinetic energy : 582.24622668 Ha 15843.72594782 eV + | Electrostatic energy : -1121.11584499 Ha -30507.11432716 eV + | Energy correction for multipole + | error in Hartree potential : 0.01978591 Ha 0.53840201 eV + | Sum of eigenvalues per atom : -4464.86685003 eV + | Total energy (T->0) per atom : -7900.10304715 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -7900.10304715 eV + Evaluating new KS density using the density matrix + Evaluating density matrix + Time summed over all CPUs for getting density from density matrix: real work 0.843 s, elapsed 0.843 s + + Evaluating density-matrix-based force terms: batch-based integration + Evaluating density matrix + Evaluating density matrix + Integration grid: deviation in total charge ( - N_e) = -2.486900E-14 + + atomic forces [eV/Ang]: + ----------------------- + atom # 1 + Hellmann-Feynman : -0.145995E-06 0.750543E-07 0.744960E-07 + Ionic forces : 0.000000E+00 0.000000E+00 0.000000E+00 + Multipole : 0.103364E-07 -0.366274E-08 -0.377878E-08 + Hartree pot. SCF incomplete : -0.358185E-09 0.103402E-09 0.222414E-09 + Pulay + GGA : 0.169233E-06 -0.805632E-07 -0.834521E-07 + ---------------------------------------------------------------- + Total forces( 1) : 0.332160E-07 -0.906822E-08 -0.125124E-07 + atom # 2 + Hellmann-Feynman : 0.146165E-06 -0.724696E-07 -0.734276E-07 + Ionic forces : 0.000000E+00 0.000000E+00 0.000000E+00 + Multipole : -0.103358E-07 0.366295E-08 0.377614E-08 + Hartree pot. SCF incomplete : 0.293215E-09 -0.158219E-09 -0.190451E-09 + Pulay + GGA : -0.183358E-06 0.756836E-07 0.762508E-07 + ---------------------------------------------------------------- + Total forces( 2) : -0.472358E-07 0.671870E-08 0.640891E-08 + + + Analytical stress tensor components [eV] xx yy zz xy xz yz + ----------------------------------------------------------------------------------------------------------------------------------------------------------- + Nuclear Hellmann-Feynman : -0.1414603250E+02 -0.1414626976E+02 -0.1414626973E+02 -0.2419395416E-07 -0.2344943180E-07 0.7515882712E-07 + Multipole Hellmann-Feynman : -0.3058493612E+02 -0.3058494702E+02 -0.3058494706E+02 -0.5452181630E-07 -0.5027800706E-07 0.2153701328E-06 + On-site Multipole corrections : -0.2833796336E+00 -0.2833796336E+00 -0.2833796336E+00 0.4306547092E-10 0.4092601380E-10 -0.1215927816E-09 + Strain deriv. of the orbitals : 0.4401780801E+02 0.4401805485E+02 0.4401805485E+02 0.2741294229E-07 0.2308618083E-07 -0.1752726495E-06 + ----------------------------------------------------------------------------------------------------------------------------------------------------------- + Sum of all contributions : -0.9965402449E+00 -0.9965415741E+00 -0.9965415777E+00 -0.5125976270E-07 -0.5060033201E-07 0.1151347177E-06 + + +-------------------------------------------------------------------+ + | Analytical stress tensor - Symmetrized | + | Cartesian components [eV/A**3] | + +-------------------------------------------------------------------+ + | x y z | + | | + | x -0.02338243 -0.00000000 -0.00000000 | + | y -0.00000000 -0.02338246 0.00000000 | + | z -0.00000000 0.00000000 -0.02338246 | + | | + | Pressure: 0.02338245 [eV/A**3] | + | | + +-------------------------------------------------------------------+ + + + Self-consistency convergence accuracy: + | Change of charge density : 0.1796E-09 + | Change of sum of eigenvalues : 0.2478E-06 eV + | Change of total energy : -0.4640E-10 eV + | Change of forces : 0.4524E-09 eV/A + + Writing Kohn-Sham eigenvalues. + K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + + State Occupation Eigenvalue [Ha] Eigenvalue [eV] + 1 2.00000 -65.744123 -1788.98861 + 2 2.00000 -65.744123 -1788.98861 + 3 2.00000 -5.104202 -138.89241 + 4 2.00000 -5.103995 -138.88676 + 5 2.00000 -3.487854 -94.90933 + 6 2.00000 -3.487854 -94.90933 + 7 2.00000 -3.487854 -94.90933 + 8 2.00000 -3.487374 -94.89627 + 9 2.00000 -3.487374 -94.89627 + 10 2.00000 -3.487374 -94.89627 + 11 2.00000 -0.620861 -16.89449 + 12 2.00000 -0.194336 -5.28814 + 13 2.00000 -0.194336 -5.28814 + 14 2.00000 -0.194336 -5.28814 + 15 0.00000 -0.105251 -2.86402 + 16 0.00000 -0.105251 -2.86402 + 17 0.00000 -0.105251 -2.86402 + 18 0.00000 -0.094315 -2.56644 + 19 0.00000 0.090720 2.46860 + 20 0.00000 0.090720 2.46860 + + What follows are estimated values for band gap, HOMO, LUMO, etc. + | They are estimated on a discrete k-point grid and not necessarily exact. + | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. + + Highest occupied state (VBM) at -5.28814064 eV (relative to internal zero) + | Occupation number: 2.00000000 + | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + + Lowest unoccupied state (CBM) at -4.53504686 eV (relative to internal zero) + | Occupation number: 0.00000000 + | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) + + ESTIMATED overall HOMO-LUMO gap: 0.75309378 eV between HOMO at k-point 1 and LUMO at k-point 4 + | This appears to be an indirect band gap. + | Smallest direct gap : 2.42412061 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, + this system is most likely an insulator or a semiconductor. + | Chemical Potential : -4.92520044 eV + + Self-consistency cycle converged. + + +------------------------------------------------------------ + End self-consistency iteration # 10 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 19.789 s 19.919 s + | Charge density & force component update : 16.791 s 16.906 s + | Density mixing : 0.002 s 0.002 s + | Hartree multipole update : 0.001 s 0.001 s + | Hartree multipole summation : 1.649 s 1.657 s + | Hartree pot. SCF incomplete forces : 0.926 s 0.931 s + | Integration : 0.415 s 0.417 s + | Solution of K.-S. eqns. : 0.005 s 0.005 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 1.632 MB (on task 0) + | Maximum: 1.632 MB (on task 0) + | Average: 1.632 MB + | Peak value for overall tracked memory usage: + | Minimum: 14.236 MB (on task 0 after allocating d_wave) + | Maximum: 14.236 MB (on task 0 after allocating d_wave) + | Average: 14.236 MB + | Largest tracked array allocation so far: + | Minimum: 3.456 MB (hamiltonian_shell on task 0) + | Maximum: 3.456 MB (hamiltonian_shell on task 0) + | Average: 3.456 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + Removing unitary transformations (pure translations, rotations) from forces on atoms. + Atomic forces before filtering: + | Net force on center of mass : -0.140198E-07 -0.234952E-08 -0.610350E-08 eV/A + Atomic forces after filtering: + | Net force on center of mass : -0.531692E-23 -0.132923E-23 0.000000E+00 eV/A + + Energy and forces in a compact form: + | Total energy uncorrected : -0.158002060942910E+05 eV + | Total energy corrected : -0.158002060942910E+05 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -0.158002060942910E+05 eV + Total atomic forces (unitary forces cleaned) [eV/Ang]: + | 1 0.402258645112855E-07 -0.789345665168126E-08 -0.946066143948756E-08 + | 2 -0.402258645112855E-07 0.789345665168126E-08 0.946066143948756E-08 + + ------------------------------------ + Start decomposition of the XC Energy + ------------------------------------ + X and C from original XC functional choice + Hartree-Fock Energy : 0.000000000 Ha 0.000000000 eV + X Energy : -40.691832894 Ha -1107.281110900 eV + C Energy : -1.085450248 Ha -29.536604044 eV + XC Energy w/o HF : -41.777283142 Ha -1136.817714944 eV + Total XC Energy : -41.777283142 Ha -1136.817714944 eV + ------------------------------------ + LDA X and C from self-consistent density + X Energy LDA : -37.625522323 Ha -1023.842554939 eV + C Energy LDA : -2.145950281 Ha -58.394278201 eV + ------------------------------------ + End decomposition of the XC Energy + ------------------------------------ + +------------------------------------------------------------ + Relaxation / MD: End force evaluation. : max(cpu_time) wall_clock(cpu1) + | Time for this force evaluation : 39.534 s 39.781 s + +------------------------------------------------------------ + Geometry optimization: Attempting to predict improved coordinates. + + +-------------------------------------------------------------------+ + | Generalized derivatives on lattice vectors [eV/A] | + +-------------------------------------------------------------------+ + |lattice_vector 0.17972412 -0.17972435 -0.17972435 | + |lattice_vector -0.17972414 0.17972439 -0.17972441 | + |lattice_vector -0.17972414 -0.17972441 0.17972440 | + +-------------------------------------------------------------------+ + | Forces on lattice vectors cleaned from atomic contributions [eV/A]| + +-------------------------------------------------------------------+ + |lattice_vector -0.17972412 0.17972435 0.17972435 | + |lattice_vector 0.17972414 -0.17972439 0.17972441 | + |lattice_vector 0.17972414 0.17972441 -0.17972440 | + +-------------------------------------------------------------------+ + Removing unitary transformations (pure translations, rotations) from forces on atoms. + Atomic forces before filtering: + | Net force on center of mass : -0.531692E-23 -0.132923E-23 0.000000E+00 eV/A + Atomic forces after filtering: + | Net force on center of mass : -0.531692E-23 -0.132923E-23 0.000000E+00 eV/A + Net remaining forces (excluding translations, rotations) in present geometry: + || Forces on atoms || = 0.402259E-07 eV/A. + || Forces on lattice || = 0.179724E+00 eV/A^3. + Maximum force component is 0.179724E+00 eV/A. + Present geometry is not yet converged. + + Relaxation step number 2: Predicting new coordinates. + + Advancing geometry using trust radius method. + | True / expected gain: -2.17E-02 eV / -1.37E-02 eV = 1.5829 + | Harmonic / expected gain: -2.31E-02 eV / -1.37E-02 eV = 1.6845 + | Hessian has 0 negative and 3 zero eigenvalues. + | Positive eigenvalues (eV/A^2): 3.92E+00 ... 3.02E+01 + | Use Quasi-Newton step of length |H^-1 F| = 9.26E-02 A. + Finished advancing geometry + | Time : 0.000 s + Updated atomic structure: + x [A] y [A] z [A] + lattice_vector 0.00000007 2.81020375 2.81020375 + lattice_vector 2.81020365 -0.00000003 2.81020369 + lattice_vector 2.81020365 2.81020369 -0.00000004 + + atom 0.00000001 -0.00000000 -0.00000000 Si + atom 1.40510183 1.40510185 1.40510185 Si + + Fractional coordinates: + L1 L2 L3 + atom_frac -0.00000000 0.00000000 0.00000000 Si + atom_frac 0.25000000 0.25000000 0.25000000 Si +------------------------------------------------------------ + Writing the current geometry to file "geometry.in.next_step". + Writing estimated Hessian matrix to file 'hessian.aims' + + Quantities derived from the lattice vectors: + | Reciprocal lattice vector 1: -1.117923 1.117923 1.117923 + | Reciprocal lattice vector 2: 1.117923 -1.117923 1.117923 + | Reciprocal lattice vector 3: 1.117923 1.117923 -1.117923 + | Unit cell volume : 0.443857E+02 A^3 + + Range separation radius for Ewald summation (hartree_convergence_parameter): 4.03797672 bohr. + +------------------------------------------------------------ + Begin self-consistency loop: Re-initialization. + + Date : 20230628, Time : 104252.172 +------------------------------------------------------------ + + Initializing index lists of integration centers etc. from given atomic structure: + Mapping all atomic coordinates to central unit cell. + + Initializing the k-points + Using symmetry for reducing the k-points + | k-points reduced from: 8 to 8 + | Number of k-points : 8 + The eigenvectors in the calculations are REAL. + | K-points in task 0: 8 + | Number of basis functions in the Hamiltonian integrals : 1771 + | Number of basis functions in a single unit cell : 50 + | Number of centers in hartree potential : 708 + | Number of centers in hartree multipole : 318 + | Number of centers in electron density summation: 190 + | Number of centers in basis integrals : 198 + | Number of centers in integrals : 101 + | Number of centers in hamiltonian : 190 + | Consuming 14 KiB for k_phase. + | Number of super-cells (origin) [n_cells] : 2197 + | Number of super-cells (after PM_index) [n_cells] : 112 + | Number of super-cells in hamiltonian [n_cells_in_hamiltonian]: 112 + | Size of matrix packed + index [n_hamiltonian_matrix_size] : 82595 + Partitioning the integration grid into batches with parallel hashing+maxmin method. + | Number of batches: 128 + | Maximal batch size: 90 + | Minimal batch size: 85 + | Average batch size: 87.562 + | Standard deviation of batch sizes: 1.493 + + Integration load balanced across 1 MPI tasks. + Work distribution over tasks is as follows: + Initializing partition tables, free-atom densities, potentials, etc. across the integration grid (initialize_grid_storage). + | Species 1: outer_partition_radius set to 5.000694715736543 AA . + | The sparse table of interatomic distances needs 194.62 kbyte instead of 313.63 kbyte of memory. + | Net number of integration points: 11208 + | of which are non-zero points : 9876 + | Numerical average free-atom electrostatic potential : -11.84315486 eV + Renormalizing the initial density to the exact electron count on the 3D integration grid. + | Initial density: Formal number of electrons (from input files) : 28.0000000000 + | Integrated number of electrons on 3D grid : 28.0038026450 + | Charge integration error : 0.0038026450 + | Normalization factor for density and gradient : 0.9998642097 + Renormalizing the free-atom superposition density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 28.0000000000 + | Integrated number of electrons on 3D grid : 28.0038026450 + | Charge integration error : 0.0038026450 + | Normalization factor for density and gradient : 0.9998642097 + Obtaining max. number of non-zero basis functions in each batch (get_n_compute_maxes). + Calculating total energy contributions from superposition of free atom densities. + Initialize hartree_potential_storage + Integrating overlap matrix. + Time summed over all CPUs for integration: real work 0.254 s, elapsed 0.254 s + Orthonormalizing eigenvectors + + End scf reinitialization - timings : max(cpu_time) wall_clock(cpu1) + | Time for scf. reinitialization : 0.560 s 0.563 s + | Boundary condition initialization : 0.064 s 0.064 s + | Integration : 0.252 s 0.254 s + | Grid partitioning : 0.032 s 0.032 s + | Preloading free-atom quantities on grid : 0.174 s 0.175 s + | Free-atom superposition energy : 0.027 s 0.027 s + | K.-S. eigenvector reorthonormalization : 0.001 s 0.001 s +------------------------------------------------------------ + Evaluating new KS density using the density matrix + Evaluating density matrix + Time summed over all CPUs for getting density from density matrix: real work 0.805 s, elapsed 0.805 s + Integration grid: deviation in total charge ( - N_e) = 7.105427E-15 + + Time for density update prior : max(cpu_time) wall_clock(cpu1) + | self-consistency iterative process : 0.801 s 0.807 s + +------------------------------------------------------------ + Begin self-consistency iteration # 1 + + Date : 20230628, Time : 104253.542 +------------------------------------------------------------ + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 28.0000000000 + | Integrated number of electrons on 3D grid : 28.0000000000 + | Charge integration error : 0.0000000000 + | Normalization factor for density and gradient : 1.0000000000 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = 0.158275E-12 + | Sum of charges compensated after spline to logarithmic grids = -0.694106E-04 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = 0.000000E+00 + Summing up the Hartree potential. + | Estimated reciprocal-space cutoff momentum G_max: 2.30767722 bohr^-1 . + | Reciprocal lattice points for long-range Hartree potential: 58 + Time summed over all CPUs for potential: real work 0.391 s, elapsed 0.391 s + | RMS charge density error from multipole expansion : 0.138738E-01 + | Average real-space part of the electrostatic potential : 0.43982773 eV + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.397 s, elapsed 0.397 s + Decreasing sparse matrix size: + | Tolerance: 0.1000E-12 + Hamiltonian matrix + | Array has 75370 nonzero elements out of 82595 elements + | Sparsity factor is 0.087 + Overlap matrix + | Array has 68470 nonzero elements out of 82595 elements + | Sparsity factor is 0.171 + New size of hamiltonian matrix: 75393 + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Singularity check in k-point 1, task 0 (analysis for other k-points/tasks may follow below): + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.000 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -5.00592993 eV + Writing Kohn-Sham eigenvalues. + K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + + State Occupation Eigenvalue [Ha] Eigenvalue [eV] + 1 2.00000 -65.749436 -1789.13317 + 2 2.00000 -65.749436 -1789.13317 + 3 2.00000 -5.106559 -138.95654 + 4 2.00000 -5.106390 -138.95195 + 5 2.00000 -3.490380 -94.97807 + 6 2.00000 -3.490380 -94.97807 + 7 2.00000 -3.490380 -94.97807 + 8 2.00000 -3.489976 -94.96707 + 9 2.00000 -3.489976 -94.96707 + 10 2.00000 -3.489976 -94.96707 + 11 2.00000 -0.609457 -16.58418 + 12 2.00000 -0.192712 -5.24397 + 13 2.00000 -0.192712 -5.24397 + 14 2.00000 -0.192712 -5.24397 + 15 0.00000 -0.109029 -2.96684 + 16 0.00000 -0.104086 -2.83233 + 17 0.00000 -0.104086 -2.83233 + 18 0.00000 -0.104086 -2.83233 + 19 0.00000 0.092607 2.51996 + 20 0.00000 0.092607 2.51996 + + What follows are estimated values for band gap, HOMO, LUMO, etc. + | They are estimated on a discrete k-point grid and not necessarily exact. + | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. + + Highest occupied state (VBM) at -5.24396793 eV (relative to internal zero) + | Occupation number: 2.00000000 + | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + + Lowest unoccupied state (CBM) at -4.41671413 eV (relative to internal zero) + | Occupation number: 0.00000000 + | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) + + ESTIMATED overall HOMO-LUMO gap: 0.82725381 eV between HOMO at k-point 1 and LUMO at k-point 4 + | This appears to be an indirect band gap. + | Smallest direct gap : 2.27712508 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, + this system is most likely an insulator or a semiconductor. + + Total energy components: + | Sum of eigenvalues : -328.17953753 Ha -8930.21958065 eV + | XC energy correction : -41.74961532 Ha -1136.06483528 eV + | XC potential correction : 53.91234167 Ha 1467.02945857 eV + | Free-atom electrostatic energy: -263.83177839 Ha -7179.22796514 eV + | Hartree energy correction : -0.79902556 Ha -21.74259165 eV + | Entropy correction : -0.00000000 Ha -0.00000000 eV + | --------------------------- + | Total energy : -580.64761512 Ha -15800.22551413 eV + | Total energy, T -> 0 : -580.64761512 Ha -15800.22551413 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -580.64761512 Ha -15800.22551413 eV + + Derived energy quantities: + | Kinetic energy : 582.08268557 Ha 15839.27576796 eV + | Electrostatic energy : -1120.98068538 Ha -30503.43644682 eV + | Energy correction for multipole + | error in Hartree potential : 0.01842747 Ha 0.50143705 eV + | Sum of eigenvalues per atom : -4465.10979032 eV + | Total energy (T->0) per atom : -7900.11275707 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -7900.11275707 eV + Evaluating new KS density using the density matrix + Evaluating density matrix + Time summed over all CPUs for getting density from density matrix: real work 0.809 s, elapsed 0.809 s + Integration grid: deviation in total charge ( - N_e) = 4.973799E-14 + + Self-consistency convergence accuracy: + | Change of charge density : 0.1325E+00 + | Change of sum of eigenvalues : -0.8930E+04 eV + | Change of total energy : -0.1580E+05 eV + + +------------------------------------------------------------ + End self-consistency iteration # 1 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 1.598 s 1.607 s + | Charge density update : 0.805 s 0.810 s + | Density mixing & preconditioning : 0.000 s 0.000 s + | Hartree multipole update : 0.001 s 0.001 s + | Hartree multipole summation : 0.392 s 0.394 s + | Integration : 0.395 s 0.398 s + | Solution of K.-S. eqns. : 0.005 s 0.004 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 1.569 MB (on task 0) + | Maximum: 1.569 MB (on task 0) + | Average: 1.569 MB + | Peak value for overall tracked memory usage: + | Minimum: 14.236 MB (on task 0 after allocating d_wave) + | Maximum: 14.236 MB (on task 0 after allocating d_wave) + | Average: 14.236 MB + | Largest tracked array allocation so far: + | Minimum: 3.456 MB (hamiltonian_shell on task 0) + | Maximum: 3.456 MB (hamiltonian_shell on task 0) + | Average: 3.456 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + +------------------------------------------------------------ + Begin self-consistency iteration # 2 + + Date : 20230628, Time : 104255.149 +------------------------------------------------------------ + Pulay mixing of updated and previous charge densities. + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 28.0000000000 + | Integrated number of electrons on 3D grid : 27.9999816483 + | Charge integration error : -0.0000183517 + | Normalization factor for density and gradient : 1.0000006554 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = 0.130890E-13 + | Sum of charges compensated after spline to logarithmic grids = -0.694375E-04 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = 0.000000E+00 + Summing up the Hartree potential. + Time summed over all CPUs for potential: real work 0.392 s, elapsed 0.392 s + | RMS charge density error from multipole expansion : 0.138614E-01 + | Average real-space part of the electrostatic potential : 0.43992626 eV + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.401 s, elapsed 0.401 s + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.000 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -5.00656759 eV + What follows are estimated values for band gap, HOMO, LUMO, etc. + | They are estimated on a discrete k-point grid and not necessarily exact. + | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. + + Highest occupied state (VBM) at -5.24455109 eV (relative to internal zero) + | Occupation number: 2.00000000 + | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + + Lowest unoccupied state (CBM) at -4.41699375 eV (relative to internal zero) + | Occupation number: 0.00000000 + | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) + + ESTIMATED overall HOMO-LUMO gap: 0.82755734 eV between HOMO at k-point 1 and LUMO at k-point 4 + | This appears to be an indirect band gap. + | Smallest direct gap : 2.27729154 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, + this system is most likely an insulator or a semiconductor. + + Total energy components: + | Sum of eigenvalues : -328.17620388 Ha -8930.12886748 eV + | XC energy correction : -41.75005579 Ha -1136.07682099 eV + | XC potential correction : 53.91291833 Ha 1467.04515027 eV + | Free-atom electrostatic energy: -263.83177839 Ha -7179.22796514 eV + | Hartree energy correction : -0.80249533 Ha -21.83700887 eV + | Entropy correction : -0.00000000 Ha -0.00000000 eV + | --------------------------- + | Total energy : -580.64761505 Ha -15800.22551221 eV + | Total energy, T -> 0 : -580.64761505 Ha -15800.22551221 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -580.64761505 Ha -15800.22551221 eV + + Derived energy quantities: + | Kinetic energy : 582.09177949 Ha 15839.52322595 eV + | Electrostatic energy : -1120.98933875 Ha -30503.67191717 eV + | Energy correction for multipole + | error in Hartree potential : 0.01842356 Ha 0.50133061 eV + | Sum of eigenvalues per atom : -4465.06443374 eV + | Total energy (T->0) per atom : -7900.11275611 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -7900.11275611 eV + Evaluating new KS density using the density matrix + Evaluating density matrix + Time summed over all CPUs for getting density from density matrix: real work 0.808 s, elapsed 0.808 s + Integration grid: deviation in total charge ( - N_e) = 4.973799E-14 + + Self-consistency convergence accuracy: + | Change of charge density : 0.2137E-02 + | Change of sum of eigenvalues : 0.9071E-01 eV + | Change of total energy : 0.1920E-05 eV + + +------------------------------------------------------------ + End self-consistency iteration # 2 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 1.778 s 1.789 s + | Charge density update : 0.804 s 0.809 s + | Density mixing & preconditioning : 0.177 s 0.178 s + | Hartree multipole update : 0.001 s 0.002 s + | Hartree multipole summation : 0.392 s 0.394 s + | Integration : 0.399 s 0.401 s + | Solution of K.-S. eqns. : 0.005 s 0.005 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 1.569 MB (on task 0) + | Maximum: 1.569 MB (on task 0) + | Average: 1.569 MB + | Peak value for overall tracked memory usage: + | Minimum: 14.236 MB (on task 0 after allocating d_wave) + | Maximum: 14.236 MB (on task 0 after allocating d_wave) + | Average: 14.236 MB + | Largest tracked array allocation so far: + | Minimum: 3.456 MB (hamiltonian_shell on task 0) + | Maximum: 3.456 MB (hamiltonian_shell on task 0) + | Average: 3.456 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + +------------------------------------------------------------ + Begin self-consistency iteration # 3 + + Date : 20230628, Time : 104256.938 +------------------------------------------------------------ + Pulay mixing of updated and previous charge densities. + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 28.0000000000 + | Integrated number of electrons on 3D grid : 27.9998999680 + | Charge integration error : -0.0001000320 + | Normalization factor for density and gradient : 1.0000035726 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = 0.191295E-14 + | Sum of charges compensated after spline to logarithmic grids = -0.695443E-04 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = 0.000000E+00 + Summing up the Hartree potential. + Time summed over all CPUs for potential: real work 0.391 s, elapsed 0.391 s + | RMS charge density error from multipole expansion : 0.138170E-01 + | Average real-space part of the electrostatic potential : 0.44042345 eV + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.400 s, elapsed 0.400 s + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.000 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -5.00875522 eV + What follows are estimated values for band gap, HOMO, LUMO, etc. + | They are estimated on a discrete k-point grid and not necessarily exact. + | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. + + Highest occupied state (VBM) at -5.24650921 eV (relative to internal zero) + | Occupation number: 2.00000000 + | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + + Lowest unoccupied state (CBM) at -4.41793384 eV (relative to internal zero) + | Occupation number: 0.00000000 + | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) + + ESTIMATED overall HOMO-LUMO gap: 0.82857537 eV between HOMO at k-point 1 and LUMO at k-point 4 + | This appears to be an indirect band gap. + | Smallest direct gap : 2.27795944 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, + this system is most likely an insulator or a semiconductor. + + Total energy components: + | Sum of eigenvalues : -328.16359582 Ha -8929.78578471 eV + | XC energy correction : -41.75168311 Ha -1136.12110253 eV + | XC potential correction : 53.91505137 Ha 1467.10319311 eV + | Free-atom electrostatic energy: -263.83177839 Ha -7179.22796514 eV + | Hartree energy correction : -0.81561003 Ha -22.19387804 eV + | Entropy correction : -0.00000000 Ha -0.00000000 eV + | --------------------------- + | Total energy : -580.64761598 Ha -15800.22553731 eV + | Total energy, T -> 0 : -580.64761598 Ha -15800.22553731 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -580.64761598 Ha -15800.22553731 eV + + Derived energy quantities: + | Kinetic energy : 582.12506692 Ha 15840.42902298 eV + | Electrostatic energy : -1121.02099979 Ha -30504.53345776 eV + | Energy correction for multipole + | error in Hartree potential : 0.01840991 Ha 0.50095915 eV + | Sum of eigenvalues per atom : -4464.89289235 eV + | Total energy (T->0) per atom : -7900.11276865 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -7900.11276865 eV + Evaluating new KS density using the density matrix + Evaluating density matrix + Time summed over all CPUs for getting density from density matrix: real work 0.808 s, elapsed 0.808 s + Integration grid: deviation in total charge ( - N_e) = 3.907985E-14 + + Self-consistency convergence accuracy: + | Change of charge density : 0.1672E-02 + | Change of sum of eigenvalues : 0.3431E+00 eV + | Change of total energy : -0.2509E-04 eV + + +------------------------------------------------------------ + End self-consistency iteration # 3 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 1.778 s 1.788 s + | Charge density update : 0.804 s 0.809 s + | Density mixing & preconditioning : 0.178 s 0.179 s + | Hartree multipole update : 0.001 s 0.001 s + | Hartree multipole summation : 0.392 s 0.394 s + | Integration : 0.398 s 0.400 s + | Solution of K.-S. eqns. : 0.005 s 0.005 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 1.569 MB (on task 0) + | Maximum: 1.569 MB (on task 0) + | Average: 1.569 MB + | Peak value for overall tracked memory usage: + | Minimum: 14.236 MB (on task 0 after allocating d_wave) + | Maximum: 14.236 MB (on task 0 after allocating d_wave) + | Average: 14.236 MB + | Largest tracked array allocation so far: + | Minimum: 3.456 MB (hamiltonian_shell on task 0) + | Maximum: 3.456 MB (hamiltonian_shell on task 0) + | Average: 3.456 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + +------------------------------------------------------------ + Begin self-consistency iteration # 4 + + Date : 20230628, Time : 104258.726 +------------------------------------------------------------ + Pulay mixing of updated and previous charge densities. + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 28.0000000000 + | Integrated number of electrons on 3D grid : 27.9999295002 + | Charge integration error : -0.0000704998 + | Normalization factor for density and gradient : 1.0000025179 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = 0.145459E-12 + | Sum of charges compensated after spline to logarithmic grids = -0.695626E-04 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = 0.000000E+00 + Summing up the Hartree potential. + Time summed over all CPUs for potential: real work 0.391 s, elapsed 0.391 s + | RMS charge density error from multipole expansion : 0.138179E-01 + | Average real-space part of the electrostatic potential : 0.44071380 eV + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.401 s, elapsed 0.401 s + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.000 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -5.00850126 eV + What follows are estimated values for band gap, HOMO, LUMO, etc. + | They are estimated on a discrete k-point grid and not necessarily exact. + | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. + + Highest occupied state (VBM) at -5.24618997 eV (relative to internal zero) + | Occupation number: 2.00000000 + | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + + Lowest unoccupied state (CBM) at -4.41778973 eV (relative to internal zero) + | Occupation number: 0.00000000 + | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) + + ESTIMATED overall HOMO-LUMO gap: 0.82840023 eV between HOMO at k-point 1 and LUMO at k-point 4 + | This appears to be an indirect band gap. + | Smallest direct gap : 2.27808000 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, + this system is most likely an insulator or a semiconductor. + + Total energy components: + | Sum of eigenvalues : -328.16275576 Ha -8929.76292551 eV + | XC energy correction : -41.75170074 Ha -1136.12158234 eV + | XC potential correction : 53.91508115 Ha 1467.10400346 eV + | Free-atom electrostatic energy: -263.83177839 Ha -7179.22796514 eV + | Hartree energy correction : -0.81646339 Ha -22.21709927 eV + | Entropy correction : -0.00000000 Ha -0.00000000 eV + | --------------------------- + | Total energy : -580.64761713 Ha -15800.22556879 eV + | Total energy, T -> 0 : -580.64761713 Ha -15800.22556879 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -580.64761713 Ha -15800.22556879 eV + + Derived energy quantities: + | Kinetic energy : 582.12482304 Ha 15840.42238664 eV + | Electrostatic energy : -1121.02073943 Ha -30504.52637309 eV + | Energy correction for multipole + | error in Hartree potential : 0.01841088 Ha 0.50098545 eV + | Sum of eigenvalues per atom : -4464.88146276 eV + | Total energy (T->0) per atom : -7900.11278440 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -7900.11278440 eV + Evaluating new KS density using the density matrix + Evaluating density matrix + Time summed over all CPUs for getting density from density matrix: real work 0.812 s, elapsed 0.812 s + Integration grid: deviation in total charge ( - N_e) = -4.263256E-14 + + Self-consistency convergence accuracy: + | Change of charge density : 0.1558E-03 + | Change of sum of eigenvalues : 0.2286E-01 eV + | Change of total energy : -0.3149E-04 eV + + +------------------------------------------------------------ + End self-consistency iteration # 4 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 1.782 s 1.794 s + | Charge density update : 0.808 s 0.814 s + | Density mixing & preconditioning : 0.178 s 0.179 s + | Hartree multipole update : 0.001 s 0.002 s + | Hartree multipole summation : 0.392 s 0.393 s + | Integration : 0.399 s 0.401 s + | Solution of K.-S. eqns. : 0.005 s 0.005 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 1.569 MB (on task 0) + | Maximum: 1.569 MB (on task 0) + | Average: 1.569 MB + | Peak value for overall tracked memory usage: + | Minimum: 14.236 MB (on task 0 after allocating d_wave) + | Maximum: 14.236 MB (on task 0 after allocating d_wave) + | Average: 14.236 MB + | Largest tracked array allocation so far: + | Minimum: 3.456 MB (hamiltonian_shell on task 0) + | Maximum: 3.456 MB (hamiltonian_shell on task 0) + | Average: 3.456 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + +------------------------------------------------------------ + Begin self-consistency iteration # 5 + + Date : 20230628, Time : 104300.520 +------------------------------------------------------------ + Pulay mixing of updated and previous charge densities. + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 28.0000000000 + | Integrated number of electrons on 3D grid : 27.9999639037 + | Charge integration error : -0.0000360963 + | Normalization factor for density and gradient : 1.0000012892 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = 0.947663E-13 + | Sum of charges compensated after spline to logarithmic grids = -0.695766E-04 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = 0.000000E+00 + Summing up the Hartree potential. + Time summed over all CPUs for potential: real work 0.391 s, elapsed 0.391 s + | RMS charge density error from multipole expansion : 0.138146E-01 + | Average real-space part of the electrostatic potential : 0.44085511 eV + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.402 s, elapsed 0.402 s + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.000 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -5.00862633 eV + What follows are estimated values for band gap, HOMO, LUMO, etc. + | They are estimated on a discrete k-point grid and not necessarily exact. + | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. + + Highest occupied state (VBM) at -5.24629314 eV (relative to internal zero) + | Occupation number: 2.00000000 + | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + + Lowest unoccupied state (CBM) at -4.41784591 eV (relative to internal zero) + | Occupation number: 0.00000000 + | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) + + ESTIMATED overall HOMO-LUMO gap: 0.82844723 eV between HOMO at k-point 1 and LUMO at k-point 4 + | This appears to be an indirect band gap. + | Smallest direct gap : 2.27813467 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, + this system is most likely an insulator or a semiconductor. + + Total energy components: + | Sum of eigenvalues : -328.16254782 Ha -8929.75726714 eV + | XC energy correction : -41.75163465 Ha -1136.11978386 eV + | XC potential correction : 53.91500339 Ha 1467.10188744 eV + | Free-atom electrostatic energy: -263.83177839 Ha -7179.22796514 eV + | Hartree energy correction : -0.81666037 Ha -22.22245928 eV + | Entropy correction : -0.00000000 Ha -0.00000000 eV + | --------------------------- + | Total energy : -580.64761784 Ha -15800.22558798 eV + | Total energy, T -> 0 : -580.64761784 Ha -15800.22558798 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -580.64761784 Ha -15800.22558798 eV + + Derived energy quantities: + | Kinetic energy : 582.12305363 Ha 15840.37423862 eV + | Electrostatic energy : -1121.01903682 Ha -30504.48004274 eV + | Energy correction for multipole + | error in Hartree potential : 0.01840905 Ha 0.50093578 eV + | Sum of eigenvalues per atom : -4464.87863357 eV + | Total energy (T->0) per atom : -7900.11279399 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -7900.11279399 eV + Evaluating new KS density using the density matrix + Evaluating density matrix + Time summed over all CPUs for getting density from density matrix: real work 0.806 s, elapsed 0.806 s + Integration grid: deviation in total charge ( - N_e) = -2.131628E-14 + + Self-consistency convergence accuracy: + | Change of charge density : 0.1220E-03 + | Change of sum of eigenvalues : 0.5658E-02 eV + | Change of total energy : -0.1918E-04 eV + + +------------------------------------------------------------ + End self-consistency iteration # 5 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 1.777 s 1.788 s + | Charge density update : 0.802 s 0.807 s + | Density mixing & preconditioning : 0.177 s 0.178 s + | Hartree multipole update : 0.001 s 0.001 s + | Hartree multipole summation : 0.392 s 0.394 s + | Integration : 0.400 s 0.402 s + | Solution of K.-S. eqns. : 0.005 s 0.005 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 1.569 MB (on task 0) + | Maximum: 1.569 MB (on task 0) + | Average: 1.569 MB + | Peak value for overall tracked memory usage: + | Minimum: 14.236 MB (on task 0 after allocating d_wave) + | Maximum: 14.236 MB (on task 0 after allocating d_wave) + | Average: 14.236 MB + | Largest tracked array allocation so far: + | Minimum: 3.456 MB (hamiltonian_shell on task 0) + | Maximum: 3.456 MB (hamiltonian_shell on task 0) + | Average: 3.456 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + +------------------------------------------------------------ + Begin self-consistency iteration # 6 + + Date : 20230628, Time : 104302.308 +------------------------------------------------------------ + Pulay mixing of updated and previous charge densities. + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 28.0000000000 + | Integrated number of electrons on 3D grid : 28.0000002635 + | Charge integration error : 0.0000002635 + | Normalization factor for density and gradient : 0.9999999906 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = 0.134233E-13 + | Sum of charges compensated after spline to logarithmic grids = -0.695774E-04 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = 0.000000E+00 + Summing up the Hartree potential. + Time summed over all CPUs for potential: real work 0.391 s, elapsed 0.391 s + | RMS charge density error from multipole expansion : 0.138149E-01 + | Average real-space part of the electrostatic potential : 0.44087742 eV + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.400 s, elapsed 0.400 s + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.000 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -5.00859466 eV + What follows are estimated values for band gap, HOMO, LUMO, etc. + | They are estimated on a discrete k-point grid and not necessarily exact. + | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. + + Highest occupied state (VBM) at -5.24625679 eV (relative to internal zero) + | Occupation number: 2.00000000 + | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + + Lowest unoccupied state (CBM) at -4.41782701 eV (relative to internal zero) + | Occupation number: 0.00000000 + | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) + + ESTIMATED overall HOMO-LUMO gap: 0.82842977 eV between HOMO at k-point 1 and LUMO at k-point 4 + | This appears to be an indirect band gap. + | Smallest direct gap : 2.27813896 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, + this system is most likely an insulator or a semiconductor. + + Total energy components: + | Sum of eigenvalues : -328.16249298 Ha -8929.75577487 eV + | XC energy correction : -41.75163831 Ha -1136.11988366 eV + | XC potential correction : 53.91500793 Ha 1467.10201098 eV + | Free-atom electrostatic energy: -263.83177839 Ha -7179.22796514 eV + | Hartree energy correction : -0.81671611 Ha -22.22397621 eV + | Entropy correction : -0.00000000 Ha -0.00000000 eV + | --------------------------- + | Total energy : -580.64761787 Ha -15800.22558889 eV + | Total energy, T -> 0 : -580.64761787 Ha -15800.22558889 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -580.64761787 Ha -15800.22558889 eV + + Derived energy quantities: + | Kinetic energy : 582.12301570 Ha 15840.37320663 eV + | Electrostatic energy : -1121.01899526 Ha -30504.47891186 eV + | Energy correction for multipole + | error in Hartree potential : 0.01840955 Ha 0.50094923 eV + | Sum of eigenvalues per atom : -4464.87788744 eV + | Total energy (T->0) per atom : -7900.11279444 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -7900.11279444 eV + Evaluating new KS density using the density matrix + Evaluating density matrix + Time summed over all CPUs for getting density from density matrix: real work 0.805 s, elapsed 0.805 s + Integration grid: deviation in total charge ( - N_e) = 2.842171E-14 + + Self-consistency convergence accuracy: + | Change of charge density : 0.6472E-05 + | Change of sum of eigenvalues : 0.1492E-02 eV + | Change of total energy : -0.9144E-06 eV + + +------------------------------------------------------------ + End self-consistency iteration # 6 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 1.775 s 1.785 s + | Charge density update : 0.802 s 0.806 s + | Density mixing & preconditioning : 0.178 s 0.178 s + | Hartree multipole update : 0.001 s 0.001 s + | Hartree multipole summation : 0.392 s 0.394 s + | Integration : 0.398 s 0.401 s + | Solution of K.-S. eqns. : 0.005 s 0.004 s + | Total energy evaluation : 0.000 s 0.001 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 1.569 MB (on task 0) + | Maximum: 1.569 MB (on task 0) + | Average: 1.569 MB + | Peak value for overall tracked memory usage: + | Minimum: 14.236 MB (on task 0 after allocating d_wave) + | Maximum: 14.236 MB (on task 0 after allocating d_wave) + | Average: 14.236 MB + | Largest tracked array allocation so far: + | Minimum: 3.456 MB (hamiltonian_shell on task 0) + | Maximum: 3.456 MB (hamiltonian_shell on task 0) + | Average: 3.456 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + +------------------------------------------------------------ + Begin self-consistency iteration # 7 + + Date : 20230628, Time : 104304.093 +------------------------------------------------------------ + Pulay mixing of updated and previous charge densities. + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 28.0000000000 + | Integrated number of electrons on 3D grid : 28.0000000212 + | Charge integration error : 0.0000000212 + | Normalization factor for density and gradient : 0.9999999992 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = 0.804936E-13 + | Sum of charges compensated after spline to logarithmic grids = -0.695777E-04 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = 0.000000E+00 + Summing up the Hartree potential. + Time summed over all CPUs for potential: real work 0.392 s, elapsed 0.392 s + | RMS charge density error from multipole expansion : 0.138148E-01 + | Average real-space part of the electrostatic potential : 0.44087905 eV + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.401 s, elapsed 0.401 s + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.000 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -5.00860015 eV + What follows are estimated values for band gap, HOMO, LUMO, etc. + | They are estimated on a discrete k-point grid and not necessarily exact. + | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. + + Highest occupied state (VBM) at -5.24626186 eV (relative to internal zero) + | Occupation number: 2.00000000 + | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + + Lowest unoccupied state (CBM) at -4.41782925 eV (relative to internal zero) + | Occupation number: 0.00000000 + | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) + + ESTIMATED overall HOMO-LUMO gap: 0.82843261 eV between HOMO at k-point 1 and LUMO at k-point 4 + | This appears to be an indirect band gap. + | Smallest direct gap : 2.27814005 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, + this system is most likely an insulator or a semiconductor. + + Total energy components: + | Sum of eigenvalues : -328.16247288 Ha -8929.75522800 eV + | XC energy correction : -41.75164027 Ha -1136.11993695 eV + | XC potential correction : 53.91501052 Ha 1467.10208164 eV + | Free-atom electrostatic energy: -263.83177839 Ha -7179.22796514 eV + | Hartree energy correction : -0.81673685 Ha -22.22454051 eV + | Entropy correction : -0.00000000 Ha -0.00000000 eV + | --------------------------- + | Total energy : -580.64761787 Ha -15800.22558896 eV + | Total energy, T -> 0 : -580.64761787 Ha -15800.22558896 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -580.64761787 Ha -15800.22558896 eV + + Derived energy quantities: + | Kinetic energy : 582.12304709 Ha 15840.37406077 eV + | Electrostatic energy : -1121.01902469 Ha -30504.47971278 eV + | Energy correction for multipole + | error in Hartree potential : 0.01840953 Ha 0.50094889 eV + | Sum of eigenvalues per atom : -4464.87761400 eV + | Total energy (T->0) per atom : -7900.11279448 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -7900.11279448 eV + Evaluating new KS density using the density matrix + Evaluating density matrix + Time summed over all CPUs for getting density from density matrix: real work 0.807 s, elapsed 0.807 s + Integration grid: deviation in total charge ( - N_e) = 0.000000E+00 + + Self-consistency convergence accuracy: + | Change of charge density : 0.3201E-05 + | Change of sum of eigenvalues : 0.5469E-03 eV + | Change of total energy : -0.6885E-07 eV + + +------------------------------------------------------------ + End self-consistency iteration # 7 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 1.777 s 1.788 s + | Charge density update : 0.803 s 0.808 s + | Density mixing & preconditioning : 0.178 s 0.180 s + | Hartree multipole update : 0.001 s 0.001 s + | Hartree multipole summation : 0.392 s 0.394 s + | Integration : 0.398 s 0.401 s + | Solution of K.-S. eqns. : 0.005 s 0.004 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 1.569 MB (on task 0) + | Maximum: 1.569 MB (on task 0) + | Average: 1.569 MB + | Peak value for overall tracked memory usage: + | Minimum: 14.236 MB (on task 0 after allocating d_wave) + | Maximum: 14.236 MB (on task 0 after allocating d_wave) + | Average: 14.236 MB + | Largest tracked array allocation so far: + | Minimum: 3.456 MB (hamiltonian_shell on task 0) + | Maximum: 3.456 MB (hamiltonian_shell on task 0) + | Average: 3.456 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + +------------------------------------------------------------ + Begin self-consistency iteration # 8 + + Date : 20230628, Time : 104305.881 +------------------------------------------------------------ + Pulay mixing of updated and previous charge densities. + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 28.0000000000 + | Integrated number of electrons on 3D grid : 27.9999999720 + | Charge integration error : -0.0000000280 + | Normalization factor for density and gradient : 1.0000000010 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = 0.113845E-12 + | Sum of charges compensated after spline to logarithmic grids = -0.695777E-04 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = 0.000000E+00 + Summing up the Hartree potential. + Time summed over all CPUs for potential: real work 0.391 s, elapsed 0.391 s + | RMS charge density error from multipole expansion : 0.138147E-01 + | Average real-space part of the electrostatic potential : 0.44087717 eV + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.400 s, elapsed 0.400 s + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.000 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -5.00860220 eV + What follows are estimated values for band gap, HOMO, LUMO, etc. + | They are estimated on a discrete k-point grid and not necessarily exact. + | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. + + Highest occupied state (VBM) at -5.24626423 eV (relative to internal zero) + | Occupation number: 2.00000000 + | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + + Lowest unoccupied state (CBM) at -4.41783017 eV (relative to internal zero) + | Occupation number: 0.00000000 + | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) + + ESTIMATED overall HOMO-LUMO gap: 0.82843406 eV between HOMO at k-point 1 and LUMO at k-point 4 + | This appears to be an indirect band gap. + | Smallest direct gap : 2.27813974 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, + this system is most likely an insulator or a semiconductor. + + Total energy components: + | Sum of eigenvalues : -328.16247913 Ha -8929.75539800 eV + | XC energy correction : -41.75163983 Ha -1136.11992500 eV + | XC potential correction : 53.91500993 Ha 1467.10206565 eV + | Free-atom electrostatic energy: -263.83177839 Ha -7179.22796514 eV + | Hartree energy correction : -0.81673045 Ha -22.22436629 eV + | Entropy correction : -0.00000000 Ha -0.00000000 eV + | --------------------------- + | Total energy : -580.64761787 Ha -15800.22558879 eV + | Total energy, T -> 0 : -580.64761787 Ha -15800.22558879 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -580.64761787 Ha -15800.22558879 eV + + Derived energy quantities: + | Kinetic energy : 582.12304576 Ha 15840.37402446 eV + | Electrostatic energy : -1121.01902379 Ha -30504.47968825 eV + | Energy correction for multipole + | error in Hartree potential : 0.01840953 Ha 0.50094875 eV + | Sum of eigenvalues per atom : -4464.87769900 eV + | Total energy (T->0) per atom : -7900.11279439 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -7900.11279439 eV + Evaluating new KS density using the density matrix + Evaluating density matrix + Time summed over all CPUs for getting density from density matrix: real work 0.808 s, elapsed 0.808 s + Integration grid: deviation in total charge ( - N_e) = -3.907985E-14 + + Self-consistency convergence accuracy: + | Change of charge density : 0.6371E-06 + | Change of sum of eigenvalues : -0.1700E-03 eV + | Change of total energy : 0.1710E-06 eV + + +------------------------------------------------------------ + End self-consistency iteration # 8 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 1.778 s 1.789 s + | Charge density update : 0.804 s 0.809 s + | Density mixing & preconditioning : 0.178 s 0.180 s + | Hartree multipole update : 0.001 s 0.001 s + | Hartree multipole summation : 0.392 s 0.394 s + | Integration : 0.398 s 0.400 s + | Solution of K.-S. eqns. : 0.005 s 0.005 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 1.569 MB (on task 0) + | Maximum: 1.569 MB (on task 0) + | Average: 1.569 MB + | Peak value for overall tracked memory usage: + | Minimum: 14.236 MB (on task 0 after allocating d_wave) + | Maximum: 14.236 MB (on task 0 after allocating d_wave) + | Average: 14.236 MB + | Largest tracked array allocation so far: + | Minimum: 3.456 MB (hamiltonian_shell on task 0) + | Maximum: 3.456 MB (hamiltonian_shell on task 0) + | Average: 3.456 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + +------------------------------------------------------------ + Begin self-consistency iteration # 9 + + Date : 20230628, Time : 104307.670 +------------------------------------------------------------ + Pulay mixing of updated and previous charge densities. + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 28.0000000000 + | Integrated number of electrons on 3D grid : 28.0000000003 + | Charge integration error : 0.0000000003 + | Normalization factor for density and gradient : 1.0000000000 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = 0.601429E-13 + | Sum of charges compensated after spline to logarithmic grids = -0.695777E-04 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = 0.000000E+00 + Summing up the Hartree potential. + Time summed over all CPUs for potential: real work 0.391 s, elapsed 0.391 s + | RMS charge density error from multipole expansion : 0.138147E-01 + | Average real-space part of the electrostatic potential : 0.44087721 eV + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.401 s, elapsed 0.401 s + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.000 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -5.00860218 eV + What follows are estimated values for band gap, HOMO, LUMO, etc. + | They are estimated on a discrete k-point grid and not necessarily exact. + | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. + + Highest occupied state (VBM) at -5.24626421 eV (relative to internal zero) + | Occupation number: 2.00000000 + | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + + Lowest unoccupied state (CBM) at -4.41783015 eV (relative to internal zero) + | Occupation number: 0.00000000 + | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) + + ESTIMATED overall HOMO-LUMO gap: 0.82843407 eV between HOMO at k-point 1 and LUMO at k-point 4 + | This appears to be an indirect band gap. + | Smallest direct gap : 2.27813973 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, + this system is most likely an insulator or a semiconductor. + + Total energy components: + | Sum of eigenvalues : -328.16247910 Ha -8929.75539715 eV + | XC energy correction : -41.75163984 Ha -1136.11992507 eV + | XC potential correction : 53.91500994 Ha 1467.10206572 eV + | Free-atom electrostatic energy: -263.83177839 Ha -7179.22796514 eV + | Hartree energy correction : -0.81673048 Ha -22.22436715 eV + | Entropy correction : -0.00000000 Ha -0.00000000 eV + | --------------------------- + | Total energy : -580.64761787 Ha -15800.22558879 eV + | Total energy, T -> 0 : -580.64761787 Ha -15800.22558879 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -580.64761787 Ha -15800.22558879 eV + + Derived energy quantities: + | Kinetic energy : 582.12304580 Ha 15840.37402565 eV + | Electrostatic energy : -1121.01902383 Ha -30504.47968937 eV + | Energy correction for multipole + | error in Hartree potential : 0.01840953 Ha 0.50094879 eV + | Sum of eigenvalues per atom : -4464.87769858 eV + | Total energy (T->0) per atom : -7900.11279439 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -7900.11279439 eV + Preliminary charge convergence reached. Turning off preconditioner. + + Evaluating new KS density using the density matrix + Evaluating density matrix + Time summed over all CPUs for getting density from density matrix: real work 0.806 s, elapsed 0.806 s + Integration grid: deviation in total charge ( - N_e) = 7.105427E-15 + + Self-consistency convergence accuracy: + | Change of charge density : 0.1012E-07 + | Change of sum of eigenvalues : 0.8489E-06 eV + | Change of total energy : -0.1237E-10 eV + + Electronic self-consistency reached - switching on the force computation. + + Electronic self-consistency reached - switching on the analytical stress tensor computation. + + +------------------------------------------------------------ + End self-consistency iteration # 9 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 1.776 s 1.786 s + | Charge density & force component update : 0.802 s 0.807 s + | Density mixing : 0.178 s 0.179 s + | Hartree multipole update : 0.001 s 0.001 s + | Hartree multipole summation : 0.392 s 0.394 s + | Hartree pot. SCF incomplete forces : 0.926 s 0.931 s + | Integration : 0.398 s 0.401 s + | Solution of K.-S. eqns. : 0.005 s 0.004 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 1.569 MB (on task 0) + | Maximum: 1.569 MB (on task 0) + | Average: 1.569 MB + | Peak value for overall tracked memory usage: + | Minimum: 14.236 MB (on task 0 after allocating d_wave) + | Maximum: 14.236 MB (on task 0 after allocating d_wave) + | Average: 14.236 MB + | Largest tracked array allocation so far: + | Minimum: 3.456 MB (hamiltonian_shell on task 0) + | Maximum: 3.456 MB (hamiltonian_shell on task 0) + | Average: 3.456 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + +------------------------------------------------------------ + Begin self-consistency iteration # 10 + + Date : 20230628, Time : 104309.457 +------------------------------------------------------------ + Pulay mixing of updated and previous charge densities. + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 28.0000000000 + | Integrated number of electrons on 3D grid : 28.0000000000 + | Charge integration error : 0.0000000000 + | Normalization factor for density and gradient : 1.0000000000 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = 0.115654E-13 + | Sum of charges compensated after spline to logarithmic grids = -0.695777E-04 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = 0.000000E+00 + Summing up the Hartree potential. + Time summed over all CPUs for potential: real work 1.652 s, elapsed 1.652 s + | RMS charge density error from multipole expansion : 0.138147E-01 + | Average real-space part of the electrostatic potential : 0.44087721 eV + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.401 s, elapsed 0.401 s + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.000 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -5.00860218 eV + What follows are estimated values for band gap, HOMO, LUMO, etc. + | They are estimated on a discrete k-point grid and not necessarily exact. + | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. + + Highest occupied state (VBM) at -5.24626422 eV (relative to internal zero) + | Occupation number: 2.00000000 + | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + + Lowest unoccupied state (CBM) at -4.41783015 eV (relative to internal zero) + | Occupation number: 0.00000000 + | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) + + ESTIMATED overall HOMO-LUMO gap: 0.82843407 eV between HOMO at k-point 1 and LUMO at k-point 4 + | This appears to be an indirect band gap. + | Smallest direct gap : 2.27813973 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, + this system is most likely an insulator or a semiconductor. + + Total energy components: + | Sum of eigenvalues : -328.16247910 Ha -8929.75539713 eV + | XC energy correction : -41.75163984 Ha -1136.11992507 eV + | XC potential correction : 53.91500994 Ha 1467.10206572 eV + | Free-atom electrostatic energy: -263.83177839 Ha -7179.22796514 eV + | Hartree energy correction : -0.81673048 Ha -22.22436717 eV + | Entropy correction : -0.00000000 Ha -0.00000000 eV + | --------------------------- + | Total energy : -580.64761787 Ha -15800.22558879 eV + | Total energy, T -> 0 : -580.64761787 Ha -15800.22558879 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -580.64761787 Ha -15800.22558879 eV + + Derived energy quantities: + | Kinetic energy : 582.12304581 Ha 15840.37402572 eV + | Electrostatic energy : -1121.01902384 Ha -30504.47968944 eV + | Energy correction for multipole + | error in Hartree potential : 0.01840953 Ha 0.50094879 eV + | Sum of eigenvalues per atom : -4464.87769857 eV + | Total energy (T->0) per atom : -7900.11279439 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -7900.11279439 eV + Evaluating new KS density using the density matrix + Evaluating density matrix + Time summed over all CPUs for getting density from density matrix: real work 0.806 s, elapsed 0.806 s + Integration grid: deviation in total charge ( - N_e) = -1.065814E-14 + + atomic forces [eV/Ang]: + ----------------------- + atom # 1 + Hellmann-Feynman : -0.542618E-06 0.229221E-06 0.236877E-06 + Ionic forces : 0.000000E+00 0.000000E+00 0.000000E+00 + Multipole : -0.108365E-07 -0.318034E-08 -0.208258E-08 + Hartree pot. SCF incomplete : 0.256616E-09 -0.279956E-10 -0.321834E-10 + Pulay + GGA : 0.000000E+00 0.000000E+00 0.000000E+00 + ---------------------------------------------------------------- + Total forces( 1) : -0.553198E-06 0.226012E-06 0.234762E-06 + atom # 2 + Hellmann-Feynman : 0.547917E-06 -0.227080E-06 -0.236616E-06 + Ionic forces : 0.000000E+00 0.000000E+00 0.000000E+00 + Multipole : 0.108364E-07 0.317865E-08 0.208329E-08 + Hartree pot. SCF incomplete : -0.278235E-09 0.101879E-10 0.602639E-10 + Pulay + GGA : 0.000000E+00 0.000000E+00 0.000000E+00 + ---------------------------------------------------------------- + Total forces( 2) : 0.558475E-06 -0.223891E-06 -0.234472E-06 + + + Self-consistency convergence accuracy: + | Change of charge density : 0.7985E-09 + | Change of sum of eigenvalues : 0.2060E-07 eV + | Change of total energy : 0.1237E-10 eV + | Change of forces : 0.6442E-06 eV/A + + +------------------------------------------------------------ + End self-consistency iteration # 10 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 3.799 s 3.819 s + | Charge density & force component update : 0.802 s 0.807 s + | Density mixing : 0.002 s 0.002 s + | Hartree multipole update : 0.001 s 0.001 s + | Hartree multipole summation : 1.648 s 1.655 s + | Hartree pot. SCF incomplete forces : 0.943 s 0.948 s + | Integration : 0.398 s 0.401 s + | Solution of K.-S. eqns. : 0.005 s 0.005 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 1.569 MB (on task 0) + | Maximum: 1.569 MB (on task 0) + | Average: 1.569 MB + | Peak value for overall tracked memory usage: + | Minimum: 14.236 MB (on task 0 after allocating d_wave) + | Maximum: 14.236 MB (on task 0 after allocating d_wave) + | Average: 14.236 MB + | Largest tracked array allocation so far: + | Minimum: 3.456 MB (hamiltonian_shell on task 0) + | Maximum: 3.456 MB (hamiltonian_shell on task 0) + | Average: 3.456 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + +------------------------------------------------------------ + Begin self-consistency iteration # 11 + + Date : 20230628, Time : 104313.276 +------------------------------------------------------------ + Pulay mixing of updated and previous charge densities. + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 28.0000000000 + | Integrated number of electrons on 3D grid : 28.0000000000 + | Charge integration error : 0.0000000000 + | Normalization factor for density and gradient : 1.0000000000 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = -0.137138E-13 + | Sum of charges compensated after spline to logarithmic grids = -0.695777E-04 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = -0.135922E-13 + Summing up the Hartree potential. + Time summed over all CPUs for potential: real work 1.652 s, elapsed 1.652 s + | RMS charge density error from multipole expansion : 0.138147E-01 + | Average real-space part of the electrostatic potential : 0.44087721 eV + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.401 s, elapsed 0.401 s + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.000 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -5.00860218 eV + What follows are estimated values for band gap, HOMO, LUMO, etc. + | They are estimated on a discrete k-point grid and not necessarily exact. + | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. + + Highest occupied state (VBM) at -5.24626422 eV (relative to internal zero) + | Occupation number: 2.00000000 + | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + + Lowest unoccupied state (CBM) at -4.41783015 eV (relative to internal zero) + | Occupation number: 0.00000000 + | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) + + ESTIMATED overall HOMO-LUMO gap: 0.82843407 eV between HOMO at k-point 1 and LUMO at k-point 4 + | This appears to be an indirect band gap. + | Smallest direct gap : 2.27813973 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, + this system is most likely an insulator or a semiconductor. + + Total energy components: + | Sum of eigenvalues : -328.16247909 Ha -8929.75539708 eV + | XC energy correction : -41.75163984 Ha -1136.11992508 eV + | XC potential correction : 53.91500994 Ha 1467.10206573 eV + | Free-atom electrostatic energy: -263.83177839 Ha -7179.22796514 eV + | Hartree energy correction : -0.81673048 Ha -22.22436722 eV + | Entropy correction : -0.00000000 Ha -0.00000000 eV + | --------------------------- + | Total energy : -580.64761787 Ha -15800.22558879 eV + | Total energy, T -> 0 : -580.64761787 Ha -15800.22558879 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -580.64761787 Ha -15800.22558879 eV + + Derived energy quantities: + | Kinetic energy : 582.12304581 Ha 15840.37402582 eV + | Electrostatic energy : -1121.01902384 Ha -30504.47968953 eV + | Energy correction for multipole + | error in Hartree potential : 0.01840953 Ha 0.50094879 eV + | Sum of eigenvalues per atom : -4464.87769854 eV + | Total energy (T->0) per atom : -7900.11279439 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -7900.11279439 eV + Evaluating new KS density using the density matrix + Evaluating density matrix + Time summed over all CPUs for getting density from density matrix: real work 0.807 s, elapsed 0.807 s + + Evaluating density-matrix-based force terms: batch-based integration + Evaluating density matrix + Evaluating density matrix + Integration grid: deviation in total charge ( - N_e) = -3.552714E-14 + + atomic forces [eV/Ang]: + ----------------------- + atom # 1 + Hellmann-Feynman : -0.542369E-06 0.229192E-06 0.236855E-06 + Ionic forces : 0.000000E+00 0.000000E+00 0.000000E+00 + Multipole : -0.108372E-07 -0.317971E-08 -0.208314E-08 + Hartree pot. SCF incomplete : 0.204530E-09 0.426881E-11 -0.411103E-10 + Pulay + GGA : 0.332299E-06 -0.197292E-06 -0.199532E-06 + ---------------------------------------------------------------- + Total forces( 1) : -0.220703E-06 0.287241E-07 0.351991E-07 + atom # 2 + Hellmann-Feynman : 0.547666E-06 -0.227067E-06 -0.236586E-06 + Ionic forces : 0.000000E+00 0.000000E+00 0.000000E+00 + Multipole : 0.108385E-07 0.318083E-08 0.208178E-08 + Hartree pot. SCF incomplete : -0.232279E-09 0.152712E-10 0.687008E-10 + Pulay + GGA : -0.334454E-06 0.187898E-06 0.189976E-06 + ---------------------------------------------------------------- + Total forces( 2) : 0.223819E-06 -0.359731E-07 -0.444596E-07 + + + Analytical stress tensor components [eV] xx yy zz xy xz yz + ----------------------------------------------------------------------------------------------------------------------------------------------------------- + Nuclear Hellmann-Feynman : -0.1215583460E+02 -0.1215602163E+02 -0.1215602163E+02 0.1223944233E-07 0.1859811812E-08 -0.2081627194E-06 + Multipole Hellmann-Feynman : -0.2784699655E+02 -0.2784700724E+02 -0.2784700725E+02 0.1401674465E-06 0.9598284490E-07 -0.7751689496E-06 + On-site Multipole corrections : -0.2839687132E+00 -0.2839687135E+00 -0.2839687135E+00 0.3702642801E-10 0.4462349828E-10 0.5734027137E-10 + Strain deriv. of the orbitals : 0.4017672923E+02 0.4017692687E+02 0.4017692687E+02 -0.2331229685E-06 -0.1839374584E-06 0.1063722946E-05 + ----------------------------------------------------------------------------------------------------------------------------------------------------------- + Sum of all contributions : -0.1100706416E+00 -0.1100707148E+00 -0.1100707131E+00 -0.8067905325E-07 -0.8605017815E-07 0.8044861777E-07 + + +-------------------------------------------------------------------+ + | Analytical stress tensor - Symmetrized | + | Cartesian components [eV/A**3] | + +-------------------------------------------------------------------+ + | x y z | + | | + | x -0.00247987 -0.00000000 -0.00000000 | + | y -0.00000000 -0.00247987 0.00000000 | + | z -0.00000000 0.00000000 -0.00247987 | + | | + | Pressure: 0.00247987 [eV/A**3] | + | | + +-------------------------------------------------------------------+ + + + Self-consistency convergence accuracy: + | Change of charge density : 0.5403E-09 + | Change of sum of eigenvalues : 0.5458E-07 eV + | Change of total energy : -0.2166E-10 eV + | Change of forces : 0.2508E-09 eV/A + + Writing Kohn-Sham eigenvalues. + K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + + State Occupation Eigenvalue [Ha] Eigenvalue [eV] + 1 2.00000 -65.747889 -1789.09108 + 2 2.00000 -65.747889 -1789.09108 + 3 2.00000 -5.105889 -138.93830 + 4 2.00000 -5.105720 -138.93370 + 5 2.00000 -3.489648 -94.95816 + 6 2.00000 -3.489648 -94.95816 + 7 2.00000 -3.489648 -94.95816 + 8 2.00000 -3.489244 -94.94715 + 9 2.00000 -3.489244 -94.94715 + 10 2.00000 -3.489244 -94.94715 + 11 2.00000 -0.609526 -16.58603 + 12 2.00000 -0.192797 -5.24626 + 13 2.00000 -0.192797 -5.24626 + 14 2.00000 -0.192797 -5.24626 + 15 0.00000 -0.109077 -2.96812 + 16 0.00000 -0.104155 -2.83419 + 17 0.00000 -0.104155 -2.83419 + 18 0.00000 -0.104155 -2.83419 + 19 0.00000 0.092547 2.51834 + 20 0.00000 0.092547 2.51834 + + What follows are estimated values for band gap, HOMO, LUMO, etc. + | They are estimated on a discrete k-point grid and not necessarily exact. + | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. + + Highest occupied state (VBM) at -5.24626422 eV (relative to internal zero) + | Occupation number: 2.00000000 + | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + + Lowest unoccupied state (CBM) at -4.41783015 eV (relative to internal zero) + | Occupation number: 0.00000000 + | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) + + ESTIMATED overall HOMO-LUMO gap: 0.82843407 eV between HOMO at k-point 1 and LUMO at k-point 4 + | This appears to be an indirect band gap. + | Smallest direct gap : 2.27813973 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, + this system is most likely an insulator or a semiconductor. + | Chemical Potential : -5.00860218 eV + + Self-consistency cycle converged. + + +------------------------------------------------------------ + End self-consistency iteration # 11 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 19.043 s 19.167 s + | Charge density & force component update : 16.048 s 16.157 s + | Density mixing : 0.002 s 0.002 s + | Hartree multipole update : 0.001 s 0.001 s + | Hartree multipole summation : 1.648 s 1.656 s + | Hartree pot. SCF incomplete forces : 0.941 s 0.946 s + | Integration : 0.398 s 0.401 s + | Solution of K.-S. eqns. : 0.005 s 0.004 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 1.569 MB (on task 0) + | Maximum: 1.569 MB (on task 0) + | Average: 1.569 MB + | Peak value for overall tracked memory usage: + | Minimum: 14.236 MB (on task 0 after allocating d_wave) + | Maximum: 14.236 MB (on task 0 after allocating d_wave) + | Average: 14.236 MB + | Largest tracked array allocation so far: + | Minimum: 3.456 MB (hamiltonian_shell on task 0) + | Maximum: 3.456 MB (hamiltonian_shell on task 0) + | Average: 3.456 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + Removing unitary transformations (pure translations, rotations) from forces on atoms. + Atomic forces before filtering: + | Net force on center of mass : 0.311585E-08 -0.724909E-08 -0.926049E-08 eV/A + Atomic forces after filtering: + | Net force on center of mass : 0.000000E+00 0.000000E+00 0.000000E+00 eV/A + + Energy and forces in a compact form: + | Total energy uncorrected : -0.158002255887876E+05 eV + | Total energy corrected : -0.158002255887876E+05 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -0.158002255887876E+05 eV + Total atomic forces (unitary forces cleaned) [eV/Ang]: + | 1 -0.222260903726852E-06 0.323486013650826E-07 0.398293064328442E-07 + | 2 0.222260903726852E-06 -0.323486013650826E-07 -0.398293064328442E-07 + + ------------------------------------ + Start decomposition of the XC Energy + ------------------------------------ + X and C from original XC functional choice + Hartree-Fock Energy : 0.000000000 Ha 0.000000000 eV + X Energy : -40.669204423 Ha -1106.665358876 eV + C Energy : -1.082435412 Ha -29.454566200 eV + XC Energy w/o HF : -41.751639836 Ha -1136.119925076 eV + Total XC Energy : -41.751639836 Ha -1136.119925076 eV + ------------------------------------ + LDA X and C from self-consistent density + X Energy LDA : -37.600440540 Ha -1023.160044893 eV + C Energy LDA : -2.144134624 Ha -58.344871663 eV + ------------------------------------ + End decomposition of the XC Energy + ------------------------------------ + +------------------------------------------------------------ + Relaxation / MD: End force evaluation. : max(cpu_time) wall_clock(cpu1) + | Time for this force evaluation : 40.030 s 40.277 s + +------------------------------------------------------------ + Geometry optimization: Attempting to predict improved coordinates. + + +-------------------------------------------------------------------+ + | Generalized derivatives on lattice vectors [eV/A] | + +-------------------------------------------------------------------+ + |lattice_vector 0.01958407 -0.01958409 -0.01958409 | + |lattice_vector -0.01958411 0.01958412 -0.01958415 | + |lattice_vector -0.01958410 -0.01958415 0.01958412 | + +-------------------------------------------------------------------+ + | Forces on lattice vectors cleaned from atomic contributions [eV/A]| + +-------------------------------------------------------------------+ + |lattice_vector -0.01958407 0.01958409 0.01958409 | + |lattice_vector 0.01958411 -0.01958412 0.01958415 | + |lattice_vector 0.01958410 0.01958415 -0.01958412 | + +-------------------------------------------------------------------+ + Removing unitary transformations (pure translations, rotations) from forces on atoms. + Atomic forces before filtering: + | Net force on center of mass : 0.000000E+00 0.000000E+00 0.000000E+00 eV/A + Atomic forces after filtering: + | Net force on center of mass : 0.000000E+00 0.000000E+00 0.000000E+00 eV/A + Net remaining forces (excluding translations, rotations) in present geometry: + || Forces on atoms || = 0.222261E-06 eV/A. + || Forces on lattice || = 0.195841E-01 eV/A^3. + Maximum force component is 0.195841E-01 eV/A. + Present geometry is not yet converged. + + Relaxation step number 3: Predicting new coordinates. + + Advancing geometry using trust radius method. + | True / expected gain: -1.95E-02 eV / -2.04E-02 eV = 0.9568 + | Harmonic / expected gain: -2.26E-02 eV / -2.04E-02 eV = 1.1090 + | Hessian has 0 negative and 3 zero eigenvalues. + | Positive eigenvalues (eV/A^2): 3.58E+00 ... 3.02E+01 + | Use Quasi-Newton step of length |H^-1 F| = 1.13E-02 A. + Finished advancing geometry + | Time : 0.000 s + Updated atomic structure: + x [A] y [A] z [A] + lattice_vector 0.00000007 2.81482492 2.81482492 + lattice_vector 2.81482482 -0.00000004 2.81482486 + lattice_vector 2.81482482 2.81482486 -0.00000004 + + atom -0.00000001 0.00000000 0.00000000 Si + atom 1.40741244 1.40741244 1.40741244 Si + + Fractional coordinates: + L1 L2 L3 + atom_frac 0.00000000 -0.00000000 -0.00000000 Si + atom_frac 0.25000000 0.25000000 0.25000000 Si +------------------------------------------------------------ + Writing the current geometry to file "geometry.in.next_step". + Writing estimated Hessian matrix to file 'hessian.aims' + + Quantities derived from the lattice vectors: + | Reciprocal lattice vector 1: -1.116088 1.116088 1.116088 + | Reciprocal lattice vector 2: 1.116088 -1.116088 1.116088 + | Reciprocal lattice vector 3: 1.116088 1.116088 -1.116088 + | Unit cell volume : 0.446051E+02 A^3 + + Range separation radius for Ewald summation (hartree_convergence_parameter): 4.04522276 bohr. + +------------------------------------------------------------ + Begin self-consistency loop: Re-initialization. + + Date : 20230628, Time : 104332.450 +------------------------------------------------------------ + + Initializing index lists of integration centers etc. from given atomic structure: + Mapping all atomic coordinates to central unit cell. + + Initializing the k-points + Using symmetry for reducing the k-points + | k-points reduced from: 8 to 8 + | Number of k-points : 8 + The eigenvectors in the calculations are REAL. + | K-points in task 0: 8 + | Number of basis functions in the Hamiltonian integrals : 1771 + | Number of basis functions in a single unit cell : 50 + | Number of centers in hartree potential : 708 + | Number of centers in hartree multipole : 318 + | Number of centers in electron density summation: 190 + | Number of centers in basis integrals : 198 + | Number of centers in integrals : 101 + | Number of centers in hamiltonian : 190 + | Consuming 14 KiB for k_phase. + | Number of super-cells (origin) [n_cells] : 2197 + | Number of super-cells (after PM_index) [n_cells] : 112 + | Number of super-cells in hamiltonian [n_cells_in_hamiltonian]: 112 + | Size of matrix packed + index [n_hamiltonian_matrix_size] : 82583 + Partitioning the integration grid into batches with parallel hashing+maxmin method. + | Number of batches: 128 + | Maximal batch size: 90 + | Minimal batch size: 85 + | Average batch size: 87.562 + | Standard deviation of batch sizes: 1.493 + + Integration load balanced across 1 MPI tasks. + Work distribution over tasks is as follows: + Initializing partition tables, free-atom densities, potentials, etc. across the integration grid (initialize_grid_storage). + | Species 1: outer_partition_radius set to 5.000694715736543 AA . + | The sparse table of interatomic distances needs 194.62 kbyte instead of 313.63 kbyte of memory. + | Net number of integration points: 11208 + | of which are non-zero points : 9876 + | Numerical average free-atom electrostatic potential : -11.78489284 eV + Renormalizing the initial density to the exact electron count on the 3D integration grid. + | Initial density: Formal number of electrons (from input files) : 28.0000000000 + | Integrated number of electrons on 3D grid : 28.0037489641 + | Charge integration error : 0.0037489641 + | Normalization factor for density and gradient : 0.9998661263 + Renormalizing the free-atom superposition density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 28.0000000000 + | Integrated number of electrons on 3D grid : 28.0037489641 + | Charge integration error : 0.0037489641 + | Normalization factor for density and gradient : 0.9998661263 + Obtaining max. number of non-zero basis functions in each batch (get_n_compute_maxes). + Calculating total energy contributions from superposition of free atom densities. + Initialize hartree_potential_storage + Integrating overlap matrix. + Time summed over all CPUs for integration: real work 0.254 s, elapsed 0.254 s + Orthonormalizing eigenvectors + + End scf reinitialization - timings : max(cpu_time) wall_clock(cpu1) + | Time for scf. reinitialization : 0.561 s 0.564 s + | Boundary condition initialization : 0.064 s 0.065 s + | Integration : 0.252 s 0.254 s + | Grid partitioning : 0.032 s 0.032 s + | Preloading free-atom quantities on grid : 0.174 s 0.175 s + | Free-atom superposition energy : 0.027 s 0.027 s + | K.-S. eigenvector reorthonormalization : 0.001 s 0.001 s +------------------------------------------------------------ + Evaluating new KS density using the density matrix + Evaluating density matrix + Time summed over all CPUs for getting density from density matrix: real work 0.802 s, elapsed 0.802 s + Integration grid: deviation in total charge ( - N_e) = -1.776357E-14 + + Time for density update prior : max(cpu_time) wall_clock(cpu1) + | self-consistency iterative process : 0.798 s 0.804 s + +------------------------------------------------------------ + Begin self-consistency iteration # 1 + + Date : 20230628, Time : 104333.818 +------------------------------------------------------------ + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 28.0000000000 + | Integrated number of electrons on 3D grid : 28.0000000000 + | Charge integration error : 0.0000000000 + | Normalization factor for density and gradient : 1.0000000000 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = 0.281885E-13 + | Sum of charges compensated after spline to logarithmic grids = -0.634484E-04 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = 0.281375E-13 + Summing up the Hartree potential. + | Estimated reciprocal-space cutoff momentum G_max: 2.30334413 bohr^-1 . + | Reciprocal lattice points for long-range Hartree potential: 58 + Time summed over all CPUs for potential: real work 0.393 s, elapsed 0.393 s + | RMS charge density error from multipole expansion : 0.137198E-01 + | Average real-space part of the electrostatic potential : 0.43641905 eV + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.398 s, elapsed 0.398 s + Decreasing sparse matrix size: + | Tolerance: 0.1000E-12 + Hamiltonian matrix + | Array has 74604 nonzero elements out of 82583 elements + | Sparsity factor is 0.097 + Overlap matrix + | Array has 68322 nonzero elements out of 82583 elements + | Sparsity factor is 0.173 + New size of hamiltonian matrix: 74633 + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Singularity check in k-point 1, task 0 (analysis for other k-points/tasks may follow below): + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.001 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -5.01844054 eV + Writing Kohn-Sham eigenvalues. + K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + + State Occupation Eigenvalue [Ha] Eigenvalue [eV] + 1 2.00000 -65.748529 -1789.10850 + 2 2.00000 -65.748529 -1789.10850 + 3 2.00000 -5.106185 -138.94637 + 4 2.00000 -5.106020 -138.94188 + 5 2.00000 -3.489964 -94.96676 + 6 2.00000 -3.489964 -94.96676 + 7 2.00000 -3.489964 -94.96676 + 8 2.00000 -3.489568 -94.95598 + 9 2.00000 -3.489568 -94.95598 + 10 2.00000 -3.489568 -94.95598 + 11 2.00000 -0.608175 -16.54927 + 12 2.00000 -0.192610 -5.24119 + 13 2.00000 -0.192610 -5.24119 + 14 2.00000 -0.192610 -5.24119 + 15 0.00000 -0.110839 -3.01608 + 16 0.00000 -0.104019 -2.83051 + 17 0.00000 -0.104019 -2.83051 + 18 0.00000 -0.104019 -2.83051 + 19 0.00000 0.092765 2.52427 + 20 0.00000 0.092765 2.52427 + + What follows are estimated values for band gap, HOMO, LUMO, etc. + | They are estimated on a discrete k-point grid and not necessarily exact. + | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. + + Highest occupied state (VBM) at -5.24118513 eV (relative to internal zero) + | Occupation number: 2.00000000 + | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + + Lowest unoccupied state (CBM) at -4.40418353 eV (relative to internal zero) + | Occupation number: 0.00000000 + | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) + + ESTIMATED overall HOMO-LUMO gap: 0.83700160 eV between HOMO at k-point 1 and LUMO at k-point 4 + | This appears to be an indirect band gap. + | Smallest direct gap : 2.22510843 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, + this system is most likely an insulator or a semiconductor. + + Total energy components: + | Sum of eigenvalues : -328.16494985 Ha -8929.82262971 eV + | XC energy correction : -41.74834478 Ha -1136.03026208 eV + | XC potential correction : 53.91061389 Ha 1466.98244316 eV + | Free-atom electrostatic energy: -263.84200016 Ha -7179.50611365 eV + | Hartree energy correction : -0.80293588 Ha -21.84899693 eV + | Entropy correction : -0.00000000 Ha -0.00000000 eV + | --------------------------- + | Total energy : -580.64761678 Ha -15800.22555921 eV + | Total energy, T -> 0 : -580.64761678 Ha -15800.22555921 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -580.64761678 Ha -15800.22555921 eV + + Derived energy quantities: + | Kinetic energy : 582.10394346 Ha 15839.85422458 eV + | Electrostatic energy : -1121.00321546 Ha -30504.04952171 eV + | Energy correction for multipole + | error in Hartree potential : 0.01825064 Ha 0.49662528 eV + | Sum of eigenvalues per atom : -4464.91131485 eV + | Total energy (T->0) per atom : -7900.11277960 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -7900.11277960 eV + Evaluating new KS density using the density matrix + Evaluating density matrix + Time summed over all CPUs for getting density from density matrix: real work 0.800 s, elapsed 0.800 s + Integration grid: deviation in total charge ( - N_e) = 6.039613E-14 + + Self-consistency convergence accuracy: + | Change of charge density : 0.1310E+00 + | Change of sum of eigenvalues : -0.8930E+04 eV + | Change of total energy : -0.1580E+05 eV + + +------------------------------------------------------------ + End self-consistency iteration # 1 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 1.595 s 1.601 s + | Charge density update : 0.800 s 0.801 s + | Density mixing & preconditioning : 0.000 s 0.000 s + | Hartree multipole update : 0.001 s 0.001 s + | Hartree multipole summation : 0.393 s 0.395 s + | Integration : 0.396 s 0.399 s + | Solution of K.-S. eqns. : 0.005 s 0.005 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 1.554 MB (on task 0) + | Maximum: 1.554 MB (on task 0) + | Average: 1.554 MB + | Peak value for overall tracked memory usage: + | Minimum: 14.236 MB (on task 0 after allocating d_wave) + | Maximum: 14.236 MB (on task 0 after allocating d_wave) + | Average: 14.236 MB + | Largest tracked array allocation so far: + | Minimum: 3.456 MB (hamiltonian_shell on task 0) + | Maximum: 3.456 MB (hamiltonian_shell on task 0) + | Average: 3.456 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + +------------------------------------------------------------ + Begin self-consistency iteration # 2 + + Date : 20230628, Time : 104335.419 +------------------------------------------------------------ + Pulay mixing of updated and previous charge densities. + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 28.0000000000 + | Integrated number of electrons on 3D grid : 27.9999917916 + | Charge integration error : -0.0000082084 + | Normalization factor for density and gradient : 1.0000002932 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = -0.429136E-13 + | Sum of charges compensated after spline to logarithmic grids = -0.634540E-04 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = 0.000000E+00 + Summing up the Hartree potential. + Time summed over all CPUs for potential: real work 0.390 s, elapsed 0.390 s + | RMS charge density error from multipole expansion : 0.137185E-01 + | Average real-space part of the electrostatic potential : 0.43644029 eV + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.396 s, elapsed 0.396 s + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.001 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -5.01850965 eV + What follows are estimated values for band gap, HOMO, LUMO, etc. + | They are estimated on a discrete k-point grid and not necessarily exact. + | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. + + Highest occupied state (VBM) at -5.24124683 eV (relative to internal zero) + | Occupation number: 2.00000000 + | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + + Lowest unoccupied state (CBM) at -4.40420932 eV (relative to internal zero) + | Occupation number: 0.00000000 + | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) + + ESTIMATED overall HOMO-LUMO gap: 0.83703751 eV between HOMO at k-point 1 and LUMO at k-point 4 + | This appears to be an indirect band gap. + | Smallest direct gap : 2.22513239 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, + this system is most likely an insulator or a semiconductor. + + Total energy components: + | Sum of eigenvalues : -328.16451174 Ha -8929.81070830 eV + | XC energy correction : -41.74840253 Ha -1136.03183343 eV + | XC potential correction : 53.91068936 Ha 1466.98449680 eV + | Free-atom electrostatic energy: -263.84200016 Ha -7179.50611365 eV + | Hartree energy correction : -0.80339175 Ha -21.86140183 eV + | Entropy correction : -0.00000000 Ha -0.00000000 eV + | --------------------------- + | Total energy : -580.64761682 Ha -15800.22556040 eV + | Total energy, T -> 0 : -580.64761682 Ha -15800.22556040 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -580.64761682 Ha -15800.22556040 eV + + Derived energy quantities: + | Kinetic energy : 582.10515597 Ha 15839.88721854 eV + | Electrostatic energy : -1121.00437027 Ha -30504.08094552 eV + | Energy correction for multipole + | error in Hartree potential : 0.01825039 Ha 0.49661835 eV + | Sum of eigenvalues per atom : -4464.90535415 eV + | Total energy (T->0) per atom : -7900.11278020 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -7900.11278020 eV + Evaluating new KS density using the density matrix + Evaluating density matrix + Time summed over all CPUs for getting density from density matrix: real work 0.798 s, elapsed 0.798 s + Integration grid: deviation in total charge ( - N_e) = -3.552714E-14 + + Self-consistency convergence accuracy: + | Change of charge density : 0.2454E-03 + | Change of sum of eigenvalues : 0.1192E-01 eV + | Change of total energy : -0.1196E-05 eV + + +------------------------------------------------------------ + End self-consistency iteration # 2 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 1.771 s 1.771 s + | Charge density update : 0.799 s 0.799 s + | Density mixing & preconditioning : 0.177 s 0.177 s + | Hartree multipole update : 0.001 s 0.001 s + | Hartree multipole summation : 0.393 s 0.392 s + | Integration : 0.396 s 0.397 s + | Solution of K.-S. eqns. : 0.005 s 0.005 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 1.554 MB (on task 0) + | Maximum: 1.554 MB (on task 0) + | Average: 1.554 MB + | Peak value for overall tracked memory usage: + | Minimum: 14.236 MB (on task 0 after allocating d_wave) + | Maximum: 14.236 MB (on task 0 after allocating d_wave) + | Average: 14.236 MB + | Largest tracked array allocation so far: + | Minimum: 3.456 MB (hamiltonian_shell on task 0) + | Maximum: 3.456 MB (hamiltonian_shell on task 0) + | Average: 3.456 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + +------------------------------------------------------------ + Begin self-consistency iteration # 3 + + Date : 20230628, Time : 104337.190 +------------------------------------------------------------ + Pulay mixing of updated and previous charge densities. + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 28.0000000000 + | Integrated number of electrons on 3D grid : 27.9999746841 + | Charge integration error : -0.0000253159 + | Normalization factor for density and gradient : 1.0000009041 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = -0.383018E-13 + | Sum of charges compensated after spline to logarithmic grids = -0.634724E-04 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = -0.383621E-13 + Summing up the Hartree potential. + Time summed over all CPUs for potential: real work 0.391 s, elapsed 0.391 s + | RMS charge density error from multipole expansion : 0.137142E-01 + | Average real-space part of the electrostatic potential : 0.43651485 eV + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.396 s, elapsed 0.396 s + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.001 s + Finished solving standard eigenproblem + | Time : 0.000 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -5.01873043 eV + What follows are estimated values for band gap, HOMO, LUMO, etc. + | They are estimated on a discrete k-point grid and not necessarily exact. + | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. + + Highest occupied state (VBM) at -5.24144412 eV (relative to internal zero) + | Occupation number: 2.00000000 + | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + + Lowest unoccupied state (CBM) at -4.40429028 eV (relative to internal zero) + | Occupation number: 0.00000000 + | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) + + ESTIMATED overall HOMO-LUMO gap: 0.83715384 eV between HOMO at k-point 1 and LUMO at k-point 4 + | This appears to be an indirect band gap. + | Smallest direct gap : 2.22520734 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, + this system is most likely an insulator or a semiconductor. + + Total energy components: + | Sum of eigenvalues : -328.16315258 Ha -8929.77372365 eV + | XC energy correction : -41.74857787 Ha -1136.03660464 eV + | XC potential correction : 53.91091893 Ha 1466.99074380 eV + | Free-atom electrostatic energy: -263.84200016 Ha -7179.50611365 eV + | Hartree energy correction : -0.80480531 Ha -21.89986660 eV + | Entropy correction : -0.00000000 Ha -0.00000000 eV + | --------------------------- + | Total energy : -580.64761698 Ha -15800.22556475 eV + | Total energy, T -> 0 : -580.64761698 Ha -15800.22556475 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -580.64761698 Ha -15800.22556475 eV + + Derived energy quantities: + | Kinetic energy : 582.10881200 Ha 15839.98670431 eV + | Electrostatic energy : -1121.00785112 Ha -30504.17566441 eV + | Energy correction for multipole + | error in Hartree potential : 0.01824968 Ha 0.49659904 eV + | Sum of eigenvalues per atom : -4464.88686183 eV + | Total energy (T->0) per atom : -7900.11278237 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -7900.11278237 eV + Evaluating new KS density using the density matrix + Evaluating density matrix + Time summed over all CPUs for getting density from density matrix: real work 0.799 s, elapsed 0.799 s + Integration grid: deviation in total charge ( - N_e) = -7.105427E-15 + + Self-consistency convergence accuracy: + | Change of charge density : 0.1866E-03 + | Change of sum of eigenvalues : 0.3698E-01 eV + | Change of total energy : -0.4348E-05 eV + + +------------------------------------------------------------ + End self-consistency iteration # 3 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 1.773 s 1.773 s + | Charge density update : 0.800 s 0.800 s + | Density mixing & preconditioning : 0.178 s 0.178 s + | Hartree multipole update : 0.001 s 0.001 s + | Hartree multipole summation : 0.393 s 0.393 s + | Integration : 0.396 s 0.396 s + | Solution of K.-S. eqns. : 0.005 s 0.005 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 1.554 MB (on task 0) + | Maximum: 1.554 MB (on task 0) + | Average: 1.554 MB + | Peak value for overall tracked memory usage: + | Minimum: 14.236 MB (on task 0 after allocating d_wave) + | Maximum: 14.236 MB (on task 0 after allocating d_wave) + | Average: 14.236 MB + | Largest tracked array allocation so far: + | Minimum: 3.456 MB (hamiltonian_shell on task 0) + | Maximum: 3.456 MB (hamiltonian_shell on task 0) + | Average: 3.456 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + +------------------------------------------------------------ + Begin self-consistency iteration # 4 + + Date : 20230628, Time : 104338.963 +------------------------------------------------------------ + Pulay mixing of updated and previous charge densities. + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 28.0000000000 + | Integrated number of electrons on 3D grid : 28.0000001275 + | Charge integration error : 0.0000001275 + | Normalization factor for density and gradient : 0.9999999954 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = -0.356423E-13 + | Sum of charges compensated after spline to logarithmic grids = -0.634774E-04 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = -0.355182E-13 + Summing up the Hartree potential. + Time summed over all CPUs for potential: real work 0.391 s, elapsed 0.391 s + | RMS charge density error from multipole expansion : 0.137135E-01 + | Average real-space part of the electrostatic potential : 0.43655206 eV + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.396 s, elapsed 0.396 s + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.001 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -5.01875904 eV + What follows are estimated values for band gap, HOMO, LUMO, etc. + | They are estimated on a discrete k-point grid and not necessarily exact. + | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. + + Highest occupied state (VBM) at -5.24147007 eV (relative to internal zero) + | Occupation number: 2.00000000 + | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + + Lowest unoccupied state (CBM) at -4.40429494 eV (relative to internal zero) + | Occupation number: 0.00000000 + | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) + + ESTIMATED overall HOMO-LUMO gap: 0.83717513 eV between HOMO at k-point 1 and LUMO at k-point 4 + | This appears to be an indirect band gap. + | Smallest direct gap : 2.22521115 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, + this system is most likely an insulator or a semiconductor. + + Total energy components: + | Sum of eigenvalues : -328.16312551 Ha -8929.77298693 eV + | XC energy correction : -41.74856597 Ha -1136.03628091 eV + | XC potential correction : 53.91090505 Ha 1466.99036601 eV + | Free-atom electrostatic energy: -263.84200016 Ha -7179.50611365 eV + | Hartree energy correction : -0.80483046 Ha -21.90055117 eV + | Entropy correction : -0.00000000 Ha -0.00000000 eV + | --------------------------- + | Total energy : -580.64761705 Ha -15800.22556665 eV + | Total energy, T -> 0 : -580.64761705 Ha -15800.22556665 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -580.64761705 Ha -15800.22556665 eV + + Derived energy quantities: + | Kinetic energy : 582.10845902 Ha 15839.97709920 eV + | Electrostatic energy : -1121.00751011 Ha -30504.16638494 eV + | Energy correction for multipole + | error in Hartree potential : 0.01825001 Ha 0.49660813 eV + | Sum of eigenvalues per atom : -4464.88649346 eV + | Total energy (T->0) per atom : -7900.11278332 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -7900.11278332 eV + Evaluating new KS density using the density matrix + Evaluating density matrix + Time summed over all CPUs for getting density from density matrix: real work 0.800 s, elapsed 0.800 s + Integration grid: deviation in total charge ( - N_e) = -7.105427E-15 + + Self-consistency convergence accuracy: + | Change of charge density : 0.2666E-04 + | Change of sum of eigenvalues : 0.7367E-03 eV + | Change of total energy : -0.1898E-05 eV + + +------------------------------------------------------------ + End self-consistency iteration # 4 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 1.773 s 1.774 s + | Charge density update : 0.801 s 0.801 s + | Density mixing & preconditioning : 0.178 s 0.178 s + | Hartree multipole update : 0.001 s 0.001 s + | Hartree multipole summation : 0.393 s 0.393 s + | Integration : 0.396 s 0.396 s + | Solution of K.-S. eqns. : 0.005 s 0.005 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 1.554 MB (on task 0) + | Maximum: 1.554 MB (on task 0) + | Average: 1.554 MB + | Peak value for overall tracked memory usage: + | Minimum: 14.236 MB (on task 0 after allocating d_wave) + | Maximum: 14.236 MB (on task 0 after allocating d_wave) + | Average: 14.236 MB + | Largest tracked array allocation so far: + | Minimum: 3.456 MB (hamiltonian_shell on task 0) + | Maximum: 3.456 MB (hamiltonian_shell on task 0) + | Average: 3.456 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + +------------------------------------------------------------ + Begin self-consistency iteration # 5 + + Date : 20230628, Time : 104340.737 +------------------------------------------------------------ + Pulay mixing of updated and previous charge densities. + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 28.0000000000 + | Integrated number of electrons on 3D grid : 27.9999999970 + | Charge integration error : -0.0000000030 + | Normalization factor for density and gradient : 1.0000000001 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = -0.408762E-13 + | Sum of charges compensated after spline to logarithmic grids = -0.634778E-04 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = -0.407702E-13 + Summing up the Hartree potential. + Time summed over all CPUs for potential: real work 0.391 s, elapsed 0.391 s + | RMS charge density error from multipole expansion : 0.137135E-01 + | Average real-space part of the electrostatic potential : 0.43655673 eV + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.396 s, elapsed 0.396 s + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.000 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -5.01875552 eV + What follows are estimated values for band gap, HOMO, LUMO, etc. + | They are estimated on a discrete k-point grid and not necessarily exact. + | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. + + Highest occupied state (VBM) at -5.24146591 eV (relative to internal zero) + | Occupation number: 2.00000000 + | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + + Lowest unoccupied state (CBM) at -4.40429219 eV (relative to internal zero) + | Occupation number: 0.00000000 + | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) + + ESTIMATED overall HOMO-LUMO gap: 0.83717372 eV between HOMO at k-point 1 and LUMO at k-point 4 + | This appears to be an indirect band gap. + | Smallest direct gap : 2.22521117 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, + this system is most likely an insulator or a semiconductor. + + Total energy components: + | Sum of eigenvalues : -328.16311891 Ha -8929.77280749 eV + | XC energy correction : -41.74856632 Ha -1136.03629037 eV + | XC potential correction : 53.91090547 Ha 1466.99037744 eV + | Free-atom electrostatic energy: -263.84200016 Ha -7179.50611365 eV + | Hartree energy correction : -0.80483714 Ha -21.90073277 eV + | Entropy correction : -0.00000000 Ha -0.00000000 eV + | --------------------------- + | Total energy : -580.64761706 Ha -15800.22556684 eV + | Total energy, T -> 0 : -580.64761706 Ha -15800.22556684 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -580.64761706 Ha -15800.22556684 eV + + Derived energy quantities: + | Kinetic energy : 582.10845957 Ha 15839.97711419 eV + | Electrostatic energy : -1121.00751032 Ha -30504.16639066 eV + | Energy correction for multipole + | error in Hartree potential : 0.01825010 Ha 0.49661059 eV + | Sum of eigenvalues per atom : -4464.88640374 eV + | Total energy (T->0) per atom : -7900.11278342 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -7900.11278342 eV + Evaluating new KS density using the density matrix + Evaluating density matrix + Time summed over all CPUs for getting density from density matrix: real work 0.798 s, elapsed 0.798 s + Integration grid: deviation in total charge ( - N_e) = 0.000000E+00 + + Self-consistency convergence accuracy: + | Change of charge density : 0.5995E-06 + | Change of sum of eigenvalues : 0.1794E-03 eV + | Change of total energy : -0.1944E-06 eV + + +------------------------------------------------------------ + End self-consistency iteration # 5 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 1.772 s 1.772 s + | Charge density update : 0.799 s 0.800 s + | Density mixing & preconditioning : 0.177 s 0.177 s + | Hartree multipole update : 0.001 s 0.001 s + | Hartree multipole summation : 0.393 s 0.393 s + | Integration : 0.396 s 0.397 s + | Solution of K.-S. eqns. : 0.005 s 0.004 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 1.554 MB (on task 0) + | Maximum: 1.554 MB (on task 0) + | Average: 1.554 MB + | Peak value for overall tracked memory usage: + | Minimum: 14.236 MB (on task 0 after allocating d_wave) + | Maximum: 14.236 MB (on task 0 after allocating d_wave) + | Average: 14.236 MB + | Largest tracked array allocation so far: + | Minimum: 3.456 MB (hamiltonian_shell on task 0) + | Maximum: 3.456 MB (hamiltonian_shell on task 0) + | Average: 3.456 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + +------------------------------------------------------------ + Begin self-consistency iteration # 6 + + Date : 20230628, Time : 104342.509 +------------------------------------------------------------ + Pulay mixing of updated and previous charge densities. + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 28.0000000000 + | Integrated number of electrons on 3D grid : 28.0000000042 + | Charge integration error : 0.0000000042 + | Normalization factor for density and gradient : 0.9999999998 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = 0.678360E-13 + | Sum of charges compensated after spline to logarithmic grids = -0.634779E-04 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = 0.679112E-13 + Summing up the Hartree potential. + Time summed over all CPUs for potential: real work 0.390 s, elapsed 0.390 s + | RMS charge density error from multipole expansion : 0.137135E-01 + | Average real-space part of the electrostatic potential : 0.43655657 eV + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.396 s, elapsed 0.396 s + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.001 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -5.01875563 eV + What follows are estimated values for band gap, HOMO, LUMO, etc. + | They are estimated on a discrete k-point grid and not necessarily exact. + | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. + + Highest occupied state (VBM) at -5.24146606 eV (relative to internal zero) + | Occupation number: 2.00000000 + | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + + Lowest unoccupied state (CBM) at -4.40429220 eV (relative to internal zero) + | Occupation number: 0.00000000 + | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) + + ESTIMATED overall HOMO-LUMO gap: 0.83717386 eV between HOMO at k-point 1 and LUMO at k-point 4 + | This appears to be an indirect band gap. + | Smallest direct gap : 2.22521105 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, + this system is most likely an insulator or a semiconductor. + + Total energy components: + | Sum of eigenvalues : -328.16312017 Ha -8929.77284167 eV + | XC energy correction : -41.74856622 Ha -1136.03628782 eV + | XC potential correction : 53.91090534 Ha 1466.99037394 eV + | Free-atom electrostatic energy: -263.84200016 Ha -7179.50611365 eV + | Hartree energy correction : -0.80483584 Ha -21.90069763 eV + | Entropy correction : -0.00000000 Ha -0.00000000 eV + | --------------------------- + | Total energy : -580.64761706 Ha -15800.22556682 eV + | Total energy, T -> 0 : -580.64761706 Ha -15800.22556682 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -580.64761706 Ha -15800.22556682 eV + + Derived energy quantities: + | Kinetic energy : 582.10845878 Ha 15839.97709252 eV + | Electrostatic energy : -1121.00750962 Ha -30504.16637153 eV + | Energy correction for multipole + | error in Hartree potential : 0.01825011 Ha 0.49661067 eV + | Sum of eigenvalues per atom : -4464.88642083 eV + | Total energy (T->0) per atom : -7900.11278341 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -7900.11278341 eV + Preliminary charge convergence reached. Turning off preconditioner. + + Evaluating new KS density using the density matrix + Evaluating density matrix + Time summed over all CPUs for getting density from density matrix: real work 0.800 s, elapsed 0.800 s + Integration grid: deviation in total charge ( - N_e) = -1.065814E-14 + + Self-consistency convergence accuracy: + | Change of charge density : 0.6807E-07 + | Change of sum of eigenvalues : -0.3418E-04 eV + | Change of total energy : 0.2030E-07 eV + + Electronic self-consistency reached - switching on the force computation. + + Electronic self-consistency reached - switching on the analytical stress tensor computation. + + +------------------------------------------------------------ + End self-consistency iteration # 6 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 1.774 s 1.774 s + | Charge density & force component update : 0.801 s 0.801 s + | Density mixing : 0.177 s 0.177 s + | Hartree multipole update : 0.001 s 0.002 s + | Hartree multipole summation : 0.393 s 0.393 s + | Hartree pot. SCF incomplete forces : 0.941 s 0.946 s + | Integration : 0.396 s 0.396 s + | Solution of K.-S. eqns. : 0.005 s 0.004 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 1.554 MB (on task 0) + | Maximum: 1.554 MB (on task 0) + | Average: 1.554 MB + | Peak value for overall tracked memory usage: + | Minimum: 14.236 MB (on task 0 after allocating d_wave) + | Maximum: 14.236 MB (on task 0 after allocating d_wave) + | Average: 14.236 MB + | Largest tracked array allocation so far: + | Minimum: 3.456 MB (hamiltonian_shell on task 0) + | Maximum: 3.456 MB (hamiltonian_shell on task 0) + | Average: 3.456 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + +------------------------------------------------------------ + Begin self-consistency iteration # 7 + + Date : 20230628, Time : 104344.283 +------------------------------------------------------------ + Pulay mixing of updated and previous charge densities. + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 28.0000000000 + | Integrated number of electrons on 3D grid : 27.9999999961 + | Charge integration error : -0.0000000039 + | Normalization factor for density and gradient : 1.0000000001 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = 0.380846E-13 + | Sum of charges compensated after spline to logarithmic grids = -0.634779E-04 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = 0.379498E-13 + Summing up the Hartree potential. + Time summed over all CPUs for potential: real work 1.649 s, elapsed 1.649 s + | RMS charge density error from multipole expansion : 0.137135E-01 + | Average real-space part of the electrostatic potential : 0.43655657 eV + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.396 s, elapsed 0.396 s + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.000 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -5.01875572 eV + What follows are estimated values for band gap, HOMO, LUMO, etc. + | They are estimated on a discrete k-point grid and not necessarily exact. + | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. + + Highest occupied state (VBM) at -5.24146615 eV (relative to internal zero) + | Occupation number: 2.00000000 + | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + + Lowest unoccupied state (CBM) at -4.40429223 eV (relative to internal zero) + | Occupation number: 0.00000000 + | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) + + ESTIMATED overall HOMO-LUMO gap: 0.83717392 eV between HOMO at k-point 1 and LUMO at k-point 4 + | This appears to be an indirect band gap. + | Smallest direct gap : 2.22521105 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, + this system is most likely an insulator or a semiconductor. + + Total energy components: + | Sum of eigenvalues : -328.16312012 Ha -8929.77284040 eV + | XC energy correction : -41.74856623 Ha -1136.03628808 eV + | XC potential correction : 53.91090535 Ha 1466.99037429 eV + | Free-atom electrostatic energy: -263.84200016 Ha -7179.50611365 eV + | Hartree energy correction : -0.80483589 Ha -21.90069898 eV + | Entropy correction : -0.00000000 Ha -0.00000000 eV + | --------------------------- + | Total energy : -580.64761706 Ha -15800.22556682 eV + | Total energy, T -> 0 : -580.64761706 Ha -15800.22556682 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -580.64761706 Ha -15800.22556682 eV + + Derived energy quantities: + | Kinetic energy : 582.10845912 Ha 15839.97710180 eV + | Electrostatic energy : -1121.00750995 Ha -30504.16638054 eV + | Energy correction for multipole + | error in Hartree potential : 0.01825011 Ha 0.49661067 eV + | Sum of eigenvalues per atom : -4464.88642020 eV + | Total energy (T->0) per atom : -7900.11278341 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -7900.11278341 eV + Evaluating new KS density using the density matrix + Evaluating density matrix + Time summed over all CPUs for getting density from density matrix: real work 0.801 s, elapsed 0.801 s + Integration grid: deviation in total charge ( - N_e) = -1.065814E-14 + + atomic forces [eV/Ang]: + ----------------------- + atom # 1 + Hellmann-Feynman : -0.174533E-06 0.132859E-06 0.162610E-06 + Ionic forces : 0.000000E+00 0.000000E+00 0.000000E+00 + Multipole : 0.458049E-07 -0.978235E-08 -0.108478E-07 + Hartree pot. SCF incomplete : 0.122555E-08 0.445755E-08 -0.423237E-08 + Pulay + GGA : 0.000000E+00 0.000000E+00 0.000000E+00 + ---------------------------------------------------------------- + Total forces( 1) : -0.127502E-06 0.127534E-06 0.147530E-06 + atom # 2 + Hellmann-Feynman : 0.175265E-06 -0.122017E-06 -0.156383E-06 + Ionic forces : 0.000000E+00 0.000000E+00 0.000000E+00 + Multipole : -0.458035E-07 0.978442E-08 0.108489E-07 + Hartree pot. SCF incomplete : -0.119578E-08 -0.463144E-08 0.434145E-08 + Pulay + GGA : 0.000000E+00 0.000000E+00 0.000000E+00 + ---------------------------------------------------------------- + Total forces( 2) : 0.128266E-06 -0.116864E-06 -0.141192E-06 + + + Self-consistency convergence accuracy: + | Change of charge density : 0.3795E-07 + | Change of sum of eigenvalues : 0.1262E-05 eV + | Change of total energy : 0.1893E-08 eV + | Change of forces : 0.2294E-06 eV/A + + +------------------------------------------------------------ + End self-consistency iteration # 7 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 3.799 s 3.799 s + | Charge density & force component update : 0.802 s 0.802 s + | Density mixing : 0.001 s 0.001 s + | Hartree multipole update : 0.001 s 0.001 s + | Hartree multipole summation : 1.652 s 1.653 s + | Hartree pot. SCF incomplete forces : 0.942 s 0.942 s + | Integration : 0.396 s 0.396 s + | Solution of K.-S. eqns. : 0.005 s 0.004 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 1.554 MB (on task 0) + | Maximum: 1.554 MB (on task 0) + | Average: 1.554 MB + | Peak value for overall tracked memory usage: + | Minimum: 14.236 MB (on task 0 after allocating d_wave) + | Maximum: 14.236 MB (on task 0 after allocating d_wave) + | Average: 14.236 MB + | Largest tracked array allocation so far: + | Minimum: 3.456 MB (hamiltonian_shell on task 0) + | Maximum: 3.456 MB (hamiltonian_shell on task 0) + | Average: 3.456 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + +------------------------------------------------------------ + Begin self-consistency iteration # 8 + + Date : 20230628, Time : 104348.082 +------------------------------------------------------------ + Pulay mixing of updated and previous charge densities. + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 28.0000000000 + | Integrated number of electrons on 3D grid : 28.0000000009 + | Charge integration error : 0.0000000009 + | Normalization factor for density and gradient : 1.0000000000 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = -0.853832E-13 + | Sum of charges compensated after spline to logarithmic grids = -0.634779E-04 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = -0.853537E-13 + Summing up the Hartree potential. + Time summed over all CPUs for potential: real work 1.645 s, elapsed 1.645 s + | RMS charge density error from multipole expansion : 0.137135E-01 + | Average real-space part of the electrostatic potential : 0.43655656 eV + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.396 s, elapsed 0.396 s + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.001 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -5.01875570 eV + What follows are estimated values for band gap, HOMO, LUMO, etc. + | They are estimated on a discrete k-point grid and not necessarily exact. + | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. + + Highest occupied state (VBM) at -5.24146614 eV (relative to internal zero) + | Occupation number: 2.00000000 + | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + + Lowest unoccupied state (CBM) at -4.40429223 eV (relative to internal zero) + | Occupation number: 0.00000000 + | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) + + ESTIMATED overall HOMO-LUMO gap: 0.83717391 eV between HOMO at k-point 1 and LUMO at k-point 4 + | This appears to be an indirect band gap. + | Smallest direct gap : 2.22521105 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, + this system is most likely an insulator or a semiconductor. + + Total energy components: + | Sum of eigenvalues : -328.16312017 Ha -8929.77284175 eV + | XC energy correction : -41.74856623 Ha -1136.03628793 eV + | XC potential correction : 53.91090535 Ha 1466.99037409 eV + | Free-atom electrostatic energy: -263.84200016 Ha -7179.50611365 eV + | Hartree energy correction : -0.80483584 Ha -21.90069758 eV + | Entropy correction : -0.00000000 Ha -0.00000000 eV + | --------------------------- + | Total energy : -580.64761706 Ha -15800.22556682 eV + | Total energy, T -> 0 : -580.64761706 Ha -15800.22556682 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -580.64761706 Ha -15800.22556682 eV + + Derived energy quantities: + | Kinetic energy : 582.10845902 Ha 15839.97709910 eV + | Electrostatic energy : -1121.00750985 Ha -30504.16637799 eV + | Energy correction for multipole + | error in Hartree potential : 0.01825011 Ha 0.49661066 eV + | Sum of eigenvalues per atom : -4464.88642088 eV + | Total energy (T->0) per atom : -7900.11278341 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -7900.11278341 eV + Evaluating new KS density using the density matrix + Evaluating density matrix + Time summed over all CPUs for getting density from density matrix: real work 0.797 s, elapsed 0.797 s + + Evaluating density-matrix-based force terms: batch-based integration + Evaluating density matrix + Evaluating density matrix + Integration grid: deviation in total charge ( - N_e) = 2.131628E-14 + + atomic forces [eV/Ang]: + ----------------------- + atom # 1 + Hellmann-Feynman : -0.133256E-06 0.186553E-06 0.959840E-07 + Ionic forces : 0.000000E+00 0.000000E+00 0.000000E+00 + Multipole : 0.458312E-07 -0.990532E-08 -0.106989E-07 + Hartree pot. SCF incomplete : -0.149097E-07 -0.997635E-08 0.151466E-07 + Pulay + GGA : 0.444819E-06 -0.209681E-06 -0.166655E-06 + ---------------------------------------------------------------- + Total forces( 1) : 0.342484E-06 -0.430094E-07 -0.662230E-07 + atom # 2 + Hellmann-Feynman : 0.134051E-06 -0.176390E-06 -0.894499E-07 + Ionic forces : 0.000000E+00 0.000000E+00 0.000000E+00 + Multipole : -0.458309E-07 0.990579E-08 0.106979E-07 + Hartree pot. SCF incomplete : 0.148654E-07 0.105211E-07 -0.153964E-07 + Pulay + GGA : -0.443163E-06 0.186049E-06 0.141031E-06 + ---------------------------------------------------------------- + Total forces( 2) : -0.340078E-06 0.300861E-07 0.468829E-07 + + + Analytical stress tensor components [eV] xx yy zz xy xz yz + ----------------------------------------------------------------------------------------------------------------------------------------------------------- + Nuclear Hellmann-Feynman : -0.1192389456E+02 -0.1192407593E+02 -0.1192407593E+02 -0.7957847272E-07 -0.5039490827E-07 0.4410918514E-06 + Multipole Hellmann-Feynman : -0.2752793058E+02 -0.2752794118E+02 -0.2752794118E+02 -0.2504360107E-06 -0.1946134947E-06 0.1412451753E-05 + On-site Multipole corrections : -0.2840312241E+00 -0.2840312244E+00 -0.2840312245E+00 0.9961793290E-10 0.8914761865E-10 -0.3776534998E-09 + Strain deriv. of the orbitals : 0.3972740784E+02 0.3972759987E+02 0.3972759987E+02 0.2202138934E-06 0.1385950070E-06 -0.1507222448E-05 + ----------------------------------------------------------------------------------------------------------------------------------------------------------- + Sum of all contributions : -0.8448519987E-02 -0.8448470439E-02 -0.8448469456E-02 -0.1097009721E-06 -0.1063242483E-06 0.3459435029E-06 + + +-------------------------------------------------------------------+ + | Analytical stress tensor - Symmetrized | + | Cartesian components [eV/A**3] | + +-------------------------------------------------------------------+ + | x y z | + | | + | x -0.00018941 -0.00000000 -0.00000000 | + | y -0.00000000 -0.00018941 0.00000001 | + | z -0.00000000 0.00000001 -0.00018941 | + | | + | Pressure: 0.00018941 [eV/A**3] | + | | + +-------------------------------------------------------------------+ + + * Warning: Stress tensor is anisotropic. Be aware that pressure is an isotropic quantity. + + + Self-consistency convergence accuracy: + | Change of charge density : 0.8719E-08 + | Change of sum of eigenvalues : -0.1351E-05 eV + | Change of total energy : 0.4053E-09 eV + | Change of forces : 0.9513E-07 eV/A + + Writing Kohn-Sham eigenvalues. + K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + + State Occupation Eigenvalue [Ha] Eigenvalue [eV] + 1 2.00000 -65.748361 -1789.10394 + 2 2.00000 -65.748361 -1789.10394 + 3 2.00000 -5.106113 -138.94441 + 4 2.00000 -5.105948 -138.93992 + 5 2.00000 -3.489886 -94.96462 + 6 2.00000 -3.489886 -94.96462 + 7 2.00000 -3.489886 -94.96462 + 8 2.00000 -3.489489 -94.95384 + 9 2.00000 -3.489489 -94.95384 + 10 2.00000 -3.489489 -94.95384 + 11 2.00000 -0.608183 -16.54950 + 12 2.00000 -0.192620 -5.24147 + 13 2.00000 -0.192620 -5.24147 + 14 2.00000 -0.192620 -5.24147 + 15 0.00000 -0.110845 -3.01626 + 16 0.00000 -0.104028 -2.83075 + 17 0.00000 -0.104028 -2.83075 + 18 0.00000 -0.104028 -2.83075 + 19 0.00000 0.092758 2.52407 + 20 0.00000 0.092758 2.52407 + + What follows are estimated values for band gap, HOMO, LUMO, etc. + | They are estimated on a discrete k-point grid and not necessarily exact. + | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. + + Highest occupied state (VBM) at -5.24146614 eV (relative to internal zero) + | Occupation number: 2.00000000 + | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + + Lowest unoccupied state (CBM) at -4.40429223 eV (relative to internal zero) + | Occupation number: 0.00000000 + | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) + + ESTIMATED overall HOMO-LUMO gap: 0.83717391 eV between HOMO at k-point 1 and LUMO at k-point 4 + | This appears to be an indirect band gap. + | Smallest direct gap : 2.22521105 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, + this system is most likely an insulator or a semiconductor. + | Chemical Potential : -5.01875570 eV + + Self-consistency cycle converged. + + +------------------------------------------------------------ + End self-consistency iteration # 8 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 19.041 s 19.042 s + | Charge density & force component update : 16.053 s 16.053 s + | Density mixing : 0.002 s 0.002 s + | Hartree multipole update : 0.001 s 0.001 s + | Hartree multipole summation : 1.648 s 1.648 s + | Hartree pot. SCF incomplete forces : 0.935 s 0.935 s + | Integration : 0.396 s 0.397 s + | Solution of K.-S. eqns. : 0.005 s 0.004 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 1.554 MB (on task 0) + | Maximum: 1.554 MB (on task 0) + | Average: 1.554 MB + | Peak value for overall tracked memory usage: + | Minimum: 14.236 MB (on task 0 after allocating d_wave) + | Maximum: 14.236 MB (on task 0 after allocating d_wave) + | Average: 14.236 MB + | Largest tracked array allocation so far: + | Minimum: 3.456 MB (hamiltonian_shell on task 0) + | Maximum: 3.456 MB (hamiltonian_shell on task 0) + | Average: 3.456 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + Removing unitary transformations (pure translations, rotations) from forces on atoms. + Atomic forces before filtering: + | Net force on center of mass : 0.240662E-08 -0.129234E-07 -0.193401E-07 eV/A + Atomic forces after filtering: + | Net force on center of mass : 0.000000E+00 -0.106338E-22 0.000000E+00 eV/A + + Energy and forces in a compact form: + | Total energy uncorrected : -0.158002255668194E+05 eV + | Total energy corrected : -0.158002255668194E+05 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -0.158002255668194E+05 eV + Total atomic forces (unitary forces cleaned) [eV/Ang]: + | 1 0.341280940656103E-06 -0.365477601296885E-07 -0.565529618943033E-07 + | 2 -0.341280940656103E-06 0.365477601296885E-07 0.565529618943033E-07 + + ------------------------------------ + Start decomposition of the XC Energy + ------------------------------------ + X and C from original XC functional choice + Hartree-Fock Energy : 0.000000000 Ha 0.000000000 eV + X Energy : -40.666493062 Ha -1106.591578968 eV + C Energy : -1.082073165 Ha -29.444708963 eV + XC Energy w/o HF : -41.748566227 Ha -1136.036287931 eV + Total XC Energy : -41.748566227 Ha -1136.036287931 eV + ------------------------------------ + LDA X and C from self-consistent density + X Energy LDA : -37.597435086 Ha -1023.078262336 eV + C Energy LDA : -2.143916094 Ha -58.338925176 eV + ------------------------------------ + End decomposition of the XC Energy + ------------------------------------ + +------------------------------------------------------------ + Relaxation / MD: End force evaluation. : max(cpu_time) wall_clock(cpu1) + | Time for this force evaluation : 34.665 s 34.680 s + +------------------------------------------------------------ + Geometry optimization: Attempting to predict improved coordinates. + + +-------------------------------------------------------------------+ + | Generalized derivatives on lattice vectors [eV/A] | + +-------------------------------------------------------------------+ + |lattice_vector 0.00150068 -0.00150063 -0.00150063 | + |lattice_vector -0.00150072 0.00150075 -0.00150079 | + |lattice_vector -0.00150072 -0.00150079 0.00150075 | + +-------------------------------------------------------------------+ + | Forces on lattice vectors cleaned from atomic contributions [eV/A]| + +-------------------------------------------------------------------+ + |lattice_vector -0.00150068 0.00150063 0.00150063 | + |lattice_vector 0.00150072 -0.00150075 0.00150079 | + |lattice_vector 0.00150072 0.00150079 -0.00150075 | + +-------------------------------------------------------------------+ + Removing unitary transformations (pure translations, rotations) from forces on atoms. + Atomic forces before filtering: + | Net force on center of mass : 0.000000E+00 -0.106338E-22 0.000000E+00 eV/A + Atomic forces after filtering: + | Net force on center of mass : 0.000000E+00 0.000000E+00 0.000000E+00 eV/A + Net remaining forces (excluding translations, rotations) in present geometry: + || Forces on atoms || = 0.341281E-06 eV/A. + || Forces on lattice || = 0.150079E-02 eV/A^3. + Maximum force component is 0.150079E-02 eV/A. + Present geometry is not yet converged. + + Relaxation step number 4: Predicting new coordinates. + + Advancing geometry using trust radius method. + | True / expected gain: 2.20E-05 eV / -2.72E-04 eV = -0.0809 + | Harmonic / expected gain: -2.92E-04 eV / -2.72E-04 eV = 1.0766 + | Using harmonic gain instead of DE to judge step. + | Hessian has 0 negative and 3 zero eigenvalues. + | Positive eigenvalues (eV/A^2): 3.35E+00 ... 3.02E+01 + | Use Quasi-Newton step of length |H^-1 F| = 9.39E-04 A. + Finished advancing geometry + | Time : 0.000 s + Updated atomic structure: + x [A] y [A] z [A] + lattice_vector 0.00000007 2.81520842 2.81520842 + lattice_vector 2.81520832 -0.00000004 2.81520837 + lattice_vector 2.81520832 2.81520837 -0.00000004 + + atom 0.00000002 -0.00000000 -0.00000000 Si + atom 1.40760416 1.40760419 1.40760419 Si + + Fractional coordinates: + L1 L2 L3 + atom_frac -0.00000000 0.00000000 0.00000000 Si + atom_frac 0.25000000 0.25000000 0.25000000 Si +------------------------------------------------------------ + Writing the current geometry to file "geometry.in.next_step". + Writing estimated Hessian matrix to file 'hessian.aims' + + Quantities derived from the lattice vectors: + | Reciprocal lattice vector 1: -1.115936 1.115936 1.115936 + | Reciprocal lattice vector 2: 1.115936 -1.115936 1.115936 + | Reciprocal lattice vector 3: 1.115936 1.115936 -1.115936 + | Unit cell volume : 0.446233E+02 A^3 + + Range separation radius for Ewald summation (hartree_convergence_parameter): 4.04582400 bohr. + +------------------------------------------------------------ + Begin self-consistency loop: Re-initialization. + + Date : 20230628, Time : 104407.131 +------------------------------------------------------------ + + Initializing index lists of integration centers etc. from given atomic structure: + Mapping all atomic coordinates to central unit cell. + + Initializing the k-points + Using symmetry for reducing the k-points + | k-points reduced from: 8 to 8 + | Number of k-points : 8 + The eigenvectors in the calculations are REAL. + | K-points in task 0: 8 + | Number of basis functions in the Hamiltonian integrals : 1771 + | Number of basis functions in a single unit cell : 50 + | Number of centers in hartree potential : 708 + | Number of centers in hartree multipole : 318 + | Number of centers in electron density summation: 190 + | Number of centers in basis integrals : 198 + | Number of centers in integrals : 101 + | Number of centers in hamiltonian : 190 + | Consuming 14 KiB for k_phase. + | Number of super-cells (origin) [n_cells] : 2197 + | Number of super-cells (after PM_index) [n_cells] : 112 + | Number of super-cells in hamiltonian [n_cells_in_hamiltonian]: 112 + | Size of matrix packed + index [n_hamiltonian_matrix_size] : 82583 + Partitioning the integration grid into batches with parallel hashing+maxmin method. + | Number of batches: 128 + | Maximal batch size: 90 + | Minimal batch size: 85 + | Average batch size: 87.562 + | Standard deviation of batch sizes: 1.493 + + Integration load balanced across 1 MPI tasks. + Work distribution over tasks is as follows: + Initializing partition tables, free-atom densities, potentials, etc. across the integration grid (initialize_grid_storage). + | Species 1: outer_partition_radius set to 5.000694715736543 AA . + | The sparse table of interatomic distances needs 194.62 kbyte instead of 313.63 kbyte of memory. + | Net number of integration points: 11208 + | of which are non-zero points : 9876 + | Numerical average free-atom electrostatic potential : -11.78007497 eV + Renormalizing the initial density to the exact electron count on the 3D integration grid. + | Initial density: Formal number of electrons (from input files) : 28.0000000000 + | Integrated number of electrons on 3D grid : 28.0037445357 + | Charge integration error : 0.0037445357 + | Normalization factor for density and gradient : 0.9998662845 + Renormalizing the free-atom superposition density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 28.0000000000 + | Integrated number of electrons on 3D grid : 28.0037445357 + | Charge integration error : 0.0037445357 + | Normalization factor for density and gradient : 0.9998662845 + Obtaining max. number of non-zero basis functions in each batch (get_n_compute_maxes). + Calculating total energy contributions from superposition of free atom densities. + Initialize hartree_potential_storage + Integrating overlap matrix. + Time summed over all CPUs for integration: real work 0.253 s, elapsed 0.253 s + Orthonormalizing eigenvectors + + End scf reinitialization - timings : max(cpu_time) wall_clock(cpu1) + | Time for scf. reinitialization : 0.562 s 0.561 s + | Boundary condition initialization : 0.064 s 0.064 s + | Integration : 0.253 s 0.253 s + | Grid partitioning : 0.032 s 0.032 s + | Preloading free-atom quantities on grid : 0.174 s 0.174 s + | Free-atom superposition energy : 0.027 s 0.027 s + | K.-S. eigenvector reorthonormalization : 0.001 s 0.000 s +------------------------------------------------------------ + Evaluating new KS density using the density matrix + Evaluating density matrix + Time summed over all CPUs for getting density from density matrix: real work 0.796 s, elapsed 0.796 s + Integration grid: deviation in total charge ( - N_e) = -7.105427E-15 + + Time for density update prior : max(cpu_time) wall_clock(cpu1) + | self-consistency iterative process : 0.797 s 0.798 s + +------------------------------------------------------------ + Begin self-consistency iteration # 1 + + Date : 20230628, Time : 104408.490 +------------------------------------------------------------ + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 28.0000000000 + | Integrated number of electrons on 3D grid : 28.0000000000 + | Charge integration error : 0.0000000000 + | Normalization factor for density and gradient : 1.0000000000 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = -0.296378E-13 + | Sum of charges compensated after spline to logarithmic grids = -0.629591E-04 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = -0.296722E-13 + Summing up the Hartree potential. + | Estimated reciprocal-space cutoff momentum G_max: 2.30298530 bohr^-1 . + | Reciprocal lattice points for long-range Hartree potential: 58 + Time summed over all CPUs for potential: real work 0.390 s, elapsed 0.390 s + | RMS charge density error from multipole expansion : 0.137057E-01 + | Average real-space part of the electrostatic potential : 0.43618715 eV + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.393 s, elapsed 0.393 s + Decreasing sparse matrix size: + | Tolerance: 0.1000E-12 + Hamiltonian matrix + | Array has 74550 nonzero elements out of 82583 elements + | Sparsity factor is 0.097 + Overlap matrix + | Array has 68306 nonzero elements out of 82583 elements + | Sparsity factor is 0.173 + New size of hamiltonian matrix: 74577 + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Singularity check in k-point 1, task 0 (analysis for other k-points/tasks may follow below): + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.001 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.000 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -5.01957146 eV + Writing Kohn-Sham eigenvalues. + K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + + State Occupation Eigenvalue [Ha] Eigenvalue [eV] + 1 2.00000 -65.748414 -1789.10539 + 2 2.00000 -65.748414 -1789.10539 + 3 2.00000 -5.106138 -138.94508 + 4 2.00000 -5.105973 -138.94060 + 5 2.00000 -3.489912 -94.96534 + 6 2.00000 -3.489912 -94.96534 + 7 2.00000 -3.489912 -94.96534 + 8 2.00000 -3.489516 -94.95457 + 9 2.00000 -3.489516 -94.95457 + 10 2.00000 -3.489516 -94.95457 + 11 2.00000 -0.608071 -16.54646 + 12 2.00000 -0.192605 -5.24105 + 13 2.00000 -0.192605 -5.24105 + 14 2.00000 -0.192605 -5.24105 + 15 0.00000 -0.110991 -3.02022 + 16 0.00000 -0.104017 -2.83044 + 17 0.00000 -0.104017 -2.83044 + 18 0.00000 -0.104017 -2.83044 + 19 0.00000 0.092776 2.52456 + 20 0.00000 0.092776 2.52456 + + What follows are estimated values for band gap, HOMO, LUMO, etc. + | They are estimated on a discrete k-point grid and not necessarily exact. + | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. + + Highest occupied state (VBM) at -5.24104779 eV (relative to internal zero) + | Occupation number: 2.00000000 + | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + + Lowest unoccupied state (CBM) at -4.40316738 eV (relative to internal zero) + | Occupation number: 0.00000000 + | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) + + ESTIMATED overall HOMO-LUMO gap: 0.83788041 eV between HOMO at k-point 1 and LUMO at k-point 4 + | This appears to be an indirect band gap. + | Smallest direct gap : 2.22082344 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, + this system is most likely an insulator or a semiconductor. + + Total energy components: + | Sum of eigenvalues : -328.16332796 Ha -8929.77849588 eV + | XC energy correction : -41.74829363 Ha -1136.02887010 eV + | XC potential correction : 53.91054166 Ha 1466.98047781 eV + | Free-atom electrostatic energy: -263.84284311 Ha -7179.52905141 eV + | Hartree energy correction : -0.80369312 Ha -21.86960252 eV + | Entropy correction : -0.00000000 Ha -0.00000000 eV + | --------------------------- + | Total energy : -580.64761615 Ha -15800.22554210 eV + | Total energy, T -> 0 : -580.64761615 Ha -15800.22554210 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -580.64761615 Ha -15800.22554210 eV + + Derived energy quantities: + | Kinetic energy : 582.10688240 Ha 15839.93419700 eV + | Electrostatic energy : -1121.00620492 Ha -30504.13086900 eV + | Energy correction for multipole + | error in Hartree potential : 0.01823700 Ha 0.49625397 eV + | Sum of eigenvalues per atom : -4464.88924794 eV + | Total energy (T->0) per atom : -7900.11277105 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -7900.11277105 eV + Evaluating new KS density using the density matrix + Evaluating density matrix + Time summed over all CPUs for getting density from density matrix: real work 0.798 s, elapsed 0.798 s + Integration grid: deviation in total charge ( - N_e) = 2.842171E-14 + + Self-consistency convergence accuracy: + | Change of charge density : 0.1308E+00 + | Change of sum of eigenvalues : -0.8930E+04 eV + | Change of total energy : -0.1580E+05 eV + + +------------------------------------------------------------ + End self-consistency iteration # 1 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 1.592 s 1.592 s + | Charge density update : 0.799 s 0.799 s + | Density mixing & preconditioning : 0.000 s 0.000 s + | Hartree multipole update : 0.001 s 0.001 s + | Hartree multipole summation : 0.393 s 0.393 s + | Integration : 0.394 s 0.394 s + | Solution of K.-S. eqns. : 0.005 s 0.005 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 1.553 MB (on task 0) + | Maximum: 1.553 MB (on task 0) + | Average: 1.553 MB + | Peak value for overall tracked memory usage: + | Minimum: 14.236 MB (on task 0 after allocating d_wave) + | Maximum: 14.236 MB (on task 0 after allocating d_wave) + | Average: 14.236 MB + | Largest tracked array allocation so far: + | Minimum: 3.456 MB (hamiltonian_shell on task 0) + | Maximum: 3.456 MB (hamiltonian_shell on task 0) + | Average: 3.456 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + +------------------------------------------------------------ + Begin self-consistency iteration # 2 + + Date : 20230628, Time : 104410.082 +------------------------------------------------------------ + Pulay mixing of updated and previous charge densities. + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 28.0000000000 + | Integrated number of electrons on 3D grid : 27.9999998182 + | Charge integration error : -0.0000001818 + | Normalization factor for density and gradient : 1.0000000065 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = -0.102120E-12 + | Sum of charges compensated after spline to logarithmic grids = -0.629596E-04 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = -0.102153E-12 + Summing up the Hartree potential. + Time summed over all CPUs for potential: real work 0.391 s, elapsed 0.391 s + | RMS charge density error from multipole expansion : 0.137056E-01 + | Average real-space part of the electrostatic potential : 0.43618904 eV + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.397 s, elapsed 0.397 s + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.000 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -5.01957712 eV + What follows are estimated values for band gap, HOMO, LUMO, etc. + | They are estimated on a discrete k-point grid and not necessarily exact. + | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. + + Highest occupied state (VBM) at -5.24105283 eV (relative to internal zero) + | Occupation number: 2.00000000 + | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + + Lowest unoccupied state (CBM) at -4.40316944 eV (relative to internal zero) + | Occupation number: 0.00000000 + | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) + + ESTIMATED overall HOMO-LUMO gap: 0.83788339 eV between HOMO at k-point 1 and LUMO at k-point 4 + | This appears to be an indirect band gap. + | Smallest direct gap : 2.22082548 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, + this system is most likely an insulator or a semiconductor. + + Total energy components: + | Sum of eigenvalues : -328.16329335 Ha -8929.77755408 eV + | XC energy correction : -41.74829799 Ha -1136.02898875 eV + | XC potential correction : 53.91054739 Ha 1466.98063355 eV + | Free-atom electrostatic energy: -263.84284311 Ha -7179.52905141 eV + | Hartree energy correction : -0.80372910 Ha -21.87058153 eV + | Entropy correction : -0.00000000 Ha -0.00000000 eV + | --------------------------- + | Total energy : -580.64761616 Ha -15800.22554222 eV + | Total energy, T -> 0 : -580.64761616 Ha -15800.22554222 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -580.64761616 Ha -15800.22554222 eV + + Derived energy quantities: + | Kinetic energy : 582.10696926 Ha 15839.93656074 eV + | Electrostatic energy : -1121.00628743 Ha -30504.13311421 eV + | Energy correction for multipole + | error in Hartree potential : 0.01823698 Ha 0.49625347 eV + | Sum of eigenvalues per atom : -4464.88877704 eV + | Total energy (T->0) per atom : -7900.11277111 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -7900.11277111 eV + Evaluating new KS density using the density matrix + Evaluating density matrix + Time summed over all CPUs for getting density from density matrix: real work 0.797 s, elapsed 0.797 s + Integration grid: deviation in total charge ( - N_e) = 2.131628E-14 + + Self-consistency convergence accuracy: + | Change of charge density : 0.2024E-04 + | Change of sum of eigenvalues : 0.9418E-03 eV + | Change of total energy : -0.1217E-06 eV + + +------------------------------------------------------------ + End self-consistency iteration # 2 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 1.771 s 1.771 s + | Charge density update : 0.799 s 0.799 s + | Density mixing & preconditioning : 0.177 s 0.177 s + | Hartree multipole update : 0.001 s 0.001 s + | Hartree multipole summation : 0.393 s 0.393 s + | Integration : 0.397 s 0.397 s + | Solution of K.-S. eqns. : 0.005 s 0.004 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 1.553 MB (on task 0) + | Maximum: 1.553 MB (on task 0) + | Average: 1.553 MB + | Peak value for overall tracked memory usage: + | Minimum: 14.236 MB (on task 0 after allocating d_wave) + | Maximum: 14.236 MB (on task 0 after allocating d_wave) + | Average: 14.236 MB + | Largest tracked array allocation so far: + | Minimum: 3.456 MB (hamiltonian_shell on task 0) + | Maximum: 3.456 MB (hamiltonian_shell on task 0) + | Average: 3.456 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + +------------------------------------------------------------ + Begin self-consistency iteration # 3 + + Date : 20230628, Time : 104411.853 +------------------------------------------------------------ + Pulay mixing of updated and previous charge densities. + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 28.0000000000 + | Integrated number of electrons on 3D grid : 27.9999993680 + | Charge integration error : -0.0000006320 + | Normalization factor for density and gradient : 1.0000000226 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = -0.198103E-12 + | Sum of charges compensated after spline to logarithmic grids = -0.629613E-04 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = -0.198260E-12 + Summing up the Hartree potential. + Time summed over all CPUs for potential: real work 0.390 s, elapsed 0.390 s + | RMS charge density error from multipole expansion : 0.137052E-01 + | Average real-space part of the electrostatic potential : 0.43619612 eV + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.397 s, elapsed 0.397 s + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.000 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -5.01959701 eV + What follows are estimated values for band gap, HOMO, LUMO, etc. + | They are estimated on a discrete k-point grid and not necessarily exact. + | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. + + Highest occupied state (VBM) at -5.24107060 eV (relative to internal zero) + | Occupation number: 2.00000000 + | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + + Lowest unoccupied state (CBM) at -4.40317657 eV (relative to internal zero) + | Occupation number: 0.00000000 + | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) + + ESTIMATED overall HOMO-LUMO gap: 0.83789403 eV between HOMO at k-point 1 and LUMO at k-point 4 + | This appears to be an indirect band gap. + | Smallest direct gap : 2.22083239 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, + this system is most likely an insulator or a semiconductor. + + Total energy components: + | Sum of eigenvalues : -328.16317457 Ha -8929.77432201 eV + | XC energy correction : -41.74831282 Ha -1136.02939240 eV + | XC potential correction : 53.91056687 Ha 1466.98116369 eV + | Free-atom electrostatic energy: -263.84284311 Ha -7179.52905141 eV + | Hartree energy correction : -0.80385254 Ha -21.87394053 eV + | Entropy correction : -0.00000000 Ha -0.00000000 eV + | --------------------------- + | Total energy : -580.64761617 Ha -15800.22554266 eV + | Total energy, T -> 0 : -580.64761617 Ha -15800.22554266 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -580.64761617 Ha -15800.22554266 eV + + Derived energy quantities: + | Kinetic energy : 582.10726704 Ha 15839.94466374 eV + | Electrostatic energy : -1121.00657039 Ha -30504.14081400 eV + | Energy correction for multipole + | error in Hartree potential : 0.01823692 Ha 0.49625195 eV + | Sum of eigenvalues per atom : -4464.88716101 eV + | Total energy (T->0) per atom : -7900.11277133 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -7900.11277133 eV + Evaluating new KS density using the density matrix + Evaluating density matrix + Time summed over all CPUs for getting density from density matrix: real work 0.798 s, elapsed 0.798 s + Integration grid: deviation in total charge ( - N_e) = 5.329071E-14 + + Self-consistency convergence accuracy: + | Change of charge density : 0.1574E-04 + | Change of sum of eigenvalues : 0.3232E-02 eV + | Change of total energy : -0.4336E-06 eV + + +------------------------------------------------------------ + End self-consistency iteration # 3 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 1.773 s 1.773 s + | Charge density update : 0.800 s 0.799 s + | Density mixing & preconditioning : 0.178 s 0.178 s + | Hartree multipole update : 0.001 s 0.001 s + | Hartree multipole summation : 0.393 s 0.393 s + | Integration : 0.397 s 0.397 s + | Solution of K.-S. eqns. : 0.005 s 0.004 s + | Total energy evaluation : 0.000 s 0.001 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 1.553 MB (on task 0) + | Maximum: 1.553 MB (on task 0) + | Average: 1.553 MB + | Peak value for overall tracked memory usage: + | Minimum: 14.236 MB (on task 0 after allocating d_wave) + | Maximum: 14.236 MB (on task 0 after allocating d_wave) + | Average: 14.236 MB + | Largest tracked array allocation so far: + | Minimum: 3.456 MB (hamiltonian_shell on task 0) + | Maximum: 3.456 MB (hamiltonian_shell on task 0) + | Average: 3.456 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + +------------------------------------------------------------ + Begin self-consistency iteration # 4 + + Date : 20230628, Time : 104413.626 +------------------------------------------------------------ + Pulay mixing of updated and previous charge densities. + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 28.0000000000 + | Integrated number of electrons on 3D grid : 27.9999999956 + | Charge integration error : -0.0000000044 + | Normalization factor for density and gradient : 1.0000000002 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = 0.862839E-14 + | Sum of charges compensated after spline to logarithmic grids = -0.629616E-04 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = 0.874725E-14 + Summing up the Hartree potential. + Time summed over all CPUs for potential: real work 0.390 s, elapsed 0.390 s + | RMS charge density error from multipole expansion : 0.137051E-01 + | Average real-space part of the electrostatic potential : 0.43619824 eV + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.397 s, elapsed 0.397 s + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.000 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -5.01959782 eV + What follows are estimated values for band gap, HOMO, LUMO, etc. + | They are estimated on a discrete k-point grid and not necessarily exact. + | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. + + Highest occupied state (VBM) at -5.24107146 eV (relative to internal zero) + | Occupation number: 2.00000000 + | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + + Lowest unoccupied state (CBM) at -4.40317637 eV (relative to internal zero) + | Occupation number: 0.00000000 + | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) + + ESTIMATED overall HOMO-LUMO gap: 0.83789509 eV between HOMO at k-point 1 and LUMO at k-point 4 + | This appears to be an indirect band gap. + | Smallest direct gap : 2.22083176 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, + this system is most likely an insulator or a semiconductor. + + Total energy components: + | Sum of eigenvalues : -328.16317903 Ha -8929.77444340 eV + | XC energy correction : -41.74831175 Ha -1136.02936317 eV + | XC potential correction : 53.91056551 Ha 1466.98112663 eV + | Free-atom electrostatic energy: -263.84284311 Ha -7179.52905141 eV + | Hartree energy correction : -0.80384779 Ha -21.87381136 eV + | Entropy correction : -0.00000000 Ha -0.00000000 eV + | --------------------------- + | Total energy : -580.64761617 Ha -15800.22554270 eV + | Total energy, T -> 0 : -580.64761617 Ha -15800.22554270 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -580.64761617 Ha -15800.22554270 eV + + Derived energy quantities: + | Kinetic energy : 582.10725382 Ha 15839.94430404 eV + | Electrostatic energy : -1121.00655825 Ha -30504.14048358 eV + | Energy correction for multipole + | error in Hartree potential : 0.01823696 Ha 0.49625293 eV + | Sum of eigenvalues per atom : -4464.88722170 eV + | Total energy (T->0) per atom : -7900.11277135 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -7900.11277135 eV + Evaluating new KS density using the density matrix + Evaluating density matrix + Time summed over all CPUs for getting density from density matrix: real work 0.799 s, elapsed 0.799 s + Integration grid: deviation in total charge ( - N_e) = 8.526513E-14 + + Self-consistency convergence accuracy: + | Change of charge density : 0.1066E-05 + | Change of sum of eigenvalues : -0.1214E-03 eV + | Change of total energy : -0.4500E-07 eV + + +------------------------------------------------------------ + End self-consistency iteration # 4 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 1.774 s 1.774 s + | Charge density update : 0.800 s 0.800 s + | Density mixing & preconditioning : 0.178 s 0.178 s + | Hartree multipole update : 0.001 s 0.002 s + | Hartree multipole summation : 0.393 s 0.392 s + | Integration : 0.397 s 0.398 s + | Solution of K.-S. eqns. : 0.005 s 0.004 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 1.553 MB (on task 0) + | Maximum: 1.553 MB (on task 0) + | Average: 1.553 MB + | Peak value for overall tracked memory usage: + | Minimum: 14.236 MB (on task 0 after allocating d_wave) + | Maximum: 14.236 MB (on task 0 after allocating d_wave) + | Average: 14.236 MB + | Largest tracked array allocation so far: + | Minimum: 3.456 MB (hamiltonian_shell on task 0) + | Maximum: 3.456 MB (hamiltonian_shell on task 0) + | Average: 3.456 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + +------------------------------------------------------------ + Begin self-consistency iteration # 5 + + Date : 20230628, Time : 104415.400 +------------------------------------------------------------ + Pulay mixing of updated and previous charge densities. + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 28.0000000000 + | Integrated number of electrons on 3D grid : 28.0000000003 + | Charge integration error : 0.0000000003 + | Normalization factor for density and gradient : 1.0000000000 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = 0.946356E-14 + | Sum of charges compensated after spline to logarithmic grids = -0.629616E-04 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = 0.934464E-14 + Summing up the Hartree potential. + Time summed over all CPUs for potential: real work 0.390 s, elapsed 0.390 s + | RMS charge density error from multipole expansion : 0.137051E-01 + | Average real-space part of the electrostatic potential : 0.43619869 eV + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.397 s, elapsed 0.397 s + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.001 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -5.01959745 eV + What follows are estimated values for band gap, HOMO, LUMO, etc. + | They are estimated on a discrete k-point grid and not necessarily exact. + | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. + + Highest occupied state (VBM) at -5.24107102 eV (relative to internal zero) + | Occupation number: 2.00000000 + | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + + Lowest unoccupied state (CBM) at -4.40317611 eV (relative to internal zero) + | Occupation number: 0.00000000 + | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) + + ESTIMATED overall HOMO-LUMO gap: 0.83789491 eV between HOMO at k-point 1 and LUMO at k-point 4 + | This appears to be an indirect band gap. + | Smallest direct gap : 2.22083180 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, + this system is most likely an insulator or a semiconductor. + + Total energy components: + | Sum of eigenvalues : -328.16317801 Ha -8929.77441560 eV + | XC energy correction : -41.74831181 Ha -1136.02936478 eV + | XC potential correction : 53.91056559 Ha 1466.98112877 eV + | Free-atom electrostatic energy: -263.84284311 Ha -7179.52905141 eV + | Hartree energy correction : -0.80384883 Ha -21.87383971 eV + | Entropy correction : -0.00000000 Ha -0.00000000 eV + | --------------------------- + | Total energy : -580.64761617 Ha -15800.22554272 eV + | Total energy, T -> 0 : -580.64761617 Ha -15800.22554272 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -580.64761617 Ha -15800.22554272 eV + + Derived energy quantities: + | Kinetic energy : 582.10725387 Ha 15839.94430542 eV + | Electrostatic energy : -1121.00655824 Ha -30504.14048337 eV + | Energy correction for multipole + | error in Hartree potential : 0.01823697 Ha 0.49625314 eV + | Sum of eigenvalues per atom : -4464.88720780 eV + | Total energy (T->0) per atom : -7900.11277136 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -7900.11277136 eV + Preliminary charge convergence reached. Turning off preconditioner. + + Evaluating new KS density using the density matrix + Evaluating density matrix + Time summed over all CPUs for getting density from density matrix: real work 0.801 s, elapsed 0.801 s + Integration grid: deviation in total charge ( - N_e) = 1.065814E-14 + + Self-consistency convergence accuracy: + | Change of charge density : 0.6149E-07 + | Change of sum of eigenvalues : 0.2780E-04 eV + | Change of total energy : -0.2328E-07 eV + + Electronic self-consistency reached - switching on the force computation. + + Electronic self-consistency reached - switching on the analytical stress tensor computation. + + +------------------------------------------------------------ + End self-consistency iteration # 5 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 1.775 s 1.776 s + | Charge density & force component update : 0.802 s 0.802 s + | Density mixing : 0.178 s 0.178 s + | Hartree multipole update : 0.001 s 0.001 s + | Hartree multipole summation : 0.393 s 0.393 s + | Hartree pot. SCF incomplete forces : 0.935 s 0.935 s + | Integration : 0.397 s 0.397 s + | Solution of K.-S. eqns. : 0.005 s 0.005 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 1.553 MB (on task 0) + | Maximum: 1.553 MB (on task 0) + | Average: 1.553 MB + | Peak value for overall tracked memory usage: + | Minimum: 14.236 MB (on task 0 after allocating d_wave) + | Maximum: 14.236 MB (on task 0 after allocating d_wave) + | Average: 14.236 MB + | Largest tracked array allocation so far: + | Minimum: 3.456 MB (hamiltonian_shell on task 0) + | Maximum: 3.456 MB (hamiltonian_shell on task 0) + | Average: 3.456 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + +------------------------------------------------------------ + Begin self-consistency iteration # 6 + + Date : 20230628, Time : 104417.176 +------------------------------------------------------------ + Pulay mixing of updated and previous charge densities. + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 28.0000000000 + | Integrated number of electrons on 3D grid : 28.0000000000 + | Charge integration error : 0.0000000000 + | Normalization factor for density and gradient : 1.0000000000 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = 0.772723E-14 + | Sum of charges compensated after spline to logarithmic grids = -0.629616E-04 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = 0.763731E-14 + Summing up the Hartree potential. + Time summed over all CPUs for potential: real work 1.644 s, elapsed 1.644 s + | RMS charge density error from multipole expansion : 0.137051E-01 + | Average real-space part of the electrostatic potential : 0.43619869 eV + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.397 s, elapsed 0.397 s + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.000 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -5.01959745 eV + What follows are estimated values for band gap, HOMO, LUMO, etc. + | They are estimated on a discrete k-point grid and not necessarily exact. + | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. + + Highest occupied state (VBM) at -5.24107102 eV (relative to internal zero) + | Occupation number: 2.00000000 + | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + + Lowest unoccupied state (CBM) at -4.40317611 eV (relative to internal zero) + | Occupation number: 0.00000000 + | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) + + ESTIMATED overall HOMO-LUMO gap: 0.83789491 eV between HOMO at k-point 1 and LUMO at k-point 4 + | This appears to be an indirect band gap. + | Smallest direct gap : 2.22083180 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, + this system is most likely an insulator or a semiconductor. + + Total energy components: + | Sum of eigenvalues : -328.16317801 Ha -8929.77441570 eV + | XC energy correction : -41.74831181 Ha -1136.02936478 eV + | XC potential correction : 53.91056559 Ha 1466.98112877 eV + | Free-atom electrostatic energy: -263.84284311 Ha -7179.52905141 eV + | Hartree energy correction : -0.80384883 Ha -21.87383961 eV + | Entropy correction : -0.00000000 Ha -0.00000000 eV + | --------------------------- + | Total energy : -580.64761617 Ha -15800.22554272 eV + | Total energy, T -> 0 : -580.64761617 Ha -15800.22554272 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -580.64761617 Ha -15800.22554272 eV + + Derived energy quantities: + | Kinetic energy : 582.10725386 Ha 15839.94430505 eV + | Electrostatic energy : -1121.00655823 Ha -30504.14048300 eV + | Energy correction for multipole + | error in Hartree potential : 0.01823697 Ha 0.49625314 eV + | Sum of eigenvalues per atom : -4464.88720785 eV + | Total energy (T->0) per atom : -7900.11277136 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -7900.11277136 eV + Evaluating new KS density using the density matrix + Evaluating density matrix + Time summed over all CPUs for getting density from density matrix: real work 0.799 s, elapsed 0.799 s + Integration grid: deviation in total charge ( - N_e) = 0.000000E+00 + + atomic forces [eV/Ang]: + ----------------------- + atom # 1 + Hellmann-Feynman : -0.591784E-06 0.154593E-06 0.163668E-06 + Ionic forces : 0.000000E+00 0.000000E+00 0.000000E+00 + Multipole : -0.528189E-07 0.315861E-08 0.748176E-08 + Hartree pot. SCF incomplete : 0.105940E-07 -0.281635E-08 0.592908E-08 + Pulay + GGA : 0.000000E+00 0.000000E+00 0.000000E+00 + ---------------------------------------------------------------- + Total forces( 1) : -0.634009E-06 0.154935E-06 0.177079E-06 + atom # 2 + Hellmann-Feynman : 0.596618E-06 -0.152609E-06 -0.157106E-06 + Ionic forces : 0.000000E+00 0.000000E+00 0.000000E+00 + Multipole : 0.528178E-07 -0.315954E-08 -0.748044E-08 + Hartree pot. SCF incomplete : -0.109746E-07 0.239156E-08 -0.598959E-08 + Pulay + GGA : 0.000000E+00 0.000000E+00 0.000000E+00 + ---------------------------------------------------------------- + Total forces( 2) : 0.638461E-06 -0.153376E-06 -0.170576E-06 + + + Self-consistency convergence accuracy: + | Change of charge density : 0.6540E-08 + | Change of sum of eigenvalues : -0.9572E-07 eV + | Change of total energy : 0.3496E-09 eV + | Change of forces : 0.6866E-06 eV/A + + +------------------------------------------------------------ + End self-consistency iteration # 6 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 3.795 s 3.795 s + | Charge density & force component update : 0.801 s 0.801 s + | Density mixing : 0.001 s 0.001 s + | Hartree multipole update : 0.001 s 0.002 s + | Hartree multipole summation : 1.648 s 1.647 s + | Hartree pot. SCF incomplete forces : 0.942 s 0.942 s + | Integration : 0.397 s 0.398 s + | Solution of K.-S. eqns. : 0.005 s 0.004 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 1.553 MB (on task 0) + | Maximum: 1.553 MB (on task 0) + | Average: 1.553 MB + | Peak value for overall tracked memory usage: + | Minimum: 14.236 MB (on task 0 after allocating d_wave) + | Maximum: 14.236 MB (on task 0 after allocating d_wave) + | Average: 14.236 MB + | Largest tracked array allocation so far: + | Minimum: 3.456 MB (hamiltonian_shell on task 0) + | Maximum: 3.456 MB (hamiltonian_shell on task 0) + | Average: 3.456 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + +------------------------------------------------------------ + Begin self-consistency iteration # 7 + + Date : 20230628, Time : 104420.971 +------------------------------------------------------------ + Pulay mixing of updated and previous charge densities. + Renormalizing the density to the exact electron count on the 3D integration grid. + | Formal number of electrons (from input files) : 28.0000000000 + | Integrated number of electrons on 3D grid : 28.0000000000 + | Charge integration error : -0.0000000000 + | Normalization factor for density and gradient : 1.0000000000 + + Evaluating partitioned Hartree potential by multipole expansion. + | Original multipole sum: apparent total charge = -0.690394E-13 + | Sum of charges compensated after spline to logarithmic grids = -0.629616E-04 + | Analytical far-field extrapolation by fixed multipoles: + | Hartree multipole sum: apparent total charge = -0.690219E-13 + Summing up the Hartree potential. + Time summed over all CPUs for potential: real work 1.647 s, elapsed 1.647 s + | RMS charge density error from multipole expansion : 0.137051E-01 + | Average real-space part of the electrostatic potential : 0.43619869 eV + + Integrating Hamiltonian matrix: batch-based integration. + Time summed over all CPUs for integration: real work 0.398 s, elapsed 0.398 s + + Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. + Starting LAPACK eigensolver + Finished Cholesky decomposition + | Time : 0.000 s + Finished transformation to standard eigenproblem + | Time : 0.000 s + Finished solving standard eigenproblem + | Time : 0.001 s + Finished back-transformation of eigenvectors + | Time : 0.000 s + + Obtaining occupation numbers and chemical potential using ELSI. + | Chemical potential (Fermi level): -5.01959746 eV + What follows are estimated values for band gap, HOMO, LUMO, etc. + | They are estimated on a discrete k-point grid and not necessarily exact. + | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. + + Highest occupied state (VBM) at -5.24107103 eV (relative to internal zero) + | Occupation number: 2.00000000 + | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + + Lowest unoccupied state (CBM) at -4.40317611 eV (relative to internal zero) + | Occupation number: 0.00000000 + | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) + + ESTIMATED overall HOMO-LUMO gap: 0.83789492 eV between HOMO at k-point 1 and LUMO at k-point 4 + | This appears to be an indirect band gap. + | Smallest direct gap : 2.22083180 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, + this system is most likely an insulator or a semiconductor. + + Total energy components: + | Sum of eigenvalues : -328.16317802 Ha -8929.77441578 eV + | XC energy correction : -41.74831181 Ha -1136.02936478 eV + | XC potential correction : 53.91056559 Ha 1466.98112878 eV + | Free-atom electrostatic energy: -263.84284311 Ha -7179.52905141 eV + | Hartree energy correction : -0.80384883 Ha -21.87383953 eV + | Entropy correction : -0.00000000 Ha -0.00000000 eV + | --------------------------- + | Total energy : -580.64761617 Ha -15800.22554272 eV + | Total energy, T -> 0 : -580.64761617 Ha -15800.22554272 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -580.64761617 Ha -15800.22554272 eV + + Derived energy quantities: + | Kinetic energy : 582.10725386 Ha 15839.94430512 eV + | Electrostatic energy : -1121.00655823 Ha -30504.14048306 eV + | Energy correction for multipole + | error in Hartree potential : 0.01823697 Ha 0.49625314 eV + | Sum of eigenvalues per atom : -4464.88720789 eV + | Total energy (T->0) per atom : -7900.11277136 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy per atom : -7900.11277136 eV + Evaluating new KS density using the density matrix + Evaluating density matrix + Time summed over all CPUs for getting density from density matrix: real work 0.800 s, elapsed 0.800 s + + Evaluating density-matrix-based force terms: batch-based integration + Evaluating density matrix + Evaluating density matrix + Integration grid: deviation in total charge ( - N_e) = 4.263256E-14 + + atomic forces [eV/Ang]: + ----------------------- + atom # 1 + Hellmann-Feynman : -0.593616E-06 0.154244E-06 0.167646E-06 + Ionic forces : 0.000000E+00 0.000000E+00 0.000000E+00 + Multipole : -0.528170E-07 0.316161E-08 0.747925E-08 + Hartree pot. SCF incomplete : 0.113701E-07 -0.273145E-08 0.453902E-08 + Pulay + GGA : 0.511538E-07 -0.880170E-07 -0.703409E-07 + ---------------------------------------------------------------- + Total forces( 1) : -0.583909E-06 0.666570E-07 0.109323E-06 + atom # 2 + Hellmann-Feynman : 0.598422E-06 -0.152266E-06 -0.161091E-06 + Ionic forces : 0.000000E+00 0.000000E+00 0.000000E+00 + Multipole : 0.528195E-07 -0.315968E-08 -0.747820E-08 + Hartree pot. SCF incomplete : -0.117211E-07 0.229555E-08 -0.457792E-08 + Pulay + GGA : -0.678800E-07 0.867322E-07 0.606676E-07 + ---------------------------------------------------------------- + Total forces( 2) : 0.571641E-06 -0.663978E-07 -0.112479E-06 + + + Analytical stress tensor components [eV] xx yy zz xy xz yz + ----------------------------------------------------------------------------------------------------------------------------------------------------------- + Nuclear Hellmann-Feynman : -0.1190475719E+02 -0.1190493809E+02 -0.1190493809E+02 0.1216492596E-06 0.5622001483E-07 -0.6683101677E-06 + Multipole Hellmann-Feynman : -0.2750159986E+02 -0.2750161039E+02 -0.2750161039E+02 0.3888406713E-06 0.2448907761E-06 -0.2201423316E-05 + On-site Multipole corrections : -0.2840362645E+00 -0.2840362649E+00 -0.2840362649E+00 -0.4332915843E-10 -0.1151778884E-10 0.3636389044E-09 + Strain deriv. of the orbitals : 0.3969034003E+02 0.3969053146E+02 0.3969053146E+02 -0.5077012238E-06 -0.3198719154E-06 0.2664048369E-05 + ----------------------------------------------------------------------------------------------------------------------------------------------------------- + Sum of all contributions : -0.5328603275E-04 -0.5328338212E-04 -0.5328212227E-04 0.2745377944E-08 -0.1877264225E-07 -0.2053214757E-06 + + +-------------------------------------------------------------------+ + | Analytical stress tensor - Symmetrized | + | Cartesian components [eV/A**3] | + +-------------------------------------------------------------------+ + | x y z | + | | + | x -0.00000119 0.00000000 -0.00000000 | + | y 0.00000000 -0.00000119 -0.00000000 | + | z -0.00000000 -0.00000000 -0.00000119 | + | | + | Pressure: 0.00000119 [eV/A**3] | + | | + +-------------------------------------------------------------------+ + + * Warning: Stress tensor is anisotropic. Be aware that pressure is an isotropic quantity. + + + Self-consistency convergence accuracy: + | Change of charge density : 0.3462E-08 + | Change of sum of eigenvalues : -0.8864E-07 eV + | Change of total energy : 0.2227E-09 eV + | Change of forces : 0.4388E-08 eV/A + + Writing Kohn-Sham eigenvalues. + K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + + State Occupation Eigenvalue [Ha] Eigenvalue [eV] + 1 2.00000 -65.748401 -1789.10501 + 2 2.00000 -65.748401 -1789.10501 + 3 2.00000 -5.106132 -138.94492 + 4 2.00000 -5.105967 -138.94044 + 5 2.00000 -3.489905 -94.96516 + 6 2.00000 -3.489905 -94.96516 + 7 2.00000 -3.489905 -94.96516 + 8 2.00000 -3.489510 -94.95440 + 9 2.00000 -3.489510 -94.95440 + 10 2.00000 -3.489510 -94.95440 + 11 2.00000 -0.608072 -16.54648 + 12 2.00000 -0.192606 -5.24107 + 13 2.00000 -0.192606 -5.24107 + 14 2.00000 -0.192606 -5.24107 + 15 0.00000 -0.110992 -3.02024 + 16 0.00000 -0.104018 -2.83046 + 17 0.00000 -0.104018 -2.83046 + 18 0.00000 -0.104018 -2.83046 + 19 0.00000 0.092775 2.52455 + 20 0.00000 0.092775 2.52455 + + What follows are estimated values for band gap, HOMO, LUMO, etc. + | They are estimated on a discrete k-point grid and not necessarily exact. + | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. + + Highest occupied state (VBM) at -5.24107103 eV (relative to internal zero) + | Occupation number: 2.00000000 + | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + + Lowest unoccupied state (CBM) at -4.40317611 eV (relative to internal zero) + | Occupation number: 0.00000000 + | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) + + ESTIMATED overall HOMO-LUMO gap: 0.83789492 eV between HOMO at k-point 1 and LUMO at k-point 4 + | This appears to be an indirect band gap. + | Smallest direct gap : 2.22083180 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) + The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, + this system is most likely an insulator or a semiconductor. + | Chemical Potential : -5.01959746 eV + + Self-consistency cycle converged. + + +------------------------------------------------------------ + End self-consistency iteration # 7 : max(cpu_time) wall_clock(cpu1) + | Time for this iteration : 18.939 s 19.008 s + | Charge density & force component update : 15.942 s 16.006 s + | Density mixing : 0.001 s 0.001 s + | Hartree multipole update : 0.001 s 0.002 s + | Hartree multipole summation : 1.651 s 1.650 s + | Hartree pot. SCF incomplete forces : 0.941 s 0.946 s + | Integration : 0.398 s 0.398 s + | Solution of K.-S. eqns. : 0.005 s 0.005 s + | Total energy evaluation : 0.000 s 0.000 s + + Partial memory accounting: + | Current value for overall tracked memory usage: + | Minimum: 1.553 MB (on task 0) + | Maximum: 1.553 MB (on task 0) + | Average: 1.553 MB + | Peak value for overall tracked memory usage: + | Minimum: 14.236 MB (on task 0 after allocating d_wave) + | Maximum: 14.236 MB (on task 0 after allocating d_wave) + | Average: 14.236 MB + | Largest tracked array allocation so far: + | Minimum: 3.456 MB (hamiltonian_shell on task 0) + | Maximum: 3.456 MB (hamiltonian_shell on task 0) + | Average: 3.456 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. +------------------------------------------------------------ + Removing unitary transformations (pure translations, rotations) from forces on atoms. + Atomic forces before filtering: + | Net force on center of mass : -0.122682E-07 0.259215E-09 -0.315608E-08 eV/A + Atomic forces after filtering: + | Net force on center of mass : -0.850707E-22 0.000000E+00 -0.212677E-22 eV/A + + Energy and forces in a compact form: + | Total energy uncorrected : -0.158002255427229E+05 eV + | Total energy corrected : -0.158002255427229E+05 eV <-- do not rely on this value for anything but (periodic) metals + | Electronic free energy : -0.158002255427229E+05 eV + Total atomic forces (unitary forces cleaned) [eV/Ang]: + | 1 -0.577774893695394E-06 0.665273903016273E-07 0.110901338442392E-06 + | 2 0.577774893695393E-06 -0.665273903016273E-07 -0.110901338442392E-06 + + ------------------------------------ + Start decomposition of the XC Energy + ------------------------------------ + X and C from original XC functional choice + Hartree-Fock Energy : 0.000000000 Ha 0.000000000 eV + X Energy : -40.666268639 Ha -1106.585472109 eV + C Energy : -1.082043167 Ha -29.443892673 eV + XC Energy w/o HF : -41.748311806 Ha -1136.029364783 eV + Total XC Energy : -41.748311806 Ha -1136.029364783 eV + ------------------------------------ + LDA X and C from self-consistent density + X Energy LDA : -37.597186314 Ha -1023.071492920 eV + C Energy LDA : -2.143897994 Ha -58.338432637 eV + ------------------------------------ + End decomposition of the XC Energy + ------------------------------------ + +------------------------------------------------------------ + Relaxation / MD: End force evaluation. : max(cpu_time) wall_clock(cpu1) + | Time for this force evaluation : 32.785 s 32.854 s + +------------------------------------------------------------ + Geometry optimization: Attempting to predict improved coordinates. + + +-------------------------------------------------------------------+ + | Generalized derivatives on lattice vectors [eV/A] | + +-------------------------------------------------------------------+ + |lattice_vector 0.00000946 -0.00000950 -0.00000950 | + |lattice_vector -0.00000947 0.00000943 -0.00000943 | + |lattice_vector -0.00000946 -0.00000943 0.00000942 | + +-------------------------------------------------------------------+ + | Forces on lattice vectors cleaned from atomic contributions [eV/A]| + +-------------------------------------------------------------------+ + |lattice_vector -0.00000946 0.00000950 0.00000950 | + |lattice_vector 0.00000947 -0.00000943 0.00000943 | + |lattice_vector 0.00000946 0.00000943 -0.00000942 | + +-------------------------------------------------------------------+ + Removing unitary transformations (pure translations, rotations) from forces on atoms. + Atomic forces before filtering: + | Net force on center of mass : -0.850707E-22 0.000000E+00 -0.212677E-22 eV/A + Atomic forces after filtering: + | Net force on center of mass : 0.850707E-22 0.000000E+00 0.212677E-22 eV/A + Net remaining forces (excluding translations, rotations) in present geometry: + || Forces on atoms || = 0.577775E-06 eV/A. + || Forces on lattice || = 0.950044E-05 eV/A^3. + Maximum force component is 0.950044E-05 eV/A. + Present geometry is converged. + +------------------------------------------------------------ + Final atomic structure: + x [A] y [A] z [A] + lattice_vector 0.00000007 2.81520842 2.81520842 + lattice_vector 2.81520832 -0.00000004 2.81520837 + lattice_vector 2.81520832 2.81520837 -0.00000004 + + atom 0.00000002 -0.00000000 -0.00000000 Si + atom 1.40760416 1.40760419 1.40760419 Si + + Fractional coordinates: + L1 L2 L3 + atom_frac -0.00000000 0.00000000 0.00000000 Si + atom_frac 0.25000000 0.25000000 0.25000000 Si +------------------------------------------------------------ + +------------------------------------------------------------------------------ + Final output of selected total energy values: + + The following output summarizes some interesting total energy values + at the end of a run (AFTER all relaxation, molecular dynamics, etc.). + + | Total energy of the DFT / Hartree-Fock s.c.f. calculation : -15800.225542723 eV + | Final zero-broadening corrected energy (caution - metals only) : -15800.225542723 eV + | For reference only, the value of 1 Hartree used in FHI-aims is : 27.211384500 eV + | For reference only, the overall average (free atom contribution + | + realspace contribution) of the electrostatic potential after + | s.c.f. convergence is : -11.343876278 eV + + Before relying on these values, please be sure to understand exactly which + total energy value is referred to by a given number. Different objects may + all carry the same name 'total energy'. Definitions: + + Total energy of the DFT / Hartree-Fock s.c.f. calculation: + | Note that this energy does not include ANY quantities calculated after the + | s.c.f. cycle, in particular not ANY RPA, MP2, etc. many-body perturbation terms. + + Final zero-broadening corrected energy: + | For metallic systems only, a broadening of the occupation numbers at the Fermi + | level can be extrapolated back to zero broadening by an electron-gas inspired + | formula. For all systems that are not real metals, this value can be + | meaningless and should be avoided. + +------------------------------------------------------------------------------ + Methods described in the following list of references were used in this FHI-aims run. + If you publish the results, please make sure to cite these reference if they apply. + FHI-aims is an academic code, and for our developers (often, Ph.D. students + and postdocs), scientific credit in the community is essential. + Thank you for helping us! + + For any use of FHI-aims, please cite: + + Volker Blum, Ralf Gehrke, Felix Hanke, Paula Havu, Ville Havu, + Xinguo Ren, Karsten Reuter, and Matthias Scheffler + 'Ab initio molecular simulations with numeric atom-centered orbitals' + Computer Physics Communications 180, 2175-2196 (2009) + http://doi.org/10.1016/j.cpc.2009.06.022 + + + For the analytical stress tensor used in your run, please cite: + + Franz Knuth, Christian Carbogno, Viktor Atalla, Volker Blum, Matthias Scheffler + 'All-electron formalism for total energy strain derivatives and + stress tensor components for numeric atom-centered orbitals' + Computer Physics Communications 190, 33-50 (2015). + http://doi.org/10.1016/j.cpc.2015.01.003 + + + The provided symmetry information was generated with SPGlib: + + Atsushi Togo, Yusuke Seto, Dimitar Pashov + SPGlib 1.7.3 obtained from http://spglib.sourceforge.net + Copyright (C) 2008 Atsushi Togo + + + The ELSI infrastructure was used in your run to solve the Kohn-Sham electronic structure. + Please check out http://elsi-interchange.org to learn more. + If scalability is important for your project, please acknowledge ELSI by citing: + + V. W-z. Yu, F. Corsetti, A. Garcia, W. P. Huhn, M. Jacquelin, W. Jia, + B. Lange, L. Lin, J. Lu, W. Mi, A. Seifitokaldani, A. Vazquez-Mayagoitia, + C. Yang, H. Yang, and V. Blum + 'ELSI: A unified software interface for Kohn-Sham electronic structure solvers' + Computer Physics Communications 222, 267-285 (2018). + http://doi.org/10.1016/j.cpc.2017.09.007 + + + For the real-space grid partitioning and parallelization used in this calculation, please cite: + + Ville Havu, Volker Blum, Paula Havu, and Matthias Scheffler, + 'Efficient O(N) integration for all-electron electronic structure calculation' + 'using numerically tabulated basis functions' + Journal of Computational Physics 228, 8367-8379 (2009). + http://doi.org/10.1016/j.jcp.2009.08.008 + + Of course, there are many other important community references, e.g., those cited in the + above references. Our list is limited to references that describe implementations in the + FHI-aims code. The reason is purely practical (length of this list) - please credit others as well. + +------------------------------------------------------------ + Leaving FHI-aims. + Date : 20230628, Time : 104439.986 + + Computational steps: + | Number of self-consistency cycles : 50 + | Number of SCF (re)initializations : 5 + | Number of relaxation steps : 4 + + Detailed time accounting : max(cpu_time) wall_clock(cpu1) + | Total time : 196.060 s 196.938 s + | Preparation time : 0.110 s 0.111 s + | Boundary condition initialization : 0.313 s 0.313 s + | Grid partitioning : 0.169 s 0.168 s + | Preloading free-atom quantities on grid : 0.908 s 0.911 s + | Free-atom superposition energy : 0.137 s 0.137 s + | Total time for integrations : 22.234 s 22.335 s + | Total time for solution of K.-S. equations : 0.238 s 0.235 s + | Total time for EV reorthonormalization : 0.003 s 0.003 s + | Total time for density & force components : 123.835 s 124.446 s + | Total time for mixing & preconditioning : 6.421 s 6.446 s + | Total time for Hartree multipole update : 0.059 s 0.059 s + | Total time for Hartree multipole sum : 32.131 s 32.238 s + | Total time for total energy evaluation : 0.002 s 0.002 s + | Total time NSC force correction : 9.394 s 9.429 s + | Total time for scaled ZORA corrections : 0.000 s 0.000 s + + Partial memory accounting: + | Residual value for overall tracked memory usage across tasks: 0.000000 MB (should be 0.000000 MB) + | Peak values for overall tracked memory usage: + | Minimum: 14.236 MB (on task 0 after allocating d_wave) + | Maximum: 14.236 MB (on task 0 after allocating d_wave) + | Average: 14.236 MB + | Largest tracked array allocation: + | Minimum: 3.456 MB (hamiltonian_shell on task 0) + | Maximum: 3.456 MB (hamiltonian_shell on task 0) + | Average: 3.456 MB + Note: These values currently only include a subset of arrays which are explicitly tracked. + The "true" memory usage will be greater. + + Have a nice day. +------------------------------------------------------------ diff --git a/tests/io/aims/aims_output_files/si_ref.json b/tests/io/aims/aims_output_files/si_ref.json new file mode 100644 index 00000000000..864fe0f3224 --- /dev/null +++ b/tests/io/aims/aims_output_files/si_ref.json @@ -0,0 +1,767 @@ +{ + "@module": "pymatgen.io.aims.output", + "@class": "AimsOutput", + "results": [ + { + "@module": "pymatgen.core.structure", + "@class": "Structure", + "charge": 0, + "lattice": { + "matrix": [ + [ + 0.0, + 2.755, + 2.755 + ], + [ + 2.755, + 0.0, + 2.755 + ], + [ + 2.755, + 2.755, + 0.0 + ] + ], + "pbc": [ + true, + true, + true + ], + "a": 3.896158364337877, + "b": 3.896158364337877, + "c": 3.896158364337877, + "alpha": 60.00000000000001, + "beta": 60.00000000000001, + "gamma": 60.00000000000001, + "volume": 41.821037749999995 + }, + "properties": { + "energy": -15800.1843792097, + "free_energy": -15800.1843792097, + "stress": { + "@module": "numpy", + "@class": "array", + "dtype": 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"properties": { + "force": { + "@module": "numpy", + "@class": "array", + "dtype": "float64", + "data": [ + 5.77774893695393e-07, + -6.65273903016273e-08, + -1.10901338442392e-07 + ] + } + }, + "label": "Si" + } + ], + "@version": null + } + ], + "metadata": { + "commit_hash": "232d594a3", + "aims_uuid": "7F959EC8-A7E1-43AC-A4DA-9302788CF7F6", + "version_number": "220309", + "fortran_compiler": "mpiifort (Intel) version 2021.6.0.20220226", + "c_compiler": "icc (Intel) version 2021.6.0.20220226", + "fortran_compiler_flags": "-O3 -ip -fp-model precise", + "c_compiler_flags": "-m64 -O3 -ip -fp-model precise -std=gnu99", + "build_type": [ + "MPI", + "ScaLAPACK", + "LibXC", + "i-PI", + "RLSY" + ], + "linked_against": [ + "/home/tpurcell/intel/oneapi/mkl/2022.1.0/lib/intel64/libmkl_scalapack_lp64.so", + "/home/tpurcell/intel/oneapi/mkl/2022.1.0/lib/intel64/libmkl_blacs_intelmpi_lp64.so", + "/home/tpurcell/intel/oneapi/mkl/2022.1.0/lib/intel64/libmkl_intel_lp64.so", + "/home/tpurcell/intel/oneapi/mkl/2022.1.0/lib/intel64/libmkl_sequential.so", + "/home/tpurcell/intel/oneapi/mkl/2022.1.0/lib/intel64/libmkl_core.so" + ] + }, + "structure_summary": { + "initial_structure": { + "@module": "pymatgen.core.structure", + "@class": "Structure", + "charge": 0.0, + "lattice": { + "matrix": [ + [ + 0.0, + 2.755, + 2.755 + ], + [ + 2.755, + 0.0, + 2.755 + ], + [ + 2.755, + 2.755, + 0.0 + ] + ], + "pbc": [ + true, + true, + true + ], + "a": 3.896158364337877, + "b": 3.896158364337877, + "c": 3.896158364337877, + "alpha": 60.00000000000001, + "beta": 60.00000000000001, + "gamma": 60.00000000000001, + "volume": 41.821037749999995 + }, + "properties": {}, + "sites": [ + { + "species": [ + { + "element": "Si", + "occu": 1 + } + ], + "abc": [ + 0.0, + 0.0, + 0.0 + ], + "xyz": [ + 0.0, + 0.0, + 0.0 + ], + "properties": { + "charge": 0.0 + }, + "label": "Si" + }, + { + "species": [ + { + "element": "Si", + "occu": 1 + } + ], + "abc": [ + 0.25, + 0.25, + 0.25 + ], + "xyz": [ + 1.3775, + 1.3775, + 1.3775 + ], + "properties": { + "charge": 0.0 + }, + "label": "Si" + } + ], + "@version": null + }, + "initial_lattice": { + "@module": "pymatgen.core.lattice", + "@class": "Lattice", + "matrix": [ + [ + 0.0, + 2.755, + 2.755 + ], + [ + 2.755, + 0.0, + 2.755 + ], + [ + 2.755, + 2.755, + 0.0 + ] + ], + "pbc": [ + true, + true, + true + ], + "@version": null + }, + "is_relaxation": true, + "is_md": false, + "n_atoms": 2, + "n_bands": 20, + "n_electrons": 28, + "n_spins": 1, + "electronic_temperature": 0.1, + "n_k_points": 8, + "k_points": null, + "k_point_weights": null + } +} From ea95182c25b17ba1fe9f09135444a4b1d75f533b Mon Sep 17 00:00:00 2001 From: Thomas Purcell Date: Mon, 30 Oct 2023 10:46:57 +0100 Subject: [PATCH 06/30] Add tests for AimsGeometryIn inputs Test for both Si and H2O --- pymatgen/io/aims/inputs.py | 142 +++++++++++++++--- .../io/aims/aims_input_files/geometry.in.h2o | 8 + .../aims/aims_input_files/geometry.in.h2o.ref | 8 + tests/io/aims/aims_input_files/geometry.in.si | 10 ++ .../aims/aims_input_files/geometry.in.si.ref | 10 ++ tests/io/aims/aims_input_files/h2o_ref.json | 72 +++++++++ tests/io/aims/aims_input_files/si_ref.json | 91 +++++++++++ tests/io/aims/test_aims_inputs.py | 78 ++++++++++ 8 files changed, 394 insertions(+), 25 deletions(-) create mode 100644 tests/io/aims/aims_input_files/geometry.in.h2o create mode 100644 tests/io/aims/aims_input_files/geometry.in.h2o.ref create mode 100644 tests/io/aims/aims_input_files/geometry.in.si create mode 100644 tests/io/aims/aims_input_files/geometry.in.si.ref create mode 100644 tests/io/aims/aims_input_files/h2o_ref.json create mode 100644 tests/io/aims/aims_input_files/si_ref.json create mode 100644 tests/io/aims/test_aims_inputs.py diff --git a/pymatgen/io/aims/inputs.py b/pymatgen/io/aims/inputs.py index ee70e0bdffc..125f0bf6e67 100644 --- a/pymatgen/io/aims/inputs.py +++ b/pymatgen/io/aims/inputs.py @@ -14,7 +14,7 @@ import numpy as np from monty.json import MontyDecoder, MSONable -from pymatgen.core import Lattice, Structure +from pymatgen.core import Lattice, Molecule, Structure if TYPE_CHECKING: from collections.abc import Sequence @@ -25,7 +25,7 @@ class AimsGeometryIn(MSONable): """Class representing an aims geometry.in file""" _content: str - _structure: Structure + _structure: Structure | Molecule @classmethod def from_str(cls, contents: str): @@ -36,7 +36,9 @@ def from_str(cls, contents: str): contents: str The content of the string """ - content_lines = [line.strip() for line in contents.split("\n") if line.strip()[0] != "#"] + content_lines = [ + line.strip() for line in contents.split("\n") if len(line.strip()) > 0 and line.strip()[0] != "#" + ] species = [] coords = [] @@ -54,9 +56,9 @@ def from_str(cls, contents: str): if inp[0] == "lattice_vector": lattice_vectors.append([float(ii) for ii in line.split()[1:4]]) if inp[0] == "initial_moment": - charges_dct[len(coords) - 1] = float(inp[1]) - if inp[0] == "initial_charge": moments_dct[len(coords) - 1] = float(inp[1]) + if inp[0] == "initial_charge": + charges_dct[len(coords) - 1] = float(inp[1]) charge = np.zeros(len(coords)) for key, val in charges_dct.items(): @@ -70,7 +72,7 @@ def from_str(cls, contents: str): lattice = Lattice(lattice_vectors) for cc in range(len(coords)): if is_frac[cc]: - coords[cc] = lattice.get_cartesian_coords(np.array(coords[cc]).reshape(3, 1)) + coords[cc] = lattice.get_cartesian_coords(np.array(coords[cc]).reshape(1, 3)).flatten() elif len(lattice_vectors) == 0: lattice = None if any(is_frac): @@ -78,17 +80,31 @@ def from_str(cls, contents: str): else: raise ValueError("Incorrect number of lattice vectors passed.") - structure = Structure( - lattice, - species, - coords, - np.sum(charge), - coords_are_cartesian=True, - site_properties={"magmom": magmom, "charge": charge}, - ) + if lattice is None: + structure = Molecule( + species, + coords, + np.sum(charge), + site_properties={"magmom": magmom, "charge": charge}, + ) + else: + structure = Structure( + lattice, + species, + coords, + np.sum(charge), + coords_are_cartesian=True, + site_properties={"magmom": magmom, "charge": charge}, + ) return cls(_content="\n".join(content_lines), _structure=structure) + @classmethod + def from_file(cls, filepath: str | Path): + with open(filepath) as infile: + content = infile.read() + return cls.from_str(content) + @classmethod def from_structure(cls, structure: Structure): """The contents of the input file @@ -100,23 +116,24 @@ def from_structure(cls, structure: Structure): """ content_lines = [] - if structure.lattice is not None: - for lv in structure.lattive.matrix: + if isinstance(structure, Structure): + for lv in structure.lattice.matrix: content_lines.append(f"lattice_vector {lv[0]: .12e} {lv[1]: .12e} {lv[2]: .12e}") charges = structure.site_properties.get("charge", np.zeros(len(structure.species))) magmoms = structure.site_properties.get("magmom", np.zeros(len(structure.species))) for species, coord, charge, magmom in zip(structure.species, structure.cart_coords, charges, magmoms): + print(coord) content_lines.append(f"atom {coord[0]: .12e} {coord[1]: .12e} {coord[2]: .12e} {species}") if charge != 0: - content_lines.append(f" initial_charge {charge}") + content_lines.append(f" initial_charge {charge:.12e}") if magmom != 0: - content_lines.append(f" initial_moment {magmom}") + content_lines.append(f" initial_moment {magmom:.12e}") return cls(_content="\n".join(content_lines), _structure=structure) @property - def structure(self) -> Structure: + def structure(self) -> Structure | Molecule: """Accses structure for the file""" return self._structure @@ -146,7 +163,9 @@ def write_file(self, directory: str | Path | None = None, overwrite: bool = Fals fd.write(f"# FHI-aims geometry file: {directory}/geometry.in\n") fd.write("# File generated from pymatgen\n") fd.write(f"# {time.asctime()}\n") + fd.write("#" + "=" * 72 + "\n") fd.write(self.content) + fd.write("\n") def as_dict(self) -> dict[str, Any]: """Get a dictionary representation of the geometry.in file. @@ -174,8 +193,8 @@ def from_dict(cls, d: dict[str, Any]): decoded = {k: MontyDecoder().process_decoded(v) for k, v in d.items() if not k.startswith("@")} return cls( - content=decoded["content"], - structure=decoded["structure"], + _content=decoded["content"], + _structure=decoded["structure"], ) @@ -237,11 +256,12 @@ class AimsCube(MSONable): The type of electron localization function to use (see FHI-aims manual) """ - name: str = "AimsCube" type: str = field(default_factory=str) - origin: Sequence[float] | tuple[float, float, float] = [0.0, 0.0, 0.0] - edges: Sequence[Sequence[float]] = [[0.1, 0.0, 0.0], [0.0, 0.1, 0.0], [0.0, 0.0, 0.1]] - points: Sequence[int] | tuple[int, int, int] = [0, 0, 0] + origin: Sequence[float] | tuple[float, float, float] = field(default_factory=lambda: [0.0, 0.0, 0.0]) + edges: Sequence[Sequence[float]] = field( + default_factory=lambda: [[0.1, 0.0, 0.0], [0.0, 0.1, 0.0], [0.0, 0.0, 0.1]] + ) + points: Sequence[int] | tuple[int, int, int] = field(default_factory=lambda: [0, 0, 0]) format: str = "cube" spinstate: int | None = None kpoint: int | None = None @@ -305,6 +325,50 @@ def control_block(self): return cb + def as_dict(self) -> dict[str, Any]: + """Get a dictionary representation of the geometry.in file. + + Returns + ------- + The dictionary representation of the input file + """ + dct: dict[str, Any] = {} + dct["@module"] = type(self).__module__ + dct["@class"] = type(self).__name__ + dct["type"] = self.type + dct["origin"] = self.origin + dct["edges"] = self.edges + dct["points"] = self.points + dct["format"] = self.format + dct["spinstate"] = self.spinstate + dct["kpoint"] = self.kpoint + dct["filename"] = self.filename + dct["elf_type"] = self.elf_type + return dct + + @classmethod + def from_dict(cls, d: dict[str, Any]): + """Initialize from dictionary. + + self.__dict__ + ---------- + d: dict[str, Any] + The MontyEncoded dictionary + """ + decoded = {k: MontyDecoder().process_decoded(v) for k, v in d.items() if not k.startswith("@")} + + return cls( + type=decoded["type"], + origin=decoded["origin"], + edges=decoded["edges"], + points=decoded["points"], + format=decoded["format"], + spinstate=decoded["spinstate"], + kpoint=decoded["kpoint"], + filename=decoded["filename"], + elf_type=decoded["elf_type"], + ) + @dataclass class AimsControlIn(MSONable): @@ -439,3 +503,31 @@ def get_species_block(self, structure, species_dir): with open(filename) as sf: sb += "\n".join(sf.readlines()) return sb + + def as_dict(self) -> dict[str, Any]: + """Get a dictionary representation of the geometry.in file. + + Returns + ------- + The dictionary representation of the input file + """ + dct = {} + dct["@module"] = type(self).__module__ + dct["@class"] = type(self).__name__ + dct["parameters"] = self.parameters + return dct + + @classmethod + def from_dict(cls, d: dict[str, Any]): + """Initialize from dictionary. + + self.__dict__ + ---------- + d: dict[str, Any] + The MontyEncoded dictionary + """ + decoded = {k: MontyDecoder().process_decoded(v) for k, v in d.items() if not k.startswith("@")} + + return cls( + _parameters=decoded["parameters"], + ) diff --git a/tests/io/aims/aims_input_files/geometry.in.h2o b/tests/io/aims/aims_input_files/geometry.in.h2o new file mode 100644 index 00000000000..fc58d0eda6d --- /dev/null +++ b/tests/io/aims/aims_input_files/geometry.in.h2o @@ -0,0 +1,8 @@ +#======================================================= +# FHI-aims file: geometry.in.h2o +# Created using the Atomic Simulation Environment (ASE) +# Mon Oct 30 09:52:33 2023 +#======================================================= +atom 0.0000000000000000 0.0000000000000000 0.1192620000000000 O +atom 0.0000000000000000 0.7632390000000000 -0.4770470000000000 H +atom 0.0000000000000000 -0.7632390000000000 -0.4770470000000000 H diff --git a/tests/io/aims/aims_input_files/geometry.in.h2o.ref b/tests/io/aims/aims_input_files/geometry.in.h2o.ref new file mode 100644 index 00000000000..3882b668553 --- /dev/null +++ b/tests/io/aims/aims_input_files/geometry.in.h2o.ref @@ -0,0 +1,8 @@ +#======================================================================== +# FHI-aims geometry file: /home/tpurcell/git/pymatgen/tests/io/aims/geometry.in +# File generated from pymatgen +# Mon Oct 30 10:43:06 2023 +#======================================================================== +atom 0.000000000000e+00 0.000000000000e+00 1.192620000000e-01 O +atom 0.000000000000e+00 7.632390000000e-01 -4.770470000000e-01 H +atom 0.000000000000e+00 -7.632390000000e-01 -4.770470000000e-01 H diff --git a/tests/io/aims/aims_input_files/geometry.in.si b/tests/io/aims/aims_input_files/geometry.in.si new file mode 100644 index 00000000000..ebeb6451dd7 --- /dev/null +++ b/tests/io/aims/aims_input_files/geometry.in.si @@ -0,0 +1,10 @@ +#======================================================= +# FHI-aims file: geometry.in.si +# Created using the Atomic Simulation Environment (ASE) +# Mon Oct 30 09:52:33 2023 +#======================================================= +lattice_vector 0.0000000000000000 2.715 2.716 +lattice_vector 2.717 0.0000000000000000 2.718 +lattice_vector 2.719 2.720 0.0000000000000000 +atom_frac 0.0000000000000000 0.0000000000000000 -0.0000000000000000 Si +atom_frac 0.2500000000000000 0.2400000000000000 0.2600000000000000 Si diff --git a/tests/io/aims/aims_input_files/geometry.in.si.ref b/tests/io/aims/aims_input_files/geometry.in.si.ref new file mode 100644 index 00000000000..de6cf81e39a --- /dev/null +++ b/tests/io/aims/aims_input_files/geometry.in.si.ref @@ -0,0 +1,10 @@ +#======================================================================== +# FHI-aims geometry file: /home/tpurcell/git/pymatgen/tests/io/aims/geometry.in +# File generated from pymatgen +# Mon Oct 30 10:35:09 2023 +#======================================================================== +lattice_vector 0.000000000000e+00 2.715000000000e+00 2.716000000000e+00 +lattice_vector 2.717000000000e+00 0.000000000000e+00 2.718000000000e+00 +lattice_vector 2.719000000000e+00 2.720000000000e+00 0.000000000000e+00 +atom 0.000000000000e+00 0.000000000000e+00 0.000000000000e+00 Si +atom 1.359020000000e+00 1.385950000000e+00 1.331320000000e+00 Si diff --git a/tests/io/aims/aims_input_files/h2o_ref.json b/tests/io/aims/aims_input_files/h2o_ref.json new file mode 100644 index 00000000000..40a0a18786f --- /dev/null +++ b/tests/io/aims/aims_input_files/h2o_ref.json @@ -0,0 +1,72 @@ +{ + "@module": "pymatgen.io.aims.inputs", + "@class": "AimsGeometryIn", + "content": "atom 0.0000000000000000 0.0000000000000000 0.1192620000000000 O\natom 0.0000000000000000 0.7632390000000000 -0.4770470000000000 H\natom 0.0000000000000000 -0.7632390000000000 -0.4770470000000000 H", + "structure": { + "@module": "pymatgen.core.structure", + "@class": "Molecule", + "charge": 0.0, + "spin_multiplicity": 1, + "sites": [ + { + "name": "O", + "species": [ + { + "element": "O", + "occu": 1 + } + ], + "xyz": [ + 0.0, + 0.0, + 0.119262 + ], + "properties": { + "magmom": 0.0, + "charge": 0.0 + }, + "label": "O" + }, + { + "name": "H", + "species": [ + { + "element": "H", + "occu": 1 + } + ], + "xyz": [ + 0.0, + 0.763239, + -0.477047 + ], + "properties": { + "magmom": 0.0, + "charge": 0.0 + }, + "label": "H" + }, + { + "name": "H", + "species": [ + { + "element": "H", + "occu": 1 + } + ], + "xyz": [ + 0.0, + -0.763239, + -0.477047 + ], + "properties": { + "magmom": 0.0, + "charge": 0.0 + }, + "label": "H" + } + ], + "properties": {}, + "@version": null + } +} diff --git a/tests/io/aims/aims_input_files/si_ref.json b/tests/io/aims/aims_input_files/si_ref.json new file mode 100644 index 00000000000..289f28243be --- /dev/null +++ b/tests/io/aims/aims_input_files/si_ref.json @@ -0,0 +1,91 @@ +{ + "@module": "pymatgen.io.aims.inputs", + "@class": "AimsGeometryIn", + "content": "lattice_vector 0.0000000000000000 2.715 2.716\nlattice_vector 2.717 0.0000000000000000 2.718\nlattice_vector 2.719 2.720 0.0000000000000000\natom_frac 0.0000000000000000 0.0000000000000000 -0.0000000000000000 Si\natom_frac 0.2500000000000000 0.2400000000000000 0.2600000000000000 Si", + "structure": { + "@module": "pymatgen.core.structure", + "@class": "Structure", + "charge": 0.0, + "lattice": { + "matrix": [ + [ + 0.0, + 2.715, + 2.716 + ], + [ + 2.717, + 0.0, + 2.718 + ], + [ + 2.719, + 2.72, + 0.0 + ] + ], + "pbc": [ + true, + true, + true + ], + "a": 3.840296993723272, + "b": 3.843125420800107, + "c": 3.8459538478770128, + "alpha": 60.01216763270818, + "beta": 60.000011198585014, + "gamma": 59.987821915280264, + "volume": 40.13639887 + }, + "properties": {}, + "sites": [ + { + "species": [ + { + "element": "Si", + "occu": 1 + } + ], + "abc": [ + 0.0, + 0.0, + 0.0 + ], + "xyz": [ + 0.0, + 0.0, + 0.0 + ], + "properties": { + "magmom": 0.0, + "charge": 0.0 + }, + "label": "Si" + }, + { + "species": [ + { + "element": "Si", + "occu": 1 + } + ], + "abc": [ + 0.25, + 0.24, + 0.26 + ], + "xyz": [ + 1.3590200000000001, + 1.38595, + 1.33132 + ], + "properties": { + "magmom": 0.0, + "charge": 0.0 + }, + "label": "Si" + } + ], + "@version": null + } +} diff --git a/tests/io/aims/test_aims_inputs.py b/tests/io/aims/test_aims_inputs.py new file mode 100644 index 00000000000..b395fdfd7e9 --- /dev/null +++ b/tests/io/aims/test_aims_inputs.py @@ -0,0 +1,78 @@ +from __future__ import annotations + +import json +import os +from pathlib import Path + +import numpy as np +from monty.json import MontyDecoder + +from pymatgen.io.aims.inputs import AimsGeometryIn + +infile_dir = Path(__file__).parent / "aims_input_files" + + +def test_read_write_si_in(tmpdir): + si = AimsGeometryIn.from_file(infile_dir / "geometry.in.si") + + in_lattice = np.array([[0.0, 2.715, 2.716], [2.717, 0.0, 2.718], [2.719, 2.720, 0.0]]) + in_coords = np.array([[0.0, 0.0, 0.0], [0.25, 0.24, 0.26]]) + + assert all(sp.symbol == "Si" for sp in si.structure.species) + assert np.allclose(si.structure.lattice.matrix, in_lattice) + assert np.allclose(si.structure.frac_coords.flatten(), in_coords.flatten()) + + si_test_from_struct = AimsGeometryIn.from_structure(si.structure) + assert si.structure == si_test_from_struct.structure + + workdir = Path.cwd() + os.chdir(tmpdir) + si_test_from_struct.write_file(overwrite=True) + + with open("geometry.in") as test_file: + test_lines = test_file.readlines()[5:] + + with open(infile_dir / "geometry.in.si.ref") as ref_file: + ref_lines = ref_file.readlines()[5:] + + for test_line, ref_line in zip(test_lines, ref_lines): + assert test_line == ref_line + + os.chdir(workdir) + + with open(f"{infile_dir}/si_ref.json") as si_ref_json: + si_from_dct = json.load(si_ref_json, cls=MontyDecoder) + + assert si.structure == si_from_dct.structure + + +def test_read_h2o_in(tmpdir): + h2o = AimsGeometryIn.from_file(infile_dir / "geometry.in.h2o") + + in_coords = np.array([[0.0, 0.0, 0.119262], [0.0, 0.763239, -0.477047], [0.0, -0.763239, -0.477047]]) + + assert all(sp.symbol == symb for sp, symb in zip(h2o.structure.species, ["O", "H", "H"])) + assert np.allclose(h2o.structure.cart_coords.flatten(), in_coords.flatten()) + + h2o_test_from_struct = AimsGeometryIn.from_structure(h2o.structure) + assert h2o.structure == h2o_test_from_struct.structure + + workdir = Path.cwd() + os.chdir(tmpdir) + h2o_test_from_struct.write_file(overwrite=True) + + with open("geometry.in") as test_file: + test_lines = test_file.readlines()[5:] + + with open(infile_dir / "geometry.in.h2o.ref") as ref_file: + ref_lines = ref_file.readlines()[5:] + + for test_line, ref_line in zip(test_lines, ref_lines): + assert test_line == ref_line + + os.chdir(workdir) + + with open(f"{infile_dir}/h2o_ref.json") as h2o_ref_json: + h2o_from_dct = json.load(h2o_ref_json, cls=MontyDecoder) + + assert h2o.structure == h2o_from_dct.structure From 41ac7bdd2b88a8dd9be1e127654829d890364e60 Mon Sep 17 00:00:00 2001 From: Thomas Purcell Date: Mon, 30 Oct 2023 15:06:43 +0100 Subject: [PATCH 07/30] Add tests for AimsCube Make sure that the AimsCubes are properly formatted --- tests/io/aims/test_aims_inputs.py | 91 ++++++++++++++++++++++++++++++- 1 file changed, 88 insertions(+), 3 deletions(-) diff --git a/tests/io/aims/test_aims_inputs.py b/tests/io/aims/test_aims_inputs.py index b395fdfd7e9..b26fdb7e5bd 100644 --- a/tests/io/aims/test_aims_inputs.py +++ b/tests/io/aims/test_aims_inputs.py @@ -5,9 +5,10 @@ from pathlib import Path import numpy as np -from monty.json import MontyDecoder +import pytest +from monty.json import MontyDecoder, MontyEncoder -from pymatgen.io.aims.inputs import AimsGeometryIn +from pymatgen.io.aims.inputs import ALLOWED_AIMS_CUBE_TYPES, ALLOWED_AIMS_CUBE_TYPES_STATE, AimsCube, AimsGeometryIn infile_dir = Path(__file__).parent / "aims_input_files" @@ -49,7 +50,13 @@ def test_read_write_si_in(tmpdir): def test_read_h2o_in(tmpdir): h2o = AimsGeometryIn.from_file(infile_dir / "geometry.in.h2o") - in_coords = np.array([[0.0, 0.0, 0.119262], [0.0, 0.763239, -0.477047], [0.0, -0.763239, -0.477047]]) + in_coords = np.array( + [ + [0.0, 0.0, 0.119262], + [0.0, 0.763239, -0.477047], + [0.0, -0.763239, -0.477047], + ] + ) assert all(sp.symbol == symb for sp, symb in zip(h2o.structure.species, ["O", "H", "H"])) assert np.allclose(h2o.structure.cart_coords.flatten(), in_coords.flatten()) @@ -76,3 +83,81 @@ def test_read_h2o_in(tmpdir): h2o_from_dct = json.load(h2o_ref_json, cls=MontyDecoder) assert h2o.structure == h2o_from_dct.structure + + +def check_wrong_type_aims_cube(type, exp_err): + with pytest.raises(ValueError, match=exp_err): + AimsCube(type=type) + + +def test_aims_cube(tmpdir): + check_wrong_type_aims_cube(type="INCORRECT_TYPE", exp_err="Cube type undefined") + + for type in ALLOWED_AIMS_CUBE_TYPES_STATE: + check_wrong_type_aims_cube( + type=type, + exp_err=f"Cube of type {type} must have a state associated with it", + ) + + for type in ALLOWED_AIMS_CUBE_TYPES: + check_wrong_type_aims_cube( + type=f"{type} 1", + exp_err=f"Cube of type {type} can not have a state associated with it", + ) + + with pytest.raises( + ValueError, + match="Cube file must have a format of cube, gOpenMol, or xsf", + ): + AimsCube(type=ALLOWED_AIMS_CUBE_TYPES[0], format="TEST_ERR") + + with pytest.raises(ValueError, match="Spin state must be 1 or 2"): + AimsCube(type=ALLOWED_AIMS_CUBE_TYPES[0], spinstate=3) + + with pytest.raises(ValueError, match="The cube origin must have 3 components"): + AimsCube(type=ALLOWED_AIMS_CUBE_TYPES[0], origin=[0]) + + with pytest.raises(ValueError, match="Only three cube edges can be passed"): + AimsCube(type=ALLOWED_AIMS_CUBE_TYPES[0], edges=[[0.0, 0.0, 0.1]]) + + with pytest.raises(ValueError, match="Each cube edge must have 3 components"): + AimsCube( + type=ALLOWED_AIMS_CUBE_TYPES[0], + edges=[[0.0, 0.0, 0.1], [0.1, 0.0, 0.0], [0.1, 0.0]], + ) + + with pytest.raises(ValueError, match="elf_type only used when the cube type is elf"): + AimsCube(type=ALLOWED_AIMS_CUBE_TYPES[0], elf_type=1) + + with pytest.raises(ValueError, match="The number of points per edge must have 3 components"): + AimsCube(type=ALLOWED_AIMS_CUBE_TYPES[0], points=[100, 100, 100, 100]) + + test_cube = AimsCube( + type="elf", + origin=[0, 0, 0], + edges=[[0.01, 0, 0], [0.0, 0.01, 0], [0.0, 0, 0.01]], + points=[100, 100, 100], + spinstate=1, + kpoint=1, + filename="test.cube", + format="cube", + elf_type=1, + ) + + test_cube_block = [ + "output cube elf", + " cube origin [0, 0, 0]", + " cube edge 100 1.000000000000e-02 0.000000000000e+00 0.000000000000e+00", + " cube edge 100 0.000000000000e+00 1.000000000000e-02 0.000000000000e+00", + " cube edge 100 0.000000000000e+00 0.000000000000e+00 1.000000000000e-02", + " cube format cube", + " cube spinstate 1", + " cube kpoint 1", + " cube filename test.cube", + " cube elf_type 1", + "", + ] + assert test_cube.control_block == "\n".join(test_cube_block) + + test_cube_from_dict = json.loads(json.dumps(test_cube.as_dict(), cls=MontyEncoder), cls=MontyDecoder) + assert test_cube_from_dict.control_block == test_cube.control_block From d9e30417ae381bf7af8c715caa8fb8d911a73c3e Mon Sep 17 00:00:00 2001 From: Thomas Purcell Date: Mon, 30 Oct 2023 20:57:24 +0100 Subject: [PATCH 08/30] Add tests for aims_control_in Add test for aims control.in file generators --- pymatgen/io/aims/inputs.py | 34 +++- tests/io/aims/aims_input_files/control.in.h2o | 170 ++++++++++++++++++ tests/io/aims/aims_input_files/control.in.si | 126 +++++++++++++ .../aims/species_directory/light/01_H_default | 64 +++++++ .../aims/species_directory/light/08_O_default | 80 +++++++++ .../species_directory/light/14_Si_default | 87 +++++++++ tests/io/aims/test_aims_inputs.py | 109 +++++++++-- 7 files changed, 645 insertions(+), 25 deletions(-) create mode 100644 tests/io/aims/aims_input_files/control.in.h2o create mode 100644 tests/io/aims/aims_input_files/control.in.si create mode 100644 tests/io/aims/species_directory/light/01_H_default create mode 100644 tests/io/aims/species_directory/light/08_O_default create mode 100644 tests/io/aims/species_directory/light/14_Si_default diff --git a/pymatgen/io/aims/inputs.py b/pymatgen/io/aims/inputs.py index 125f0bf6e67..feb48e8e0a7 100644 --- a/pymatgen/io/aims/inputs.py +++ b/pymatgen/io/aims/inputs.py @@ -123,7 +123,6 @@ def from_structure(cls, structure: Structure): charges = structure.site_properties.get("charge", np.zeros(len(structure.species))) magmoms = structure.site_properties.get("magmom", np.zeros(len(structure.species))) for species, coord, charge, magmom in zip(structure.species, structure.cart_coords, charges, magmoms): - print(coord) content_lines.append(f"atom {coord[0]: .12e} {coord[1]: .12e} {coord[2]: .12e} {species}") if charge != 0: content_lines.append(f" initial_charge {charge:.12e}") @@ -259,7 +258,11 @@ class AimsCube(MSONable): type: str = field(default_factory=str) origin: Sequence[float] | tuple[float, float, float] = field(default_factory=lambda: [0.0, 0.0, 0.0]) edges: Sequence[Sequence[float]] = field( - default_factory=lambda: [[0.1, 0.0, 0.0], [0.0, 0.1, 0.0], [0.0, 0.0, 0.1]] + default_factory=lambda: [ + [0.1, 0.0, 0.0], + [0.0, 0.1, 0.0], + [0.0, 0.0, 0.1], + ] ) points: Sequence[int] | tuple[int, int, int] = field(default_factory=lambda: [0, 0, 0]) format: str = "cube" @@ -307,7 +310,7 @@ def __post_init__(self): @property def control_block(self): cb = f"output cube {self.type}\n" - cb += f" cube origin {self.origin}\n" + cb += f" cube origin {self.origin[0]: .12e} {self.origin[1]: .12e} {self.origin[2]: .12e}\n" for ii in range(3): cb += f" cube edge {self.points[ii]} " cb += f"{self.edges[ii][0]: .12e} " @@ -376,7 +379,7 @@ class AimsControlIn(MSONable): _parameters: dict[str, Any] = field(default_factory=dict) - def __postinit__(self): + def __post_init__(self): if "output" not in self._parameters: self._parameters["output"] = [] @@ -395,6 +398,16 @@ def __setitem__(self, key: str, value: Any): else: self._parameters[key] = value + def __delitem__(self, key: str) -> Any: + """Delete a parameter from the input object + + Parameters + ---------- + key: str + The key in the parameter to remove + """ + return self._parameters.pop(key, None) + @property def parameters(self): return self._parameters @@ -403,6 +416,8 @@ def parameters(self): def parameters(self, parameters: dict[str, Any]): """reload a control.in inputs from a parameters dictionary""" self._parameters = parameters + if "output" not in self._parameters: + self._parameters["output"] = [] def get_aims_control_parameter_str(self, key, value, format): return f"{key :35s}" + (format % value) + "\n" @@ -435,14 +450,19 @@ def write_file( lim = "#" + "=" * 79 + if isinstance(structure, Structure) and ( + "k_grid" not in self._parameters and "k_grid_density" not in self._parameters + ): + raise ValueError("k-grid must be defined for periodic systems") + parameters = deepcopy(self._parameters) - with open(f"{directory}/geometry.in", "w") as fd: + with open(f"{directory}/control.in", "w") as fd: fd.write("#" + "=" * 72 + "\n") fd.write(f"# FHI-aims geometry file: {directory}/geometry.in\n") fd.write("# File generated from pymatgen\n") fd.write(f"# {time.asctime()}\n") - fd.write(self.content) + fd.write("#" + "=" * 72 + "\n") if parameters["xc"] == "LDA": parameters["xc"] = "pw-lda" @@ -501,7 +521,7 @@ def get_species_block(self, structure, species_dir): for sp in species: filename = f"{species_dir}/{sp.Z:02d}_{sp.symbol}_default" with open(filename) as sf: - sb += "\n".join(sf.readlines()) + sb += "".join(sf.readlines()) return sb def as_dict(self) -> dict[str, Any]: diff --git a/tests/io/aims/aims_input_files/control.in.h2o b/tests/io/aims/aims_input_files/control.in.h2o new file mode 100644 index 00000000000..057c24be7fb --- /dev/null +++ b/tests/io/aims/aims_input_files/control.in.h2o @@ -0,0 +1,170 @@ +#======================================================================== +# FHI-aims geometry file: /home/tpurcell/git/pymatgen/tests/io/aims/testing/geometry.in +# File generated from pymatgen +# Mon Oct 30 20:29:48 2023 +#======================================================================== +#=============================================================================== +xc pw-lda +occupation_type fermi 0.010000 +vdw_correction_hirshfeld +compute_forces .true. +relax_geometry trm 1e-3 +batch_size_limit 200 +output cube eigenstate 1 + cube origin 0.000000000000e+00 0.000000000000e+00 0.000000000000e+00 + cube edge 10 1.000000000000e-01 0.000000000000e+00 0.000000000000e+00 + cube edge 10 0.000000000000e+00 1.000000000000e-01 0.000000000000e+00 + cube edge 10 0.000000000000e+00 0.000000000000e+00 1.000000000000e-01 + cube format cube +output cube total_density + cube origin 0.000000000000e+00 0.000000000000e+00 0.000000000000e+00 + cube edge 10 1.000000000000e-01 0.000000000000e+00 0.000000000000e+00 + cube edge 10 0.000000000000e+00 1.000000000000e-01 0.000000000000e+00 + cube edge 10 0.000000000000e+00 0.000000000000e+00 1.000000000000e-01 + cube format cube +#=============================================================================== + +################################################################################ +# +# FHI-aims code project +# VB, Fritz-Haber Institut, 2009 +# +# Suggested "light" defaults for H atom (to be pasted into control.in file) +# Be sure to double-check any results obtained with these settings for post-processing, +# e.g., with the "tight" defaults and larger basis sets. +# +################################################################################ + species H +# global species definitions + nucleus 1 + mass 1.00794 +# + l_hartree 4 +# + cut_pot 3.5 1.5 1.0 + basis_dep_cutoff 1e-4 +# + radial_base 24 5.0 + radial_multiplier 1 + angular_grids specified + division 0.2421 50 + division 0.3822 110 + division 0.4799 194 + division 0.5341 302 +# division 0.5626 434 +# division 0.5922 590 +# division 0.6542 770 +# division 0.6868 1202 +# outer_grid 770 + outer_grid 302 +################################################################################ +# +# Definition of "minimal" basis +# +################################################################################ +# valence basis states + valence 1 s 1. +# ion occupancy + ion_occ 1 s 0.5 +################################################################################ +# +# Suggested additional basis functions. For production calculations, +# uncomment them one after another (the most important basis functions are +# listed first). +# +# Basis constructed for dimers: 0.5 A, 0.7 A, 1.0 A, 1.5 A, 2.5 A +# +################################################################################ +# "First tier" - improvements: -1014.90 meV to -62.69 meV + hydro 2 s 2.1 + hydro 2 p 3.5 +# "Second tier" - improvements: -12.89 meV to -1.83 meV +# hydro 1 s 0.85 +# hydro 2 p 3.7 +# hydro 2 s 1.2 +# hydro 3 d 7 +# "Third tier" - improvements: -0.25 meV to -0.12 meV +# hydro 4 f 11.2 +# hydro 3 p 4.8 +# hydro 4 d 9 +# hydro 3 s 3.2 +################################################################################ +# +# FHI-aims code project +# VB, Fritz-Haber Institut, 2009 +# +# Suggested "light" defaults for O atom (to be pasted into control.in file) +# Be sure to double-check any results obtained with these settings for post-processing, +# e.g., with the "tight" defaults and larger basis sets. +# +################################################################################ + species O +# global species definitions + nucleus 8 + mass 15.9994 +# + l_hartree 4 +# + cut_pot 3.5 1.5 1.0 + basis_dep_cutoff 1e-4 +# + radial_base 36 5.0 + radial_multiplier 1 + angular_grids specified + division 0.2659 50 + division 0.4451 110 + division 0.6052 194 + division 0.7543 302 +# division 0.8014 434 +# division 0.8507 590 +# division 0.8762 770 +# division 0.9023 974 +# division 1.2339 1202 +# outer_grid 974 + outer_grid 302 +################################################################################ +# +# Definition of "minimal" basis +# +################################################################################ +# valence basis states + valence 2 s 2. + valence 2 p 4. +# ion occupancy + ion_occ 2 s 1. + ion_occ 2 p 3. +################################################################################ +# +# Suggested additional basis functions. For production calculations, +# uncomment them one after another (the most important basis functions are +# listed first). +# +# Constructed for dimers: 1.0 A, 1.208 A, 1.5 A, 2.0 A, 3.0 A +# +################################################################################ +# "First tier" - improvements: -699.05 meV to -159.38 meV + hydro 2 p 1.8 + hydro 3 d 7.6 + hydro 3 s 6.4 +# "Second tier" - improvements: -49.91 meV to -5.39 meV +# hydro 4 f 11.6 +# hydro 3 p 6.2 +# hydro 3 d 5.6 +# hydro 5 g 17.6 +# hydro 1 s 0.75 +# "Third tier" - improvements: -2.83 meV to -0.50 meV +# ionic 2 p auto +# hydro 4 f 10.8 +# hydro 4 d 4.7 +# hydro 2 s 6.8 +# "Fourth tier" - improvements: -0.40 meV to -0.12 meV +# hydro 3 p 5 +# hydro 3 s 3.3 +# hydro 5 g 15.6 +# hydro 4 f 17.6 +# hydro 4 d 14 +# Further basis functions - -0.08 meV and below +# hydro 3 s 2.1 +# hydro 4 d 11.6 +# hydro 3 p 16 +# hydro 2 s 17.2 diff --git a/tests/io/aims/aims_input_files/control.in.si b/tests/io/aims/aims_input_files/control.in.si new file mode 100644 index 00000000000..5d086ac5880 --- /dev/null +++ b/tests/io/aims/aims_input_files/control.in.si @@ -0,0 +1,126 @@ +#======================================================================== +# FHI-aims geometry file: /home/tpurcell/git/pymatgen/tests/io/aims/testing/geometry.in +# File generated from pymatgen +# Mon Oct 30 20:47:24 2023 +#======================================================================== +# +# List of parameters used to initialize the calculator:# xc:pw-lda +# smearing:['fermi-dirac', 0.01] +# vdw_correction_hirshfeld:True +# compute_forces:True +# relax_geometry:['trm', '1e-3'] +# batch_size_limit:200 +# species_dir:/home/tpurcell/git/pymatgen/tests/io/aims/species_directory/light +# output:['band 0 0 0 0.5 0 0.5 10 G X', 'band 0 0 0 0.5 0.5 0.5 10 G L'] +# k_grid:[1, 1, 1] +#=============================================================================== +xc pw-lda +occupation_type fermi 0.010000 +vdw_correction_hirshfeld +compute_forces .true. +relax_geometry trm 1e-3 +batch_size_limit 200 +output band 0 0 0 0.5 0 0.5 10 G X +output band 0 0 0 0.5 0.5 0.5 10 G L +k_grid 1 1 1 +output cube eigenstate 1 + cube origin 0.000000000000e+00 0.000000000000e+00 0.000000000000e+00 + cube edge 10 1.000000000000e-01 0.000000000000e+00 0.000000000000e+00 + cube edge 10 0.000000000000e+00 1.000000000000e-01 0.000000000000e+00 + cube edge 10 0.000000000000e+00 0.000000000000e+00 1.000000000000e-01 + cube format cube +output cube total_density + cube origin 0.000000000000e+00 0.000000000000e+00 0.000000000000e+00 + cube edge 10 1.000000000000e-01 0.000000000000e+00 0.000000000000e+00 + cube edge 10 0.000000000000e+00 1.000000000000e-01 0.000000000000e+00 + cube edge 10 0.000000000000e+00 0.000000000000e+00 1.000000000000e-01 + cube format cube +#=============================================================================== + +################################################################################ +# +# FHI-aims code project +# VB, Fritz-Haber Institut, 2009 +# +# Suggested "light" defaults for Si atom (to be pasted into control.in file) +# Be sure to double-check any results obtained with these settings for post-processing, +# e.g., with the "tight" defaults and larger basis sets. +# +# 2020/09/08 Added f function to "light" after reinspection of Delta test outcomes. +# This was done for all of Al-Cl and is a tricky decision since it makes +# "light" calculations measurably more expensive for these elements. +# Nevertheless, outcomes for P, S, Cl (and to some extent, Si) appear +# to justify this choice. +# +################################################################################ + species Si +# global species definitions + nucleus 14 + mass 28.0855 +# + l_hartree 4 +# + cut_pot 3.5 1.5 1.0 + basis_dep_cutoff 1e-4 +# + radial_base 42 5.0 + radial_multiplier 1 + angular_grids specified + division 0.5866 50 + division 0.9616 110 + division 1.2249 194 + division 1.3795 302 +# division 1.4810 434 +# division 1.5529 590 +# division 1.6284 770 +# division 1.7077 974 +# division 2.4068 1202 +# outer_grid 974 + outer_grid 302 +################################################################################ +# +# Definition of "minimal" basis +# +################################################################################ +# valence basis states + valence 3 s 2. + valence 3 p 2. +# ion occupancy + ion_occ 3 s 1. + ion_occ 3 p 1. +################################################################################ +# +# Suggested additional basis functions. For production calculations, +# uncomment them one after another (the most important basis functions are +# listed first). +# +# Constructed for dimers: 1.75 A, 2.0 A, 2.25 A, 2.75 A, 3.75 A +# +################################################################################ +# "First tier" - improvements: -571.96 meV to -37.03 meV + hydro 3 d 4.2 + hydro 2 p 1.4 + hydro 4 f 6.2 + ionic 3 s auto +# "Second tier" - improvements: -16.76 meV to -3.03 meV +# hydro 3 d 9 +# hydro 5 g 9.4 +# hydro 4 p 4 +# hydro 1 s 0.65 +# "Third tier" - improvements: -3.89 meV to -0.60 meV +# ionic 3 d auto +# hydro 3 s 2.6 +# hydro 4 f 8.4 +# hydro 3 d 3.4 +# hydro 3 p 7.8 +# "Fourth tier" - improvements: -0.33 meV to -0.11 meV +# hydro 2 p 1.6 +# hydro 5 g 10.8 +# hydro 5 f 11.2 +# hydro 3 d 1 +# hydro 4 s 4.5 +# Further basis functions that fell out of the optimization - noise +# level... < -0.08 meV +# hydro 4 d 6.6 +# hydro 5 g 16.4 +# hydro 4 d 9 diff --git a/tests/io/aims/species_directory/light/01_H_default b/tests/io/aims/species_directory/light/01_H_default new file mode 100644 index 00000000000..8938a1587b4 --- /dev/null +++ b/tests/io/aims/species_directory/light/01_H_default @@ -0,0 +1,64 @@ +################################################################################ +# +# FHI-aims code project +# VB, Fritz-Haber Institut, 2009 +# +# Suggested "light" defaults for H atom (to be pasted into control.in file) +# Be sure to double-check any results obtained with these settings for post-processing, +# e.g., with the "tight" defaults and larger basis sets. +# +################################################################################ + species H +# global species definitions + nucleus 1 + mass 1.00794 +# + l_hartree 4 +# + cut_pot 3.5 1.5 1.0 + basis_dep_cutoff 1e-4 +# + radial_base 24 5.0 + radial_multiplier 1 + angular_grids specified + division 0.2421 50 + division 0.3822 110 + division 0.4799 194 + division 0.5341 302 +# division 0.5626 434 +# division 0.5922 590 +# division 0.6542 770 +# division 0.6868 1202 +# outer_grid 770 + outer_grid 302 +################################################################################ +# +# Definition of "minimal" basis +# +################################################################################ +# valence basis states + valence 1 s 1. +# ion occupancy + ion_occ 1 s 0.5 +################################################################################ +# +# Suggested additional basis functions. For production calculations, +# uncomment them one after another (the most important basis functions are +# listed first). +# +# Basis constructed for dimers: 0.5 A, 0.7 A, 1.0 A, 1.5 A, 2.5 A +# +################################################################################ +# "First tier" - improvements: -1014.90 meV to -62.69 meV + hydro 2 s 2.1 + hydro 2 p 3.5 +# "Second tier" - improvements: -12.89 meV to -1.83 meV +# hydro 1 s 0.85 +# hydro 2 p 3.7 +# hydro 2 s 1.2 +# hydro 3 d 7 +# "Third tier" - improvements: -0.25 meV to -0.12 meV +# hydro 4 f 11.2 +# hydro 3 p 4.8 +# hydro 4 d 9 +# hydro 3 s 3.2 diff --git a/tests/io/aims/species_directory/light/08_O_default b/tests/io/aims/species_directory/light/08_O_default new file mode 100644 index 00000000000..9232a9aab7d --- /dev/null +++ b/tests/io/aims/species_directory/light/08_O_default @@ -0,0 +1,80 @@ +################################################################################ +# +# FHI-aims code project +# VB, Fritz-Haber Institut, 2009 +# +# Suggested "light" defaults for O atom (to be pasted into control.in file) +# Be sure to double-check any results obtained with these settings for post-processing, +# e.g., with the "tight" defaults and larger basis sets. +# +################################################################################ + species O +# global species definitions + nucleus 8 + mass 15.9994 +# + l_hartree 4 +# + cut_pot 3.5 1.5 1.0 + basis_dep_cutoff 1e-4 +# + radial_base 36 5.0 + radial_multiplier 1 + angular_grids specified + division 0.2659 50 + division 0.4451 110 + division 0.6052 194 + division 0.7543 302 +# division 0.8014 434 +# division 0.8507 590 +# division 0.8762 770 +# division 0.9023 974 +# division 1.2339 1202 +# outer_grid 974 + outer_grid 302 +################################################################################ +# +# Definition of "minimal" basis +# +################################################################################ +# valence basis states + valence 2 s 2. + valence 2 p 4. +# ion occupancy + ion_occ 2 s 1. + ion_occ 2 p 3. +################################################################################ +# +# Suggested additional basis functions. For production calculations, +# uncomment them one after another (the most important basis functions are +# listed first). +# +# Constructed for dimers: 1.0 A, 1.208 A, 1.5 A, 2.0 A, 3.0 A +# +################################################################################ +# "First tier" - improvements: -699.05 meV to -159.38 meV + hydro 2 p 1.8 + hydro 3 d 7.6 + hydro 3 s 6.4 +# "Second tier" - improvements: -49.91 meV to -5.39 meV +# hydro 4 f 11.6 +# hydro 3 p 6.2 +# hydro 3 d 5.6 +# hydro 5 g 17.6 +# hydro 1 s 0.75 +# "Third tier" - improvements: -2.83 meV to -0.50 meV +# ionic 2 p auto +# hydro 4 f 10.8 +# hydro 4 d 4.7 +# hydro 2 s 6.8 +# "Fourth tier" - improvements: -0.40 meV to -0.12 meV +# hydro 3 p 5 +# hydro 3 s 3.3 +# hydro 5 g 15.6 +# hydro 4 f 17.6 +# hydro 4 d 14 +# Further basis functions - -0.08 meV and below +# hydro 3 s 2.1 +# hydro 4 d 11.6 +# hydro 3 p 16 +# hydro 2 s 17.2 diff --git a/tests/io/aims/species_directory/light/14_Si_default b/tests/io/aims/species_directory/light/14_Si_default new file mode 100644 index 00000000000..83008b4edf3 --- /dev/null +++ b/tests/io/aims/species_directory/light/14_Si_default @@ -0,0 +1,87 @@ +################################################################################ +# +# FHI-aims code project +# VB, Fritz-Haber Institut, 2009 +# +# Suggested "light" defaults for Si atom (to be pasted into control.in file) +# Be sure to double-check any results obtained with these settings for post-processing, +# e.g., with the "tight" defaults and larger basis sets. +# +# 2020/09/08 Added f function to "light" after reinspection of Delta test outcomes. +# This was done for all of Al-Cl and is a tricky decision since it makes +# "light" calculations measurably more expensive for these elements. +# Nevertheless, outcomes for P, S, Cl (and to some extent, Si) appear +# to justify this choice. +# +################################################################################ + species Si +# global species definitions + nucleus 14 + mass 28.0855 +# + l_hartree 4 +# + cut_pot 3.5 1.5 1.0 + basis_dep_cutoff 1e-4 +# + radial_base 42 5.0 + radial_multiplier 1 + angular_grids specified + division 0.5866 50 + division 0.9616 110 + division 1.2249 194 + division 1.3795 302 +# division 1.4810 434 +# division 1.5529 590 +# division 1.6284 770 +# division 1.7077 974 +# division 2.4068 1202 +# outer_grid 974 + outer_grid 302 +################################################################################ +# +# Definition of "minimal" basis +# +################################################################################ +# valence basis states + valence 3 s 2. + valence 3 p 2. +# ion occupancy + ion_occ 3 s 1. + ion_occ 3 p 1. +################################################################################ +# +# Suggested additional basis functions. For production calculations, +# uncomment them one after another (the most important basis functions are +# listed first). +# +# Constructed for dimers: 1.75 A, 2.0 A, 2.25 A, 2.75 A, 3.75 A +# +################################################################################ +# "First tier" - improvements: -571.96 meV to -37.03 meV + hydro 3 d 4.2 + hydro 2 p 1.4 + hydro 4 f 6.2 + ionic 3 s auto +# "Second tier" - improvements: -16.76 meV to -3.03 meV +# hydro 3 d 9 +# hydro 5 g 9.4 +# hydro 4 p 4 +# hydro 1 s 0.65 +# "Third tier" - improvements: -3.89 meV to -0.60 meV +# ionic 3 d auto +# hydro 3 s 2.6 +# hydro 4 f 8.4 +# hydro 3 d 3.4 +# hydro 3 p 7.8 +# "Fourth tier" - improvements: -0.33 meV to -0.11 meV +# hydro 2 p 1.6 +# hydro 5 g 10.8 +# hydro 5 f 11.2 +# hydro 3 d 1 +# hydro 4 s 4.5 +# Further basis functions that fell out of the optimization - noise +# level... < -0.08 meV +# hydro 4 d 6.6 +# hydro 5 g 16.4 +# hydro 4 d 9 diff --git a/tests/io/aims/test_aims_inputs.py b/tests/io/aims/test_aims_inputs.py index b26fdb7e5bd..58e711c0d58 100644 --- a/tests/io/aims/test_aims_inputs.py +++ b/tests/io/aims/test_aims_inputs.py @@ -8,11 +8,28 @@ import pytest from monty.json import MontyDecoder, MontyEncoder -from pymatgen.io.aims.inputs import ALLOWED_AIMS_CUBE_TYPES, ALLOWED_AIMS_CUBE_TYPES_STATE, AimsCube, AimsGeometryIn +from pymatgen.io.aims.inputs import ( + ALLOWED_AIMS_CUBE_TYPES, + ALLOWED_AIMS_CUBE_TYPES_STATE, + AimsControlIn, + AimsCube, + AimsGeometryIn, +) infile_dir = Path(__file__).parent / "aims_input_files" +def compare_files(ref_file, test_file): + with open(test_file) as tf: + test_lines = tf.readlines()[5:] + + with open(ref_file) as rf: + ref_lines = rf.readlines()[5:] + + for test_line, ref_line in zip(test_lines, ref_lines): + assert test_line.strip() == ref_line.strip() + + def test_read_write_si_in(tmpdir): si = AimsGeometryIn.from_file(infile_dir / "geometry.in.si") @@ -29,15 +46,13 @@ def test_read_write_si_in(tmpdir): workdir = Path.cwd() os.chdir(tmpdir) si_test_from_struct.write_file(overwrite=True) + with pytest.raises( + ValueError, + match="geometry.in file exists in ", + ): + si_test_from_struct.write_file(overwrite=False) - with open("geometry.in") as test_file: - test_lines = test_file.readlines()[5:] - - with open(infile_dir / "geometry.in.si.ref") as ref_file: - ref_lines = ref_file.readlines()[5:] - - for test_line, ref_line in zip(test_lines, ref_lines): - assert test_line == ref_line + compare_files(infile_dir / "geometry.in.si.ref", "geometry.in") os.chdir(workdir) @@ -68,14 +83,13 @@ def test_read_h2o_in(tmpdir): os.chdir(tmpdir) h2o_test_from_struct.write_file(overwrite=True) - with open("geometry.in") as test_file: - test_lines = test_file.readlines()[5:] + with pytest.raises( + ValueError, + match="geometry.in file exists in ", + ): + h2o_test_from_struct.write_file(overwrite=False) - with open(infile_dir / "geometry.in.h2o.ref") as ref_file: - ref_lines = ref_file.readlines()[5:] - - for test_line, ref_line in zip(test_lines, ref_lines): - assert test_line == ref_line + compare_files(infile_dir / "geometry.in.h2o.ref", "geometry.in") os.chdir(workdir) @@ -90,7 +104,7 @@ def check_wrong_type_aims_cube(type, exp_err): AimsCube(type=type) -def test_aims_cube(tmpdir): +def test_aims_cube(): check_wrong_type_aims_cube(type="INCORRECT_TYPE", exp_err="Cube type undefined") for type in ALLOWED_AIMS_CUBE_TYPES_STATE: @@ -146,7 +160,7 @@ def test_aims_cube(tmpdir): test_cube_block = [ "output cube elf", - " cube origin [0, 0, 0]", + " cube origin 0.000000000000e+00 0.000000000000e+00 0.000000000000e+00", " cube edge 100 1.000000000000e-02 0.000000000000e+00 0.000000000000e+00", " cube edge 100 0.000000000000e+00 1.000000000000e-02 0.000000000000e+00", " cube edge 100 0.000000000000e+00 0.000000000000e+00 1.000000000000e-02", @@ -161,3 +175,62 @@ def test_aims_cube(tmpdir): test_cube_from_dict = json.loads(json.dumps(test_cube.as_dict(), cls=MontyEncoder), cls=MontyDecoder) assert test_cube_from_dict.control_block == test_cube.control_block + + +def test_aims_control_in(tmpdir): + parameters = { + "cubes": [ + AimsCube(type="eigenstate 1", points=[10, 10, 10]), + AimsCube(type="total_density", points=[10, 10, 10]), + ], + "xc": "LDA", + "smearing": ["fermi-dirac", 0.01], + "vdw_correction_hirshfeld": True, + "compute_forces": True, + "relax_geometry": ["trm", "1e-3"], + "batch_size_limit": 200, + "species_dir": str(infile_dir.parent / "species_directory/light"), + } + + workdir = Path.cwd() + aims_control = AimsControlIn(parameters.copy()) + + for key, val in parameters.items(): + assert aims_control[key] == val + + del aims_control["xc"] + assert "xc" not in aims_control.parameters + aims_control.parameters = parameters + + # os.chdir(tmpdir) + h2o = AimsGeometryIn.from_file(infile_dir / "geometry.in.h2o").structure + + si = AimsGeometryIn.from_file(infile_dir / "geometry.in.si").structure + aims_control.write_file(h2o, overwrite=True) + + compare_files(infile_dir / "control.in.h2o", "control.in") + + with pytest.raises( + ValueError, + match="k-grid must be defined for periodic systems", + ): + aims_control.write_file(si, overwrite=True) + aims_control["k_grid"] = [1, 1, 1] + + with pytest.raises( + ValueError, + match="control.in file already in ", + ): + aims_control.write_file(si, overwrite=False) + + aims_control["output"] = "band 0 0 0 0.5 0 0.5 10 G X" + aims_control["output"] = "band 0 0 0 0.5 0.5 0.5 10 G L" + + aims_control_from_dict = json.loads(json.dumps(aims_control.as_dict(), cls=MontyEncoder), cls=MontyDecoder) + for key, val in aims_control.parameters.items(): + assert aims_control_from_dict[key] == val + + aims_control_from_dict.write_file(si, verbose_header=True, overwrite=True) + compare_files(infile_dir / "control.in.si", "control.in") + + os.chdir(workdir) From 9da0f6f588da88bd99f7e2eaa916b4649061130b Mon Sep 17 00:00:00 2001 From: Thomas Purcell Date: Tue, 31 Oct 2023 06:52:50 +0100 Subject: [PATCH 09/30] gzip all output files as requested all output files are gzipped --- tests/io/aims/aims_output_files/h2o.out | 4244 --------- tests/io/aims/aims_output_files/h2o.out.gz | Bin 0 -> 27959 bytes tests/io/aims/aims_output_files/h2o_ref.json | 403 - .../io/aims/aims_output_files/h2o_ref.json.gz | Bin 0 -> 1415 bytes tests/io/aims/aims_output_files/si.out | 8198 ----------------- tests/io/aims/aims_output_files/si.out.gz | Bin 0 -> 49958 bytes tests/io/aims/aims_output_files/si_ref.json | 767 -- .../io/aims/aims_output_files/si_ref.json.gz | Bin 0 -> 2518 bytes tests/io/aims/test_aims_outputs.py | 18 +- 9 files changed, 10 insertions(+), 13620 deletions(-) delete mode 100644 tests/io/aims/aims_output_files/h2o.out create mode 100644 tests/io/aims/aims_output_files/h2o.out.gz delete mode 100644 tests/io/aims/aims_output_files/h2o_ref.json create mode 100644 tests/io/aims/aims_output_files/h2o_ref.json.gz delete mode 100644 tests/io/aims/aims_output_files/si.out create mode 100644 tests/io/aims/aims_output_files/si.out.gz delete mode 100644 tests/io/aims/aims_output_files/si_ref.json create mode 100644 tests/io/aims/aims_output_files/si_ref.json.gz diff --git a/tests/io/aims/aims_output_files/h2o.out b/tests/io/aims/aims_output_files/h2o.out deleted file mode 100644 index cbcf8b1f574..00000000000 --- a/tests/io/aims/aims_output_files/h2o.out +++ /dev/null @@ -1,4244 +0,0 @@ ------------------------------------------------------------- - Invoking FHI-aims ... - - When using FHI-aims, please cite the following reference: - - Volker Blum, Ralf Gehrke, Felix Hanke, Paula Havu, - Ville Havu, Xinguo Ren, Karsten Reuter, and Matthias Scheffler, - 'Ab Initio Molecular Simulations with Numeric Atom-Centered Orbitals', - Computer Physics Communications 180, 2175-2196 (2009) - - In addition, many other developments in FHI-aims are likely important for - your particular application. A partial list of references is given at the end of - this file. Thank you for giving credit to the authors of these developments. - - For any questions about FHI-aims, please visit our slack channel at - - https://fhi-aims.slack.com - - and our main development and support site at - - https://aims-git.rz-berlin.mpg.de . - - The latter site, in particular, has a wiki to collect information, as well - as an issue tracker to log discussions, suggest improvements, and report issues - or bugs. https://aims-git.rz-berlin.mpg.de is also the main development site - of the project and all new and updated code versions can be obtained there. - Please send an email to aims-coordinators@fhi-berlin.mpg.de and we will add - you to these sites. They are for you and everyone is welcome there. - ------------------------------------------------------------- - - - - Date : 20230628, Time : 095500.899 - Time zero on CPU 1 : 0.163200300000000E+01 s. - Internal wall clock time zero : 457178100.899 s. - - FHI-aims created a unique identifier for this run for later identification - aims_uuid : 099AC112-61D8-44F8-AB69-102154672282 - - Build configuration of the current instance of FHI-aims - ------------------------------------------------------- - FHI-aims version : 220309 - Commit number : 232d594a3 - CMake host system : Linux-5.4.0-146-generic - CMake version : 3.26.3 - Fortran compiler : /home/tpurcell/intel/oneapi/mpi/2021.6.0/bin/mpiifort (Intel) version 2021.6.0.20220226 - Fortran compiler flags: -O3 -ip -fp-model precise - C compiler : /home/tpurcell/intel/oneapi/compiler/2022.1.0/linux/bin/intel64/icc (Intel) version 2021.6.0.20220226 - C compiler flags : -m64 -O3 -ip -fp-model precise -std=gnu99 - Using MPI - Using ScaLAPACK - Using LibXC - Using i-PI - Using RLSY - Linking against: /home/tpurcell/intel/oneapi/mkl/2022.1.0/lib/intel64/libmkl_scalapack_lp64.so - /home/tpurcell/intel/oneapi/mkl/2022.1.0/lib/intel64/libmkl_blacs_intelmpi_lp64.so - /home/tpurcell/intel/oneapi/mkl/2022.1.0/lib/intel64/libmkl_intel_lp64.so - /home/tpurcell/intel/oneapi/mkl/2022.1.0/lib/intel64/libmkl_sequential.so - /home/tpurcell/intel/oneapi/mkl/2022.1.0/lib/intel64/libmkl_core.so - - Using 1 parallel tasks. - Task 0 on host nomadbook-7 reporting. - - Performing system and environment tests: - *** Environment variable OMP_NUM_THREADS is set to - 2 - *** For performance reasons you might want to set it to 1 - | Checking for ScaLAPACK... - | Testing pdtran()... - | All pdtran() tests passed. - - Obtaining array dimensions for all initial allocations: - - ----------------------------------------------------------------------- - Parsing control.in (first pass over file, find array dimensions only). - The contents of control.in will be repeated verbatim below - unless switched off by setting 'verbatim_writeout .false.' . - in the first line of control.in . - ----------------------------------------------------------------------- - - #=============================================================================== - # Created using the Atomic Simulation Environment (ASE) - - # Tue Jun 27 18:06:33 2023 - - #=============================================================================== - xc pbe - relativistic atomic_zora scalar - relax_geometry trm 1e-3 - #=============================================================================== - - ################################################################################ - # - # FHI-aims code project - # VB, Fritz-Haber Institut, 2009 - # - # Suggested "light" defaults for O atom (to be pasted into control.in file) - # Be sure to double-check any results obtained with these settings for post-processing, - # e.g., with the "tight" defaults and larger basis sets. - # - ################################################################################ - species O - # global species definitions - nucleus 8 - mass 15.9994 - # - l_hartree 4 - # - cut_pot 3.5 1.5 1.0 - basis_dep_cutoff 1e-4 - # - radial_base 36 5.0 - radial_multiplier 1 - angular_grids specified - division 0.2659 50 - division 0.4451 110 - division 0.6052 194 - division 0.7543 302 - # division 0.8014 434 - # division 0.8507 590 - # division 0.8762 770 - # division 0.9023 974 - # division 1.2339 1202 - # outer_grid 974 - outer_grid 302 - ################################################################################ - # - # Definition of "minimal" basis - # - ################################################################################ - # valence basis states - valence 2 s 2. - valence 2 p 4. - # ion occupancy - ion_occ 2 s 1. - ion_occ 2 p 3. - ################################################################################ - # - # Suggested additional basis functions. For production calculations, - # uncomment them one after another (the most important basis functions are - # listed first). - # - # Constructed for dimers: 1.0 A, 1.208 A, 1.5 A, 2.0 A, 3.0 A - # - ################################################################################ - # "First tier" - improvements: -699.05 meV to -159.38 meV - hydro 2 p 1.8 - hydro 3 d 7.6 - hydro 3 s 6.4 - # "Second tier" - improvements: -49.91 meV to -5.39 meV - # hydro 4 f 11.6 - # hydro 3 p 6.2 - # hydro 3 d 5.6 - # hydro 5 g 17.6 - # hydro 1 s 0.75 - # "Third tier" - improvements: -2.83 meV to -0.50 meV - # ionic 2 p auto - # hydro 4 f 10.8 - # hydro 4 d 4.7 - # hydro 2 s 6.8 - # "Fourth tier" - improvements: -0.40 meV to -0.12 meV - # hydro 3 p 5 - # hydro 3 s 3.3 - # hydro 5 g 15.6 - # hydro 4 f 17.6 - # hydro 4 d 14 - # Further basis functions - -0.08 meV and below - # hydro 3 s 2.1 - # hydro 4 d 11.6 - # hydro 3 p 16 - # hydro 2 s 17.2 - ################################################################################ - # - # FHI-aims code project - # VB, Fritz-Haber Institut, 2009 - # - # Suggested "light" defaults for H atom (to be pasted into control.in file) - # Be sure to double-check any results obtained with these settings for post-processing, - # e.g., with the "tight" defaults and larger basis sets. - # - ################################################################################ - species H - # global species definitions - nucleus 1 - mass 1.00794 - # - l_hartree 4 - # - cut_pot 3.5 1.5 1.0 - basis_dep_cutoff 1e-4 - # - radial_base 24 5.0 - radial_multiplier 1 - angular_grids specified - division 0.2421 50 - division 0.3822 110 - division 0.4799 194 - division 0.5341 302 - # division 0.5626 434 - # division 0.5922 590 - # division 0.6542 770 - # division 0.6868 1202 - # outer_grid 770 - outer_grid 302 - ################################################################################ - # - # Definition of "minimal" basis - # - ################################################################################ - # valence basis states - valence 1 s 1. - # ion occupancy - ion_occ 1 s 0.5 - ################################################################################ - # - # Suggested additional basis functions. For production calculations, - # uncomment them one after another (the most important basis functions are - # listed first). - # - # Basis constructed for dimers: 0.5 A, 0.7 A, 1.0 A, 1.5 A, 2.5 A - # - ################################################################################ - # "First tier" - improvements: -1014.90 meV to -62.69 meV - hydro 2 s 2.1 - hydro 2 p 3.5 - # "Second tier" - improvements: -12.89 meV to -1.83 meV - # hydro 1 s 0.85 - # hydro 2 p 3.7 - # hydro 2 s 1.2 - # hydro 3 d 7 - # "Third tier" - improvements: -0.25 meV to -0.12 meV - # hydro 4 f 11.2 - # hydro 3 p 4.8 - # hydro 4 d 9 - # hydro 3 s 3.2 - - ----------------------------------------------------------------------- - Completed first pass over input file control.in . - ----------------------------------------------------------------------- - - - ----------------------------------------------------------------------- - Parsing geometry.in (first pass over file, find array dimensions only). - The contents of geometry.in will be repeated verbatim below - unless switched off by setting 'verbatim_writeout .false.' . - in the first line of geometry.in . - ----------------------------------------------------------------------- - - #=============================================================================== - # Created using the Atomic Simulation Environment (ASE) - - # Tue Jun 27 18:06:33 2023 - - #======================================================= - atom 0.0000000000000000 0.0000000000000000 0.1192620000000000 O - atom 0.0000000000000000 0.7632390000000000 -0.4770470000000000 H - atom 0.0000000000000000 -0.7632390000000000 -0.4770470000000000 H - - ----------------------------------------------------------------------- - Completed first pass over input file geometry.in . - ----------------------------------------------------------------------- - - - Basic array size parameters: - | Number of species : 2 - | Number of atoms : 3 - | Max. basis fn. angular momentum : 2 - | Max. atomic/ionic basis occupied n: 2 - | Max. number of basis fn. types : 2 - | Max. radial fns per species/type : 3 - | Max. logarithmic grid size : 1301 - | Max. radial integration grid size : 36 - | Max. angular integration grid size: 302 - | Max. angular grid division number : 8 - | Radial grid for Hartree potential : 1301 - | Number of spin channels : 1 - ------------------------------------------------------------- - Reading file control.in. ------------------------------------------------------------- - XC: Using PBE gradient-corrected functionals. - Scalar relativistic treatment of kinetic energy: on-site free-atom approximation to ZORA. - Geometry relaxation: Modified BFGS - TRM (trust radius method) for lattice optimization. - Convergence accuracy for geometry relaxation: Maximum force < 0.100000E-02 eV/A. - - Reading configuration options for species O . - | Found nuclear charge : 8.0000 - | Found atomic mass : 15.9994000000000 amu - | Found l_max for Hartree potential : 4 - | Found cutoff potl. onset [A], width [A], scale factor : 3.50000 1.50000 1.00000 - | Threshold for basis-dependent cutoff potential is 0.100000E-03 - | Found data for basic radial integration grid : 36 points, outermost radius = 5.000 A - | Found multiplier for basic radial grid : 1 - | Found angular grid specification: user-specified. - | Specified grid contains 5 separate shells. - | Check grid settings after all constraints further below. - | Found free-atom valence shell : 2 s 2.000 - | Found free-atom valence shell : 2 p 4.000 - | No ionic wave fns used. Skipping ion_occ. - | No ionic wave fns used. Skipping ion_occ. - | Found hydrogenic basis function : 2 p 1.800 - | Found hydrogenic basis function : 3 d 7.600 - | Found hydrogenic basis function : 3 s 6.400 - Species O : Missing cutoff potential type. - Defaulting to exp(1/x)/(1-x)^2 type cutoff potential. - Species O : No 'logarithmic' tag. Using default grid for free atom: - | Default logarithmic grid data [bohr] : 0.1000E-03 0.1000E+03 0.1012E+01 - Species O : On-site basis accuracy parameter (for Gram-Schmidt orthonormalisation) not specified. - Using default value basis_acc = 0.1000000E-03. - Species O : Using default innermost maximum threshold i_radial= 2 for radial functions. - Species O : Default cutoff onset for free atom density etc. : 0.35000000E+01 AA. - Species O : Basic radial grid will be enhanced according to radial_multiplier = 1, to contain 36 grid points. - - Reading configuration options for species H . - | Found nuclear charge : 1.0000 - | Found atomic mass : 1.00794000000000 amu - | Found l_max for Hartree potential : 4 - | Found cutoff potl. onset [A], width [A], scale factor : 3.50000 1.50000 1.00000 - | Threshold for basis-dependent cutoff potential is 0.100000E-03 - | Found data for basic radial integration grid : 24 points, outermost radius = 5.000 A - | Found multiplier for basic radial grid : 1 - | Found angular grid specification: user-specified. - | Specified grid contains 5 separate shells. - | Check grid settings after all constraints further below. - | Found free-atom valence shell : 1 s 1.000 - | No ionic wave fns used. Skipping ion_occ. - | Found hydrogenic basis function : 2 s 2.100 - | Found hydrogenic basis function : 2 p 3.500 - Species H : Missing cutoff potential type. - Defaulting to exp(1/x)/(1-x)^2 type cutoff potential. - Species H : No 'logarithmic' tag. Using default grid for free atom: - | Default logarithmic grid data [bohr] : 0.1000E-03 0.1000E+03 0.1012E+01 - Species H : On-site basis accuracy parameter (for Gram-Schmidt orthonormalisation) not specified. - Using default value basis_acc = 0.1000000E-03. - Species H : Using default innermost maximum threshold i_radial= 2 for radial functions. - Species H : Default cutoff onset for free atom density etc. : 0.35000000E+01 AA. - Species H : Basic radial grid will be enhanced according to radial_multiplier = 1, to contain 24 grid points. - - Finished reading input file 'control.in'. - ------------------------------------------------------------- - - ------------------------------------------------------------- - Reading geometry description geometry.in. ------------------------------------------------------------- - | The smallest distance between any two atoms is 0.96856502 AA. - | The first atom of this pair is atom number 1 . - | The second atom of this pair is atom number 2 . - Input structure read successfully. - The structure contains 3 atoms, and a total of 10.000 electrons. - - Input geometry: - | No unit cell requested. - | Atomic structure: - | Atom x [A] y [A] z [A] - | 1: Species O 0.00000000 0.00000000 0.11926200 - | 2: Species H 0.00000000 0.76323900 -0.47704700 - | 3: Species H 0.00000000 -0.76323900 -0.47704700 - - - Finished reading input file 'control.in'. - - ------------------------------------------------------------- - Reading geometry description geometry.in. ------------------------------------------------------------- - - Consistency checks for stacksize environment parameter are next. - - | Maximum stacksize for task 0: unlimited - | Current stacksize for task 0: unlimited - - Consistency checks for the contents of control.in are next. - - MPI_IN_PLACE appears to work with this MPI implementation. - | Keeping use_mpi_in_place .true. (see manual). - Target number of points in a grid batch is not set. Defaulting to 100 - Method for grid partitioning is not set. Defaulting to parallel hash+maxmin partitioning. - Batch size limit is not set. Defaulting to 200 - By default, will store active basis functions for each batch. - If in need of memory, prune_basis_once .false. can be used to disable this option. - communication_type for Hartree potential was not specified. - Defaulting to calc_hartree . - Defaulting to Pulay charge density mixer. - Pulay mixer: Number of relevant iterations not set. - Defaulting to 8 iterations. - Pulay mixer: Number of initial linear mixing iterations not set. - Defaulting to 0 iterations. - Work space size for distributed Hartree potential not set. - Defaulting to 0.200000E+03 MB. - Mixing parameter for charge density mixing has not been set. - Using default: charge_mix_param = 0.0500. - The mixing parameter will be adjusted in iteration number 2 of the first full s.c.f. cycle only. - Algorithm-dependent basis array size parameters: - | n_max_pulay : 8 - Maximum number of self-consistency iterations not provided. - Presetting 1000 iterations. - Presetting 1001 iterations before the initial mixing cycle - is restarted anyway using the sc_init_iter criterion / keyword. - Presetting a factor 1.000 between actual scf density residual - and density convergence criterion sc_accuracy_rho below which sc_init_iter - takes no effect. - * No s.c.f. convergence criteria (sc_accuracy_*) were provided in control.in. - * The run will proceed with a reasonable default guess, but please check whether. - * the s.c.f. cycles seem to take too much or too little time. - No maximum number of relaxation steps, defaulting to 1000 - Default initial Hessian is Lindh matrix (thres = 15.00) plus 0.200000E+01 eV/A^2 times unity. - No maximum energy tolerance for TRM/BFGS moves, defaulting to 0.100000E-02 - Maximum energy tolerance by which TRM/BFGS trajectory may increase over multiple steps: 0.300000E-02 - No harmonic length scale. Defaulting to 0.250000E-01 A. - No trust radius initializer. Defaulting to 0.200000E+00 A. - Forces evaluation will include force correction term due to incomplete self-consistency (default). - * Notice: The s.c.f. convergence criterion sc_accuracy_rho was not provided. - * We used to stop in this case, and ask the user to provide reasonable - * scf convergence criteria. However, this led some users to employ criteria - * that led to extremely long run times, e.g., for simple relaxation. - * We now preset a default value for sc_accuracy_rho if it is not set. - * You may still wish to check if this setting is too tight or too loose for your needs. - * Based on n_atoms and forces and force-correction status, FHI-aims chose sc_accuracy_rho = 0.266667E-05 . - Force calculation: scf convergence accuracy of forces not set. - Defaulting to 'sc_accuracy_forces not_checked'. - Handling of forces: Unphysical translation and rotation will be removed from forces. - No accuracy limit for integral partition fn. given. Defaulting to 0.1000E-14. - No threshold value for u(r) in integrations given. Defaulting to 0.1000E-05. - No occupation type (smearing scheme) given. Defaulting to Gaussian broadening, width = 0.1000E-01 eV. - The width will be adjusted in iteration number 2 of the first full s.c.f. cycle only. - S.C.F. convergence parameters will be adjusted in iteration number 2 of the first full s.c.f. cycle only. - No accuracy for occupation numbers given. Defaulting to 0.1000E-12. - No threshold value for occupation numbers given. Defaulting to 0.0000E+00. - No accuracy for fermi level given. Defaulting to 0.1000E-19. - Maximum # of iterations to find E_F not set. Defaulting to 200. - Preferred method for the eigenvalue solver ('KS_method') not specified in 'control.in'. - Defaulting to serial version LAPACK (via ELSI). - Will not use alltoall communication since running on < 1024 CPUs. - Threshold for basis singularities not set. - Default threshold for basis singularities: 0.1000E-04 - partition_type (choice of integration weights) for integrals was not specified. - | Using a version of the partition function of Stratmann and coworkers ('stratmann_sparse'). - | At each grid point, the set of atoms used to build the partition table is smoothly restricted to - | only those atoms whose free-atom density would be non-zero at that grid point. - Partitioning for Hartree potential was not defined. Using partition_type for integrals. - | Adjusted default value of keyword multip_moments_threshold to: 0.10000000E-11 - | This value may affect high angular momentum components of the Hartree potential in periodic systems. - Spin handling was not defined in control.in. Defaulting to unpolarized case. - No q(lm)/r^(l+1) cutoff set for long-range Hartree potential. - | Using default value of 0.100000E-09 . - | Verify using the multipole_threshold keyword. - Defaulting to new monopole extrapolation. - Density update method: automatic selection selected. - Geometry relaxation: A file "geometry.in.next_step" is written out by default after each step. - | This file contains the geometry of the current relaxation step as well as - | the current Hessian matrix needed to restart the relaxation algorithm. - | If you do not want part or all of this information, use the keywords - | "write_restart_geometry" or "hessian_to_restart_geometry" to switch the output off. - Charge integration errors on the 3D integration grid will be compensated - by explicit normalization and distribution of residual charges. - Use the "compensate_multipole_errors" flag to change this behaviour. - Set 'collect_eigenvectors' to be '.true.' for all serial calculations. This is mandatory. - Set 'collect_eigenvectors' to be '.true.' for use_density_matrix .false. - Set 'collect_eigenvectors' to be '.true.' for KS_method lapack_fast and serial. - - Consistency checks for the contents of geometry.in are next. - - Number of empty states per atom not set in control.in - providing a guess from actual geometry. - | Total number of empty states used during s.c.f. cycle: 6 - If you use a very high smearing, use empty_states (per atom!) in control.in to increase this value. - - Structure-dependent array size parameters: - | Maximum number of distinct radial functions : 9 - | Maximum number of basis functions : 24 - | Number of Kohn-Sham states (occupied + empty): 11 ------------------------------------------------------------- - ------------------------------------------------------------- - Preparing all fixed parts of the calculation. ------------------------------------------------------------- - Determining machine precision: - 2.225073858507201E-308 - Setting up grids for atomic and cluster calculations. - - Creating wave function, potential, and density for free atoms. - Runtime choices for atomic solver: - | atomic solver xc : PBE - | compute density gradient: 1 - | compute kinetic density : F - - Species: O - - List of occupied orbitals and eigenvalues: - n l occ energy [Ha] energy [eV] - 1 0 2.0000 -18.926989 -515.0296 - 2 0 2.0000 -0.880247 -23.9527 - 2 1 4.0000 -0.331514 -9.0210 - - - Species: H - - List of occupied orbitals and eigenvalues: - n l occ energy [Ha] energy [eV] - 1 0 1.0000 -0.237593 -6.4652 - - - Adding cutoff potential to free-atom effective potential. - Creating fixed part of basis set: Ionic, confined, hydrogenic. - - O hydrogenic: - - List of hydrogenic basis orbitals: - n l effective z eigenvalue [eV] inner max. [A] outer max. [A] outer radius [A] - 2 1 1.800000 -10.9749 1.164242 1.164242 4.578029 - 3 2 7.600000 -87.3180 0.624125 0.624125 3.251020 - 3 0 6.400000 -61.9207 0.061167 1.081902 4.001998 - - - H hydrogenic: - - List of hydrogenic basis orbitals: - n l effective z eigenvalue [eV] inner max. [A] outer max. [A] outer radius [A] - 2 0 2.100000 -14.9728 0.193243 1.317208 4.583499 - 2 1 3.500000 -41.6669 0.602369 0.602369 3.723403 - - Creating atomic-like basis functions for current effective potential. - - Species O : - - List of atomic basis orbitals and eigenvalues: - n l energy [Ha] energy [eV] outer radius [A] - 1 0 -18.926989 -515.0296 1.415765 - 2 0 -0.880247 -23.9527 4.413171 - 2 1 -0.331514 -9.0210 4.522403 - - - Species H : - - List of atomic basis orbitals and eigenvalues: - n l energy [Ha] energy [eV] outer radius [A] - 1 0 -0.237593 -6.4652 4.527807 - - Assembling full basis from fixed parts. - | Species O : atomic orbital 1 s accepted. - | Species O : hydro orbital 3 s accepted. - | Species O : atomic orbital 2 s accepted. - | Species O : atomic orbital 2 p accepted. - | Species O : hydro orbital 2 p accepted. - | Species O : hydro orbital 3 d accepted. - | Species H : atomic orbital 1 s accepted. - | Species H : hydro orbital 2 s accepted. - | Species H : hydro orbital 2 p accepted. - - Basis size parameters after reduction: - | Total number of radial functions: 9 - | Total number of basis functions : 24 - - Per-task memory consumption for arrays in subroutine allocate_ext: - | 2.998708MB. - Testing on-site integration grid accuracy. - | Species Function (log., in eV) (rad., in eV) - 1 1 -515.0295626295 -515.0294562738 - 1 2 15.1698434419 15.1699322204 - 1 3 -21.6038822678 -21.6039118105 - 1 4 -9.0211123393 -9.0212703513 - 1 5 8.3047696391 8.2854840999 - 1 6 45.8428042125 45.8427461222 - 2 7 -6.4664147733 -6.4652229287 - 2 8 13.7099062243 13.7158503352 - 2 9 25.2661739479 25.2663166526 - - Preparing densities etc. for the partition functions (integrals / Hartree potential). - - Preparations completed. - max(cpu_time) : 0.064 s. - Wall clock time (cpu1) : 0.064 s. ------------------------------------------------------------- - ------------------------------------------------------------- - Begin self-consistency loop: Initialization. - - Date : 20230628, Time : 095500.973 ------------------------------------------------------------- - - Initializing index lists of integration centers etc. from given atomic structure: - | Number of centers in hartree potential : 3 - | Number of centers in hartree multipole : 3 - | Number of centers in electron density summation: 3 - | Number of centers in basis integrals : 3 - | Number of centers in integrals : 3 - | Number of centers in hamiltonian : 3 - - Initializing relaxation algorithms. - Finished initialization of distributed Hessian storage. - | Global dimension: 9 - | BLACS block size: 9 - | Number of workers: 1 - - Partitioning the integration grid into batches with parallel hashing+maxmin method. - | Number of batches: 256 - | Maximal batch size: 67 - | Minimal batch size: 58 - | Average batch size: 62.203 - | Standard deviation of batch sizes: 2.500 - - Integration load balanced across 1 MPI tasks. - Work distribution over tasks is as follows: - Task 0 has 15924 integration points. - Initializing partition tables, free-atom densities, potentials, etc. across the integration grid (initialize_grid_storage). - | initialize_grid_storage: Actual outermost partition radius vs. multipole_radius_free - | (-- VB: in principle, multipole_radius_free should be larger, hence this output) - | Species 1: Confinement radius = 4.999999999999999 AA, multipole_radius_free = 5.048384829883283 AA. - | Species 1: outer_partition_radius set to 5.048384829883283 AA . - | Species 2: Confinement radius = 4.999999999999999 AA, multipole_radius_free = 5.054417573612229 AA. - | Species 2: outer_partition_radius set to 5.054417573612229 AA . - | The sparse table of interatomic distances needs 0.09 kbyte instead of 0.07 kbyte of memory. - | Using the partition_type stratmann_smoother will reduce your memory usage. - | Net number of integration points: 15924 - | of which are non-zero points : 14536 - Renormalizing the initial density to the exact electron count on the 3D integration grid. - | Initial density: Formal number of electrons (from input files) : 10.0000000000 - | Integrated number of electrons on 3D grid : 9.9999431549 - | Charge integration error : -0.0000568451 - | Normalization factor for density and gradient : 1.0000056845 - Renormalizing the free-atom superposition density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 10.0000000000 - | Integrated number of electrons on 3D grid : 9.9999431549 - | Charge integration error : -0.0000568451 - | Normalization factor for density and gradient : 1.0000056845 - Obtaining max. number of non-zero basis functions in each batch (get_n_compute_maxes). - | Maximal number of non-zero basis functions: 24 in task 0 - Selecting the method for density update. - Loop over occupied states selected for charge density update. - Allocating 0.002 MB for KS_eigenvector - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.021 s, elapsed 0.021 s - Integrating overlap matrix. - Time summed over all CPUs for integration: real work 0.006 s, elapsed 0.006 s - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Overlap matrix is not singular - | Lowest and highest eigenvalues : 0.1639E-01, 0.2709E+01 - Finished singularity check of overlap matrix - | Time : 0.000 s - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.000 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -2.79227000 eV - Writing Kohn-Sham eigenvalues. - - State Occupation Eigenvalue [Ha] Eigenvalue [eV] - 1 2.00000 -19.032811 -517.90915 - 2 2.00000 -1.096687 -29.84238 - 3 2.00000 -0.625757 -17.02772 - 4 2.00000 -0.509068 -13.85246 - 5 2.00000 -0.435914 -11.86183 - 6 0.00000 -0.049192 -1.33858 - 7 0.00000 0.033225 0.90409 - 8 0.00000 0.215393 5.86114 - 9 0.00000 0.249072 6.77760 - 10 0.00000 0.301761 8.21135 - 11 0.00000 0.508037 13.82440 - - Highest occupied state (VBM) at -11.86182706 eV - | Occupation number: 2.00000000 - - Lowest unoccupied state (CBM) at -1.33858062 eV - | Occupation number: 0.00000000 - - Overall HOMO-LUMO gap: 10.52324644 eV. - Calculating total energy contributions from superposition of free atom densities. - - Total energy components: - | Sum of eigenvalues : -43.40047679 Ha -1180.98706138 eV - | XC energy correction : -9.02427629 Ha -245.56305186 eV - | XC potential correction : 11.60300934 Ha 315.73394853 eV - | Free-atom electrostatic energy: -35.72127400 Ha -972.02532155 eV - | Hartree energy correction : 0.00000000 Ha 0.00000000 eV - | Entropy correction : 0.00000000 Ha 0.00000000 eV - | --------------------------- - | Total energy : -76.54301773 Ha -2082.84148626 eV - | Total energy, T -> 0 : -76.54301773 Ha -2082.84148626 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -76.54301773 Ha -2082.84148626 eV - - Derived energy quantities: - | Kinetic energy : 75.72371465 Ha 2060.54711517 eV - | Electrostatic energy : -143.24245610 Ha -3897.82554957 eV - | Energy correction for multipole - | error in Hartree potential : 0.00000000 Ha 0.00000000 eV - | Sum of eigenvalues per atom : -393.66235379 eV - | Total energy (T->0) per atom : -694.28049542 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -694.28049542 eV - Initialize hartree_potential_storage - Max. number of atoms included in rho_multipole: 3 - - End scf initialization - timings : max(cpu_time) wall_clock(cpu1) - | Time for scf. initialization : 0.058 s 0.058 s - | Boundary condition initialization : 0.000 s 0.000 s - | Relaxation initialization : 0.000 s 0.000 s - | Integration : 0.028 s 0.027 s - | Solution of K.-S. eqns. : 0.000 s 0.001 s - | Grid partitioning : 0.012 s 0.012 s - | Preloading free-atom quantities on grid : 0.009 s 0.009 s - | Free-atom superposition energy : 0.008 s 0.008 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 0.009 MB (on task 0) - | Maximum: 0.009 MB (on task 0) - | Average: 0.009 MB - | Peak value for overall tracked memory usage: - | Minimum: 0.549 MB (on task 0 after allocating grid_partition) - | Maximum: 0.549 MB (on task 0 after allocating grid_partition) - | Average: 0.549 MB - | Largest tracked array allocation so far: - | Minimum: 0.364 MB (all_coords on task 0) - | Maximum: 0.364 MB (all_coords on task 0) - | Average: 0.364 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - Evaluating new KS density. - Integration grid: deviation in total charge ( - N_e) = -8.881784E-15 - - Time for density update prior : max(cpu_time) wall_clock(cpu1) - | self-consistency iterative process : 0.014 s 0.013 s - ------------------------------------------------------------- - Begin self-consistency iteration # 1 - - Date : 20230628, Time : 095501.044 ------------------------------------------------------------- - Pulay mixing of updated and previous charge densities. - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 10.0000000000 - | Integrated number of electrons on 3D grid : 10.0000000000 - | Charge integration error : 0.0000000000 - | Normalization factor for density and gradient : 1.0000000000 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = 0.480609E-13 - | Sum of charges compensated after spline to logarithmic grids = 0.121981E-04 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = 0.479102E-13 - Summing up the Hartree potential. - Time summed over all CPUs for potential: real work 0.008 s, elapsed 0.008 s - | RMS charge density error from multipole expansion : 0.353198E-03 - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.021 s, elapsed 0.021 s - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.000 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -2.61100247 eV - Writing Kohn-Sham eigenvalues. - - State Occupation Eigenvalue [Ha] Eigenvalue [eV] - 1 2.00000 -18.993769 -516.84676 - 2 2.00000 -1.077613 -29.32333 - 3 2.00000 -0.609308 -16.58011 - 4 2.00000 -0.489541 -13.32110 - 5 2.00000 -0.415574 -11.30835 - 6 0.00000 -0.044601 -1.21365 - 7 0.00000 0.039616 1.07801 - 8 0.00000 0.223818 6.09038 - 9 0.00000 0.257915 7.01823 - 10 0.00000 0.307769 8.37482 - 11 0.00000 0.513654 13.97725 - - Highest occupied state (VBM) at -11.30835240 eV - | Occupation number: 2.00000000 - - Lowest unoccupied state (CBM) at -1.21365069 eV - | Occupation number: 0.00000000 - - Overall HOMO-LUMO gap: 10.09470171 eV. - - Total energy components: - | Sum of eigenvalues : -43.17161059 Ha -1174.75929518 eV - | XC energy correction : -9.04989993 Ha -246.26030676 eV - | XC potential correction : 11.63658499 Ha 316.64758837 eV - | Free-atom electrostatic energy: -35.72127400 Ha -972.02532155 eV - | Hartree energy correction : -0.21960533 Ha -5.97576519 eV - | Entropy correction : 0.00000000 Ha 0.00000000 eV - | --------------------------- - | Total energy : -76.52580486 Ha -2082.37310032 eV - | Total energy, T -> 0 : -76.52580486 Ha -2082.37310032 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -76.52580486 Ha -2082.37310032 eV - - Derived energy quantities: - | Kinetic energy : 75.87943483 Ha 2064.78447672 eV - | Electrostatic energy : -143.35533976 Ha -3900.89727028 eV - | Energy correction for multipole - | error in Hartree potential : 0.00010724 Ha 0.00291817 eV - | Sum of eigenvalues per atom : -391.58643173 eV - | Total energy (T->0) per atom : -694.12436677 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -694.12436677 eV - Evaluating new KS density. - Integration grid: deviation in total charge ( - N_e) = -2.664535E-14 - - Self-consistency convergence accuracy: - | Change of charge density : 0.3070E+00 - | Change of sum of eigenvalues : 0.6228E+01 eV - | Change of total energy : 0.4684E+00 eV - - ------------------------------------------------------------- - End self-consistency iteration # 1 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 0.045 s 0.046 s - | Charge density update : 0.013 s 0.013 s - | Density mixing : 0.001 s 0.001 s - | Hartree multipole update : 0.002 s 0.002 s - | Hartree multipole summation : 0.008 s 0.008 s - | Integration : 0.022 s 0.021 s - | Solution of K.-S. eqns. : 0.000 s 0.001 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 0.009 MB (on task 0) - | Maximum: 0.009 MB (on task 0) - | Average: 0.009 MB - | Peak value for overall tracked memory usage: - | Minimum: 0.549 MB (on task 0 after allocating grid_partition) - | Maximum: 0.549 MB (on task 0 after allocating grid_partition) - | Average: 0.549 MB - | Largest tracked array allocation so far: - | Minimum: 0.364 MB (all_coords on task 0) - | Maximum: 0.364 MB (all_coords on task 0) - | Average: 0.364 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - ------------------------------------------------------------- - Begin self-consistency iteration # 2 - - Date : 20230628, Time : 095501.090 ------------------------------------------------------------- - Pulay mixing of updated and previous charge densities. - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 10.0000000000 - | Integrated number of electrons on 3D grid : 10.0000000000 - | Charge integration error : -0.0000000000 - | Normalization factor for density and gradient : 1.0000000000 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = -0.272912E-13 - | Sum of charges compensated after spline to logarithmic grids = 0.868881E-04 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = -0.276848E-13 - Summing up the Hartree potential. - Time summed over all CPUs for potential: real work 0.008 s, elapsed 0.008 s - | RMS charge density error from multipole expansion : 0.249403E-02 - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.021 s, elapsed 0.021 s - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.001 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -1.50966676 eV - Highest occupied state (VBM) at -8.17692053 eV - | Occupation number: 2.00000000 - - Lowest unoccupied state (CBM) at -0.44769917 eV - | Occupation number: 0.00000000 - - Overall HOMO-LUMO gap: 7.72922136 eV. - - Checking to see if s.c.f. parameters should be adjusted. - The system likely has a gap. Increased the default Pulay mixing parameter (charge_mix_param). Value: 0.200000 . - Kept the default occupation width. Value: 0.010000 eV. - - Total energy components: - | Sum of eigenvalues : -41.86980201 Ha -1139.33528147 eV - | XC energy correction : -9.20277869 Ha -250.42034953 eV - | XC potential correction : 11.83691214 Ha 322.09876756 eV - | Free-atom electrostatic energy: -35.72127400 Ha -972.02532155 eV - | Hartree energy correction : -1.51668467 Ha -41.27108979 eV - | Entropy correction : 0.00000000 Ha 0.00000000 eV - | --------------------------- - | Total energy : -76.47362723 Ha -2080.95327478 eV - | Total energy, T -> 0 : -76.47362723 Ha -2080.95327478 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -76.47362723 Ha -2080.95327478 eV - - Derived energy quantities: - | Kinetic energy : 76.68903147 Ha 2086.81472232 eV - | Electrostatic energy : -143.95988001 Ha -3917.34764757 eV - | Energy correction for multipole - | error in Hartree potential : 0.00051820 Ha 0.01410099 eV - | Sum of eigenvalues per atom : -379.77842716 eV - | Total energy (T->0) per atom : -693.65109159 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -693.65109159 eV - Evaluating new KS density. - Integration grid: deviation in total charge ( - N_e) = 3.730349E-14 - - Self-consistency convergence accuracy: - | Change of charge density : 0.2694E+00 - | Change of sum of eigenvalues : 0.3542E+02 eV - | Change of total energy : 0.1420E+01 eV - - ------------------------------------------------------------- - End self-consistency iteration # 2 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 0.045 s 0.045 s - | Charge density update : 0.013 s 0.013 s - | Density mixing : 0.001 s 0.001 s - | Hartree multipole update : 0.002 s 0.002 s - | Hartree multipole summation : 0.008 s 0.008 s - | Integration : 0.021 s 0.020 s - | Solution of K.-S. eqns. : 0.000 s 0.001 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 0.009 MB (on task 0) - | Maximum: 0.009 MB (on task 0) - | Average: 0.009 MB - | Peak value for overall tracked memory usage: - | Minimum: 0.549 MB (on task 0 after allocating grid_partition) - | Maximum: 0.549 MB (on task 0 after allocating grid_partition) - | Average: 0.549 MB - | Largest tracked array allocation so far: - | Minimum: 0.364 MB (all_coords on task 0) - | Maximum: 0.364 MB (all_coords on task 0) - | Average: 0.364 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - ------------------------------------------------------------- - Begin self-consistency iteration # 3 - - Date : 20230628, Time : 095501.135 ------------------------------------------------------------- - Pulay mixing of updated and previous charge densities. - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 10.0000000000 - | Integrated number of electrons on 3D grid : 10.0000000000 - | Charge integration error : -0.0000000000 - | Normalization factor for density and gradient : 1.0000000000 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = -0.358512E-13 - | Sum of charges compensated after spline to logarithmic grids = 0.608613E-04 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = -0.356667E-13 - Summing up the Hartree potential. - Time summed over all CPUs for potential: real work 0.008 s, elapsed 0.008 s - | RMS charge density error from multipole expansion : 0.373864E-02 - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.021 s, elapsed 0.021 s - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.000 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -1.83276307 eV - Highest occupied state (VBM) at -9.47939984 eV - | Occupation number: 2.00000000 - - Lowest unoccupied state (CBM) at -0.67075811 eV - | Occupation number: 0.00000000 - - Overall HOMO-LUMO gap: 8.80864173 eV. - - Total energy components: - | Sum of eigenvalues : -42.51834920 Ha -1156.98314838 eV - | XC energy correction : -9.12444892 Ha -248.28888805 eV - | XC potential correction : 11.73383120 Ha 319.29379235 eV - | Free-atom electrostatic energy: -35.72127400 Ha -972.02532155 eV - | Hartree energy correction : -0.85867394 Ha -23.36570686 eV - | Entropy correction : 0.00000000 Ha 0.00000000 eV - | --------------------------- - | Total energy : -76.48891487 Ha -2081.36927249 eV - | Total energy, T -> 0 : -76.48891487 Ha -2081.36927249 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -76.48891487 Ha -2081.36927249 eV - - Derived energy quantities: - | Kinetic energy : 75.97577172 Ha 2067.40593692 eV - | Electrostatic energy : -143.34023766 Ha -3900.48632136 eV - | Energy correction for multipole - | error in Hartree potential : -0.00170401 Ha -0.04636857 eV - | Sum of eigenvalues per atom : -385.66104946 eV - | Total energy (T->0) per atom : -693.78975750 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -693.78975750 eV - Evaluating new KS density. - Integration grid: deviation in total charge ( - N_e) = 0.000000E+00 - - Self-consistency convergence accuracy: - | Change of charge density : 0.1194E+00 - | Change of sum of eigenvalues : -0.1765E+02 eV - | Change of total energy : -0.4160E+00 eV - - ------------------------------------------------------------- - End self-consistency iteration # 3 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 0.046 s 0.045 s - | Charge density update : 0.013 s 0.013 s - | Density mixing : 0.002 s 0.001 s - | Hartree multipole update : 0.002 s 0.002 s - | Hartree multipole summation : 0.008 s 0.008 s - | Integration : 0.021 s 0.021 s - | Solution of K.-S. eqns. : 0.000 s 0.000 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 0.009 MB (on task 0) - | Maximum: 0.009 MB (on task 0) - | Average: 0.009 MB - | Peak value for overall tracked memory usage: - | Minimum: 0.549 MB (on task 0 after allocating grid_partition) - | Maximum: 0.549 MB (on task 0 after allocating grid_partition) - | Average: 0.549 MB - | Largest tracked array allocation so far: - | Minimum: 0.364 MB (all_coords on task 0) - | Maximum: 0.364 MB (all_coords on task 0) - | Average: 0.364 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - ------------------------------------------------------------- - Begin self-consistency iteration # 4 - - Date : 20230628, Time : 095501.181 ------------------------------------------------------------- - Pulay mixing of updated and previous charge densities. - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 10.0000000000 - | Integrated number of electrons on 3D grid : 10.0000000000 - | Charge integration error : -0.0000000000 - | Normalization factor for density and gradient : 1.0000000000 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = 0.447679E-13 - | Sum of charges compensated after spline to logarithmic grids = 0.117137E-03 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = 0.456534E-13 - Summing up the Hartree potential. - Time summed over all CPUs for potential: real work 0.008 s, elapsed 0.008 s - | RMS charge density error from multipole expansion : 0.612177E-02 - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.021 s, elapsed 0.021 s - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.001 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -1.00486968 eV - Highest occupied state (VBM) at -7.58224787 eV - | Occupation number: 2.00000000 - - Lowest unoccupied state (CBM) at -0.09841615 eV - | Occupation number: 0.00000000 - - Overall HOMO-LUMO gap: 7.48383172 eV. - - Total energy components: - | Sum of eigenvalues : -41.78332068 Ha -1136.98200470 eV - | XC energy correction : -9.21749844 Ha -250.82089418 eV - | XC potential correction : 11.85563613 Ha 322.60827311 eV - | Free-atom electrostatic energy: -35.72127400 Ha -972.02532155 eV - | Hartree energy correction : -1.60353532 Ha -43.63441626 eV - | Entropy correction : 0.00000000 Ha 0.00000000 eV - | --------------------------- - | Total energy : -76.46999231 Ha -2080.85436358 eV - | Total energy, T -> 0 : -76.46999231 Ha -2080.85436358 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -76.46999231 Ha -2080.85436358 eV - - Derived energy quantities: - | Kinetic energy : 76.23184146 Ha 2074.37394903 eV - | Electrostatic energy : -143.48433533 Ha -3904.40741844 eV - | Energy correction for multipole - | error in Hartree potential : -0.00273119 Ha -0.07431933 eV - | Sum of eigenvalues per atom : -378.99400157 eV - | Total energy (T->0) per atom : -693.61812119 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -693.61812119 eV - Evaluating new KS density. - Integration grid: deviation in total charge ( - N_e) = 1.065814E-14 - - Self-consistency convergence accuracy: - | Change of charge density : 0.1621E+00 - | Change of sum of eigenvalues : 0.2000E+02 eV - | Change of total energy : 0.5149E+00 eV - - ------------------------------------------------------------- - End self-consistency iteration # 4 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 0.047 s 0.046 s - | Charge density update : 0.013 s 0.012 s - | Density mixing : 0.003 s 0.002 s - | Hartree multipole update : 0.002 s 0.002 s - | Hartree multipole summation : 0.008 s 0.008 s - | Integration : 0.021 s 0.021 s - | Solution of K.-S. eqns. : 0.000 s 0.001 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 0.009 MB (on task 0) - | Maximum: 0.009 MB (on task 0) - | Average: 0.009 MB - | Peak value for overall tracked memory usage: - | Minimum: 0.549 MB (on task 0 after allocating grid_partition) - | Maximum: 0.549 MB (on task 0 after allocating grid_partition) - | Average: 0.549 MB - | Largest tracked array allocation so far: - | Minimum: 0.364 MB (all_coords on task 0) - | Maximum: 0.364 MB (all_coords on task 0) - | Average: 0.364 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - ------------------------------------------------------------- - Begin self-consistency iteration # 5 - - Date : 20230628, Time : 095501.228 ------------------------------------------------------------- - Pulay mixing of updated and previous charge densities. - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 10.0000000000 - | Integrated number of electrons on 3D grid : 10.0000000000 - | Charge integration error : 0.0000000000 - | Normalization factor for density and gradient : 1.0000000000 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = 0.930286E-13 - | Sum of charges compensated after spline to logarithmic grids = 0.120298E-03 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = 0.929549E-13 - Summing up the Hartree potential. - Time summed over all CPUs for potential: real work 0.008 s, elapsed 0.008 s - | RMS charge density error from multipole expansion : 0.613785E-02 - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.022 s, elapsed 0.022 s - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.000 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -0.98598576 eV - Highest occupied state (VBM) at -7.54693784 eV - | Occupation number: 2.00000000 - - Lowest unoccupied state (CBM) at -0.08558240 eV - | Occupation number: 0.00000000 - - Overall HOMO-LUMO gap: 7.46135544 eV. - - Total energy components: - | Sum of eigenvalues : -41.76913271 Ha -1136.59593031 eV - | XC energy correction : -9.21934311 Ha -250.87109021 eV - | XC potential correction : 11.85806416 Ha 322.67434318 eV - | Free-atom electrostatic energy: -35.72127400 Ha -972.02532155 eV - | Hartree energy correction : -1.61818974 Ha -44.03318308 eV - | Entropy correction : 0.00000000 Ha 0.00000000 eV - | --------------------------- - | Total energy : -76.46987539 Ha -2080.85118197 eV - | Total energy, T -> 0 : -76.46987539 Ha -2080.85118197 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -76.46987539 Ha -2080.85118197 eV - - Derived energy quantities: - | Kinetic energy : 76.23723292 Ha 2074.52065823 eV - | Electrostatic energy : -143.48776520 Ha -3904.50074999 eV - | Energy correction for multipole - | error in Hartree potential : -0.00277183 Ha -0.07542532 eV - | Sum of eigenvalues per atom : -378.86531010 eV - | Total energy (T->0) per atom : -693.61706066 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -693.61706066 eV - Evaluating new KS density. - Integration grid: deviation in total charge ( - N_e) = -2.486900E-14 - - Self-consistency convergence accuracy: - | Change of charge density : 0.3224E-01 - | Change of sum of eigenvalues : 0.3861E+00 eV - | Change of total energy : 0.3182E-02 eV - - ------------------------------------------------------------- - End self-consistency iteration # 5 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 0.047 s 0.047 s - | Charge density update : 0.013 s 0.013 s - | Density mixing : 0.003 s 0.002 s - | Hartree multipole update : 0.002 s 0.002 s - | Hartree multipole summation : 0.008 s 0.008 s - | Integration : 0.022 s 0.022 s - | Solution of K.-S. eqns. : 0.000 s 0.000 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 0.009 MB (on task 0) - | Maximum: 0.009 MB (on task 0) - | Average: 0.009 MB - | Peak value for overall tracked memory usage: - | Minimum: 0.549 MB (on task 0 after allocating grid_partition) - | Maximum: 0.549 MB (on task 0 after allocating grid_partition) - | Average: 0.549 MB - | Largest tracked array allocation so far: - | Minimum: 0.364 MB (all_coords on task 0) - | Maximum: 0.364 MB (all_coords on task 0) - | Average: 0.364 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - ------------------------------------------------------------- - Begin self-consistency iteration # 6 - - Date : 20230628, Time : 095501.275 ------------------------------------------------------------- - Pulay mixing of updated and previous charge densities. - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 10.0000000000 - | Integrated number of electrons on 3D grid : 10.0000000000 - | Charge integration error : -0.0000000000 - | Normalization factor for density and gradient : 1.0000000000 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = 0.237368E-13 - | Sum of charges compensated after spline to logarithmic grids = 0.145012E-03 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = 0.237860E-13 - Summing up the Hartree potential. - Time summed over all CPUs for potential: real work 0.008 s, elapsed 0.008 s - | RMS charge density error from multipole expansion : 0.636222E-02 - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.021 s, elapsed 0.021 s - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.000 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -0.83114754 eV - Highest occupied state (VBM) at -7.26694753 eV - | Occupation number: 2.00000000 - - Lowest unoccupied state (CBM) at 0.02109373 eV - | Occupation number: 0.00000000 - - Overall HOMO-LUMO gap: 7.28804126 eV. - - Total energy components: - | Sum of eigenvalues : -41.66008202 Ha -1133.62851024 eV - | XC energy correction : -9.23378999 Ha -251.26420986 eV - | XC potential correction : 11.87707254 Ha 323.19158760 eV - | Free-atom electrostatic energy: -35.72127400 Ha -972.02532155 eV - | Hartree energy correction : -1.73119749 Ha -47.10828065 eV - | Entropy correction : 0.00000000 Ha 0.00000000 eV - | --------------------------- - | Total energy : -76.46927097 Ha -2080.83473471 eV - | Total energy, T -> 0 : -76.46927097 Ha -2080.83473471 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -76.46927097 Ha -2080.83473471 eV - - Derived energy quantities: - | Kinetic energy : 76.26661039 Ha 2075.32005989 eV - | Electrostatic energy : -143.50209137 Ha -3904.89058474 eV - | Energy correction for multipole - | error in Hartree potential : -0.00315687 Ha -0.08590286 eV - | Sum of eigenvalues per atom : -377.87617008 eV - | Total energy (T->0) per atom : -693.61157824 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -693.61157824 eV - Evaluating new KS density. - Integration grid: deviation in total charge ( - N_e) = -1.953993E-14 - - Self-consistency convergence accuracy: - | Change of charge density : 0.2988E-01 - | Change of sum of eigenvalues : 0.2967E+01 eV - | Change of total energy : 0.1645E-01 eV - - ------------------------------------------------------------- - End self-consistency iteration # 6 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 0.051 s 0.051 s - | Charge density update : 0.013 s 0.013 s - | Density mixing : 0.006 s 0.006 s - | Hartree multipole update : 0.002 s 0.002 s - | Hartree multipole summation : 0.008 s 0.008 s - | Integration : 0.022 s 0.022 s - | Solution of K.-S. eqns. : 0.000 s 0.000 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 0.009 MB (on task 0) - | Maximum: 0.009 MB (on task 0) - | Average: 0.009 MB - | Peak value for overall tracked memory usage: - | Minimum: 0.549 MB (on task 0 after allocating grid_partition) - | Maximum: 0.549 MB (on task 0 after allocating grid_partition) - | Average: 0.549 MB - | Largest tracked array allocation so far: - | Minimum: 0.364 MB (all_coords on task 0) - | Maximum: 0.364 MB (all_coords on task 0) - | Average: 0.364 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - ------------------------------------------------------------- - Begin self-consistency iteration # 7 - - Date : 20230628, Time : 095501.326 ------------------------------------------------------------- - Pulay mixing of updated and previous charge densities. - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 10.0000000000 - | Integrated number of electrons on 3D grid : 10.0000000000 - | Charge integration error : 0.0000000000 - | Normalization factor for density and gradient : 1.0000000000 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = 0.350518E-13 - | Sum of charges compensated after spline to logarithmic grids = 0.161509E-03 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = 0.354207E-13 - Summing up the Hartree potential. - Time summed over all CPUs for potential: real work 0.008 s, elapsed 0.008 s - | RMS charge density error from multipole expansion : 0.647720E-02 - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.021 s, elapsed 0.021 s - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.000 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -0.74168939 eV - Highest occupied state (VBM) at -7.09752919 eV - | Occupation number: 2.00000000 - - Lowest unoccupied state (CBM) at 0.08405329 eV - | Occupation number: 0.00000000 - - Overall HOMO-LUMO gap: 7.18158248 eV. - - Total energy components: - | Sum of eigenvalues : -41.59374938 Ha -1131.82350724 eV - | XC energy correction : -9.24249280 Ha -251.50102532 eV - | XC potential correction : 11.88854091 Ha 323.50365794 eV - | Free-atom electrostatic energy: -35.72127400 Ha -972.02532155 eV - | Hartree energy correction : -1.80017602 Ha -48.98528182 eV - | Entropy correction : 0.00000000 Ha 0.00000000 eV - | --------------------------- - | Total energy : -76.46915128 Ha -2080.83147799 eV - | Total energy, T -> 0 : -76.46915128 Ha -2080.83147799 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -76.46915128 Ha -2080.83147799 eV - - Derived energy quantities: - | Kinetic energy : 76.28493278 Ha 2075.81863733 eV - | Electrostatic energy : -143.51159126 Ha -3905.14909000 eV - | Energy correction for multipole - | error in Hartree potential : -0.00340166 Ha -0.09256383 eV - | Sum of eigenvalues per atom : -377.27450241 eV - | Total energy (T->0) per atom : -693.61049266 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -693.61049266 eV - Evaluating new KS density. - Integration grid: deviation in total charge ( - N_e) = 2.842171E-14 - - Self-consistency convergence accuracy: - | Change of charge density : 0.1231E-01 - | Change of sum of eigenvalues : 0.1805E+01 eV - | Change of total energy : 0.3257E-02 eV - - ------------------------------------------------------------- - End self-consistency iteration # 7 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 0.049 s 0.049 s - | Charge density update : 0.013 s 0.013 s - | Density mixing : 0.004 s 0.004 s - | Hartree multipole update : 0.002 s 0.002 s - | Hartree multipole summation : 0.008 s 0.008 s - | Integration : 0.022 s 0.022 s - | Solution of K.-S. eqns. : 0.000 s 0.000 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 0.009 MB (on task 0) - | Maximum: 0.009 MB (on task 0) - | Average: 0.009 MB - | Peak value for overall tracked memory usage: - | Minimum: 0.549 MB (on task 0 after allocating grid_partition) - | Maximum: 0.549 MB (on task 0 after allocating grid_partition) - | Average: 0.549 MB - | Largest tracked array allocation so far: - | Minimum: 0.364 MB (all_coords on task 0) - | Maximum: 0.364 MB (all_coords on task 0) - | Average: 0.364 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - ------------------------------------------------------------- - Begin self-consistency iteration # 8 - - Date : 20230628, Time : 095501.375 ------------------------------------------------------------- - Pulay mixing of updated and previous charge densities. - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 10.0000000000 - | Integrated number of electrons on 3D grid : 10.0000000000 - | Charge integration error : 0.0000000000 - | Normalization factor for density and gradient : 1.0000000000 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = 0.404879E-13 - | Sum of charges compensated after spline to logarithmic grids = 0.164296E-03 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = 0.404879E-13 - Summing up the Hartree potential. - Time summed over all CPUs for potential: real work 0.008 s, elapsed 0.008 s - | RMS charge density error from multipole expansion : 0.650047E-02 - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.022 s, elapsed 0.022 s - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.000 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -0.72702459 eV - Highest occupied state (VBM) at -7.07120848 eV - | Occupation number: 2.00000000 - - Lowest unoccupied state (CBM) at 0.09449783 eV - | Occupation number: 0.00000000 - - Overall HOMO-LUMO gap: 7.16570631 eV. - - Total energy components: - | Sum of eigenvalues : -41.58376611 Ha -1131.55184853 eV - | XC energy correction : -9.24381832 Ha -251.53709447 eV - | XC potential correction : 11.89028876 Ha 323.55121924 eV - | Free-atom electrostatic energy: -35.72127400 Ha -972.02532155 eV - | Hartree energy correction : -1.81058075 Ha -49.26840907 eV - | Entropy correction : 0.00000000 Ha 0.00000000 eV - | --------------------------- - | Total energy : -76.46915042 Ha -2080.83145438 eV - | Total energy, T -> 0 : -76.46915042 Ha -2080.83145438 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -76.46915042 Ha -2080.83145438 eV - - Derived energy quantities: - | Kinetic energy : 76.28672331 Ha 2075.86736033 eV - | Electrostatic energy : -143.51205541 Ha -3905.16172024 eV - | Energy correction for multipole - | error in Hartree potential : -0.00344832 Ha -0.09383351 eV - | Sum of eigenvalues per atom : -377.18394951 eV - | Total energy (T->0) per atom : -693.61048479 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -693.61048479 eV - Evaluating new KS density. - Integration grid: deviation in total charge ( - N_e) = 3.552714E-14 - - Self-consistency convergence accuracy: - | Change of charge density : 0.1250E-02 - | Change of sum of eigenvalues : 0.2717E+00 eV - | Change of total energy : 0.2361E-04 eV - - ------------------------------------------------------------- - End self-consistency iteration # 8 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 0.048 s 0.048 s - | Charge density update : 0.013 s 0.013 s - | Density mixing : 0.003 s 0.003 s - | Hartree multipole update : 0.002 s 0.002 s - | Hartree multipole summation : 0.008 s 0.008 s - | Integration : 0.022 s 0.022 s - | Solution of K.-S. eqns. : 0.000 s 0.000 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 0.009 MB (on task 0) - | Maximum: 0.009 MB (on task 0) - | Average: 0.009 MB - | Peak value for overall tracked memory usage: - | Minimum: 0.549 MB (on task 0 after allocating grid_partition) - | Maximum: 0.549 MB (on task 0 after allocating grid_partition) - | Average: 0.549 MB - | Largest tracked array allocation so far: - | Minimum: 0.364 MB (all_coords on task 0) - | Maximum: 0.364 MB (all_coords on task 0) - | Average: 0.364 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - ------------------------------------------------------------- - Begin self-consistency iteration # 9 - - Date : 20230628, Time : 095501.423 ------------------------------------------------------------- - Pulay mixing of updated and previous charge densities. - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 10.0000000000 - | Integrated number of electrons on 3D grid : 10.0000000000 - | Charge integration error : 0.0000000000 - | Normalization factor for density and gradient : 1.0000000000 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = 0.123087E-12 - | Sum of charges compensated after spline to logarithmic grids = 0.163432E-03 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = 0.124711E-12 - Summing up the Hartree potential. - Time summed over all CPUs for potential: real work 0.008 s, elapsed 0.008 s - | RMS charge density error from multipole expansion : 0.649308E-02 - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.021 s, elapsed 0.021 s - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.000 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -0.73150611 eV - Highest occupied state (VBM) at -7.07781963 eV - | Occupation number: 2.00000000 - - Lowest unoccupied state (CBM) at 0.09138305 eV - | Occupation number: 0.00000000 - - Overall HOMO-LUMO gap: 7.16920268 eV. - - Total energy components: - | Sum of eigenvalues : -41.58620402 Ha -1131.61818755 eV - | XC energy correction : -9.24347846 Ha -251.52784639 eV - | XC potential correction : 11.88984104 Ha 323.53903622 eV - | Free-atom electrostatic energy: -35.72127400 Ha -972.02532155 eV - | Hartree energy correction : -1.80803473 Ha -49.19912835 eV - | Entropy correction : 0.00000000 Ha 0.00000000 eV - | --------------------------- - | Total energy : -76.46915017 Ha -2080.83144762 eV - | Total energy, T -> 0 : -76.46915017 Ha -2080.83144762 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -76.46915017 Ha -2080.83144762 eV - - Derived energy quantities: - | Kinetic energy : 76.28677355 Ha 2075.86872736 eV - | Electrostatic energy : -143.51244526 Ha -3905.17232859 eV - | Energy correction for multipole - | error in Hartree potential : -0.00343219 Ha -0.09339472 eV - | Sum of eigenvalues per atom : -377.20606252 eV - | Total energy (T->0) per atom : -693.61048254 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -693.61048254 eV - Evaluating new KS density. - Integration grid: deviation in total charge ( - N_e) = 1.776357E-15 - - Self-consistency convergence accuracy: - | Change of charge density : 0.3854E-03 - | Change of sum of eigenvalues : -0.6634E-01 eV - | Change of total energy : 0.6755E-05 eV - - ------------------------------------------------------------- - End self-consistency iteration # 9 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 0.047 s 0.047 s - | Charge density update : 0.013 s 0.013 s - | Density mixing : 0.003 s 0.003 s - | Hartree multipole update : 0.002 s 0.002 s - | Hartree multipole summation : 0.008 s 0.008 s - | Integration : 0.021 s 0.021 s - | Solution of K.-S. eqns. : 0.000 s 0.000 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 0.010 MB (on task 0) - | Maximum: 0.010 MB (on task 0) - | Average: 0.010 MB - | Peak value for overall tracked memory usage: - | Minimum: 0.549 MB (on task 0 after allocating grid_partition) - | Maximum: 0.549 MB (on task 0 after allocating grid_partition) - | Average: 0.549 MB - | Largest tracked array allocation so far: - | Minimum: 0.364 MB (all_coords on task 0) - | Maximum: 0.364 MB (all_coords on task 0) - | Average: 0.364 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - ------------------------------------------------------------- - Begin self-consistency iteration # 10 - - Date : 20230628, Time : 095501.470 ------------------------------------------------------------- - Pulay mixing of updated and previous charge densities. - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 10.0000000000 - | Integrated number of electrons on 3D grid : 10.0000000000 - | Charge integration error : 0.0000000000 - | Normalization factor for density and gradient : 1.0000000000 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = 0.434642E-13 - | Sum of charges compensated after spline to logarithmic grids = 0.163336E-03 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = 0.436118E-13 - Summing up the Hartree potential. - Time summed over all CPUs for potential: real work 0.008 s, elapsed 0.008 s - | RMS charge density error from multipole expansion : 0.649266E-02 - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.021 s, elapsed 0.021 s - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.000 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -0.73194815 eV - Highest occupied state (VBM) at -7.07878555 eV - | Occupation number: 2.00000000 - - Lowest unoccupied state (CBM) at 0.09105437 eV - | Occupation number: 0.00000000 - - Overall HOMO-LUMO gap: 7.16983991 eV. - - Total energy components: - | Sum of eigenvalues : -41.58658022 Ha -1131.62842454 eV - | XC energy correction : -9.24343119 Ha -251.52656013 eV - | XC potential correction : 11.88977861 Ha 323.53733745 eV - | Free-atom electrostatic energy: -35.72127400 Ha -972.02532155 eV - | Hartree energy correction : -1.80764338 Ha -49.18847899 eV - | Entropy correction : 0.00000000 Ha 0.00000000 eV - | --------------------------- - | Total energy : -76.46915017 Ha -2080.83144776 eV - | Total energy, T -> 0 : -76.46915017 Ha -2080.83144776 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -76.46915017 Ha -2080.83144776 eV - - Derived energy quantities: - | Kinetic energy : 76.28667075 Ha 2075.86592990 eV - | Electrostatic energy : -143.51238973 Ha -3905.17081753 eV - | Energy correction for multipole - | error in Hartree potential : -0.00343077 Ha -0.09335597 eV - | Sum of eigenvalues per atom : -377.20947485 eV - | Total energy (T->0) per atom : -693.61048259 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -693.61048259 eV - Evaluating new KS density. - Integration grid: deviation in total charge ( - N_e) = -2.486900E-14 - - Self-consistency convergence accuracy: - | Change of charge density : 0.4204E-04 - | Change of sum of eigenvalues : -0.1024E-01 eV - | Change of total energy : -0.1338E-06 eV - - ------------------------------------------------------------- - End self-consistency iteration # 10 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 0.047 s 0.047 s - | Charge density update : 0.013 s 0.013 s - | Density mixing : 0.003 s 0.003 s - | Hartree multipole update : 0.002 s 0.002 s - | Hartree multipole summation : 0.008 s 0.007 s - | Integration : 0.021 s 0.022 s - | Solution of K.-S. eqns. : 0.000 s 0.000 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 0.010 MB (on task 0) - | Maximum: 0.010 MB (on task 0) - | Average: 0.010 MB - | Peak value for overall tracked memory usage: - | Minimum: 0.549 MB (on task 0 after allocating grid_partition) - | Maximum: 0.549 MB (on task 0 after allocating grid_partition) - | Average: 0.549 MB - | Largest tracked array allocation so far: - | Minimum: 0.364 MB (all_coords on task 0) - | Maximum: 0.364 MB (all_coords on task 0) - | Average: 0.364 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - ------------------------------------------------------------- - Begin self-consistency iteration # 11 - - Date : 20230628, Time : 095501.517 ------------------------------------------------------------- - Pulay mixing of updated and previous charge densities. - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 10.0000000000 - | Integrated number of electrons on 3D grid : 10.0000000000 - | Charge integration error : -0.0000000000 - | Normalization factor for density and gradient : 1.0000000000 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = 0.382003E-13 - | Sum of charges compensated after spline to logarithmic grids = 0.163377E-03 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = 0.378313E-13 - Summing up the Hartree potential. - Time summed over all CPUs for potential: real work 0.009 s, elapsed 0.009 s - | RMS charge density error from multipole expansion : 0.649286E-02 - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.021 s, elapsed 0.021 s - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.000 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -0.73176936 eV - Highest occupied state (VBM) at -7.07842135 eV - | Occupation number: 2.00000000 - - Lowest unoccupied state (CBM) at 0.09118270 eV - | Occupation number: 0.00000000 - - Overall HOMO-LUMO gap: 7.16960405 eV. - - Total energy components: - | Sum of eigenvalues : -41.58643672 Ha -1131.62451950 eV - | XC energy correction : -9.24344966 Ha -251.52706278 eV - | XC potential correction : 11.88980299 Ha 323.53800085 eV - | Free-atom electrostatic energy: -35.72127400 Ha -972.02532155 eV - | Hartree energy correction : -1.80779279 Ha -49.19254463 eV - | Entropy correction : 0.00000000 Ha 0.00000000 eV - | --------------------------- - | Total energy : -76.46915017 Ha -2080.83144761 eV - | Total energy, T -> 0 : -76.46915017 Ha -2080.83144761 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -76.46915017 Ha -2080.83144761 eV - - Derived energy quantities: - | Kinetic energy : 76.28671545 Ha 2075.86714629 eV - | Electrostatic energy : -143.51241596 Ha -3905.17153112 eV - | Energy correction for multipole - | error in Hartree potential : -0.00343129 Ha -0.09337004 eV - | Sum of eigenvalues per atom : -377.20817317 eV - | Total energy (T->0) per atom : -693.61048254 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -693.61048254 eV - Evaluating new KS density. - Integration grid: deviation in total charge ( - N_e) = 1.598721E-14 - - Self-consistency convergence accuracy: - | Change of charge density : 0.2545E-04 - | Change of sum of eigenvalues : 0.3905E-02 eV - | Change of total energy : 0.1444E-06 eV - - ------------------------------------------------------------- - End self-consistency iteration # 11 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 0.048 s 0.048 s - | Charge density update : 0.013 s 0.014 s - | Density mixing : 0.003 s 0.003 s - | Hartree multipole update : 0.002 s 0.001 s - | Hartree multipole summation : 0.009 s 0.009 s - | Integration : 0.021 s 0.021 s - | Solution of K.-S. eqns. : 0.000 s 0.000 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 0.010 MB (on task 0) - | Maximum: 0.010 MB (on task 0) - | Average: 0.010 MB - | Peak value for overall tracked memory usage: - | Minimum: 0.549 MB (on task 0 after allocating grid_partition) - | Maximum: 0.549 MB (on task 0 after allocating grid_partition) - | Average: 0.549 MB - | Largest tracked array allocation so far: - | Minimum: 0.364 MB (all_coords on task 0) - | Maximum: 0.364 MB (all_coords on task 0) - | Average: 0.364 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - ------------------------------------------------------------- - Begin self-consistency iteration # 12 - - Date : 20230628, Time : 095501.565 ------------------------------------------------------------- - Pulay mixing of updated and previous charge densities. - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 10.0000000000 - | Integrated number of electrons on 3D grid : 10.0000000000 - | Charge integration error : 0.0000000000 - | Normalization factor for density and gradient : 1.0000000000 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = 0.373394E-13 - | Sum of charges compensated after spline to logarithmic grids = 0.163375E-03 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = 0.380035E-13 - Summing up the Hartree potential. - Time summed over all CPUs for potential: real work 0.007 s, elapsed 0.007 s - | RMS charge density error from multipole expansion : 0.649285E-02 - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.021 s, elapsed 0.021 s - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.000 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -0.73177804 eV - Highest occupied state (VBM) at -7.07842907 eV - | Occupation number: 2.00000000 - - Lowest unoccupied state (CBM) at 0.09117707 eV - | Occupation number: 0.00000000 - - Overall HOMO-LUMO gap: 7.16960614 eV. - - Total energy components: - | Sum of eigenvalues : -41.58643930 Ha -1131.62458986 eV - | XC energy correction : -9.24344918 Ha -251.52704966 eV - | XC potential correction : 11.88980236 Ha 323.53798377 eV - | Free-atom electrostatic energy: -35.72127400 Ha -972.02532155 eV - | Hartree energy correction : -1.80779006 Ha -49.19247030 eV - | Entropy correction : 0.00000000 Ha 0.00000000 eV - | --------------------------- - | Total energy : -76.46915017 Ha -2080.83144760 eV - | Total energy, T -> 0 : -76.46915017 Ha -2080.83144760 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -76.46915017 Ha -2080.83144760 eV - - Derived energy quantities: - | Kinetic energy : 76.28671580 Ha 2075.86715580 eV - | Electrostatic energy : -143.51241679 Ha -3905.17155374 eV - | Energy correction for multipole - | error in Hartree potential : -0.00343126 Ha -0.09336937 eV - | Sum of eigenvalues per atom : -377.20819662 eV - | Total energy (T->0) per atom : -693.61048253 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -693.61048253 eV - Evaluating new KS density. - Integration grid: deviation in total charge ( - N_e) = 1.421085E-14 - - Self-consistency convergence accuracy: - | Change of charge density : 0.6725E-06 - | Change of sum of eigenvalues : -0.7036E-04 eV - | Change of total energy : 0.1583E-07 eV - - Electronic self-consistency reached - switching on the force computation. - - ------------------------------------------------------------- - End self-consistency iteration # 12 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 0.047 s 0.046 s - | Charge density & force component update : 0.013 s 0.013 s - | Density mixing : 0.003 s 0.003 s - | Hartree multipole update : 0.002 s 0.001 s - | Hartree multipole summation : 0.008 s 0.008 s - | Hartree pot. SCF incomplete forces : 0.000 s 0.000 s - | Integration : 0.021 s 0.021 s - | Solution of K.-S. eqns. : 0.000 s 0.000 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 0.010 MB (on task 0) - | Maximum: 0.010 MB (on task 0) - | Average: 0.010 MB - | Peak value for overall tracked memory usage: - | Minimum: 0.549 MB (on task 0 after allocating grid_partition) - | Maximum: 0.549 MB (on task 0 after allocating grid_partition) - | Average: 0.549 MB - | Largest tracked array allocation so far: - | Minimum: 0.364 MB (all_coords on task 0) - | Maximum: 0.364 MB (all_coords on task 0) - | Average: 0.364 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - ------------------------------------------------------------- - Begin self-consistency iteration # 13 - - Date : 20230628, Time : 095501.612 ------------------------------------------------------------- - Pulay mixing of updated and previous charge densities. - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 10.0000000000 - | Integrated number of electrons on 3D grid : 10.0000000000 - | Charge integration error : -0.0000000000 - | Normalization factor for density and gradient : 1.0000000000 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = -0.312391E-14 - | Sum of charges compensated after spline to logarithmic grids = 0.163375E-03 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = -0.209081E-14 - Summing up the Hartree potential. - Time summed over all CPUs for potential: real work 0.024 s, elapsed 0.024 s - | RMS charge density error from multipole expansion : 0.649285E-02 - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.021 s, elapsed 0.021 s - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.000 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -0.73177723 eV - Highest occupied state (VBM) at -7.07842768 eV - | Occupation number: 2.00000000 - - Lowest unoccupied state (CBM) at 0.09117765 eV - | Occupation number: 0.00000000 - - Overall HOMO-LUMO gap: 7.16960533 eV. - - Total energy components: - | Sum of eigenvalues : -41.58643878 Ha -1131.62457563 eV - | XC energy correction : -9.24344925 Ha -251.52705153 eV - | XC potential correction : 11.88980246 Ha 323.53798624 eV - | Free-atom electrostatic energy: -35.72127400 Ha -972.02532155 eV - | Hartree energy correction : -1.80779060 Ha -49.19248513 eV - | Entropy correction : 0.00000000 Ha 0.00000000 eV - | --------------------------- - | Total energy : -76.46915017 Ha -2080.83144760 eV - | Total energy, T -> 0 : -76.46915017 Ha -2080.83144760 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -76.46915017 Ha -2080.83144760 eV - - Derived energy quantities: - | Kinetic energy : 76.28671582 Ha 2075.86715635 eV - | Electrostatic energy : -143.51241674 Ha -3905.17155242 eV - | Energy correction for multipole - | error in Hartree potential : -0.00343126 Ha -0.09336945 eV - | Sum of eigenvalues per atom : -377.20819188 eV - | Total energy (T->0) per atom : -693.61048253 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -693.61048253 eV - Evaluating new KS density and force components. - Integration grid: deviation in total charge ( - N_e) = 2.486900E-14 - - atomic forces [eV/Ang]: - ----------------------- - atom # 1 - Hellmann-Feynman : -0.329545E-12 -0.107615E-11 0.176407E+02 - Ionic forces : 0.000000E+00 0.000000E+00 0.000000E+00 - Multipole : 0.168077E-12 -0.141368E-12 -0.897884E-01 - Hartree pot. SCF incomplete : 0.144342E-12 0.296708E-12 -0.390350E-06 - Pulay + GGA : 0.981201E-12 -0.399171E-11 -0.173658E+02 - ---------------------------------------------------------------- - Total forces( 1) : 0.964076E-12 -0.491252E-11 0.185135E+00 - atom # 2 - Hellmann-Feynman : -0.252432E-14 0.468977E+00 -0.413666E+00 - Ionic forces : 0.000000E+00 0.000000E+00 0.000000E+00 - Multipole : -0.626561E-15 -0.448375E-02 -0.317610E-01 - Hartree pot. SCF incomplete : 0.259584E-14 -0.130223E-06 -0.879668E-07 - Pulay + GGA : -0.145540E-13 -0.293948E+00 0.341633E+00 - ---------------------------------------------------------------- - Total forces( 2) : -0.151091E-13 0.170545E+00 -0.103795E+00 - atom # 3 - Hellmann-Feynman : 0.890643E-15 -0.468977E+00 -0.413666E+00 - Ionic forces : 0.000000E+00 0.000000E+00 0.000000E+00 - Multipole : -0.224484E-15 0.448375E-02 -0.317610E-01 - Hartree pot. SCF incomplete : -0.330869E-14 0.130223E-06 -0.879668E-07 - Pulay + GGA : 0.245841E-13 0.293948E+00 0.341633E+00 - ---------------------------------------------------------------- - Total forces( 3) : 0.219416E-13 -0.170545E+00 -0.103795E+00 - - - Self-consistency convergence accuracy: - | Change of charge density : 0.8667E-07 - | Change of sum of eigenvalues : 0.1423E-04 eV - | Change of total energy : -0.2718E-09 eV - | Change of forces : 0.4057E+00 eV/A - - Writing Kohn-Sham eigenvalues. - - State Occupation Eigenvalue [Ha] Eigenvalue [eV] - 1 2.00000 -18.788144 -511.25140 - 2 2.00000 -0.926801 -25.21953 - 3 2.00000 -0.479271 -13.04164 - 4 2.00000 -0.338876 -9.22128 - 5 2.00000 -0.260127 -7.07843 - 6 0.00000 0.003351 0.09118 - 7 0.00000 0.101965 2.77460 - 8 0.00000 0.297791 8.10331 - 9 0.00000 0.334106 9.09149 - 10 0.00000 0.368731 10.03368 - 11 0.00000 0.578309 15.73660 - - Highest occupied state (VBM) at -7.07842768 eV - | Occupation number: 2.00000000 - - Lowest unoccupied state (CBM) at 0.09117765 eV - | Occupation number: 0.00000000 - - Overall HOMO-LUMO gap: 7.16960533 eV. - | Chemical Potential : -0.73177723 eV - - Self-consistency cycle converged. - - ------------------------------------------------------------- - End self-consistency iteration # 13 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 0.121 s 0.120 s - | Charge density & force component update : 0.054 s 0.054 s - | Density mixing : 0.004 s 0.004 s - | Hartree multipole update : 0.002 s 0.002 s - | Hartree multipole summation : 0.024 s 0.024 s - | Hartree pot. SCF incomplete forces : 0.015 s 0.015 s - | Integration : 0.021 s 0.021 s - | Solution of K.-S. eqns. : 0.000 s 0.000 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 0.010 MB (on task 0) - | Maximum: 0.010 MB (on task 0) - | Average: 0.010 MB - | Peak value for overall tracked memory usage: - | Minimum: 0.549 MB (on task 0 after allocating grid_partition) - | Maximum: 0.549 MB (on task 0 after allocating grid_partition) - | Average: 0.549 MB - | Largest tracked array allocation so far: - | Minimum: 0.364 MB (all_coords on task 0) - | Maximum: 0.364 MB (all_coords on task 0) - | Average: 0.364 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - Removing unitary transformations (pure translations, rotations) from forces on atoms. - Atomic forces before filtering: - | Net force on center of mass : 0.970908E-12 -0.489462E-11 -0.224546E-01 eV/A - | Net torque on center of mass: 0.196541E-11 0.381900E-12 0.282785E-13 eV - Atomic forces after filtering: - | Net force on center of mass : -0.365084E-27 0.223008E-16 -0.223008E-16 eV/A - | Net torque on center of mass: 0.118011E-16 -0.241892E-28 0.309607E-28 eV - - Energy and forces in a compact form: - | Total energy uncorrected : -0.208083144759841E+04 eV - | Total energy corrected : -0.208083144759841E+04 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -0.208083144759841E+04 eV - Total atomic forces (unitary forces cleaned) [eV/Ang]: - | 1 -0.162259424656531E-27 -0.272372884812723E-11 0.192619418545703E+00 - | 2 -0.121694568492398E-27 0.170544629723911E+00 -0.963097092739153E-01 - | 3 -0.811297123282653E-28 -0.170544629721187E+00 -0.963097092717873E-01 - - ------------------------------------ - Start decomposition of the XC Energy - ------------------------------------ - X and C from original XC functional choice - Hartree-Fock Energy : 0.000000000 Ha 0.000000000 eV - X Energy : -8.918299910 Ha -242.679287946 eV - C Energy : -0.325149335 Ha -8.847763582 eV - XC Energy w/o HF : -9.243449246 Ha -251.527051528 eV - Total XC Energy : -9.243449246 Ha -251.527051528 eV - ------------------------------------ - LDA X and C from self-consistent density - X Energy LDA : -8.102145071 Ha -220.470584797 eV - C Energy LDA : -0.659545176 Ha -17.947137392 eV - ------------------------------------ - End decomposition of the XC Energy - ------------------------------------ - ------------------------------------------------------------- - Relaxation / MD: End force evaluation. : max(cpu_time) wall_clock(cpu1) - | Time for this force evaluation : 0.768 s 0.768 s - ------------------------------------------------------------- - Geometry optimization: Attempting to predict improved coordinates. - - Removing unitary transformations (pure translations, rotations) from forces on atoms. - Atomic forces before filtering: - | Net force on center of mass : -0.365084E-27 0.223008E-16 -0.223008E-16 eV/A - | Net torque on center of mass: 0.118011E-16 -0.241892E-28 0.309607E-28 eV - Atomic forces after filtering: - | Net force on center of mass : 0.108086E-42 0.223008E-16 -0.223008E-16 eV/A - | Net torque on center of mass: -0.118011E-16 0.211671E-59 0.000000E+00 eV - Net remaining forces (excluding translations, rotations) in present geometry: - || Forces on atoms || = 0.192619E+00 eV/A. - Maximum force component is 0.192619E+00 eV/A. - Present geometry is not yet converged. - - Relaxation step number 1: Predicting new coordinates. - - Advancing geometry using trust radius method. - Allocating 0.002 MB for stored_KS_eigenvector - | Hessian has 0 negative and 6 zero eigenvalues. - | Positive eigenvalues (eV/A^2): 3.26E+01 ... 1.51E+02 - | Use Quasi-Newton step of length |H^-1 F| = 4.31E-03 A. - Finished advancing geometry - | Time : 0.001 s - Updated atomic structure: - x [A] y [A] z [A] - atom -0.00000000 -0.00000000 0.11975785 O - atom 0.00000000 0.76625386 -0.47729492 H - atom -0.00000000 -0.76625386 -0.47729492 H ------------------------------------------------------------- - Writing the current geometry to file "geometry.in.next_step". - Writing estimated Hessian matrix to file 'hessian.aims' - ------------------------------------------------------------- - Begin self-consistency loop: Re-initialization. - - Date : 20230628, Time : 095501.742 ------------------------------------------------------------- - - Initializing index lists of integration centers etc. from given atomic structure: - | Number of centers in hartree potential : 3 - | Number of centers in hartree multipole : 3 - | Number of centers in electron density summation: 3 - | Number of centers in basis integrals : 3 - | Number of centers in integrals : 3 - | Number of centers in hamiltonian : 3 - Partitioning the integration grid into batches with parallel hashing+maxmin method. - | Number of batches: 256 - | Maximal batch size: 65 - | Minimal batch size: 60 - | Average batch size: 62.203 - | Standard deviation of batch sizes: 1.470 - - Integration load balanced across 1 MPI tasks. - Work distribution over tasks is as follows: - Initializing partition tables, free-atom densities, potentials, etc. across the integration grid (initialize_grid_storage). - | Species 1: outer_partition_radius set to 5.048384829883283 AA . - | Species 2: outer_partition_radius set to 5.054417573612229 AA . - | The sparse table of interatomic distances needs 0.09 kbyte instead of 0.07 kbyte of memory. - | Using the partition_type stratmann_smoother will reduce your memory usage. - | Net number of integration points: 15924 - | of which are non-zero points : 14544 - Renormalizing the initial density to the exact electron count on the 3D integration grid. - | Initial density: Formal number of electrons (from input files) : 10.0000000000 - | Integrated number of electrons on 3D grid : 9.9999452850 - | Charge integration error : -0.0000547150 - | Normalization factor for density and gradient : 1.0000054715 - Renormalizing the free-atom superposition density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 10.0000000000 - | Integrated number of electrons on 3D grid : 9.9999452850 - | Charge integration error : -0.0000547150 - | Normalization factor for density and gradient : 1.0000054715 - Obtaining max. number of non-zero basis functions in each batch (get_n_compute_maxes). - Calculating total energy contributions from superposition of free atom densities. - Initialize hartree_potential_storage - Integrating overlap matrix. - Time summed over all CPUs for integration: real work 0.006 s, elapsed 0.006 s - Orthonormalizing eigenvectors - - End scf reinitialization - timings : max(cpu_time) wall_clock(cpu1) - | Time for scf. reinitialization : 0.034 s 0.035 s - | Boundary condition initialization : 0.000 s 0.000 s - | Integration : 0.006 s 0.006 s - | Grid partitioning : 0.012 s 0.012 s - | Preloading free-atom quantities on grid : 0.008 s 0.008 s - | Free-atom superposition energy : 0.008 s 0.008 s - | K.-S. eigenvector reorthonormalization : 0.000 s 0.000 s ------------------------------------------------------------- - Evaluating new KS density. - Integration grid: deviation in total charge ( - N_e) = 3.197442E-14 - - Time for density update prior : max(cpu_time) wall_clock(cpu1) - | self-consistency iterative process : 0.013 s 0.013 s - ------------------------------------------------------------- - Begin self-consistency iteration # 1 - - Date : 20230628, Time : 095501.790 ------------------------------------------------------------- - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 10.0000000000 - | Integrated number of electrons on 3D grid : 10.0000000000 - | Charge integration error : -0.0000000000 - | Normalization factor for density and gradient : 1.0000000000 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = -0.275495E-13 - | Sum of charges compensated after spline to logarithmic grids = 0.163522E-03 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = -0.263688E-13 - Summing up the Hartree potential. - Time summed over all CPUs for potential: real work 0.007 s, elapsed 0.007 s - | RMS charge density error from multipole expansion : 0.648259E-02 - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.021 s, elapsed 0.021 s - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.000 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -0.78602879 eV - Writing Kohn-Sham eigenvalues. - - State Occupation Eigenvalue [Ha] Eigenvalue [eV] - 1 2.00000 -18.786961 -511.21921 - 2 2.00000 -0.924744 -25.16357 - 3 2.00000 -0.477899 -13.00430 - 4 2.00000 -0.337826 -9.19272 - 5 2.00000 -0.259220 -7.05374 - 6 0.00000 0.002973 0.08091 - 7 0.00000 0.101163 2.75279 - 8 0.00000 0.298452 8.12129 - 9 0.00000 0.334566 9.10401 - 10 0.00000 0.369686 10.05966 - 11 0.00000 0.576213 15.67956 - - Highest occupied state (VBM) at -7.05373863 eV - | Occupation number: 2.00000000 - - Lowest unoccupied state (CBM) at 0.08091291 eV - | Occupation number: 0.00000000 - - Overall HOMO-LUMO gap: 7.13465154 eV. - - Total energy components: - | Sum of eigenvalues : -41.57330097 Ha -1131.26707776 eV - | XC energy correction : -9.24195258 Ha -251.48632509 eV - | XC potential correction : 11.88782558 Ha 323.48419268 eV - | Free-atom electrostatic energy: -35.73400870 Ha -972.37185039 eV - | Hartree energy correction : -1.80774296 Ha -49.19118864 eV - | Entropy correction : 0.00000000 Ha 0.00000000 eV - | --------------------------- - | Total energy : -76.46917963 Ha -2080.83224920 eV - | Total energy, T -> 0 : -76.46917963 Ha -2080.83224920 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -76.46917963 Ha -2080.83224920 eV - - Derived energy quantities: - | Kinetic energy : 76.28290527 Ha 2075.76346597 eV - | Electrostatic energy : -143.51013232 Ha -3905.10939008 eV - | Energy correction for multipole - | error in Hartree potential : -0.00337689 Ha -0.09188981 eV - | Sum of eigenvalues per atom : -377.08902592 eV - | Total energy (T->0) per atom : -693.61074973 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -693.61074973 eV - Evaluating new KS density. - Integration grid: deviation in total charge ( - N_e) = -1.065814E-14 - - Self-consistency convergence accuracy: - | Change of charge density : 0.1749E+00 - | Change of sum of eigenvalues : -0.1131E+04 eV - | Change of total energy : -0.2081E+04 eV - - ------------------------------------------------------------- - End self-consistency iteration # 1 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 0.045 s 0.044 s - | Charge density update : 0.013 s 0.013 s - | Density mixing : 0.000 s 0.000 s - | Hartree multipole update : 0.002 s 0.002 s - | Hartree multipole summation : 0.008 s 0.007 s - | Integration : 0.021 s 0.022 s - | Solution of K.-S. eqns. : 0.000 s 0.000 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 0.012 MB (on task 0) - | Maximum: 0.012 MB (on task 0) - | Average: 0.012 MB - | Peak value for overall tracked memory usage: - | Minimum: 0.558 MB (on task 0 after allocating grid_partition) - | Maximum: 0.558 MB (on task 0 after allocating grid_partition) - | Average: 0.558 MB - | Largest tracked array allocation so far: - | Minimum: 0.364 MB (all_coords on task 0) - | Maximum: 0.364 MB (all_coords on task 0) - | Average: 0.364 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - ------------------------------------------------------------- - Begin self-consistency iteration # 2 - - Date : 20230628, Time : 095501.835 ------------------------------------------------------------- - Pulay mixing of updated and previous charge densities. - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 10.0000000000 - | Integrated number of electrons on 3D grid : 10.0000000000 - | Charge integration error : 0.0000000000 - | Normalization factor for density and gradient : 1.0000000000 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = -0.597725E-14 - | Sum of charges compensated after spline to logarithmic grids = 0.163328E-03 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = -0.619863E-14 - Summing up the Hartree potential. - Time summed over all CPUs for potential: real work 0.008 s, elapsed 0.008 s - | RMS charge density error from multipole expansion : 0.648262E-02 - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.021 s, elapsed 0.021 s - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.000 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -0.79074788 eV - Highest occupied state (VBM) at -7.06351364 eV - | Occupation number: 2.00000000 - - Lowest unoccupied state (CBM) at 0.07777841 eV - | Occupation number: 0.00000000 - - Overall HOMO-LUMO gap: 7.14129205 eV. - - Total energy components: - | Sum of eigenvalues : -41.57785097 Ha -1131.39088942 eV - | XC energy correction : -9.24136553 Ha -251.47035076 eV - | XC potential correction : 11.88705618 Ha 323.46325637 eV - | Free-atom electrostatic energy: -35.73400870 Ha -972.37185039 eV - | Hartree energy correction : -1.80300942 Ha -49.06238254 eV - | Entropy correction : 0.00000000 Ha 0.00000000 eV - | --------------------------- - | Total energy : -76.46917843 Ha -2080.83221673 eV - | Total energy, T -> 0 : -76.46917843 Ha -2080.83221673 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -76.46917843 Ha -2080.83221673 eV - - Derived energy quantities: - | Kinetic energy : 76.27940659 Ha 2075.66826204 eV - | Electrostatic energy : -143.50721949 Ha -3905.03012801 eV - | Energy correction for multipole - | error in Hartree potential : -0.00338681 Ha -0.09215988 eV - | Sum of eigenvalues per atom : -377.13029647 eV - | Total energy (T->0) per atom : -693.61073891 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -693.61073891 eV - Evaluating new KS density. - Integration grid: deviation in total charge ( - N_e) = 3.730349E-14 - - Self-consistency convergence accuracy: - | Change of charge density : 0.1768E-02 - | Change of sum of eigenvalues : -0.1238E+00 eV - | Change of total energy : 0.3246E-04 eV - - ------------------------------------------------------------- - End self-consistency iteration # 2 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 0.045 s 0.044 s - | Charge density update : 0.013 s 0.013 s - | Density mixing : 0.001 s 0.000 s - | Hartree multipole update : 0.002 s 0.002 s - | Hartree multipole summation : 0.008 s 0.008 s - | Integration : 0.021 s 0.021 s - | Solution of K.-S. eqns. : 0.000 s 0.000 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 0.012 MB (on task 0) - | Maximum: 0.012 MB (on task 0) - | Average: 0.012 MB - | Peak value for overall tracked memory usage: - | Minimum: 0.558 MB (on task 0 after allocating grid_partition) - | Maximum: 0.558 MB (on task 0 after allocating grid_partition) - | Average: 0.558 MB - | Largest tracked array allocation so far: - | Minimum: 0.364 MB (all_coords on task 0) - | Maximum: 0.364 MB (all_coords on task 0) - | Average: 0.364 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - ------------------------------------------------------------- - Begin self-consistency iteration # 3 - - Date : 20230628, Time : 095501.879 ------------------------------------------------------------- - Pulay mixing of updated and previous charge densities. - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 10.0000000000 - | Integrated number of electrons on 3D grid : 10.0000000000 - | Charge integration error : -0.0000000000 - | Normalization factor for density and gradient : 1.0000000000 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = -0.102179E-12 - | Sum of charges compensated after spline to logarithmic grids = 0.163184E-03 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = -0.102671E-12 - Summing up the Hartree potential. - Time summed over all CPUs for potential: real work 0.008 s, elapsed 0.008 s - | RMS charge density error from multipole expansion : 0.648125E-02 - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.021 s, elapsed 0.021 s - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.000 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -0.79492051 eV - Highest occupied state (VBM) at -7.07052261 eV - | Occupation number: 2.00000000 - - Lowest unoccupied state (CBM) at 0.07510135 eV - | Occupation number: 0.00000000 - - Overall HOMO-LUMO gap: 7.14562396 eV. - - Total energy components: - | Sum of eigenvalues : -41.58115491 Ha -1131.48079421 eV - | XC energy correction : -9.24092567 Ha -251.45838141 eV - | XC potential correction : 11.88648080 Ha 323.44759935 eV - | Free-atom electrostatic energy: -35.73400870 Ha -972.37185039 eV - | Hartree energy correction : -1.79956965 Ha -48.96878163 eV - | Entropy correction : 0.00000000 Ha 0.00000000 eV - | --------------------------- - | Total energy : -76.46917812 Ha -2080.83220829 eV - | Total energy, T -> 0 : -76.46917812 Ha -2080.83220829 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -76.46917812 Ha -2080.83220829 eV - - Derived energy quantities: - | Kinetic energy : 76.27702007 Ha 2075.60332155 eV - | Electrostatic energy : -143.50527252 Ha -3904.97714843 eV - | Energy correction for multipole - | error in Hartree potential : -0.00339473 Ha -0.09237528 eV - | Sum of eigenvalues per atom : -377.16026474 eV - | Total energy (T->0) per atom : -693.61073610 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -693.61073610 eV - Evaluating new KS density. - Integration grid: deviation in total charge ( - N_e) = 2.842171E-14 - - Self-consistency convergence accuracy: - | Change of charge density : 0.8560E-03 - | Change of sum of eigenvalues : -0.8990E-01 eV - | Change of total energy : 0.8441E-05 eV - - ------------------------------------------------------------- - End self-consistency iteration # 3 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 0.046 s 0.046 s - | Charge density update : 0.013 s 0.013 s - | Density mixing : 0.002 s 0.002 s - | Hartree multipole update : 0.002 s 0.002 s - | Hartree multipole summation : 0.008 s 0.008 s - | Integration : 0.021 s 0.021 s - | Solution of K.-S. eqns. : 0.000 s 0.000 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 0.012 MB (on task 0) - | Maximum: 0.012 MB (on task 0) - | Average: 0.012 MB - | Peak value for overall tracked memory usage: - | Minimum: 0.558 MB (on task 0 after allocating grid_partition) - | Maximum: 0.558 MB (on task 0 after allocating grid_partition) - | Average: 0.558 MB - | Largest tracked array allocation so far: - | Minimum: 0.364 MB (all_coords on task 0) - | Maximum: 0.364 MB (all_coords on task 0) - | Average: 0.364 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - ------------------------------------------------------------- - Begin self-consistency iteration # 4 - - Date : 20230628, Time : 095501.925 ------------------------------------------------------------- - Pulay mixing of updated and previous charge densities. - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 10.0000000000 - | Integrated number of electrons on 3D grid : 10.0000000000 - | Charge integration error : -0.0000000000 - | Normalization factor for density and gradient : 1.0000000000 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = -0.100851E-13 - | Sum of charges compensated after spline to logarithmic grids = 0.163145E-03 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = -0.956852E-14 - Summing up the Hartree potential. - Time summed over all CPUs for potential: real work 0.008 s, elapsed 0.008 s - | RMS charge density error from multipole expansion : 0.647691E-02 - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.021 s, elapsed 0.021 s - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.000 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -0.79780277 eV - Highest occupied state (VBM) at -7.07168466 eV - | Occupation number: 2.00000000 - - Lowest unoccupied state (CBM) at 0.07346652 eV - | Occupation number: 0.00000000 - - Overall HOMO-LUMO gap: 7.14515119 eV. - - Total energy components: - | Sum of eigenvalues : -41.58182615 Ha -1131.49905950 eV - | XC energy correction : -9.24079857 Ha -251.45492285 eV - | XC potential correction : 11.88631758 Ha 323.44315793 eV - | Free-atom electrostatic energy: -35.73400870 Ha -972.37185039 eV - | Hartree energy correction : -1.79886203 Ha -48.94952637 eV - | Entropy correction : 0.00000000 Ha 0.00000000 eV - | --------------------------- - | Total energy : -76.46917786 Ha -2080.83220117 eV - | Total energy, T -> 0 : -76.46917786 Ha -2080.83220117 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -76.46917786 Ha -2080.83220117 eV - - Derived energy quantities: - | Kinetic energy : 76.27701160 Ha 2075.60309121 eV - | Electrostatic energy : -143.50539090 Ha -3904.98036954 eV - | Energy correction for multipole - | error in Hartree potential : -0.00339850 Ha -0.09247781 eV - | Sum of eigenvalues per atom : -377.16635317 eV - | Total energy (T->0) per atom : -693.61073372 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -693.61073372 eV - Evaluating new KS density. - Integration grid: deviation in total charge ( - N_e) = 1.776357E-14 - - Self-consistency convergence accuracy: - | Change of charge density : 0.3853E-03 - | Change of sum of eigenvalues : -0.1827E-01 eV - | Change of total energy : 0.7116E-05 eV - - ------------------------------------------------------------- - End self-consistency iteration # 4 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 0.047 s 0.048 s - | Charge density update : 0.013 s 0.014 s - | Density mixing : 0.002 s 0.003 s - | Hartree multipole update : 0.002 s 0.002 s - | Hartree multipole summation : 0.008 s 0.008 s - | Integration : 0.021 s 0.021 s - | Solution of K.-S. eqns. : 0.000 s 0.000 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 0.012 MB (on task 0) - | Maximum: 0.012 MB (on task 0) - | Average: 0.012 MB - | Peak value for overall tracked memory usage: - | Minimum: 0.558 MB (on task 0 after allocating grid_partition) - | Maximum: 0.558 MB (on task 0 after allocating grid_partition) - | Average: 0.558 MB - | Largest tracked array allocation so far: - | Minimum: 0.364 MB (all_coords on task 0) - | Maximum: 0.364 MB (all_coords on task 0) - | Average: 0.364 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - ------------------------------------------------------------- - Begin self-consistency iteration # 5 - - Date : 20230628, Time : 095501.973 ------------------------------------------------------------- - Pulay mixing of updated and previous charge densities. - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 10.0000000000 - | Integrated number of electrons on 3D grid : 10.0000000000 - | Charge integration error : 0.0000000000 - | Normalization factor for density and gradient : 1.0000000000 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = 0.734734E-13 - | Sum of charges compensated after spline to logarithmic grids = 0.163149E-03 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = 0.722190E-13 - Summing up the Hartree potential. - Time summed over all CPUs for potential: real work 0.008 s, elapsed 0.008 s - | RMS charge density error from multipole expansion : 0.647648E-02 - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.021 s, elapsed 0.021 s - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.000 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -0.79766159 eV - Highest occupied state (VBM) at -7.07161384 eV - | Occupation number: 2.00000000 - - Lowest unoccupied state (CBM) at 0.07355349 eV - | Occupation number: 0.00000000 - - Overall HOMO-LUMO gap: 7.14516733 eV. - - Total energy components: - | Sum of eigenvalues : -41.58180799 Ha -1131.49856536 eV - | XC energy correction : -9.24080192 Ha -251.45501412 eV - | XC potential correction : 11.88632210 Ha 323.44328082 eV - | Free-atom electrostatic energy: -35.73400870 Ha -972.37185039 eV - | Hartree energy correction : -1.79888135 Ha -48.95005198 eV - | Entropy correction : 0.00000000 Ha 0.00000000 eV - | --------------------------- - | Total energy : -76.46917786 Ha -2080.83220103 eV - | Total energy, T -> 0 : -76.46917786 Ha -2080.83220103 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -76.46917786 Ha -2080.83220103 eV - - Derived energy quantities: - | Kinetic energy : 76.27714979 Ha 2075.60685147 eV - | Electrostatic energy : -143.50552573 Ha -3904.98403838 eV - | Energy correction for multipole - | error in Hartree potential : -0.00339898 Ha -0.09249098 eV - | Sum of eigenvalues per atom : -377.16618845 eV - | Total energy (T->0) per atom : -693.61073368 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -693.61073368 eV - Evaluating new KS density. - Integration grid: deviation in total charge ( - N_e) = 1.065814E-14 - - Self-consistency convergence accuracy: - | Change of charge density : 0.5809E-04 - | Change of sum of eigenvalues : 0.4941E-03 eV - | Change of total energy : 0.1457E-06 eV - - ------------------------------------------------------------- - End self-consistency iteration # 5 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 0.045 s 0.045 s - | Charge density update : 0.013 s 0.013 s - | Density mixing : 0.002 s 0.002 s - | Hartree multipole update : 0.002 s 0.001 s - | Hartree multipole summation : 0.008 s 0.008 s - | Integration : 0.021 s 0.021 s - | Solution of K.-S. eqns. : 0.000 s 0.000 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 0.012 MB (on task 0) - | Maximum: 0.012 MB (on task 0) - | Average: 0.012 MB - | Peak value for overall tracked memory usage: - | Minimum: 0.558 MB (on task 0 after allocating grid_partition) - | Maximum: 0.558 MB (on task 0 after allocating grid_partition) - | Average: 0.558 MB - | Largest tracked array allocation so far: - | Minimum: 0.364 MB (all_coords on task 0) - | Maximum: 0.364 MB (all_coords on task 0) - | Average: 0.364 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - ------------------------------------------------------------- - Begin self-consistency iteration # 6 - - Date : 20230628, Time : 095502.018 ------------------------------------------------------------- - Pulay mixing of updated and previous charge densities. - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 10.0000000000 - | Integrated number of electrons on 3D grid : 10.0000000000 - | Charge integration error : -0.0000000000 - | Normalization factor for density and gradient : 1.0000000000 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = -0.293451E-13 - | Sum of charges compensated after spline to logarithmic grids = 0.163149E-03 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = -0.294189E-13 - Summing up the Hartree potential. - Time summed over all CPUs for potential: real work 0.008 s, elapsed 0.008 s - | RMS charge density error from multipole expansion : 0.647651E-02 - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.021 s, elapsed 0.021 s - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.000 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -0.79766462 eV - Highest occupied state (VBM) at -7.07163976 eV - | Occupation number: 2.00000000 - - Lowest unoccupied state (CBM) at 0.07354940 eV - | Occupation number: 0.00000000 - - Overall HOMO-LUMO gap: 7.14518917 eV. - - Total energy components: - | Sum of eigenvalues : -41.58181936 Ha -1131.49887469 eV - | XC energy correction : -9.24080079 Ha -251.45498348 eV - | XC potential correction : 11.88632061 Ha 323.44324034 eV - | Free-atom electrostatic energy: -35.73400870 Ha -972.37185039 eV - | Hartree energy correction : -1.79886962 Ha -48.94973278 eV - | Entropy correction : 0.00000000 Ha 0.00000000 eV - | --------------------------- - | Total energy : -76.46917785 Ha -2080.83220101 eV - | Total energy, T -> 0 : -76.46917785 Ha -2080.83220101 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -76.46917785 Ha -2080.83220101 eV - - Derived energy quantities: - | Kinetic energy : 76.27714255 Ha 2075.60665457 eV - | Electrostatic energy : -143.50551961 Ha -3904.98387210 eV - | Energy correction for multipole - | error in Hartree potential : -0.00339903 Ha -0.09249230 eV - | Sum of eigenvalues per atom : -377.16629156 eV - | Total energy (T->0) per atom : -693.61073367 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -693.61073367 eV - Evaluating new KS density. - Integration grid: deviation in total charge ( - N_e) = -1.598721E-14 - - Self-consistency convergence accuracy: - | Change of charge density : 0.3640E-05 - | Change of sum of eigenvalues : -0.3093E-03 eV - | Change of total energy : 0.2309E-07 eV - - ------------------------------------------------------------- - End self-consistency iteration # 6 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 0.046 s 0.046 s - | Charge density update : 0.013 s 0.013 s - | Density mixing : 0.002 s 0.002 s - | Hartree multipole update : 0.002 s 0.002 s - | Hartree multipole summation : 0.008 s 0.008 s - | Integration : 0.021 s 0.021 s - | Solution of K.-S. eqns. : 0.000 s 0.000 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 0.012 MB (on task 0) - | Maximum: 0.012 MB (on task 0) - | Average: 0.012 MB - | Peak value for overall tracked memory usage: - | Minimum: 0.558 MB (on task 0 after allocating grid_partition) - | Maximum: 0.558 MB (on task 0 after allocating grid_partition) - | Average: 0.558 MB - | Largest tracked array allocation so far: - | Minimum: 0.364 MB (all_coords on task 0) - | Maximum: 0.364 MB (all_coords on task 0) - | Average: 0.364 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - ------------------------------------------------------------- - Begin self-consistency iteration # 7 - - Date : 20230628, Time : 095502.065 ------------------------------------------------------------- - Pulay mixing of updated and previous charge densities. - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 10.0000000000 - | Integrated number of electrons on 3D grid : 10.0000000000 - | Charge integration error : 0.0000000000 - | Normalization factor for density and gradient : 1.0000000000 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = 0.478672E-13 - | Sum of charges compensated after spline to logarithmic grids = 0.163150E-03 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = 0.480148E-13 - Summing up the Hartree potential. - Time summed over all CPUs for potential: real work 0.007 s, elapsed 0.007 s - | RMS charge density error from multipole expansion : 0.647652E-02 - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.022 s, elapsed 0.022 s - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.000 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -0.79764716 eV - Highest occupied state (VBM) at -7.07161517 eV - | Occupation number: 2.00000000 - - Lowest unoccupied state (CBM) at 0.07355967 eV - | Occupation number: 0.00000000 - - Overall HOMO-LUMO gap: 7.14517483 eV. - - Total energy components: - | Sum of eigenvalues : -41.58180747 Ha -1131.49855116 eV - | XC energy correction : -9.24080255 Ha -251.45503119 eV - | XC potential correction : 11.88632290 Ha 323.44330269 eV - | Free-atom electrostatic energy: -35.73400870 Ha -972.37185039 eV - | Hartree energy correction : -1.79888204 Ha -48.95007091 eV - | Entropy correction : 0.00000000 Ha 0.00000000 eV - | --------------------------- - | Total energy : -76.46917785 Ha -2080.83220096 eV - | Total energy, T -> 0 : -76.46917785 Ha -2080.83220096 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -76.46917785 Ha -2080.83220096 eV - - Derived energy quantities: - | Kinetic energy : 76.27715281 Ha 2075.60693365 eV - | Electrostatic energy : -143.50552812 Ha -3904.98410342 eV - | Energy correction for multipole - | error in Hartree potential : -0.00339902 Ha -0.09249210 eV - | Sum of eigenvalues per atom : -377.16618372 eV - | Total energy (T->0) per atom : -693.61073365 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -693.61073365 eV - Evaluating new KS density. - Integration grid: deviation in total charge ( - N_e) = -1.776357E-14 - - Self-consistency convergence accuracy: - | Change of charge density : 0.2447E-05 - | Change of sum of eigenvalues : 0.3235E-03 eV - | Change of total energy : 0.4341E-07 eV - - Electronic self-consistency reached - switching on the force computation. - - ------------------------------------------------------------- - End self-consistency iteration # 7 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 0.047 s 0.046 s - | Charge density & force component update : 0.013 s 0.012 s - | Density mixing : 0.003 s 0.003 s - | Hartree multipole update : 0.002 s 0.001 s - | Hartree multipole summation : 0.008 s 0.008 s - | Hartree pot. SCF incomplete forces : 0.015 s 0.015 s - | Integration : 0.022 s 0.021 s - | Solution of K.-S. eqns. : 0.000 s 0.000 s - | Total energy evaluation : 0.000 s 0.001 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 0.012 MB (on task 0) - | Maximum: 0.012 MB (on task 0) - | Average: 0.012 MB - | Peak value for overall tracked memory usage: - | Minimum: 0.558 MB (on task 0 after allocating grid_partition) - | Maximum: 0.558 MB (on task 0 after allocating grid_partition) - | Average: 0.558 MB - | Largest tracked array allocation so far: - | Minimum: 0.364 MB (all_coords on task 0) - | Maximum: 0.364 MB (all_coords on task 0) - | Average: 0.364 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - ------------------------------------------------------------- - Begin self-consistency iteration # 8 - - Date : 20230628, Time : 095502.112 ------------------------------------------------------------- - Pulay mixing of updated and previous charge densities. - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 10.0000000000 - | Integrated number of electrons on 3D grid : 10.0000000000 - | Charge integration error : -0.0000000000 - | Normalization factor for density and gradient : 1.0000000000 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = 0.154966E-14 - | Sum of charges compensated after spline to logarithmic grids = 0.163150E-03 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = 0.491955E-15 - Summing up the Hartree potential. - Time summed over all CPUs for potential: real work 0.024 s, elapsed 0.024 s - | RMS charge density error from multipole expansion : 0.647652E-02 - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.022 s, elapsed 0.022 s - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.000 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -0.79764888 eV - Highest occupied state (VBM) at -7.07161657 eV - | Occupation number: 2.00000000 - - Lowest unoccupied state (CBM) at 0.07355876 eV - | Occupation number: 0.00000000 - - Overall HOMO-LUMO gap: 7.14517533 eV. - - Total energy components: - | Sum of eigenvalues : -41.58180820 Ha -1131.49857114 eV - | XC energy correction : -9.24080241 Ha -251.45502746 eV - | XC potential correction : 11.88632272 Ha 323.44329787 eV - | Free-atom electrostatic energy: -35.73400870 Ha -972.37185039 eV - | Hartree energy correction : -1.79888127 Ha -48.95004984 eV - | Entropy correction : 0.00000000 Ha 0.00000000 eV - | --------------------------- - | Total energy : -76.46917785 Ha -2080.83220096 eV - | Total energy, T -> 0 : -76.46917785 Ha -2080.83220096 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -76.46917785 Ha -2080.83220096 eV - - Derived energy quantities: - | Kinetic energy : 76.27715179 Ha 2075.60690600 eV - | Electrostatic energy : -143.50552724 Ha -3904.98407951 eV - | Energy correction for multipole - | error in Hartree potential : -0.00339903 Ha -0.09249223 eV - | Sum of eigenvalues per atom : -377.16619038 eV - | Total energy (T->0) per atom : -693.61073365 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -693.61073365 eV - Evaluating new KS density and force components. - Integration grid: deviation in total charge ( - N_e) = 2.309264E-14 - - atomic forces [eV/Ang]: - ----------------------- - atom # 1 - Hellmann-Feynman : 0.201844E-12 0.174695E-11 0.175356E+02 - Ionic forces : 0.000000E+00 0.000000E+00 0.000000E+00 - Multipole : 0.327274E-14 -0.151196E-12 -0.901744E-01 - Hartree pot. SCF incomplete : -0.268758E-12 -0.585313E-12 0.126175E-06 - Pulay + GGA : -0.376705E-11 -0.965991E-11 -0.174065E+02 - ---------------------------------------------------------------- - Total forces( 1) : -0.383069E-11 -0.864947E-11 0.389048E-01 - atom # 2 - Hellmann-Feynman : 0.222344E-14 0.338393E+00 -0.336427E+00 - Ionic forces : 0.000000E+00 0.000000E+00 0.000000E+00 - Multipole : 0.388560E-15 -0.450322E-02 -0.316752E-01 - Hartree pot. SCF incomplete : -0.186922E-13 -0.193470E-06 0.484390E-06 - Pulay + GGA : 0.205836E-13 -0.291714E+00 0.338461E+00 - ---------------------------------------------------------------- - Total forces( 2) : 0.450345E-14 0.421758E-01 -0.296398E-01 - atom # 3 - Hellmann-Feynman : 0.186135E-13 -0.338393E+00 -0.336427E+00 - Ionic forces : 0.000000E+00 0.000000E+00 0.000000E+00 - Multipole : 0.587569E-16 0.450322E-02 -0.316752E-01 - Hartree pot. SCF incomplete : -0.201227E-14 0.193470E-06 0.484390E-06 - Pulay + GGA : -0.338477E-13 0.291714E+00 0.338461E+00 - ---------------------------------------------------------------- - Total forces( 3) : -0.171877E-13 -0.421758E-01 -0.296398E-01 - - - Self-consistency convergence accuracy: - | Change of charge density : 0.2123E-06 - | Change of sum of eigenvalues : -0.1998E-04 eV - | Change of total energy : 0.1053E-08 eV - | Change of forces : 0.4504E+00 eV/A - - Writing Kohn-Sham eigenvalues. - - State Occupation Eigenvalue [Ha] Eigenvalue [eV] - 1 2.00000 -18.788449 -511.25972 - 2 2.00000 -0.925547 -25.18540 - 3 2.00000 -0.478591 -13.02311 - 4 2.00000 -0.338440 -9.20943 - 5 2.00000 -0.259877 -7.07162 - 6 0.00000 0.002703 0.07356 - 7 0.00000 0.100819 2.74341 - 8 0.00000 0.298122 8.11233 - 9 0.00000 0.334207 9.09425 - 10 0.00000 0.369442 10.05302 - 11 0.00000 0.575820 15.66887 - - Highest occupied state (VBM) at -7.07161657 eV - | Occupation number: 2.00000000 - - Lowest unoccupied state (CBM) at 0.07355876 eV - | Occupation number: 0.00000000 - - Overall HOMO-LUMO gap: 7.14517533 eV. - | Chemical Potential : -0.79764888 eV - - Self-consistency cycle converged. - - ------------------------------------------------------------- - End self-consistency iteration # 8 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 0.118 s 0.118 s - | Charge density & force component update : 0.054 s 0.054 s - | Density mixing : 0.002 s 0.002 s - | Hartree multipole update : 0.002 s 0.001 s - | Hartree multipole summation : 0.024 s 0.024 s - | Hartree pot. SCF incomplete forces : 0.015 s 0.015 s - | Integration : 0.022 s 0.022 s - | Solution of K.-S. eqns. : 0.000 s 0.000 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 0.012 MB (on task 0) - | Maximum: 0.012 MB (on task 0) - | Average: 0.012 MB - | Peak value for overall tracked memory usage: - | Minimum: 0.558 MB (on task 0 after allocating grid_partition) - | Maximum: 0.558 MB (on task 0 after allocating grid_partition) - | Average: 0.558 MB - | Largest tracked array allocation so far: - | Minimum: 0.364 MB (all_coords on task 0) - | Maximum: 0.364 MB (all_coords on task 0) - | Average: 0.364 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - Removing unitary transformations (pure translations, rotations) from forces on atoms. - Atomic forces before filtering: - | Net force on center of mass : -0.384337E-11 -0.107254E-10 -0.203748E-01 eV/A - | Net torque on center of mass: 0.424425E-11 -0.152222E-11 -0.166209E-13 eV - Atomic forces after filtering: - | Net force on center of mass : 0.811297E-27 0.000000E+00 0.000000E+00 eV/A - | Net torque on center of mass: -0.590053E-17 -0.645850E-28 0.644757E-35 eV - - Energy and forces in a compact form: - | Total energy uncorrected : -0.208083220096086E+04 eV - | Total energy corrected : -0.208083220096086E+04 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -0.208083220096086E+04 eV - Total atomic forces (unitary forces cleaned) [eV/Ang]: - | 1 0.162259424656531E-27 -0.387786774244967E-11 0.456963966289359E-01 - | 2 0.324518849313061E-27 0.421757890961139E-01 -0.228481983159783E-01 - | 3 0.324518849313061E-27 -0.421757890922361E-01 -0.228481983129576E-01 - - ------------------------------------ - Start decomposition of the XC Energy - ------------------------------------ - X and C from original XC functional choice - Hartree-Fock Energy : 0.000000000 Ha 0.000000000 eV - X Energy : -8.915793610 Ha -242.611088036 eV - C Energy : -0.325008800 Ha -8.843939422 eV - XC Energy w/o HF : -9.240802410 Ha -251.455027457 eV - Total XC Energy : -9.240802410 Ha -251.455027457 eV - ------------------------------------ - LDA X and C from self-consistent density - X Energy LDA : -8.099651011 Ha -220.402717964 eV - C Energy LDA : -0.659406655 Ha -17.943368043 eV - ------------------------------------ - End decomposition of the XC Energy - ------------------------------------ - ------------------------------------------------------------- - Relaxation / MD: End force evaluation. : max(cpu_time) wall_clock(cpu1) - | Time for this force evaluation : 0.496 s 0.497 s - ------------------------------------------------------------- - Geometry optimization: Attempting to predict improved coordinates. - - Removing unitary transformations (pure translations, rotations) from forces on atoms. - Atomic forces before filtering: - | Net force on center of mass : 0.811297E-27 0.000000E+00 0.000000E+00 eV/A - | Net torque on center of mass: -0.590053E-17 -0.645850E-28 0.644757E-35 eV - Atomic forces after filtering: - | Net force on center of mass : -0.324259E-42 0.000000E+00 0.000000E+00 eV/A - | Net torque on center of mass: 0.000000E+00 0.790178E-39 0.209879E-38 eV - Net remaining forces (excluding translations, rotations) in present geometry: - || Forces on atoms || = 0.456964E-01 eV/A. - Maximum force component is 0.456964E-01 eV/A. - Present geometry is not yet converged. - - Relaxation step number 2: Predicting new coordinates. - - Advancing geometry using trust radius method. - | True / expected gain: -7.53E-04 eV / -5.86E-04 eV = 1.2860 - | Harmonic / expected gain: -7.30E-04 eV / -5.86E-04 eV = 1.2461 - | Using harmonic gain instead of DE to judge step. - | Hessian has 0 negative and 6 zero eigenvalues. - | Positive eigenvalues (eV/A^2): 2.88E+01 ... 1.51E+02 - | Use Quasi-Newton step of length |H^-1 F| = 1.44E-03 A. - Finished advancing geometry - | Time : 0.000 s - Updated atomic structure: - x [A] y [A] z [A] - atom 0.00000000 -0.00000000 0.11989040 O - atom 0.00000000 0.76726299 -0.47736120 H - atom -0.00000000 -0.76726299 -0.47736120 H ------------------------------------------------------------- - Writing the current geometry to file "geometry.in.next_step". - Writing estimated Hessian matrix to file 'hessian.aims' - ------------------------------------------------------------- - Begin self-consistency loop: Re-initialization. - - Date : 20230628, Time : 095502.239 ------------------------------------------------------------- - - Initializing index lists of integration centers etc. from given atomic structure: - | Number of centers in hartree potential : 3 - | Number of centers in hartree multipole : 3 - | Number of centers in electron density summation: 3 - | Number of centers in basis integrals : 3 - | Number of centers in integrals : 3 - | Number of centers in hamiltonian : 3 - Partitioning the integration grid into batches with parallel hashing+maxmin method. - | Number of batches: 256 - | Maximal batch size: 65 - | Minimal batch size: 60 - | Average batch size: 62.203 - | Standard deviation of batch sizes: 1.470 - - Integration load balanced across 1 MPI tasks. - Work distribution over tasks is as follows: - Initializing partition tables, free-atom densities, potentials, etc. across the integration grid (initialize_grid_storage). - | Species 1: outer_partition_radius set to 5.048384829883283 AA . - | Species 2: outer_partition_radius set to 5.054417573612229 AA . - | The sparse table of interatomic distances needs 0.09 kbyte instead of 0.07 kbyte of memory. - | Using the partition_type stratmann_smoother will reduce your memory usage. - | Net number of integration points: 15924 - | of which are non-zero points : 14544 - Renormalizing the initial density to the exact electron count on the 3D integration grid. - | Initial density: Formal number of electrons (from input files) : 10.0000000000 - | Integrated number of electrons on 3D grid : 9.9999460462 - | Charge integration error : -0.0000539538 - | Normalization factor for density and gradient : 1.0000053954 - Renormalizing the free-atom superposition density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 10.0000000000 - | Integrated number of electrons on 3D grid : 9.9999460462 - | Charge integration error : -0.0000539538 - | Normalization factor for density and gradient : 1.0000053954 - Obtaining max. number of non-zero basis functions in each batch (get_n_compute_maxes). - Calculating total energy contributions from superposition of free atom densities. - Initialize hartree_potential_storage - Integrating overlap matrix. - Time summed over all CPUs for integration: real work 0.006 s, elapsed 0.006 s - Orthonormalizing eigenvectors - - End scf reinitialization - timings : max(cpu_time) wall_clock(cpu1) - | Time for scf. reinitialization : 0.034 s 0.034 s - | Boundary condition initialization : 0.000 s 0.000 s - | Integration : 0.006 s 0.006 s - | Grid partitioning : 0.012 s 0.012 s - | Preloading free-atom quantities on grid : 0.008 s 0.008 s - | Free-atom superposition energy : 0.008 s 0.008 s - | K.-S. eigenvector reorthonormalization : 0.000 s 0.000 s ------------------------------------------------------------- - Evaluating new KS density. - Integration grid: deviation in total charge ( - N_e) = 1.776357E-15 - - Time for density update prior : max(cpu_time) wall_clock(cpu1) - | self-consistency iterative process : 0.013 s 0.014 s - ------------------------------------------------------------- - Begin self-consistency iteration # 1 - - Date : 20230628, Time : 095502.287 ------------------------------------------------------------- - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 10.0000000000 - | Integrated number of electrons on 3D grid : 10.0000000000 - | Charge integration error : -0.0000000000 - | Normalization factor for density and gradient : 1.0000000000 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = -0.126678E-13 - | Sum of charges compensated after spline to logarithmic grids = 0.163201E-03 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = -0.129138E-13 - Summing up the Hartree potential. - Time summed over all CPUs for potential: real work 0.008 s, elapsed 0.008 s - | RMS charge density error from multipole expansion : 0.647320E-02 - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.021 s, elapsed 0.021 s - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.000 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -0.81584664 eV - Writing Kohn-Sham eigenvalues. - - State Occupation Eigenvalue [Ha] Eigenvalue [eV] - 1 2.00000 -18.788066 -511.24929 - 2 2.00000 -0.924879 -25.16724 - 3 2.00000 -0.478157 -13.01133 - 4 2.00000 -0.338091 -9.19992 - 5 2.00000 -0.259583 -7.06362 - 6 0.00000 0.002580 0.07021 - 7 0.00000 0.100559 2.73636 - 8 0.00000 0.298340 8.11825 - 9 0.00000 0.334356 9.09828 - 10 0.00000 0.369759 10.06166 - 11 0.00000 0.575118 15.64975 - - Highest occupied state (VBM) at -7.06361568 eV - | Occupation number: 2.00000000 - - Lowest unoccupied state (CBM) at 0.07021039 eV - | Occupation number: 0.00000000 - - Overall HOMO-LUMO gap: 7.13382606 eV. - - Total energy components: - | Sum of eigenvalues : -41.57755222 Ha -1131.38275999 eV - | XC energy correction : -9.24031874 Ha -251.44186625 eV - | XC potential correction : 11.88568386 Ha 323.42591349 eV - | Free-atom electrostatic energy: -35.73811056 Ha -972.48346788 eV - | Hartree energy correction : -1.79888236 Ha -48.95007960 eV - | Entropy correction : 0.00000000 Ha 0.00000000 eV - | --------------------------- - | Total energy : -76.46918003 Ha -2080.83226023 eV - | Total energy, T -> 0 : -76.46918003 Ha -2080.83226023 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -76.46918003 Ha -2080.83226023 eV - - Derived energy quantities: - | Kinetic energy : 76.27592956 Ha 2075.57364729 eV - | Electrostatic energy : -143.50479084 Ha -3904.96404126 eV - | Energy correction for multipole - | error in Hartree potential : -0.00338139 Ha -0.09201220 eV - | Sum of eigenvalues per atom : -377.12758666 eV - | Total energy (T->0) per atom : -693.61075341 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -693.61075341 eV - Evaluating new KS density. - Integration grid: deviation in total charge ( - N_e) = 5.329071E-15 - - Self-consistency convergence accuracy: - | Change of charge density : 0.1747E+00 - | Change of sum of eigenvalues : -0.1131E+04 eV - | Change of total energy : -0.2081E+04 eV - - ------------------------------------------------------------- - End self-consistency iteration # 1 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 0.044 s 0.043 s - | Charge density update : 0.013 s 0.013 s - | Density mixing : 0.000 s 0.000 s - | Hartree multipole update : 0.002 s 0.002 s - | Hartree multipole summation : 0.008 s 0.007 s - | Integration : 0.021 s 0.021 s - | Solution of K.-S. eqns. : 0.000 s 0.000 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 0.012 MB (on task 0) - | Maximum: 0.012 MB (on task 0) - | Average: 0.012 MB - | Peak value for overall tracked memory usage: - | Minimum: 0.558 MB (on task 0 after allocating grid_partition) - | Maximum: 0.558 MB (on task 0 after allocating grid_partition) - | Average: 0.558 MB - | Largest tracked array allocation so far: - | Minimum: 0.364 MB (all_coords on task 0) - | Maximum: 0.364 MB (all_coords on task 0) - | Average: 0.364 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - ------------------------------------------------------------- - Begin self-consistency iteration # 2 - - Date : 20230628, Time : 095502.330 ------------------------------------------------------------- - Pulay mixing of updated and previous charge densities. - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 10.0000000000 - | Integrated number of electrons on 3D grid : 10.0000000000 - | Charge integration error : 0.0000000000 - | Normalization factor for density and gradient : 1.0000000000 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = 0.718254E-14 - | Sum of charges compensated after spline to logarithmic grids = 0.163136E-03 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = 0.755151E-14 - Summing up the Hartree potential. - Time summed over all CPUs for potential: real work 0.008 s, elapsed 0.008 s - | RMS charge density error from multipole expansion : 0.647322E-02 - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.021 s, elapsed 0.021 s - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.000 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -0.81737047 eV - Highest occupied state (VBM) at -7.06676776 eV - | Occupation number: 2.00000000 - - Lowest unoccupied state (CBM) at 0.06919607 eV - | Occupation number: 0.00000000 - - Overall HOMO-LUMO gap: 7.13596383 eV. - - Total energy components: - | Sum of eigenvalues : -41.57901894 Ha -1131.42267146 eV - | XC energy correction : -9.24012938 Ha -251.43671332 eV - | XC potential correction : 11.88543568 Ha 323.41916031 eV - | Free-atom electrostatic energy: -35.73811056 Ha -972.48346788 eV - | Hartree energy correction : -1.79735675 Ha -48.90856569 eV - | Entropy correction : 0.00000000 Ha 0.00000000 eV - | --------------------------- - | Total energy : -76.46917995 Ha -2080.83225804 eV - | Total energy, T -> 0 : -76.46917995 Ha -2080.83225804 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -76.46917995 Ha -2080.83225804 eV - - Derived energy quantities: - | Kinetic energy : 76.27479953 Ha 2075.54289761 eV - | Electrostatic energy : -143.50385010 Ha -3904.93844233 eV - | Energy correction for multipole - | error in Hartree potential : -0.00338459 Ha -0.09209942 eV - | Sum of eigenvalues per atom : -377.14089049 eV - | Total energy (T->0) per atom : -693.61075268 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -693.61075268 eV - Evaluating new KS density. - Integration grid: deviation in total charge ( - N_e) = -3.375078E-14 - - Self-consistency convergence accuracy: - | Change of charge density : 0.5698E-03 - | Change of sum of eigenvalues : -0.3991E-01 eV - | Change of total energy : 0.2186E-05 eV - - ------------------------------------------------------------- - End self-consistency iteration # 2 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 0.045 s 0.045 s - | Charge density update : 0.013 s 0.013 s - | Density mixing : 0.001 s 0.001 s - | Hartree multipole update : 0.002 s 0.002 s - | Hartree multipole summation : 0.008 s 0.007 s - | Integration : 0.021 s 0.022 s - | Solution of K.-S. eqns. : 0.000 s 0.000 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 0.012 MB (on task 0) - | Maximum: 0.012 MB (on task 0) - | Average: 0.012 MB - | Peak value for overall tracked memory usage: - | Minimum: 0.558 MB (on task 0 after allocating grid_partition) - | Maximum: 0.558 MB (on task 0 after allocating grid_partition) - | Average: 0.558 MB - | Largest tracked array allocation so far: - | Minimum: 0.364 MB (all_coords on task 0) - | Maximum: 0.364 MB (all_coords on task 0) - | Average: 0.364 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - ------------------------------------------------------------- - Begin self-consistency iteration # 3 - - Date : 20230628, Time : 095502.375 ------------------------------------------------------------- - Pulay mixing of updated and previous charge densities. - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 10.0000000000 - | Integrated number of electrons on 3D grid : 10.0000000000 - | Charge integration error : 0.0000000000 - | Normalization factor for density and gradient : 1.0000000000 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = 0.342155E-13 - | Sum of charges compensated after spline to logarithmic grids = 0.163089E-03 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = 0.350026E-13 - Summing up the Hartree potential. - Time summed over all CPUs for potential: real work 0.008 s, elapsed 0.008 s - | RMS charge density error from multipole expansion : 0.647279E-02 - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.021 s, elapsed 0.021 s - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.000 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -0.81872111 eV - Highest occupied state (VBM) at -7.06902905 eV - | Occupation number: 2.00000000 - - Lowest unoccupied state (CBM) at 0.06832818 eV - | Occupation number: 0.00000000 - - Overall HOMO-LUMO gap: 7.13735724 eV. - - Total energy components: - | Sum of eigenvalues : -41.58008451 Ha -1131.45166724 eV - | XC energy correction : -9.23998730 Ha -251.43284728 eV - | XC potential correction : 11.88524985 Ha 323.41410357 eV - | Free-atom electrostatic energy: -35.73811056 Ha -972.48346788 eV - | Hartree energy correction : -1.79624740 Ha -48.87837868 eV - | Entropy correction : 0.00000000 Ha 0.00000000 eV - | --------------------------- - | Total energy : -76.46917993 Ha -2080.83225751 eV - | Total energy, T -> 0 : -76.46917993 Ha -2080.83225751 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -76.46917993 Ha -2080.83225751 eV - - Derived energy quantities: - | Kinetic energy : 76.27402717 Ha 2075.52188073 eV - | Electrostatic energy : -143.50321980 Ha -3904.92129097 eV - | Energy correction for multipole - | error in Hartree potential : -0.00338715 Ha -0.09216904 eV - | Sum of eigenvalues per atom : -377.15055575 eV - | Total energy (T->0) per atom : -693.61075250 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -693.61075250 eV - Evaluating new KS density. - Integration grid: deviation in total charge ( - N_e) = 7.105427E-15 - - Self-consistency convergence accuracy: - | Change of charge density : 0.2761E-03 - | Change of sum of eigenvalues : -0.2900E-01 eV - | Change of total energy : 0.5288E-06 eV - - ------------------------------------------------------------- - End self-consistency iteration # 3 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 0.047 s 0.047 s - | Charge density update : 0.013 s 0.013 s - | Density mixing : 0.002 s 0.002 s - | Hartree multipole update : 0.002 s 0.002 s - | Hartree multipole summation : 0.008 s 0.009 s - | Integration : 0.021 s 0.021 s - | Solution of K.-S. eqns. : 0.000 s 0.000 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 0.012 MB (on task 0) - | Maximum: 0.012 MB (on task 0) - | Average: 0.012 MB - | Peak value for overall tracked memory usage: - | Minimum: 0.558 MB (on task 0 after allocating grid_partition) - | Maximum: 0.558 MB (on task 0 after allocating grid_partition) - | Average: 0.558 MB - | Largest tracked array allocation so far: - | Minimum: 0.364 MB (all_coords on task 0) - | Maximum: 0.364 MB (all_coords on task 0) - | Average: 0.364 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - ------------------------------------------------------------- - Begin self-consistency iteration # 4 - - Date : 20230628, Time : 095502.422 ------------------------------------------------------------- - Pulay mixing of updated and previous charge densities. - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 10.0000000000 - | Integrated number of electrons on 3D grid : 10.0000000000 - | Charge integration error : -0.0000000000 - | Normalization factor for density and gradient : 1.0000000000 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = -0.440300E-13 - | Sum of charges compensated after spline to logarithmic grids = 0.163076E-03 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = -0.448417E-13 - Summing up the Hartree potential. - Time summed over all CPUs for potential: real work 0.008 s, elapsed 0.008 s - | RMS charge density error from multipole expansion : 0.647142E-02 - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.021 s, elapsed 0.021 s - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.000 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -0.81965761 eV - Highest occupied state (VBM) at -7.06940695 eV - | Occupation number: 2.00000000 - - Lowest unoccupied state (CBM) at 0.06779685 eV - | Occupation number: 0.00000000 - - Overall HOMO-LUMO gap: 7.13720380 eV. - - Total energy components: - | Sum of eigenvalues : -41.58030203 Ha -1131.45758603 eV - | XC energy correction : -9.23994587 Ha -251.43171988 eV - | XC potential correction : 11.88519665 Ha 323.41265594 eV - | Free-atom electrostatic energy: -35.73811056 Ha -972.48346788 eV - | Hartree energy correction : -1.79601805 Ha -48.87213773 eV - | Entropy correction : 0.00000000 Ha 0.00000000 eV - | --------------------------- - | Total energy : -76.46917986 Ha -2080.83225557 eV - | Total energy, T -> 0 : -76.46917986 Ha -2080.83225557 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -76.46917986 Ha -2080.83225557 eV - - Derived energy quantities: - | Kinetic energy : 76.27401887 Ha 2075.52165471 eV - | Electrostatic energy : -143.50325285 Ha -3904.92219040 eV - | Energy correction for multipole - | error in Hartree potential : -0.00338837 Ha -0.09220225 eV - | Sum of eigenvalues per atom : -377.15252868 eV - | Total energy (T->0) per atom : -693.61075186 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -693.61075186 eV - Evaluating new KS density. - Integration grid: deviation in total charge ( - N_e) = 7.105427E-15 - - Self-consistency convergence accuracy: - | Change of charge density : 0.1243E-03 - | Change of sum of eigenvalues : -0.5919E-02 eV - | Change of total energy : 0.1944E-05 eV - - ------------------------------------------------------------- - End self-consistency iteration # 4 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 0.046 s 0.046 s - | Charge density update : 0.013 s 0.013 s - | Density mixing : 0.001 s 0.002 s - | Hartree multipole update : 0.002 s 0.001 s - | Hartree multipole summation : 0.008 s 0.008 s - | Integration : 0.021 s 0.022 s - | Solution of K.-S. eqns. : 0.000 s 0.000 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 0.012 MB (on task 0) - | Maximum: 0.012 MB (on task 0) - | Average: 0.012 MB - | Peak value for overall tracked memory usage: - | Minimum: 0.558 MB (on task 0 after allocating grid_partition) - | Maximum: 0.558 MB (on task 0 after allocating grid_partition) - | Average: 0.558 MB - | Largest tracked array allocation so far: - | Minimum: 0.364 MB (all_coords on task 0) - | Maximum: 0.364 MB (all_coords on task 0) - | Average: 0.364 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - ------------------------------------------------------------- - Begin self-consistency iteration # 5 - - Date : 20230628, Time : 095502.468 ------------------------------------------------------------- - Pulay mixing of updated and previous charge densities. - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 10.0000000000 - | Integrated number of electrons on 3D grid : 10.0000000000 - | Charge integration error : -0.0000000000 - | Normalization factor for density and gradient : 1.0000000000 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = -0.172430E-13 - | Sum of charges compensated after spline to logarithmic grids = 0.163077E-03 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = -0.169724E-13 - Summing up the Hartree potential. - Time summed over all CPUs for potential: real work 0.008 s, elapsed 0.008 s - | RMS charge density error from multipole expansion : 0.647128E-02 - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.021 s, elapsed 0.021 s - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.000 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -0.81961572 eV - Highest occupied state (VBM) at -7.06938908 eV - | Occupation number: 2.00000000 - - Lowest unoccupied state (CBM) at 0.06782280 eV - | Occupation number: 0.00000000 - - Overall HOMO-LUMO gap: 7.13721189 eV. - - Total energy components: - | Sum of eigenvalues : -41.58029853 Ha -1131.45749082 eV - | XC energy correction : -9.23994659 Ha -251.43173953 eV - | XC potential correction : 11.88519764 Ha 323.41268286 eV - | Free-atom electrostatic energy: -35.73811056 Ha -972.48346788 eV - | Hartree energy correction : -1.79602181 Ha -48.87224016 eV - | Entropy correction : 0.00000000 Ha 0.00000000 eV - | --------------------------- - | Total energy : -76.46917986 Ha -2080.83225553 eV - | Total energy, T -> 0 : -76.46917986 Ha -2080.83225553 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -76.46917986 Ha -2080.83225553 eV - - Derived energy quantities: - | Kinetic energy : 76.27406155 Ha 2075.52281628 eV - | Electrostatic energy : -143.50329482 Ha -3904.92333228 eV - | Energy correction for multipole - | error in Hartree potential : -0.00338853 Ha -0.09220664 eV - | Sum of eigenvalues per atom : -377.15249694 eV - | Total energy (T->0) per atom : -693.61075184 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -693.61075184 eV - Evaluating new KS density. - Integration grid: deviation in total charge ( - N_e) = -3.019807E-14 - - Self-consistency convergence accuracy: - | Change of charge density : 0.1883E-04 - | Change of sum of eigenvalues : 0.9521E-04 eV - | Change of total energy : 0.3472E-07 eV - - ------------------------------------------------------------- - End self-consistency iteration # 5 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 0.046 s 0.047 s - | Charge density update : 0.013 s 0.014 s - | Density mixing : 0.002 s 0.002 s - | Hartree multipole update : 0.002 s 0.002 s - | Hartree multipole summation : 0.008 s 0.008 s - | Integration : 0.021 s 0.021 s - | Solution of K.-S. eqns. : 0.000 s 0.000 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 0.012 MB (on task 0) - | Maximum: 0.012 MB (on task 0) - | Average: 0.012 MB - | Peak value for overall tracked memory usage: - | Minimum: 0.558 MB (on task 0 after allocating grid_partition) - | Maximum: 0.558 MB (on task 0 after allocating grid_partition) - | Average: 0.558 MB - | Largest tracked array allocation so far: - | Minimum: 0.364 MB (all_coords on task 0) - | Maximum: 0.364 MB (all_coords on task 0) - | Average: 0.364 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - ------------------------------------------------------------- - Begin self-consistency iteration # 6 - - Date : 20230628, Time : 095502.515 ------------------------------------------------------------- - Pulay mixing of updated and previous charge densities. - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 10.0000000000 - | Integrated number of electrons on 3D grid : 10.0000000000 - | Charge integration error : -0.0000000000 - | Normalization factor for density and gradient : 1.0000000000 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = 0.122989E-14 - | Sum of charges compensated after spline to logarithmic grids = 0.163077E-03 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = 0.393564E-15 - Summing up the Hartree potential. - Time summed over all CPUs for potential: real work 0.007 s, elapsed 0.008 s - | RMS charge density error from multipole expansion : 0.647129E-02 - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.021 s, elapsed 0.021 s - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.000 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -0.81961221 eV - Highest occupied state (VBM) at -7.06939046 eV - | Occupation number: 2.00000000 - - Lowest unoccupied state (CBM) at 0.06782418 eV - | Occupation number: 0.00000000 - - Overall HOMO-LUMO gap: 7.13721465 eV. - - Total energy components: - | Sum of eigenvalues : -41.58029885 Ha -1131.45749970 eV - | XC energy correction : -9.23994671 Ha -251.43174263 eV - | XC potential correction : 11.88519778 Ha 323.41268677 eV - | Free-atom electrostatic energy: -35.73811056 Ha -972.48346788 eV - | Hartree energy correction : -1.79602152 Ha -48.87223208 eV - | Entropy correction : 0.00000000 Ha 0.00000000 eV - | --------------------------- - | Total energy : -76.46917986 Ha -2080.83225552 eV - | Total energy, T -> 0 : -76.46917986 Ha -2080.83225552 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -76.46917986 Ha -2080.83225552 eV - - Derived energy quantities: - | Kinetic energy : 76.27406201 Ha 2075.52282880 eV - | Electrostatic energy : -143.50329516 Ha -3904.92334169 eV - | Energy correction for multipole - | error in Hartree potential : -0.00338854 Ha -0.09220694 eV - | Sum of eigenvalues per atom : -377.15249990 eV - | Total energy (T->0) per atom : -693.61075184 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -693.61075184 eV - Evaluating new KS density. - Integration grid: deviation in total charge ( - N_e) = -4.618528E-14 - - Self-consistency convergence accuracy: - | Change of charge density : 0.1111E-05 - | Change of sum of eigenvalues : -0.8881E-05 eV - | Change of total energy : 0.1723E-07 eV - - Electronic self-consistency reached - switching on the force computation. - - ------------------------------------------------------------- - End self-consistency iteration # 6 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 0.046 s 0.046 s - | Charge density & force component update : 0.013 s 0.013 s - | Density mixing : 0.003 s 0.002 s - | Hartree multipole update : 0.002 s 0.002 s - | Hartree multipole summation : 0.008 s 0.008 s - | Hartree pot. SCF incomplete forces : 0.015 s 0.015 s - | Integration : 0.021 s 0.021 s - | Solution of K.-S. eqns. : 0.000 s 0.000 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 0.012 MB (on task 0) - | Maximum: 0.012 MB (on task 0) - | Average: 0.012 MB - | Peak value for overall tracked memory usage: - | Minimum: 0.558 MB (on task 0 after allocating grid_partition) - | Maximum: 0.558 MB (on task 0 after allocating grid_partition) - | Average: 0.558 MB - | Largest tracked array allocation so far: - | Minimum: 0.364 MB (all_coords on task 0) - | Maximum: 0.364 MB (all_coords on task 0) - | Average: 0.364 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - ------------------------------------------------------------- - Begin self-consistency iteration # 7 - - Date : 20230628, Time : 095502.561 ------------------------------------------------------------- - Pulay mixing of updated and previous charge densities. - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 10.0000000000 - | Integrated number of electrons on 3D grid : 10.0000000000 - | Charge integration error : 0.0000000000 - | Normalization factor for density and gradient : 1.0000000000 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = 0.228513E-13 - | Sum of charges compensated after spline to logarithmic grids = 0.163077E-03 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = 0.225807E-13 - Summing up the Hartree potential. - Time summed over all CPUs for potential: real work 0.024 s, elapsed 0.024 s - | RMS charge density error from multipole expansion : 0.647129E-02 - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.021 s, elapsed 0.021 s - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.000 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -0.81960980 eV - Highest occupied state (VBM) at -7.06938675 eV - | Occupation number: 2.00000000 - - Lowest unoccupied state (CBM) at 0.06782564 eV - | Occupation number: 0.00000000 - - Overall HOMO-LUMO gap: 7.13721240 eV. - - Total energy components: - | Sum of eigenvalues : -41.58029708 Ha -1131.45745146 eV - | XC energy correction : -9.23994696 Ha -251.43174949 eV - | XC potential correction : 11.88519811 Ha 323.41269575 eV - | Free-atom electrostatic energy: -35.73811056 Ha -972.48346788 eV - | Hartree energy correction : -1.79602337 Ha -48.87228244 eV - | Entropy correction : 0.00000000 Ha 0.00000000 eV - | --------------------------- - | Total energy : -76.46917986 Ha -2080.83225551 eV - | Total energy, T -> 0 : -76.46917986 Ha -2080.83225551 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -76.46917986 Ha -2080.83225551 eV - - Derived energy quantities: - | Kinetic energy : 76.27406348 Ha 2075.52286864 eV - | Electrostatic energy : -143.50329637 Ha -3904.92337465 eV - | Energy correction for multipole - | error in Hartree potential : -0.00338854 Ha -0.09220690 eV - | Sum of eigenvalues per atom : -377.15248382 eV - | Total energy (T->0) per atom : -693.61075184 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -693.61075184 eV - Evaluating new KS density and force components. - Integration grid: deviation in total charge ( - N_e) = 3.375078E-14 - - atomic forces [eV/Ang]: - ----------------------- - atom # 1 - Hellmann-Feynman : -0.748664E-13 0.595448E-11 0.175027E+02 - Ionic forces : 0.000000E+00 0.000000E+00 0.000000E+00 - Multipole : 0.290398E-13 -0.721957E-14 -0.902990E-01 - Hartree pot. SCF incomplete : -0.278847E-12 0.302588E-12 0.116426E-04 - Pulay + GGA : 0.107576E-11 -0.100303E-10 -0.174195E+02 - ---------------------------------------------------------------- - Total forces( 1) : 0.751090E-12 -0.378045E-11 -0.710329E-02 - atom # 2 - Hellmann-Feynman : -0.105808E-13 0.296175E+00 -0.312050E+00 - Ionic forces : 0.000000E+00 0.000000E+00 0.000000E+00 - Multipole : 0.402699E-15 -0.451209E-02 -0.316561E-01 - Hartree pot. SCF incomplete : 0.868541E-14 0.890914E-06 0.188241E-05 - Pulay + GGA : 0.851889E-14 -0.291007E+00 0.337412E+00 - ---------------------------------------------------------------- - Total forces( 2) : 0.702617E-14 0.657031E-03 -0.629131E-02 - atom # 3 - Hellmann-Feynman : -0.319427E-14 -0.296175E+00 -0.312050E+00 - Ionic forces : 0.000000E+00 0.000000E+00 0.000000E+00 - Multipole : -0.783889E-16 0.451209E-02 -0.316561E-01 - Hartree pot. SCF incomplete : 0.781889E-14 -0.890914E-06 0.188241E-05 - Pulay + GGA : -0.101225E-13 0.291007E+00 0.337412E+00 - ---------------------------------------------------------------- - Total forces( 3) : -0.557627E-14 -0.657031E-03 -0.629131E-02 - - - Self-consistency convergence accuracy: - | Change of charge density : 0.3543E-06 - | Change of sum of eigenvalues : 0.4825E-04 eV - | Change of total energy : 0.5599E-08 eV - | Change of forces : 0.4731E+00 eV/A - - Writing Kohn-Sham eigenvalues. - - State Occupation Eigenvalue [Ha] Eigenvalue [eV] - 1 2.00000 -18.788546 -511.26235 - 2 2.00000 -0.925138 -25.17429 - 3 2.00000 -0.478381 -13.01741 - 4 2.00000 -0.338288 -9.20530 - 5 2.00000 -0.259795 -7.06939 - 6 0.00000 0.002493 0.06783 - 7 0.00000 0.100448 2.73333 - 8 0.00000 0.298234 8.11536 - 9 0.00000 0.334240 9.09513 - 10 0.00000 0.369680 10.05951 - 11 0.00000 0.574990 15.64628 - - Highest occupied state (VBM) at -7.06938675 eV - | Occupation number: 2.00000000 - - Lowest unoccupied state (CBM) at 0.06782564 eV - | Occupation number: 0.00000000 - - Overall HOMO-LUMO gap: 7.13721240 eV. - | Chemical Potential : -0.81960980 eV - - Self-consistency cycle converged. - - ------------------------------------------------------------- - End self-consistency iteration # 7 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 0.118 s 0.119 s - | Charge density & force component update : 0.054 s 0.054 s - | Density mixing : 0.003 s 0.003 s - | Hartree multipole update : 0.002 s 0.002 s - | Hartree multipole summation : 0.024 s 0.024 s - | Hartree pot. SCF incomplete forces : 0.015 s 0.015 s - | Integration : 0.021 s 0.021 s - | Solution of K.-S. eqns. : 0.000 s 0.000 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 0.012 MB (on task 0) - | Maximum: 0.012 MB (on task 0) - | Average: 0.012 MB - | Peak value for overall tracked memory usage: - | Minimum: 0.558 MB (on task 0 after allocating grid_partition) - | Maximum: 0.558 MB (on task 0 after allocating grid_partition) - | Average: 0.558 MB - | Largest tracked array allocation so far: - | Minimum: 0.364 MB (all_coords on task 0) - | Maximum: 0.364 MB (all_coords on task 0) - | Average: 0.364 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - Removing unitary transformations (pure translations, rotations) from forces on atoms. - Atomic forces before filtering: - | Net force on center of mass : 0.752540E-12 -0.972825E-11 -0.196859E-01 eV/A - | Net torque on center of mass: 0.387025E-11 0.298771E-12 -0.966938E-14 eV - Atomic forces after filtering: - | Net force on center of mass : -0.202824E-27 0.000000E+00 0.696899E-17 eV/A - | Net torque on center of mass: 0.103720E-17 0.646065E-28 0.133932E-36 eV - - Energy and forces in a compact form: - | Total energy uncorrected : -0.208083225551071E+04 eV - | Total energy corrected : -0.208083225551071E+04 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -0.208083225551071E+04 eV - Total atomic forces (unitary forces cleaned) [eV/Ang]: - | 1 0.405648561641326E-28 0.551198801267693E-12 -0.541321794005289E-03 - | 2 -0.121694568492398E-27 0.657031192731074E-03 0.270660897217135E-03 - | 3 -0.121694568492398E-27 -0.657031193282273E-03 0.270660896788161E-03 - - ------------------------------------ - Start decomposition of the XC Energy - ------------------------------------ - X and C from original XC functional choice - Hartree-Fock Energy : 0.000000000 Ha 0.000000000 eV - X Energy : -8.914983781 Ha -242.589051486 eV - C Energy : -0.324963179 Ha -8.842698008 eV - XC Energy w/o HF : -9.239946960 Ha -251.431749494 eV - Total XC Energy : -9.239946960 Ha -251.431749494 eV - ------------------------------------ - LDA X and C from self-consistent density - X Energy LDA : -8.098845171 Ha -220.380789948 eV - C Energy LDA : -0.659361820 Ha -17.942148003 eV - ------------------------------------ - End decomposition of the XC Energy - ------------------------------------ - ------------------------------------------------------------- - Relaxation / MD: End force evaluation. : max(cpu_time) wall_clock(cpu1) - | Time for this force evaluation : 0.449 s 0.449 s - ------------------------------------------------------------- - Geometry optimization: Attempting to predict improved coordinates. - - Removing unitary transformations (pure translations, rotations) from forces on atoms. - Atomic forces before filtering: - | Net force on center of mass : -0.202824E-27 0.000000E+00 0.696899E-17 eV/A - | Net torque on center of mass: 0.103720E-17 0.646065E-28 0.133932E-36 eV - Atomic forces after filtering: - | Net force on center of mass : 0.540432E-43 -0.871124E-19 0.000000E+00 eV/A - | Net torque on center of mass: -0.691468E-19 0.215273E-39 0.746290E-44 eV - Net remaining forces (excluding translations, rotations) in present geometry: - || Forces on atoms || = 0.657031E-03 eV/A. - Maximum force component is 0.657031E-03 eV/A. - Present geometry is converged. - ------------------------------------------------------------- - Final atomic structure: - x [A] y [A] z [A] - atom 0.00000000 -0.00000000 0.11989040 O - atom 0.00000000 0.76726299 -0.47736120 H - atom -0.00000000 -0.76726299 -0.47736120 H ------------------------------------------------------------- - ------------------------------------------------------------------------------- - Final output of selected total energy values: - - The following output summarizes some interesting total energy values - at the end of a run (AFTER all relaxation, molecular dynamics, etc.). - - | Total energy of the DFT / Hartree-Fock s.c.f. calculation : -2080.832255511 eV - | Final zero-broadening corrected energy (caution - metals only) : -2080.832255511 eV - | For reference only, the value of 1 Hartree used in FHI-aims is : 27.211384500 eV - - Before relying on these values, please be sure to understand exactly which - total energy value is referred to by a given number. Different objects may - all carry the same name 'total energy'. Definitions: - - Total energy of the DFT / Hartree-Fock s.c.f. calculation: - | Note that this energy does not include ANY quantities calculated after the - | s.c.f. cycle, in particular not ANY RPA, MP2, etc. many-body perturbation terms. - - Final zero-broadening corrected energy: - | For metallic systems only, a broadening of the occupation numbers at the Fermi - | level can be extrapolated back to zero broadening by an electron-gas inspired - | formula. For all systems that are not real metals, this value can be - | meaningless and should be avoided. - ------------------------------------------------------------------------------- - Methods described in the following list of references were used in this FHI-aims run. - If you publish the results, please make sure to cite these reference if they apply. - FHI-aims is an academic code, and for our developers (often, Ph.D. students - and postdocs), scientific credit in the community is essential. - Thank you for helping us! - - For any use of FHI-aims, please cite: - - Volker Blum, Ralf Gehrke, Felix Hanke, Paula Havu, Ville Havu, - Xinguo Ren, Karsten Reuter, and Matthias Scheffler - 'Ab initio molecular simulations with numeric atom-centered orbitals' - Computer Physics Communications 180, 2175-2196 (2009) - http://doi.org/10.1016/j.cpc.2009.06.022 - - - The ELSI infrastructure was used in your run to solve the Kohn-Sham electronic structure. - Please check out http://elsi-interchange.org to learn more. - If scalability is important for your project, please acknowledge ELSI by citing: - - V. W-z. Yu, F. Corsetti, A. Garcia, W. P. Huhn, M. Jacquelin, W. Jia, - B. Lange, L. Lin, J. Lu, W. Mi, A. Seifitokaldani, A. Vazquez-Mayagoitia, - C. Yang, H. Yang, and V. Blum - 'ELSI: A unified software interface for Kohn-Sham electronic structure solvers' - Computer Physics Communications 222, 267-285 (2018). - http://doi.org/10.1016/j.cpc.2017.09.007 - - - For the real-space grid partitioning and parallelization used in this calculation, please cite: - - Ville Havu, Volker Blum, Paula Havu, and Matthias Scheffler, - 'Efficient O(N) integration for all-electron electronic structure calculation' - 'using numerically tabulated basis functions' - Journal of Computational Physics 228, 8367-8379 (2009). - http://doi.org/10.1016/j.jcp.2009.08.008 - - Of course, there are many other important community references, e.g., those cited in the - above references. Our list is limited to references that describe implementations in the - FHI-aims code. The reason is purely practical (length of this list) - please credit others as well. - ------------------------------------------------------------- - Leaving FHI-aims. - Date : 20230628, Time : 095502.689 - - Computational steps: - | Number of self-consistency cycles : 28 - | Number of SCF (re)initializations : 3 - | Number of relaxation steps : 2 - - Detailed time accounting : max(cpu_time) wall_clock(cpu1) - | Total time : 1.789 s 1.790 s - | Preparation time : 0.064 s 0.064 s - | Boundary condition initialization : 0.000 s 0.000 s - | Grid partitioning : 0.035 s 0.036 s - | Preloading free-atom quantities on grid : 0.026 s 0.025 s - | Free-atom superposition energy : 0.024 s 0.024 s - | Total time for integrations : 0.636 s 0.635 s - | Total time for solution of K.-S. equations : 0.006 s 0.004 s - | Total time for EV reorthonormalization : 0.000 s 0.000 s - | Total time for density & force components : 0.528 s 0.528 s - | Total time for mixing : 0.064 s 0.062 s - | Total time for Hartree multipole update : 0.047 s 0.050 s - | Total time for Hartree multipole sum : 0.268 s 0.270 s - | Total time for total energy evaluation : 0.001 s 0.001 s - | Total time NSC force correction : 0.045 s 0.045 s - | Total time for scaled ZORA corrections : 0.000 s 0.000 s - - Partial memory accounting: - | Residual value for overall tracked memory usage across tasks: 0.000000 MB (should be 0.000000 MB) - | Peak values for overall tracked memory usage: - | Minimum: 0.558 MB (on task 0 after allocating grid_partition) - | Maximum: 0.558 MB (on task 0 after allocating grid_partition) - | Average: 0.558 MB - | Largest tracked array allocation: - | Minimum: 0.364 MB (all_coords on task 0) - | Maximum: 0.364 MB (all_coords on task 0) - | Average: 0.364 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. - - Have a nice day. ------------------------------------------------------------- diff --git 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A partial list of references is given at the end of - this file. Thank you for giving credit to the authors of these developments. - - For any questions about FHI-aims, please visit our slack channel at - - https://fhi-aims.slack.com - - and our main development and support site at - - https://aims-git.rz-berlin.mpg.de . - - The latter site, in particular, has a wiki to collect information, as well - as an issue tracker to log discussions, suggest improvements, and report issues - or bugs. https://aims-git.rz-berlin.mpg.de is also the main development site - of the project and all new and updated code versions can be obtained there. - Please send an email to aims-coordinators@fhi-berlin.mpg.de and we will add - you to these sites. They are for you and everyone is welcome there. - ------------------------------------------------------------- - - - - Date : 20230628, Time : 104123.048 - Time zero on CPU 1 : 0.162197700000000E+01 s. - Internal wall clock time zero : 457180883.048 s. - - FHI-aims created a unique identifier for this run for later identification - aims_uuid : 7F959EC8-A7E1-43AC-A4DA-9302788CF7F6 - - Build configuration of the current instance of FHI-aims - ------------------------------------------------------- - FHI-aims version : 220309 - Commit number : 232d594a3 - CMake host system : Linux-5.4.0-146-generic - CMake version : 3.26.3 - Fortran compiler : /home/tpurcell/intel/oneapi/mpi/2021.6.0/bin/mpiifort (Intel) version 2021.6.0.20220226 - Fortran compiler flags: -O3 -ip -fp-model precise - C compiler : /home/tpurcell/intel/oneapi/compiler/2022.1.0/linux/bin/intel64/icc (Intel) version 2021.6.0.20220226 - C compiler flags : -m64 -O3 -ip -fp-model precise -std=gnu99 - Using MPI - Using ScaLAPACK - Using LibXC - Using i-PI - Using RLSY - Linking against: /home/tpurcell/intel/oneapi/mkl/2022.1.0/lib/intel64/libmkl_scalapack_lp64.so - /home/tpurcell/intel/oneapi/mkl/2022.1.0/lib/intel64/libmkl_blacs_intelmpi_lp64.so - /home/tpurcell/intel/oneapi/mkl/2022.1.0/lib/intel64/libmkl_intel_lp64.so - /home/tpurcell/intel/oneapi/mkl/2022.1.0/lib/intel64/libmkl_sequential.so - /home/tpurcell/intel/oneapi/mkl/2022.1.0/lib/intel64/libmkl_core.so - - Using 1 parallel tasks. - Task 0 on host nomadbook-7 reporting. - - Performing system and environment tests: - *** Environment variable OMP_NUM_THREADS is set to - 2 - *** For performance reasons you might want to set it to 1 - | Checking for ScaLAPACK... - | Testing pdtran()... - | All pdtran() tests passed. - - Obtaining array dimensions for all initial allocations: - - ----------------------------------------------------------------------- - Parsing control.in (first pass over file, find array dimensions only). - The contents of control.in will be repeated verbatim below - unless switched off by setting 'verbatim_writeout .false.' . - in the first line of control.in . - ----------------------------------------------------------------------- - - #=============================================================================== - # Created using the Atomic Simulation Environment (ASE) - - # Tue Jun 27 18:06:33 2023 - - #=============================================================================== - xc pbe - relativistic atomic_zora scalar - relax_geometry trm 1e-3 - relax_unit_cell full - k_grid 2 2 2 - #=============================================================================== - - ################################################################################ - # - # FHI-aims code project - # VB, Fritz-Haber Institut, 2009 - # - # Suggested "light" defaults for Si atom (to be pasted into control.in file) - # Be sure to double-check any results obtained with these settings for post-processing, - # e.g., with the "tight" defaults and larger basis sets. - # - # 2020/09/08 Added f function to "light" after reinspection of Delta test outcomes. - # This was done for all of Al-Cl and is a tricky decision since it makes - # "light" calculations measurably more expensive for these elements. - # Nevertheless, outcomes for P, S, Cl (and to some extent, Si) appear - # to justify this choice. - # - ################################################################################ - species Si - # global species definitions - nucleus 14 - mass 28.0855 - # - l_hartree 4 - # - cut_pot 3.5 1.5 1.0 - basis_dep_cutoff 1e-4 - # - radial_base 42 5.0 - radial_multiplier 1 - angular_grids specified - division 0.5866 50 - division 0.9616 110 - division 1.2249 194 - division 1.3795 302 - # division 1.4810 434 - # division 1.5529 590 - # division 1.6284 770 - # division 1.7077 974 - # division 2.4068 1202 - # outer_grid 974 - outer_grid 302 - ################################################################################ - # - # Definition of "minimal" basis - # - ################################################################################ - # valence basis states - valence 3 s 2. - valence 3 p 2. - # ion occupancy - ion_occ 3 s 1. - ion_occ 3 p 1. - ################################################################################ - # - # Suggested additional basis functions. For production calculations, - # uncomment them one after another (the most important basis functions are - # listed first). - # - # Constructed for dimers: 1.75 A, 2.0 A, 2.25 A, 2.75 A, 3.75 A - # - ################################################################################ - # "First tier" - improvements: -571.96 meV to -37.03 meV - hydro 3 d 4.2 - hydro 2 p 1.4 - hydro 4 f 6.2 - ionic 3 s auto - # "Second tier" - improvements: -16.76 meV to -3.03 meV - # hydro 3 d 9 - # hydro 5 g 9.4 - # hydro 4 p 4 - # hydro 1 s 0.65 - # "Third tier" - improvements: -3.89 meV to -0.60 meV - # ionic 3 d auto - # hydro 3 s 2.6 - # hydro 4 f 8.4 - # hydro 3 d 3.4 - # hydro 3 p 7.8 - # "Fourth tier" - improvements: -0.33 meV to -0.11 meV - # hydro 2 p 1.6 - # hydro 5 g 10.8 - # hydro 5 f 11.2 - # hydro 3 d 1 - # hydro 4 s 4.5 - # Further basis functions that fell out of the optimization - noise - # level... < -0.08 meV - # hydro 4 d 6.6 - # hydro 5 g 16.4 - # hydro 4 d 9 - - ----------------------------------------------------------------------- - Completed first pass over input file control.in . - ----------------------------------------------------------------------- - - - ----------------------------------------------------------------------- - Parsing geometry.in (first pass over file, find array dimensions only). - The contents of geometry.in will be repeated verbatim below - unless switched off by setting 'verbatim_writeout .false.' . - in the first line of geometry.in . - ----------------------------------------------------------------------- - - #=============================================================================== - # Created using the Atomic Simulation Environment (ASE) - - # Tue Jun 27 18:06:33 2023 - - #======================================================= - lattice_vector 0.0000000000000000 2.7549999999999999 2.7549999999999999 - lattice_vector 2.7549999999999999 0.0000000000000000 2.7549999999999999 - lattice_vector 2.7549999999999999 2.7549999999999999 0.0000000000000000 - atom_frac 0.0000000000000000 0.0000000000000000 -0.0000000000000000 Si - atom_frac 0.2500000000000000 0.2500000000000000 0.2500000000000000 Si - - ----------------------------------------------------------------------- - Completed first pass over input file geometry.in . - ----------------------------------------------------------------------- - - - Basic array size parameters: - | Number of species : 1 - | Number of atoms : 2 - | Number of lattice vectors : 3 - | Max. basis fn. angular momentum : 3 - | Max. atomic/ionic basis occupied n: 3 - | Max. number of basis fn. types : 3 - | Max. radial fns per species/type : 5 - | Max. logarithmic grid size : 1346 - | Max. radial integration grid size : 42 - | Max. angular integration grid size: 302 - | Max. angular grid division number : 8 - | Radial grid for Hartree potential : 1346 - | Number of spin channels : 1 - ------------------------------------------------------------- - Reading file control.in. ------------------------------------------------------------- - XC: Using PBE gradient-corrected functionals. - Scalar relativistic treatment of kinetic energy: on-site free-atom approximation to ZORA. - Geometry relaxation: Modified BFGS - TRM (trust radius method) for lattice optimization. - Convergence accuracy for geometry relaxation: Maximum force < 0.100000E-02 eV/A. - Found k-point grid: 2 2 2 - - Reading configuration options for species Si . - | Found nuclear charge : 14.0000 - | Found atomic mass : 28.0855000000000 amu - | Found l_max for Hartree potential : 4 - | Found cutoff potl. onset [A], width [A], scale factor : 3.50000 1.50000 1.00000 - | Threshold for basis-dependent cutoff potential is 0.100000E-03 - | Found data for basic radial integration grid : 42 points, outermost radius = 5.000 A - | Found multiplier for basic radial grid : 1 - | Found angular grid specification: user-specified. - | Specified grid contains 5 separate shells. - | Check grid settings after all constraints further below. - | Found free-atom valence shell : 3 s 2.000 - | Found free-atom valence shell : 3 p 2.000 - | Found free-ion valence shell : 3 s 1.000 - | Found free-ion valence shell : 3 p 1.000 - | Found hydrogenic basis function : 3 d 4.200 - | Found hydrogenic basis function : 2 p 1.400 - | Found hydrogenic basis function : 4 f 6.200 - | Found ionic basis function : 3 s , default cutoff radius. - Species Si : Missing cutoff potential type. - Defaulting to exp(1/x)/(1-x)^2 type cutoff potential. - Species Si: No 'logarithmic' tag. Using default grid for free atom: - | Default logarithmic grid data [bohr] : 0.1000E-03 0.1000E+03 0.1012E+01 - | Will include ionic basis functions of 2.0-fold positive Si ion. - Species Si: On-site basis accuracy parameter (for Gram-Schmidt orthonormalisation) not specified. - Using default value basis_acc = 0.1000000E-03. - Species Si : Using default innermost maximum threshold i_radial= 2 for radial functions. - Species Si : Default cutoff onset for free atom density etc. : 0.35000000E+01 AA. - Species Si : Basic radial grid will be enhanced according to radial_multiplier = 1, to contain 42 grid points. - - Finished reading input file 'control.in'. - ------------------------------------------------------------- - - ------------------------------------------------------------- - Reading geometry description geometry.in. ------------------------------------------------------------- - | The smallest distance between any two atoms is 2.38589999 AA. - | The first atom of this pair is atom number 1 . - | The second atom of this pair is atom number 2 . - | Wigner-Seitz cell of the first atom image 0 1 0 . - | (The Wigner-Seitz cell of the second atom is 0 0 0 by definition.) - - Symmetry information by spglib: - | Precision set to 0.1E-04 - | Number of Operations : 48 - | Space group : 227 - | International : Fd-3m - | Schoenflies : Oh^7 - Input structure read successfully. - The structure contains 2 atoms, and a total of 28.000 electrons. - - Input geometry: - | Unit cell: - | 0.00000000 2.75500000 2.75500000 - | 2.75500000 0.00000000 2.75500000 - | 2.75500000 2.75500000 0.00000000 - | Atomic structure: - | Atom x [A] y [A] z [A] - | 1: Species Si 0.00000000 0.00000000 0.00000000 - | 2: Species Si 1.37750000 1.37750000 1.37750000 - - Lattice parameters for 3D lattice (in Angstroms) : 3.896158 3.896158 3.896158 - Angle(s) between unit vectors (in degrees) : 60.000000 60.000000 60.000000 - - - Quantities derived from the lattice vectors: - | Reciprocal lattice vector 1: -1.140324 1.140324 1.140324 - | Reciprocal lattice vector 2: 1.140324 -1.140324 1.140324 - | Reciprocal lattice vector 3: 1.140324 1.140324 -1.140324 - | Unit cell volume : 0.418210E+02 A^3 - - Fractional coordinates: - L1 L2 L3 - atom_frac 0.00000000 0.00000000 0.00000000 Si - atom_frac 0.25000000 0.25000000 0.25000000 Si - - - Finished reading input file 'control.in'. - - ------------------------------------------------------------- - Reading geometry description geometry.in. ------------------------------------------------------------- - - Consistency checks for stacksize environment parameter are next. - - | Maximum stacksize for task 0: unlimited - | Current stacksize for task 0: unlimited - - Consistency checks for the contents of control.in are next. - - MPI_IN_PLACE appears to work with this MPI implementation. - | Keeping use_mpi_in_place .true. (see manual). - Target number of points in a grid batch is not set. Defaulting to 100 - Method for grid partitioning is not set. Defaulting to parallel hash+maxmin partitioning. - Batch size limit is not set. Defaulting to 200 - By default, will store active basis functions for each batch. - If in need of memory, prune_basis_once .false. can be used to disable this option. - communication_type for Hartree potential was not specified. - Defaulting to calc_hartree . - Defaulting to Pulay charge density mixer. - Pulay mixer: Number of relevant iterations not set. - Defaulting to 8 iterations. - Pulay mixer: Number of initial linear mixing iterations not set. - Defaulting to 0 iterations. - Work space size for distributed Hartree potential not set. - Defaulting to 0.200000E+03 MB. - Mixing parameter for charge density mixing has not been set. - Using default: charge_mix_param = 0.0500. - The mixing parameter will be adjusted in iteration number 2 of the first full s.c.f. cycle only. - Algorithm-dependent basis array size parameters: - | n_max_pulay : 8 - Maximum number of self-consistency iterations not provided. - Presetting 1000 iterations. - Presetting 1001 iterations before the initial mixing cycle - is restarted anyway using the sc_init_iter criterion / keyword. - Presetting a factor 1.000 between actual scf density residual - and density convergence criterion sc_accuracy_rho below which sc_init_iter - takes no effect. - * No s.c.f. convergence criteria (sc_accuracy_*) were provided in control.in. - * The run will proceed with a reasonable default guess, but please check whether. - * the s.c.f. cycles seem to take too much or too little time. - No maximum number of relaxation steps, defaulting to 1000 - Default initial Hessian is Lindh matrix (thres = 15.00) plus 0.200000E+01 eV/A^2 times unity. - No maximum energy tolerance for TRM/BFGS moves, defaulting to 0.100000E-02 - Maximum energy tolerance by which TRM/BFGS trajectory may increase over multiple steps: 0.300000E-02 - No harmonic length scale. Defaulting to 0.250000E-01 A. - No trust radius initializer. Defaulting to 0.200000E+00 A. - Unit cell relaxation: Unit cell will be relaxed fully. - Unit cell relaxation: Analytical stress will be used. - Analytical stress will be computed. - Analytical stress calculation: Only the upper triangle is calculated. - Final output is symmetrized. - Analytical stress calculation: scf convergence accuracy of stress not set. - Analytical stress self-consistency will not be checked explicitly. - Be sure to set other criteria like sc_accuracy_rho tight enough. - Forces evaluation will include force correction term due to incomplete self-consistency (default). - * Notice: The s.c.f. convergence criterion sc_accuracy_rho was not provided. - * We used to stop in this case, and ask the user to provide reasonable - * scf convergence criteria. However, this led some users to employ criteria - * that led to extremely long run times, e.g., for simple relaxation. - * We now preset a default value for sc_accuracy_rho if it is not set. - * You may still wish to check if this setting is too tight or too loose for your needs. - * Based on n_atoms and forces and force-correction status, FHI-aims chose sc_accuracy_rho = 0.500000E-06 . - Force calculation: scf convergence accuracy of forces not set. - Defaulting to 'sc_accuracy_forces not_checked'. - Handling of forces: Unphysical translation and rotation will be removed from forces. - No accuracy limit for integral partition fn. given. Defaulting to 0.1000E-14. - No threshold value for u(r) in integrations given. Defaulting to 0.1000E-05. - No occupation type (smearing scheme) given. Defaulting to Gaussian broadening, width = 0.1000E-01 eV. - The width will be adjusted in iteration number 2 of the first full s.c.f. cycle only. - S.C.F. convergence parameters will be adjusted in iteration number 2 of the first full s.c.f. cycle only. - No accuracy for occupation numbers given. Defaulting to 0.1000E-12. - No threshold value for occupation numbers given. Defaulting to 0.0000E+00. - No accuracy for fermi level given. Defaulting to 0.1000E-19. - Maximum # of iterations to find E_F not set. Defaulting to 200. - Preferred method for the eigenvalue solver ('KS_method') not specified in 'control.in'. - Defaulting to serial version LAPACK (via ELSI). - Will not use alltoall communication since running on < 1024 CPUs. - Threshold for basis singularities not set. - Default threshold for basis singularities: 0.1000E-04 - partition_type (choice of integration weights) for integrals was not specified. - | Using a version of the partition function of Stratmann and coworkers ('stratmann_sparse'). - | At each grid point, the set of atoms used to build the partition table is smoothly restricted to - | only those atoms whose free-atom density would be non-zero at that grid point. - Partitioning for Hartree potential was not defined. Using partition_type for integrals. - | Adjusted default value of keyword multip_moments_threshold to: 0.10000000E-11 - | This value may affect high angular momentum components of the Hartree potential in periodic systems. - Spin handling was not defined in control.in. Defaulting to unpolarized case. - Angular momentum expansion for Kerker preconditioner not set explicitly. - | Using default value of 0 - No explicit requirement for turning off preconditioner. - | By default, it will be turned off when the charge convergence reaches - | sc_accuracy_rho = 0.500000E-06 - No special mixing parameter while Kerker preconditioner is on. - Using default: charge_mix_param = 0.0500. - No q(lm)/r^(l+1) cutoff set for long-range Hartree potential. - | Using default value of 0.100000E-09 . - | Verify using the multipole_threshold keyword. - Defaulting to new monopole extrapolation. - Density update method: automatic selection selected. - Using density matrix based charge density update. - Using density matrix based charge density update. - Using packed matrix style: index . - Geometry relaxation: A file "geometry.in.next_step" is written out by default after each step. - | This file contains the geometry of the current relaxation step as well as - | the current Hessian matrix needed to restart the relaxation algorithm. - | If you do not want part or all of this information, use the keywords - | "write_restart_geometry" or "hessian_to_restart_geometry" to switch the output off. - Defaulting to use time-reversal symmetry for k-point grid. - Charge integration errors on the 3D integration grid will be compensated - by explicit normalization and distribution of residual charges. - Use the "compensate_multipole_errors" flag to change this behaviour. - Set 'collect_eigenvectors' to be '.true.' for all serial calculations. This is mandatory. - Set 'collect_eigenvectors' to be '.true.' for KS_method lapack_fast and serial. - - Consistency checks for the contents of geometry.in are next. - - - Range separation radius for Ewald summation (hartree_convergence_parameter): 3.95124372 bohr. - Number of empty states per atom not set in control.in - providing a guess from actual geometry. - | Total number of empty states used during s.c.f. cycle: 6 - If you use a very high smearing, use empty_states (per atom!) in control.in to increase this value. - - Structure-dependent array size parameters: - | Maximum number of distinct radial functions : 9 - | Maximum number of basis functions : 50 - | Number of Kohn-Sham states (occupied + empty): 20 ------------------------------------------------------------- - ------------------------------------------------------------- - Preparing all fixed parts of the calculation. ------------------------------------------------------------- - Determining machine precision: - 2.225073858507201E-308 - Setting up grids for atomic and cluster calculations. - - Creating wave function, potential, and density for free atoms. - Runtime choices for atomic solver: - | atomic solver xc : PBE - | compute density gradient: 1 - | compute kinetic density : F - - Species: Si - - List of occupied orbitals and eigenvalues: - n l occ energy [Ha] energy [eV] - 1 0 2.0000 -65.767597 -1789.6274 - 2 0 2.0000 -5.115610 -139.2028 - 3 0 2.0000 -0.388877 -10.5819 - 2 1 6.0000 -3.500197 -95.2452 - 3 1 2.0000 -0.140803 -3.8315 - - - Adding cutoff potential to free-atom effective potential. - Creating fixed part of basis set: Ionic, confined, hydrogenic. - - Si ion: - - List of free ionic orbitals and eigenvalues: - n l energy [Ha] energy [eV] - 1 0 -66.641157 -1813.3982 - 2 0 -5.964274 -162.2962 - 3 0 -1.073878 -29.2217 - 2 1 -4.350005 -118.3697 - 3 1 -0.776571 -21.1316 - - - List of ionic basis orbitals and eigenvalues: - n l energy [Ha] energy [eV] outer radius [A] - 3 0 -1.073857 -29.2211 4.214062 - - - Si hydrogenic: - - List of hydrogenic basis orbitals: - n l effective z eigenvalue [eV] inner max. [A] outer max. [A] outer radius [A] - 3 2 4.200000 -26.6624 1.139231 1.139231 4.534782 - 2 1 1.400000 -6.4613 1.472672 1.472672 4.590560 - 4 3 6.200000 -32.6778 1.368518 1.368518 4.534782 - - Creating atomic-like basis functions for current effective potential. - - Species Si : - - List of atomic basis orbitals and eigenvalues: - n l energy [Ha] energy [eV] outer radius [A] - 1 0 -65.767597 -1789.6274 0.789468 - 2 0 -5.115610 -139.2028 2.815114 - 3 0 -0.388877 -10.5819 4.534782 - 2 1 -3.500197 -95.2452 3.259919 - 3 1 -0.140803 -3.8315 4.590560 - - Assembling full basis from fixed parts. - | Species Si : atomic orbital 1 s accepted. - | Species Si : atomic orbital 2 s accepted. - | Species Si : ionic orbital 3 s accepted. - | Species Si : atomic orbital 3 s accepted. - | Species Si : atomic orbital 2 p accepted. - | Species Si : atomic orbital 3 p accepted. - | Species Si : hydro orbital 2 p accepted. - | Species Si : hydro orbital 3 d accepted. - | Species Si : hydro orbital 4 f accepted. - - Basis size parameters after reduction: - | Total number of radial functions: 9 - | Total number of basis functions : 50 - - Per-task memory consumption for arrays in subroutine allocate_ext: - | 3.102808MB. - Testing on-site integration grid accuracy. - | Species Function (log., in eV) (rad., in eV) - 1 1 -1789.6273740966 -1789.6266345813 - 1 2 -139.2028173376 -139.2028132357 - 1 3 -10.2237226190 -10.2235219160 - 1 4 5.6355365073 5.5558633521 *** - 1 5 -95.2452114632 -95.2452114537 - 1 6 -3.8413965043 -3.8571292824 - 1 7 6.4035522332 6.2277973139 *** - 1 8 6.3860095444 6.3839142324 - 1 9 19.3722793793 19.3677446767 - * Note: Onsite integrals marked "***" above are less accurate than - * onsite_accuracy_threshold = 0.03000 eV. Usually, this is harmless. - * When in doubt, tighten the "radial" and/or "radial_multiplier" flags to check. - - Preparing densities etc. for the partition functions (integrals / Hartree potential). - - Preparations completed. - max(cpu_time) : 0.110 s. - Wall clock time (cpu1) : 0.111 s. ------------------------------------------------------------- - ------------------------------------------------------------- - Begin self-consistency loop: Initialization. - - Date : 20230628, Time : 104123.175 ------------------------------------------------------------- - - Initializing index lists of integration centers etc. from given atomic structure: - Mapping all atomic coordinates to central unit cell. - - Initializing the k-points - Using symmetry for reducing the k-points - | k-points reduced from: 8 to 8 - | Number of k-points : 8 - The eigenvectors in the calculations are REAL. - | K-points in task 0: 8 - | Number of basis functions in the Hamiltonian integrals : 2161 - | Number of basis functions in a single unit cell : 50 - | Number of centers in hartree potential : 708 - | Number of centers in hartree multipole : 318 - | Number of centers in electron density summation: 190 - | Number of centers in basis integrals : 198 - | Number of centers in integrals : 101 - | Number of centers in hamiltonian : 190 - | Consuming 14 KiB for k_phase. - | Number of super-cells (origin) [n_cells] : 2197 - | Number of super-cells (after PM_index) [n_cells] : 112 - | Number of super-cells in hamiltonian [n_cells_in_hamiltonian]: 112 - | Size of matrix packed + index [n_hamiltonian_matrix_size] : 86003 - - Initializing relaxation algorithms. - Finished initialization of distributed Hessian storage. - | Global dimension: 15 - | BLACS block size: 15 - | Number of workers: 1 - - | Estimated reciprocal-space cutoff momentum G_max: 2.36080402 bohr^-1 . - | Reciprocal lattice points for long-range Hartree potential: 58 - Partitioning the integration grid into batches with parallel hashing+maxmin method. - | Number of batches: 128 - | Maximal batch size: 90 - | Minimal batch size: 85 - | Average batch size: 87.562 - | Standard deviation of batch sizes: 1.493 - - Integration load balanced across 1 MPI tasks. - Work distribution over tasks is as follows: - Task 0 has 11208 integration points. - Initializing partition tables, free-atom densities, potentials, etc. across the integration grid (initialize_grid_storage). - | initialize_grid_storage: Actual outermost partition radius vs. multipole_radius_free - | (-- VB: in principle, multipole_radius_free should be larger, hence this output) - | Species 1: Confinement radius = 4.999999999999999 AA, multipole_radius_free = 5.000694715736543 AA. - | Species 1: outer_partition_radius set to 5.000694715736543 AA . - | The sparse table of interatomic distances needs 212.76 kbyte instead of 313.63 kbyte of memory. - | Net number of integration points: 11208 - | of which are non-zero points : 9844 - | Numerical average free-atom electrostatic potential : -12.56983149 eV - Renormalizing the initial density to the exact electron count on the 3D integration grid. - | Initial density: Formal number of electrons (from input files) : 28.0000000000 - | Integrated number of electrons on 3D grid : 28.0044890464 - | Charge integration error : 0.0044890464 - | Normalization factor for density and gradient : 0.9998397026 - Renormalizing the free-atom superposition density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 28.0000000000 - | Integrated number of electrons on 3D grid : 28.0044890464 - | Charge integration error : 0.0044890464 - | Normalization factor for density and gradient : 0.9998397026 - Obtaining max. number of non-zero basis functions in each batch (get_n_compute_maxes). - | Maximal number of non-zero basis functions: 673 in task 0 - Allocating 0.061 MB for KS_eigenvector - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.435 s, elapsed 0.435 s - Integrating overlap matrix. - Time summed over all CPUs for integration: real work 0.286 s, elapsed 0.286 s - Decreasing sparse matrix size: - | Tolerance: 0.1000E-12 - Hamiltonian matrix - | Array has 76538 nonzero elements out of 86003 elements - | Sparsity factor is 0.110 - Overlap matrix - | Array has 69730 nonzero elements out of 86003 elements - | Sparsity factor is 0.189 - New size of hamiltonian matrix: 77039 - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Singularity check in k-point 1, task 0 (analysis for other k-points/tasks may follow below): - Overlap matrix is not singular - | Lowest and highest eigenvalues : 0.9901E-03, 0.6283E+01 - Finished singularity check of overlap matrix - | Time : 0.000 s - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.000 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -5.54754229 eV - Writing Kohn-Sham eigenvalues. - K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - - State Occupation Eigenvalue [Ha] Eigenvalue [eV] - 1 2.00000 -65.786672 -1790.14643 - 2 2.00000 -65.786672 -1790.14643 - 3 2.00000 -5.138850 -139.83522 - 4 2.00000 -5.138620 -139.82897 - 5 2.00000 -3.523444 -95.87778 - 6 2.00000 -3.523444 -95.87778 - 7 2.00000 -3.523444 -95.87778 - 8 2.00000 -3.522920 -95.86354 - 9 2.00000 -3.522920 -95.86354 - 10 2.00000 -3.522920 -95.86354 - 11 2.00000 -0.648513 -17.64694 - 12 2.00000 -0.222890 -6.06515 - 13 2.00000 -0.222890 -6.06515 - 14 2.00000 -0.222890 -6.06515 - 15 0.00000 -0.122072 -3.32176 - 16 0.00000 -0.122072 -3.32176 - 17 0.00000 -0.122072 -3.32176 - 18 0.00000 -0.117492 -3.19713 - 19 0.00000 0.074623 2.03061 - 20 0.00000 0.074623 2.03061 - - What follows are estimated values for band gap, HOMO, LUMO, etc. - | They are estimated on a discrete k-point grid and not necessarily exact. - | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. - - Highest occupied state (VBM) at -6.06515226 eV (relative to internal zero) - | Occupation number: 2.00000000 - | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - - Lowest unoccupied state (CBM) at -4.99146902 eV (relative to internal zero) - | Occupation number: 0.00000000 - | K-point: 6 at 0.500000 0.000000 0.500000 (in units of recip. lattice) - - ESTIMATED overall HOMO-LUMO gap: 1.07368323 eV between HOMO at k-point 1 and LUMO at k-point 6 - | This appears to be an indirect band gap. - | Smallest direct gap : 2.62680162 eV for k_point 3 at 0.000000 0.500000 0.000000 (in units of recip. lattice) - The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, - this system is most likely an insulator or a semiconductor. - Calculating total energy contributions from superposition of free atom densities. - - Total energy components: - | Sum of eigenvalues : -329.10882970 Ha -8955.50690722 eV - | XC energy correction : -41.70173345 Ha -1134.76190321 eV - | XC potential correction : 53.85472519 Ha 1465.46163427 eV - | Free-atom electrostatic energy: -263.69998542 Ha -7175.64169592 eV - | Hartree energy correction : 0.00000000 Ha 0.00000000 eV - | Entropy correction : 0.00000000 Ha 0.00000000 eV - | --------------------------- - | Total energy : -580.65582338 Ha -15800.44887208 eV - | Total energy, T -> 0 : -580.65582338 Ha -15800.44887208 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -580.65582338 Ha -15800.44887208 eV - - Derived energy quantities: - | Kinetic energy : 582.33599532 Ha 15846.16867687 eV - | Electrostatic energy : -1121.29008525 Ha -30511.85564573 eV - | Energy correction for multipole - | error in Hartree potential : 0.00000000 Ha 0.00000000 eV - | Sum of eigenvalues per atom : -4477.75345361 eV - | Total energy (T->0) per atom : -7900.22443604 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -7900.22443604 eV - Initialize hartree_potential_storage - Max. number of atoms included in rho_multipole: 2 - - End scf initialization - timings : max(cpu_time) wall_clock(cpu1) - | Time for scf. initialization : 1.052 s 1.052 s - | Boundary condition initialization : 0.062 s 0.061 s - | Relaxation initialization : 0.000 s 0.001 s - | Integration : 0.723 s 0.723 s - | Solution of K.-S. eqns. : 0.006 s 0.006 s - | Grid partitioning : 0.037 s 0.036 s - | Preloading free-atom quantities on grid : 0.196 s 0.197 s - | Free-atom superposition energy : 0.028 s 0.028 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 1.537 MB (on task 0) - | Maximum: 1.537 MB (on task 0) - | Average: 1.537 MB - | Peak value for overall tracked memory usage: - | Minimum: 6.565 MB (on task 0 after allocating wave) - | Maximum: 6.565 MB (on task 0 after allocating wave) - | Average: 6.565 MB - | Largest tracked array allocation so far: - | Minimum: 3.456 MB (hamiltonian_shell on task 0) - | Maximum: 3.456 MB (hamiltonian_shell on task 0) - | Average: 3.456 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - Evaluating new KS density using the density matrix - Evaluating density matrix - Time summed over all CPUs for getting density from density matrix: real work 0.918 s, elapsed 0.918 s - Integration grid: deviation in total charge ( - N_e) = -4.618528E-14 - - Time for density update prior : max(cpu_time) wall_clock(cpu1) - | self-consistency iterative process : 0.914 s 0.919 s - ------------------------------------------------------------- - Begin self-consistency iteration # 1 - - Date : 20230628, Time : 104125.146 ------------------------------------------------------------- - Pulay mixing of updated and previous charge densities. - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 28.0000000000 - | Integrated number of electrons on 3D grid : 27.9997706824 - | Charge integration error : -0.0002293176 - | Normalization factor for density and gradient : 1.0000081900 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = 0.174607E-12 - | Sum of charges compensated after spline to logarithmic grids = -0.539729E-05 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = 0.000000E+00 - Summing up the Hartree potential. - Time summed over all CPUs for potential: real work 0.329 s, elapsed 0.329 s - | RMS charge density error from multipole expansion : 0.688731E-03 - | Average real-space part of the electrostatic potential : 0.02728917 eV - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.432 s, elapsed 0.432 s - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.000 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -5.51709006 eV - Writing Kohn-Sham eigenvalues. - K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - - State Occupation Eigenvalue [Ha] Eigenvalue [eV] - 1 2.00000 -65.783258 -1790.05352 - 2 2.00000 -65.783258 -1790.05352 - 3 2.00000 -5.136258 -139.76468 - 4 2.00000 -5.136028 -139.75842 - 5 2.00000 -3.520781 -95.80534 - 6 2.00000 -3.520781 -95.80534 - 7 2.00000 -3.520781 -95.80534 - 8 2.00000 -3.520258 -95.79108 - 9 2.00000 -3.520258 -95.79108 - 10 2.00000 -3.520258 -95.79108 - 11 2.00000 -0.647408 -17.61686 - 12 2.00000 -0.221469 -6.02649 - 13 2.00000 -0.221469 -6.02649 - 14 2.00000 -0.221469 -6.02649 - 15 0.00000 -0.121223 -3.29865 - 16 0.00000 -0.121223 -3.29865 - 17 0.00000 -0.121223 -3.29865 - 18 0.00000 -0.115839 -3.15215 - 19 0.00000 0.075426 2.05244 - 20 0.00000 0.075426 2.05244 - - What follows are estimated values for band gap, HOMO, LUMO, etc. - | They are estimated on a discrete k-point grid and not necessarily exact. - | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. - - Highest occupied state (VBM) at -6.02649044 eV (relative to internal zero) - | Occupation number: 2.00000000 - | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - - Lowest unoccupied state (CBM) at -4.97745287 eV (relative to internal zero) - | Occupation number: 0.00000000 - | K-point: 6 at 0.500000 0.000000 0.500000 (in units of recip. lattice) - - ESTIMATED overall HOMO-LUMO gap: 1.04903757 eV between HOMO at k-point 1 and LUMO at k-point 6 - | This appears to be an indirect band gap. - | Smallest direct gap : 2.62049196 eV for k_point 3 at 0.000000 0.500000 0.000000 (in units of recip. lattice) - The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, - this system is most likely an insulator or a semiconductor. - - Total energy components: - | Sum of eigenvalues : -329.04311153 Ha -8953.71862494 eV - | XC energy correction : -41.70627212 Ha -1134.88540669 eV - | XC potential correction : 53.86059820 Ha 1465.62144695 eV - | Free-atom electrostatic energy: -263.69998542 Ha -7175.64169592 eV - | Hartree energy correction : -0.06595607 Ha -1.79475600 eV - | Entropy correction : 0.00000000 Ha 0.00000000 eV - | --------------------------- - | Total energy : -580.65472694 Ha -15800.41903659 eV - | Total energy, T -> 0 : -580.65472694 Ha -15800.41903659 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -580.65472694 Ha -15800.41903659 eV - - Derived energy quantities: - | Kinetic energy : 582.35664842 Ha 15846.73067623 eV - | Electrostatic energy : -1121.30510324 Ha -30512.26430613 eV - | Energy correction for multipole - | error in Hartree potential : 0.00092076 Ha 0.02505523 eV - | Sum of eigenvalues per atom : -4476.85931247 eV - | Total energy (T->0) per atom : -7900.20951830 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -7900.20951830 eV - Evaluating new KS density using the density matrix - Evaluating density matrix - Time summed over all CPUs for getting density from density matrix: real work 0.878 s, elapsed 0.878 s - Integration grid: deviation in total charge ( - N_e) = 5.684342E-14 - - Self-consistency convergence accuracy: - | Change of charge density : 0.1472E+00 - | Change of sum of eigenvalues : 0.1788E+01 eV - | Change of total energy : 0.2984E-01 eV - - ------------------------------------------------------------- - End self-consistency iteration # 1 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 1.820 s 1.831 s - | Charge density update : 0.873 s 0.879 s - | Density mixing & preconditioning : 0.180 s 0.181 s - | Hartree multipole update : 0.001 s 0.001 s - | Hartree multipole summation : 0.329 s 0.332 s - | Integration : 0.431 s 0.433 s - | Solution of K.-S. eqns. : 0.005 s 0.005 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 1.537 MB (on task 0) - | Maximum: 1.537 MB (on task 0) - | Average: 1.537 MB - | Peak value for overall tracked memory usage: - | Minimum: 7.765 MB (on task 0 after allocating gradient_basis_wave) - | Maximum: 7.765 MB (on task 0 after allocating gradient_basis_wave) - | Average: 7.765 MB - | Largest tracked array allocation so far: - | Minimum: 3.456 MB (hamiltonian_shell on task 0) - | Maximum: 3.456 MB (hamiltonian_shell on task 0) - | Average: 3.456 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - ------------------------------------------------------------- - Begin self-consistency iteration # 2 - - Date : 20230628, Time : 104126.977 ------------------------------------------------------------- - Pulay mixing of updated and previous charge densities. - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 28.0000000000 - | Integrated number of electrons on 3D grid : 27.9958223750 - | Charge integration error : -0.0041776250 - | Normalization factor for density and gradient : 1.0001492232 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = 0.248636E-12 - | Sum of charges compensated after spline to logarithmic grids = -0.103125E-03 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = 0.000000E+00 - Summing up the Hartree potential. - Time summed over all CPUs for potential: real work 0.392 s, elapsed 0.392 s - | RMS charge density error from multipole expansion : 0.131324E-01 - | Average real-space part of the electrostatic potential : 0.51574400 eV - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.432 s, elapsed 0.432 s - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.000 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -4.86564087 eV - What follows are estimated values for band gap, HOMO, LUMO, etc. - | They are estimated on a discrete k-point grid and not necessarily exact. - | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. - - Highest occupied state (VBM) at -5.26885362 eV (relative to internal zero) - | Occupation number: 2.00000000 - | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - - Lowest unoccupied state (CBM) at -4.61373730 eV (relative to internal zero) - | Occupation number: 0.00000000 - | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) - - ESTIMATED overall HOMO-LUMO gap: 0.65511632 eV between HOMO at k-point 1 and LUMO at k-point 4 - | This appears to be an indirect band gap. - | Smallest direct gap : 2.43194692 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, - this system is most likely an insulator or a semiconductor. - - Checking to see if s.c.f. parameters should be adjusted. - The system likely has a gap. Increased the default Pulay mixing parameter (charge_mix_param). Value: 0.200000 . - Kept the default occupation width. Value: 0.010000 eV. - - Total energy components: - | Sum of eigenvalues : -327.86163892 Ha -8921.56911953 eV - | XC energy correction : -41.81168620 Ha -1137.75386970 eV - | XC potential correction : 53.99474106 Ha 1469.27165986 eV - | Free-atom electrostatic energy: -263.69998542 Ha -7175.64169592 eV - | Hartree energy correction : -1.26787332 Ha -34.50058828 eV - | Entropy correction : -0.00000000 Ha -0.00000000 eV - | --------------------------- - | Total energy : -580.64644280 Ha -15800.19361357 eV - | Total energy, T -> 0 : -580.64644280 Ha -15800.19361357 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -580.64644280 Ha -15800.19361357 eV - - Derived energy quantities: - | Kinetic energy : 582.68623392 Ha 15855.69915398 eV - | Electrostatic energy : -1121.52099052 Ha -30518.13889784 eV - | Energy correction for multipole - | error in Hartree potential : 0.01752068 Ha 0.47676194 eV - | Sum of eigenvalues per atom : -4460.78455977 eV - | Total energy (T->0) per atom : -7900.09680678 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -7900.09680678 eV - Evaluating new KS density using the density matrix - Evaluating density matrix - Time summed over all CPUs for getting density from density matrix: real work 0.878 s, elapsed 0.878 s - Integration grid: deviation in total charge ( - N_e) = 1.065814E-13 - - Self-consistency convergence accuracy: - | Change of charge density : 0.1397E+00 - | Change of sum of eigenvalues : 0.3215E+02 eV - | Change of total energy : 0.2254E+00 eV - - ------------------------------------------------------------- - End self-consistency iteration # 2 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 1.879 s 1.891 s - | Charge density update : 0.874 s 0.880 s - | Density mixing & preconditioning : 0.178 s 0.179 s - | Hartree multipole update : 0.001 s 0.001 s - | Hartree multipole summation : 0.392 s 0.394 s - | Integration : 0.430 s 0.433 s - | Solution of K.-S. eqns. : 0.005 s 0.004 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 1.537 MB (on task 0) - | Maximum: 1.537 MB (on task 0) - | Average: 1.537 MB - | Peak value for overall tracked memory usage: - | Minimum: 7.766 MB (on task 0 after allocating gradient_basis_wave) - | Maximum: 7.766 MB (on task 0 after allocating gradient_basis_wave) - | Average: 7.766 MB - | Largest tracked array allocation so far: - | Minimum: 3.456 MB (hamiltonian_shell on task 0) - | Maximum: 3.456 MB (hamiltonian_shell on task 0) - | Average: 3.456 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - ------------------------------------------------------------- - Begin self-consistency iteration # 3 - - Date : 20230628, Time : 104128.868 ------------------------------------------------------------- - Pulay mixing of updated and previous charge densities. - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 28.0000000000 - | Integrated number of electrons on 3D grid : 27.9993663856 - | Charge integration error : -0.0006336144 - | Normalization factor for density and gradient : 1.0000226296 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = -0.386371E-13 - | Sum of charges compensated after spline to logarithmic grids = -0.111544E-03 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = 0.000000E+00 - Summing up the Hartree potential. - Time summed over all CPUs for potential: real work 0.392 s, elapsed 0.392 s - | RMS charge density error from multipole expansion : 0.138367E-01 - | Average real-space part of the electrostatic potential : 0.50527974 eV - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.432 s, elapsed 0.433 s - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.000 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -4.88620788 eV - What follows are estimated values for band gap, HOMO, LUMO, etc. - | They are estimated on a discrete k-point grid and not necessarily exact. - | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. - - Highest occupied state (VBM) at -5.29937334 eV (relative to internal zero) - | Occupation number: 2.00000000 - | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - - Lowest unoccupied state (CBM) at -4.61132158 eV (relative to internal zero) - | Occupation number: 0.00000000 - | K-point: 6 at 0.500000 0.000000 0.500000 (in units of recip. lattice) - - ESTIMATED overall HOMO-LUMO gap: 0.68805176 eV between HOMO at k-point 1 and LUMO at k-point 6 - | This appears to be an indirect band gap. - | Smallest direct gap : 2.43473574 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, - this system is most likely an insulator or a semiconductor. - - Total energy components: - | Sum of eigenvalues : -328.00561270 Ha -8925.48684534 eV - | XC energy correction : -41.79877840 Ha -1137.40263057 eV - | XC potential correction : 53.97806660 Ha 1468.81792492 eV - | Free-atom electrostatic energy: -263.69998542 Ha -7175.64169592 eV - | Hartree energy correction : -1.12001652 Ha -30.47720020 eV - | Entropy correction : 0.00000000 Ha 0.00000000 eV - | --------------------------- - | Total energy : -580.64632643 Ha -15800.19044711 eV - | Total energy, T -> 0 : -580.64632643 Ha -15800.19044711 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -580.64632643 Ha -15800.19044711 eV - - Derived energy quantities: - | Kinetic energy : 582.50125777 Ha 15850.66569691 eV - | Electrostatic energy : -1121.34880581 Ha -30513.45351345 eV - | Energy correction for multipole - | error in Hartree potential : 0.01868691 Ha 0.50849666 eV - | Sum of eigenvalues per atom : -4462.74342267 eV - | Total energy (T->0) per atom : -7900.09522355 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -7900.09522355 eV - Evaluating new KS density using the density matrix - Evaluating density matrix - Time summed over all CPUs for getting density from density matrix: real work 0.877 s, elapsed 0.877 s - Integration grid: deviation in total charge ( - N_e) = 2.842171E-14 - - Self-consistency convergence accuracy: - | Change of charge density : 0.2064E-01 - | Change of sum of eigenvalues : -0.3918E+01 eV - | Change of total energy : 0.3166E-02 eV - - ------------------------------------------------------------- - End self-consistency iteration # 3 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 1.881 s 1.893 s - | Charge density update : 0.872 s 0.879 s - | Density mixing & preconditioning : 0.181 s 0.181 s - | Hartree multipole update : 0.001 s 0.001 s - | Hartree multipole summation : 0.392 s 0.394 s - | Integration : 0.430 s 0.433 s - | Solution of K.-S. eqns. : 0.005 s 0.005 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 1.538 MB (on task 0) - | Maximum: 1.538 MB (on task 0) - | Average: 1.538 MB - | Peak value for overall tracked memory usage: - | Minimum: 7.766 MB (on task 0 after allocating gradient_basis_wave) - | Maximum: 7.766 MB (on task 0 after allocating gradient_basis_wave) - | Average: 7.766 MB - | Largest tracked array allocation so far: - | Minimum: 3.456 MB (hamiltonian_shell on task 0) - | Maximum: 3.456 MB (hamiltonian_shell on task 0) - | Average: 3.456 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - ------------------------------------------------------------- - Begin self-consistency iteration # 4 - - Date : 20230628, Time : 104130.761 ------------------------------------------------------------- - Pulay mixing of updated and previous charge densities. - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 28.0000000000 - | Integrated number of electrons on 3D grid : 27.9993017485 - | Charge integration error : -0.0006982515 - | Normalization factor for density and gradient : 1.0000249382 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = 0.127016E-12 - | Sum of charges compensated after spline to logarithmic grids = -0.124177E-03 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = 0.000000E+00 - Summing up the Hartree potential. - Time summed over all CPUs for potential: real work 0.394 s, elapsed 0.394 s - | RMS charge density error from multipole expansion : 0.151234E-01 - | Average real-space part of the electrostatic potential : 0.51490697 eV - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.432 s, elapsed 0.432 s - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.001 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.000 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -4.87204434 eV - What follows are estimated values for band gap, HOMO, LUMO, etc. - | They are estimated on a discrete k-point grid and not necessarily exact. - | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. - - Highest occupied state (VBM) at -5.29286016 eV (relative to internal zero) - | Occupation number: 2.00000000 - | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - - Lowest unoccupied state (CBM) at -4.58355519 eV (relative to internal zero) - | Occupation number: 0.00000000 - | K-point: 7 at 0.500000 0.500000 0.000000 (in units of recip. lattice) - - ESTIMATED overall HOMO-LUMO gap: 0.70930496 eV between HOMO at k-point 1 and LUMO at k-point 7 - | This appears to be an indirect band gap. - | Smallest direct gap : 2.42480865 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, - this system is most likely an insulator or a semiconductor. - - Total energy components: - | Sum of eigenvalues : -328.10105415 Ha -8928.08393921 eV - | XC energy correction : -41.79191602 Ha -1137.21589584 eV - | XC potential correction : 53.96893080 Ha 1468.56932705 eV - | Free-atom electrostatic energy: -263.69998542 Ha -7175.64169592 eV - | Hartree energy correction : -1.02214339 Ha -27.81393683 eV - | Entropy correction : 0.00000000 Ha 0.00000000 eV - | --------------------------- - | Total energy : -580.64616818 Ha -15800.18614075 eV - | Total energy, T -> 0 : -580.64616818 Ha -15800.18614075 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -580.64616818 Ha -15800.18614075 eV - - Derived energy quantities: - | Kinetic energy : 582.32598076 Ha 15845.89616684 eV - | Electrostatic energy : -1121.18023292 Ha -30508.86641175 eV - | Energy correction for multipole - | error in Hartree potential : 0.02061469 Ha 0.56095417 eV - | Sum of eigenvalues per atom : -4464.04196961 eV - | Total energy (T->0) per atom : -7900.09307038 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -7900.09307038 eV - Evaluating new KS density using the density matrix - Evaluating density matrix - Time summed over all CPUs for getting density from density matrix: real work 0.878 s, elapsed 0.878 s - Integration grid: deviation in total charge ( - N_e) = 5.684342E-14 - - Self-consistency convergence accuracy: - | Change of charge density : 0.1231E-01 - | Change of sum of eigenvalues : -0.2597E+01 eV - | Change of total energy : 0.4306E-02 eV - - ------------------------------------------------------------- - End self-consistency iteration # 4 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 1.881 s 1.892 s - | Charge density update : 0.874 s 0.879 s - | Density mixing & preconditioning : 0.178 s 0.179 s - | Hartree multipole update : 0.001 s 0.001 s - | Hartree multipole summation : 0.394 s 0.396 s - | Integration : 0.430 s 0.432 s - | Solution of K.-S. eqns. : 0.005 s 0.005 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 1.538 MB (on task 0) - | Maximum: 1.538 MB (on task 0) - | Average: 1.538 MB - | Peak value for overall tracked memory usage: - | Minimum: 7.766 MB (on task 0 after allocating gradient_basis_wave) - | Maximum: 7.766 MB (on task 0 after allocating gradient_basis_wave) - | Average: 7.766 MB - | Largest tracked array allocation so far: - | Minimum: 3.456 MB (hamiltonian_shell on task 0) - | Maximum: 3.456 MB (hamiltonian_shell on task 0) - | Average: 3.456 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - ------------------------------------------------------------- - Begin self-consistency iteration # 5 - - Date : 20230628, Time : 104132.653 ------------------------------------------------------------- - Pulay mixing of updated and previous charge densities. - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 28.0000000000 - | Integrated number of electrons on 3D grid : 28.0007654108 - | Charge integration error : 0.0007654108 - | Normalization factor for density and gradient : 0.9999726646 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = 0.113849E-12 - | Sum of charges compensated after spline to logarithmic grids = -0.121847E-03 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = 0.000000E+00 - Summing up the Hartree potential. - Time summed over all CPUs for potential: real work 0.392 s, elapsed 0.392 s - | RMS charge density error from multipole expansion : 0.150727E-01 - | Average real-space part of the electrostatic potential : 0.49589346 eV - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.432 s, elapsed 0.432 s - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.000 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -4.88328636 eV - What follows are estimated values for band gap, HOMO, LUMO, etc. - | They are estimated on a discrete k-point grid and not necessarily exact. - | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. - - Highest occupied state (VBM) at -5.30466705 eV (relative to internal zero) - | Occupation number: 2.00000000 - | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - - Lowest unoccupied state (CBM) at -4.59249490 eV (relative to internal zero) - | Occupation number: 0.00000000 - | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) - - ESTIMATED overall HOMO-LUMO gap: 0.71217215 eV between HOMO at k-point 1 and LUMO at k-point 4 - | This appears to be an indirect band gap. - | Smallest direct gap : 2.42925330 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, - this system is most likely an insulator or a semiconductor. - - Total energy components: - | Sum of eigenvalues : -328.15577741 Ha -8929.57303500 eV - | XC energy correction : -41.78965399 Ha -1137.15434277 eV - | XC potential correction : 53.96575153 Ha 1468.48281475 eV - | Free-atom electrostatic energy: -263.69998542 Ha -7175.64169592 eV - | Hartree energy correction : -0.96645644 Ha -26.29861771 eV - | Entropy correction : 0.00000000 Ha 0.00000000 eV - | --------------------------- - | Total energy : -580.64612172 Ha -15800.18487664 eV - | Total energy, T -> 0 : -580.64612172 Ha -15800.18487664 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -580.64612172 Ha -15800.18487664 eV - - Derived energy quantities: - | Kinetic energy : 582.29516914 Ha 15845.05773999 eV - | Electrostatic energy : -1121.15163688 Ha -30508.08827387 eV - | Energy correction for multipole - | error in Hartree potential : 0.02040284 Ha 0.55518946 eV - | Sum of eigenvalues per atom : -4464.78651750 eV - | Total energy (T->0) per atom : -7900.09243832 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -7900.09243832 eV - Evaluating new KS density using the density matrix - Evaluating density matrix - Time summed over all CPUs for getting density from density matrix: real work 0.878 s, elapsed 0.878 s - Integration grid: deviation in total charge ( - N_e) = 5.329071E-14 - - Self-consistency convergence accuracy: - | Change of charge density : 0.3697E-02 - | Change of sum of eigenvalues : -0.1489E+01 eV - | Change of total energy : 0.1264E-02 eV - - ------------------------------------------------------------- - End self-consistency iteration # 5 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 1.880 s 1.892 s - | Charge density update : 0.874 s 0.880 s - | Density mixing & preconditioning : 0.178 s 0.179 s - | Hartree multipole update : 0.001 s 0.001 s - | Hartree multipole summation : 0.393 s 0.395 s - | Integration : 0.430 s 0.432 s - | Solution of K.-S. eqns. : 0.005 s 0.005 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 1.538 MB (on task 0) - | Maximum: 1.538 MB (on task 0) - | Average: 1.538 MB - | Peak value for overall tracked memory usage: - | Minimum: 7.766 MB (on task 0 after allocating gradient_basis_wave) - | Maximum: 7.766 MB (on task 0 after allocating gradient_basis_wave) - | Average: 7.766 MB - | Largest tracked array allocation so far: - | Minimum: 3.456 MB (hamiltonian_shell on task 0) - | Maximum: 3.456 MB (hamiltonian_shell on task 0) - | Average: 3.456 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - ------------------------------------------------------------- - Begin self-consistency iteration # 6 - - Date : 20230628, Time : 104134.545 ------------------------------------------------------------- - Pulay mixing of updated and previous charge densities. - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 28.0000000000 - | Integrated number of electrons on 3D grid : 28.0001271580 - | Charge integration error : 0.0001271580 - | Normalization factor for density and gradient : 0.9999954587 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = 0.170005E-12 - | Sum of charges compensated after spline to logarithmic grids = -0.121146E-03 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = 0.000000E+00 - Summing up the Hartree potential. - Time summed over all CPUs for potential: real work 0.392 s, elapsed 0.392 s - | RMS charge density error from multipole expansion : 0.149973E-01 - | Average real-space part of the electrostatic potential : 0.48838703 eV - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.432 s, elapsed 0.432 s - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.001 s - Finished solving standard eigenproblem - | Time : 0.000 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -4.89304867 eV - What follows are estimated values for band gap, HOMO, LUMO, etc. - | They are estimated on a discrete k-point grid and not necessarily exact. - | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. - - Highest occupied state (VBM) at -5.31568837 eV (relative to internal zero) - | Occupation number: 2.00000000 - | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - - Lowest unoccupied state (CBM) at -4.59826078 eV (relative to internal zero) - | Occupation number: 0.00000000 - | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) - - ESTIMATED overall HOMO-LUMO gap: 0.71742759 eV between HOMO at k-point 1 and LUMO at k-point 4 - | This appears to be an indirect band gap. - | Smallest direct gap : 2.43284984 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, - this system is most likely an insulator or a semiconductor. - - Total energy components: - | Sum of eigenvalues : -328.17991453 Ha -8930.22983952 eV - | XC energy correction : -41.78779479 Ha -1137.10375136 eV - | XC potential correction : 53.96336410 Ha 1468.41784950 eV - | Free-atom electrostatic energy: -263.69998542 Ha -7175.64169592 eV - | Hartree energy correction : -0.94177100 Ha -25.62689267 eV - | Entropy correction : 0.00000000 Ha 0.00000000 eV - | --------------------------- - | Total energy : -580.64610163 Ha -15800.18432997 eV - | Total energy, T -> 0 : -580.64610163 Ha -15800.18432997 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -580.64610163 Ha -15800.18432997 eV - - Derived energy quantities: - | Kinetic energy : 582.28772081 Ha 15844.85506064 eV - | Electrostatic energy : -1121.14602766 Ha -30507.93563924 eV - | Energy correction for multipole - | error in Hartree potential : 0.02029783 Ha 0.55233193 eV - | Sum of eigenvalues per atom : -4465.11491976 eV - | Total energy (T->0) per atom : -7900.09216498 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -7900.09216498 eV - Evaluating new KS density using the density matrix - Evaluating density matrix - Time summed over all CPUs for getting density from density matrix: real work 0.878 s, elapsed 0.878 s - Integration grid: deviation in total charge ( - N_e) = -5.684342E-14 - - Self-consistency convergence accuracy: - | Change of charge density : 0.1082E-02 - | Change of sum of eigenvalues : -0.6568E+00 eV - | Change of total energy : 0.5467E-03 eV - - ------------------------------------------------------------- - End self-consistency iteration # 6 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 1.880 s 1.891 s - | Charge density update : 0.873 s 0.879 s - | Density mixing & preconditioning : 0.178 s 0.179 s - | Hartree multipole update : 0.001 s 0.001 s - | Hartree multipole summation : 0.392 s 0.394 s - | Integration : 0.430 s 0.433 s - | Solution of K.-S. eqns. : 0.005 s 0.005 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 1.538 MB (on task 0) - | Maximum: 1.538 MB (on task 0) - | Average: 1.538 MB - | Peak value for overall tracked memory usage: - | Minimum: 7.766 MB (on task 0 after allocating gradient_basis_wave) - | Maximum: 7.766 MB (on task 0 after allocating gradient_basis_wave) - | Average: 7.766 MB - | Largest tracked array allocation so far: - | Minimum: 3.456 MB (hamiltonian_shell on task 0) - | Maximum: 3.456 MB (hamiltonian_shell on task 0) - | Average: 3.456 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - ------------------------------------------------------------- - Begin self-consistency iteration # 7 - - Date : 20230628, Time : 104136.436 ------------------------------------------------------------- - Pulay mixing of updated and previous charge densities. - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 28.0000000000 - | Integrated number of electrons on 3D grid : 27.9999503327 - | Charge integration error : -0.0000496673 - | Normalization factor for density and gradient : 1.0000017738 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = 0.874785E-13 - | Sum of charges compensated after spline to logarithmic grids = -0.122079E-03 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = 0.000000E+00 - Summing up the Hartree potential. - Time summed over all CPUs for potential: real work 0.392 s, elapsed 0.392 s - | RMS charge density error from multipole expansion : 0.151009E-01 - | Average real-space part of the electrostatic potential : 0.49319331 eV - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.433 s, elapsed 0.433 s - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.000 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -4.88720335 eV - What follows are estimated values for band gap, HOMO, LUMO, etc. - | They are estimated on a discrete k-point grid and not necessarily exact. - | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. - - Highest occupied state (VBM) at -5.30957832 eV (relative to internal zero) - | Occupation number: 2.00000000 - | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - - Lowest unoccupied state (CBM) at -4.59363164 eV (relative to internal zero) - | Occupation number: 0.00000000 - | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) - - ESTIMATED overall HOMO-LUMO gap: 0.71594668 eV between HOMO at k-point 1 and LUMO at k-point 4 - | This appears to be an indirect band gap. - | Smallest direct gap : 2.43056833 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, - this system is most likely an insulator or a semiconductor. - - Total energy components: - | Sum of eigenvalues : -328.16539134 Ha -8929.83464325 eV - | XC energy correction : -41.78931786 Ha -1137.14519629 eV - | XC potential correction : 53.96533763 Ha 1468.47155192 eV - | Free-atom electrostatic energy: -263.69998542 Ha -7175.64169592 eV - | Hartree energy correction : -0.95674602 Ha -26.03438384 eV - | Entropy correction : 0.00000000 Ha 0.00000000 eV - | --------------------------- - | Total energy : -580.64610301 Ha -15800.18436738 eV - | Total energy, T -> 0 : -580.64610301 Ha -15800.18436738 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -580.64610301 Ha -15800.18436738 eV - - Derived energy quantities: - | Kinetic energy : 582.30449763 Ha 15845.31158105 eV - | Electrostatic energy : -1121.16128278 Ha -30508.35075214 eV - | Energy correction for multipole - | error in Hartree potential : 0.02045069 Ha 0.55649154 eV - | Sum of eigenvalues per atom : -4464.91732162 eV - | Total energy (T->0) per atom : -7900.09218369 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -7900.09218369 eV - Evaluating new KS density using the density matrix - Evaluating density matrix - Time summed over all CPUs for getting density from density matrix: real work 0.878 s, elapsed 0.878 s - Integration grid: deviation in total charge ( - N_e) = 0.000000E+00 - - Self-consistency convergence accuracy: - | Change of charge density : 0.9762E-03 - | Change of sum of eigenvalues : 0.3952E+00 eV - | Change of total energy : -0.3741E-04 eV - - ------------------------------------------------------------- - End self-consistency iteration # 7 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 1.881 s 1.893 s - | Charge density update : 0.874 s 0.880 s - | Density mixing & preconditioning : 0.178 s 0.179 s - | Hartree multipole update : 0.001 s 0.001 s - | Hartree multipole summation : 0.393 s 0.395 s - | Integration : 0.431 s 0.434 s - | Solution of K.-S. eqns. : 0.005 s 0.004 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 1.538 MB (on task 0) - | Maximum: 1.538 MB (on task 0) - | Average: 1.538 MB - | Peak value for overall tracked memory usage: - | Minimum: 7.766 MB (on task 0 after allocating gradient_basis_wave) - | Maximum: 7.766 MB (on task 0 after allocating gradient_basis_wave) - | Average: 7.766 MB - | Largest tracked array allocation so far: - | Minimum: 3.456 MB (hamiltonian_shell on task 0) - | Maximum: 3.456 MB (hamiltonian_shell on task 0) - | Average: 3.456 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - ------------------------------------------------------------- - Begin self-consistency iteration # 8 - - Date : 20230628, Time : 104138.329 ------------------------------------------------------------- - Pulay mixing of updated and previous charge densities. - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 28.0000000000 - | Integrated number of electrons on 3D grid : 27.9999822413 - | Charge integration error : -0.0000177587 - | Normalization factor for density and gradient : 1.0000006342 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = 0.311694E-12 - | Sum of charges compensated after spline to logarithmic grids = -0.122168E-03 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = 0.000000E+00 - Summing up the Hartree potential. - Time summed over all CPUs for potential: real work 0.393 s, elapsed 0.393 s - | RMS charge density error from multipole expansion : 0.151074E-01 - | Average real-space part of the electrostatic potential : 0.49358685 eV - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.432 s, elapsed 0.432 s - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.000 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -4.88678031 eV - What follows are estimated values for band gap, HOMO, LUMO, etc. - | They are estimated on a discrete k-point grid and not necessarily exact. - | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. - - Highest occupied state (VBM) at -5.30913777 eV (relative to internal zero) - | Occupation number: 2.00000000 - | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - - Lowest unoccupied state (CBM) at -4.59330002 eV (relative to internal zero) - | Occupation number: 0.00000000 - | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) - - ESTIMATED overall HOMO-LUMO gap: 0.71583774 eV between HOMO at k-point 1 and LUMO at k-point 4 - | This appears to be an indirect band gap. - | Smallest direct gap : 2.43040051 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, - this system is most likely an insulator or a semiconductor. - - Total energy components: - | Sum of eigenvalues : -328.16455080 Ha -8929.81177108 eV - | XC energy correction : -41.78939437 Ha -1137.14727826 eV - | XC potential correction : 53.96543501 Ha 1468.47420172 eV - | Free-atom electrostatic energy: -263.69998542 Ha -7175.64169592 eV - | Hartree energy correction : -0.95760741 Ha -26.05782341 eV - | Entropy correction : 0.00000000 Ha 0.00000000 eV - | --------------------------- - | Total energy : -580.64610299 Ha -15800.18436694 eV - | Total energy, T -> 0 : -580.64610299 Ha -15800.18436694 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -580.64610299 Ha -15800.18436694 eV - - Derived energy quantities: - | Kinetic energy : 582.30488896 Ha 15845.32222982 eV - | Electrostatic energy : -1121.16159758 Ha -30508.35931850 eV - | Energy correction for multipole - | error in Hartree potential : 0.02046340 Ha 0.55683750 eV - | Sum of eigenvalues per atom : -4464.90588554 eV - | Total energy (T->0) per atom : -7900.09218347 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -7900.09218347 eV - Evaluating new KS density using the density matrix - Evaluating density matrix - Time summed over all CPUs for getting density from density matrix: real work 0.881 s, elapsed 0.881 s - Integration grid: deviation in total charge ( - N_e) = -6.039613E-14 - - Self-consistency convergence accuracy: - | Change of charge density : 0.5217E-04 - | Change of sum of eigenvalues : 0.2287E-01 eV - | Change of total energy : 0.4390E-06 eV - - ------------------------------------------------------------- - End self-consistency iteration # 8 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 1.888 s 1.900 s - | Charge density update : 0.876 s 0.883 s - | Density mixing & preconditioning : 0.183 s 0.184 s - | Hartree multipole update : 0.001 s 0.001 s - | Hartree multipole summation : 0.393 s 0.395 s - | Integration : 0.430 s 0.433 s - | Solution of K.-S. eqns. : 0.005 s 0.004 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 1.538 MB (on task 0) - | Maximum: 1.538 MB (on task 0) - | Average: 1.538 MB - | Peak value for overall tracked memory usage: - | Minimum: 7.766 MB (on task 0 after allocating gradient_basis_wave) - | Maximum: 7.766 MB (on task 0 after allocating gradient_basis_wave) - | Average: 7.766 MB - | Largest tracked array allocation so far: - | Minimum: 3.456 MB (hamiltonian_shell on task 0) - | Maximum: 3.456 MB (hamiltonian_shell on task 0) - | Average: 3.456 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - ------------------------------------------------------------- - Begin self-consistency iteration # 9 - - Date : 20230628, Time : 104140.229 ------------------------------------------------------------- - Pulay mixing of updated and previous charge densities. - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 28.0000000000 - | Integrated number of electrons on 3D grid : 27.9999984129 - | Charge integration error : -0.0000015871 - | Normalization factor for density and gradient : 1.0000000567 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = 0.183238E-12 - | Sum of charges compensated after spline to logarithmic grids = -0.122152E-03 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = 0.000000E+00 - Summing up the Hartree potential. - Time summed over all CPUs for potential: real work 0.393 s, elapsed 0.393 s - | RMS charge density error from multipole expansion : 0.151052E-01 - | Average real-space part of the electrostatic potential : 0.49360086 eV - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.432 s, elapsed 0.432 s - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.000 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -4.88679696 eV - What follows are estimated values for band gap, HOMO, LUMO, etc. - | They are estimated on a discrete k-point grid and not necessarily exact. - | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. - - Highest occupied state (VBM) at -5.30914296 eV (relative to internal zero) - | Occupation number: 2.00000000 - | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - - Lowest unoccupied state (CBM) at -4.59333953 eV (relative to internal zero) - | Occupation number: 0.00000000 - | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) - - ESTIMATED overall HOMO-LUMO gap: 0.71580344 eV between HOMO at k-point 1 and LUMO at k-point 4 - | This appears to be an indirect band gap. - | Smallest direct gap : 2.43041245 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, - this system is most likely an insulator or a semiconductor. - - Total energy components: - | Sum of eigenvalues : -328.16438111 Ha -8929.80715350 eV - | XC energy correction : -41.78939735 Ha -1137.14735920 eV - | XC potential correction : 53.96543963 Ha 1468.47432741 eV - | Free-atom electrostatic energy: -263.69998542 Ha -7175.64169592 eV - | Hartree energy correction : -0.95777908 Ha -26.06249469 eV - | Entropy correction : 0.00000000 Ha 0.00000000 eV - | --------------------------- - | Total energy : -580.64610332 Ha -15800.18437589 eV - | Total energy, T -> 0 : -580.64610332 Ha -15800.18437589 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -580.64610332 Ha -15800.18437589 eV - - Derived energy quantities: - | Kinetic energy : 582.30500669 Ha 15845.32543330 eV - | Electrostatic energy : -1121.16171266 Ha -30508.36245000 eV - | Energy correction for multipole - | error in Hartree potential : 0.02046055 Ha 0.55675977 eV - | Sum of eigenvalues per atom : -4464.90357675 eV - | Total energy (T->0) per atom : -7900.09218795 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -7900.09218795 eV - Evaluating new KS density using the density matrix - Evaluating density matrix - Time summed over all CPUs for getting density from density matrix: real work 0.878 s, elapsed 0.878 s - Integration grid: deviation in total charge ( - N_e) = -4.263256E-14 - - Self-consistency convergence accuracy: - | Change of charge density : 0.2570E-04 - | Change of sum of eigenvalues : 0.4618E-02 eV - | Change of total energy : -0.8952E-05 eV - - ------------------------------------------------------------- - End self-consistency iteration # 9 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 1.880 s 1.891 s - | Charge density update : 0.873 s 0.879 s - | Density mixing & preconditioning : 0.178 s 0.178 s - | Hartree multipole update : 0.001 s 0.001 s - | Hartree multipole summation : 0.393 s 0.395 s - | Integration : 0.430 s 0.433 s - | Solution of K.-S. eqns. : 0.005 s 0.005 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 1.538 MB (on task 0) - | Maximum: 1.538 MB (on task 0) - | Average: 1.538 MB - | Peak value for overall tracked memory usage: - | Minimum: 7.766 MB (on task 0 after allocating gradient_basis_wave) - | Maximum: 7.766 MB (on task 0 after allocating gradient_basis_wave) - | Average: 7.766 MB - | Largest tracked array allocation so far: - | Minimum: 3.456 MB (hamiltonian_shell on task 0) - | Maximum: 3.456 MB (hamiltonian_shell on task 0) - | Average: 3.456 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - ------------------------------------------------------------- - Begin self-consistency iteration # 10 - - Date : 20230628, Time : 104142.120 ------------------------------------------------------------- - Pulay mixing of updated and previous charge densities. - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 28.0000000000 - | Integrated number of electrons on 3D grid : 27.9999978066 - | Charge integration error : -0.0000021934 - | Normalization factor for density and gradient : 1.0000000783 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = 0.194108E-12 - | Sum of charges compensated after spline to logarithmic grids = -0.122150E-03 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = 0.000000E+00 - Summing up the Hartree potential. - Time summed over all CPUs for potential: real work 0.393 s, elapsed 0.393 s - | RMS charge density error from multipole expansion : 0.151049E-01 - | Average real-space part of the electrostatic potential : 0.49364677 eV - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.432 s, elapsed 0.432 s - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.000 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -4.88676148 eV - What follows are estimated values for band gap, HOMO, LUMO, etc. - | They are estimated on a discrete k-point grid and not necessarily exact. - | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. - - Highest occupied state (VBM) at -5.30910305 eV (relative to internal zero) - | Occupation number: 2.00000000 - | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - - Lowest unoccupied state (CBM) at -4.59332232 eV (relative to internal zero) - | Occupation number: 0.00000000 - | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) - - ESTIMATED overall HOMO-LUMO gap: 0.71578073 eV between HOMO at k-point 1 and LUMO at k-point 4 - | This appears to be an indirect band gap. - | Smallest direct gap : 2.43040185 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, - this system is most likely an insulator or a semiconductor. - - Total energy components: - | Sum of eigenvalues : -328.16424229 Ha -8929.80337620 eV - | XC energy correction : -41.78940489 Ha -1137.14756448 eV - | XC potential correction : 53.96544959 Ha 1468.47459850 eV - | Free-atom electrostatic energy: -263.69998542 Ha -7175.64169592 eV - | Hartree energy correction : -0.95792043 Ha -26.06634104 eV - | Entropy correction : 0.00000000 Ha 0.00000000 eV - | --------------------------- - | Total energy : -580.64610344 Ha -15800.18437914 eV - | Total energy, T -> 0 : -580.64610344 Ha -15800.18437914 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -580.64610344 Ha -15800.18437914 eV - - Derived energy quantities: - | Kinetic energy : 582.30510406 Ha 15845.32808287 eV - | Electrostatic energy : -1121.16180261 Ha -30508.36489753 eV - | Energy correction for multipole - | error in Hartree potential : 0.02046059 Ha 0.55676111 eV - | Sum of eigenvalues per atom : -4464.90168810 eV - | Total energy (T->0) per atom : -7900.09218957 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -7900.09218957 eV - Evaluating new KS density using the density matrix - Evaluating density matrix - Time summed over all CPUs for getting density from density matrix: real work 0.879 s, elapsed 0.879 s - Integration grid: deviation in total charge ( - N_e) = -2.842171E-14 - - Self-consistency convergence accuracy: - | Change of charge density : 0.8655E-05 - | Change of sum of eigenvalues : 0.3777E-02 eV - | Change of total energy : -0.3241E-05 eV - - ------------------------------------------------------------- - End self-consistency iteration # 10 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 1.880 s 1.892 s - | Charge density update : 0.874 s 0.880 s - | Density mixing & preconditioning : 0.177 s 0.178 s - | Hartree multipole update : 0.001 s 0.002 s - | Hartree multipole summation : 0.393 s 0.394 s - | Integration : 0.430 s 0.432 s - | Solution of K.-S. eqns. : 0.005 s 0.004 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 1.538 MB (on task 0) - | Maximum: 1.538 MB (on task 0) - | Average: 1.538 MB - | Peak value for overall tracked memory usage: - | Minimum: 7.766 MB (on task 0 after allocating gradient_basis_wave) - | Maximum: 7.766 MB (on task 0 after allocating gradient_basis_wave) - | Average: 7.766 MB - | Largest tracked array allocation so far: - | Minimum: 3.456 MB (hamiltonian_shell on task 0) - | Maximum: 3.456 MB (hamiltonian_shell on task 0) - | Average: 3.456 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - ------------------------------------------------------------- - Begin self-consistency iteration # 11 - - Date : 20230628, Time : 104144.012 ------------------------------------------------------------- - Pulay mixing of updated and previous charge densities. - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 28.0000000000 - | Integrated number of electrons on 3D grid : 27.9999998400 - | Charge integration error : -0.0000001600 - | Normalization factor for density and gradient : 1.0000000057 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = 0.336367E-12 - | Sum of charges compensated after spline to logarithmic grids = -0.122151E-03 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = 0.000000E+00 - Summing up the Hartree potential. - Time summed over all CPUs for potential: real work 0.393 s, elapsed 0.393 s - | RMS charge density error from multipole expansion : 0.151050E-01 - | Average real-space part of the electrostatic potential : 0.49365281 eV - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.432 s, elapsed 0.432 s - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.000 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -4.88675747 eV - What follows are estimated values for band gap, HOMO, LUMO, etc. - | They are estimated on a discrete k-point grid and not necessarily exact. - | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. - - Highest occupied state (VBM) at -5.30909890 eV (relative to internal zero) - | Occupation number: 2.00000000 - | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - - Lowest unoccupied state (CBM) at -4.59331868 eV (relative to internal zero) - | Occupation number: 0.00000000 - | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) - - ESTIMATED overall HOMO-LUMO gap: 0.71578022 eV between HOMO at k-point 1 and LUMO at k-point 4 - | This appears to be an indirect band gap. - | Smallest direct gap : 2.43039979 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, - this system is most likely an insulator or a semiconductor. - - Total energy components: - | Sum of eigenvalues : -328.16422868 Ha -8929.80300586 eV - | XC energy correction : -41.78940590 Ha -1137.14759207 eV - | XC potential correction : 53.96545094 Ha 1468.47463513 eV - | Free-atom electrostatic energy: -263.69998542 Ha -7175.64169592 eV - | Hartree energy correction : -0.95793437 Ha -26.06672043 eV - | Entropy correction : 0.00000000 Ha 0.00000000 eV - | --------------------------- - | Total energy : -580.64610344 Ha -15800.18437915 eV - | Total energy, T -> 0 : -580.64610344 Ha -15800.18437915 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -580.64610344 Ha -15800.18437915 eV - - Derived energy quantities: - | Kinetic energy : 582.30511413 Ha 15845.32835703 eV - | Electrostatic energy : -1121.16181167 Ha -30508.36514411 eV - | Energy correction for multipole - | error in Hartree potential : 0.02046076 Ha 0.55676574 eV - | Sum of eigenvalues per atom : -4464.90150293 eV - | Total energy (T->0) per atom : -7900.09218958 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -7900.09218958 eV - Evaluating new KS density using the density matrix - Evaluating density matrix - Time summed over all CPUs for getting density from density matrix: real work 0.878 s, elapsed 0.878 s - Integration grid: deviation in total charge ( - N_e) = -3.552714E-14 - - Self-consistency convergence accuracy: - | Change of charge density : 0.6808E-06 - | Change of sum of eigenvalues : 0.3703E-03 eV - | Change of total energy : -0.1404E-07 eV - - ------------------------------------------------------------- - End self-consistency iteration # 11 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 1.881 s 1.892 s - | Charge density update : 0.874 s 0.880 s - | Density mixing & preconditioning : 0.177 s 0.178 s - | Hartree multipole update : 0.001 s 0.002 s - | Hartree multipole summation : 0.393 s 0.395 s - | Integration : 0.430 s 0.433 s - | Solution of K.-S. eqns. : 0.005 s 0.004 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 1.538 MB (on task 0) - | Maximum: 1.538 MB (on task 0) - | Average: 1.538 MB - | Peak value for overall tracked memory usage: - | Minimum: 7.766 MB (on task 0 after allocating gradient_basis_wave) - | Maximum: 7.766 MB (on task 0 after allocating gradient_basis_wave) - | Average: 7.766 MB - | Largest tracked array allocation so far: - | Minimum: 3.456 MB (hamiltonian_shell on task 0) - | Maximum: 3.456 MB (hamiltonian_shell on task 0) - | Average: 3.456 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - ------------------------------------------------------------- - Begin self-consistency iteration # 12 - - Date : 20230628, Time : 104145.904 ------------------------------------------------------------- - Pulay mixing of updated and previous charge densities. - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 28.0000000000 - | Integrated number of electrons on 3D grid : 28.0000000145 - | Charge integration error : 0.0000000145 - | Normalization factor for density and gradient : 0.9999999995 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = 0.273819E-12 - | Sum of charges compensated after spline to logarithmic grids = -0.122151E-03 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = 0.000000E+00 - Summing up the Hartree potential. - Time summed over all CPUs for potential: real work 0.393 s, elapsed 0.393 s - | RMS charge density error from multipole expansion : 0.151050E-01 - | Average real-space part of the electrostatic potential : 0.49365232 eV - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.432 s, elapsed 0.432 s - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.000 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -4.88675744 eV - What follows are estimated values for band gap, HOMO, LUMO, etc. - | They are estimated on a discrete k-point grid and not necessarily exact. - | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. - - Highest occupied state (VBM) at -5.30909879 eV (relative to internal zero) - | Occupation number: 2.00000000 - | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - - Lowest unoccupied state (CBM) at -4.59331890 eV (relative to internal zero) - | Occupation number: 0.00000000 - | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) - - ESTIMATED overall HOMO-LUMO gap: 0.71577988 eV between HOMO at k-point 1 and LUMO at k-point 4 - | This appears to be an indirect band gap. - | Smallest direct gap : 2.43039988 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, - this system is most likely an insulator or a semiconductor. - - Total energy components: - | Sum of eigenvalues : -328.16422901 Ha -8929.80301477 eV - | XC energy correction : -41.78940590 Ha -1137.14759207 eV - | XC potential correction : 53.96545093 Ha 1468.47463491 eV - | Free-atom electrostatic energy: -263.69998542 Ha -7175.64169592 eV - | Hartree energy correction : -0.95793403 Ha -26.06671134 eV - | Entropy correction : 0.00000000 Ha 0.00000000 eV - | --------------------------- - | Total energy : -580.64610344 Ha -15800.18437919 eV - | Total energy, T -> 0 : -580.64610344 Ha -15800.18437919 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -580.64610344 Ha -15800.18437919 eV - - Derived energy quantities: - | Kinetic energy : 582.30511376 Ha 15845.32834691 eV - | Electrostatic energy : -1121.16181130 Ha -30508.36513403 eV - | Energy correction for multipole - | error in Hartree potential : 0.02046074 Ha 0.55676512 eV - | Sum of eigenvalues per atom : -4464.90150738 eV - | Total energy (T->0) per atom : -7900.09218960 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -7900.09218960 eV - Preliminary charge convergence reached. Turning off preconditioner. - - Evaluating new KS density using the density matrix - Evaluating density matrix - Time summed over all CPUs for getting density from density matrix: real work 0.877 s, elapsed 0.877 s - Integration grid: deviation in total charge ( - N_e) = -1.350031E-13 - - Self-consistency convergence accuracy: - | Change of charge density : 0.1818E-06 - | Change of sum of eigenvalues : -0.8910E-05 eV - | Change of total energy : -0.4207E-07 eV - - Electronic self-consistency reached - switching on the force computation. - - Electronic self-consistency reached - switching on the analytical stress tensor computation. - - ------------------------------------------------------------- - End self-consistency iteration # 12 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 1.880 s 1.891 s - | Charge density & force component update : 0.873 s 0.879 s - | Density mixing : 0.178 s 0.178 s - | Hartree multipole update : 0.001 s 0.002 s - | Hartree multipole summation : 0.393 s 0.395 s - | Hartree pot. SCF incomplete forces : 0.000 s 0.000 s - | Integration : 0.430 s 0.432 s - | Solution of K.-S. eqns. : 0.005 s 0.005 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 1.538 MB (on task 0) - | Maximum: 1.538 MB (on task 0) - | Average: 1.538 MB - | Peak value for overall tracked memory usage: - | Minimum: 7.766 MB (on task 0 after allocating gradient_basis_wave) - | Maximum: 7.766 MB (on task 0 after allocating gradient_basis_wave) - | Average: 7.766 MB - | Largest tracked array allocation so far: - | Minimum: 3.456 MB (hamiltonian_shell on task 0) - | Maximum: 3.456 MB (hamiltonian_shell on task 0) - | Average: 3.456 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - ------------------------------------------------------------- - Begin self-consistency iteration # 13 - - Date : 20230628, Time : 104147.795 ------------------------------------------------------------- - Pulay mixing of updated and previous charge densities. - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 28.0000000000 - | Integrated number of electrons on 3D grid : 27.9999999788 - | Charge integration error : -0.0000000212 - | Normalization factor for density and gradient : 1.0000000008 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = 0.220709E-12 - | Sum of charges compensated after spline to logarithmic grids = -0.122151E-03 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = 0.000000E+00 - Summing up the Hartree potential. - Time summed over all CPUs for potential: real work 1.656 s, elapsed 1.656 s - | RMS charge density error from multipole expansion : 0.151050E-01 - | Average real-space part of the electrostatic potential : 0.49365270 eV - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.433 s, elapsed 0.433 s - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.000 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -4.88675710 eV - What follows are estimated values for band gap, HOMO, LUMO, etc. - | They are estimated on a discrete k-point grid and not necessarily exact. - | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. - - Highest occupied state (VBM) at -5.30909840 eV (relative to internal zero) - | Occupation number: 2.00000000 - | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - - Lowest unoccupied state (CBM) at -4.59331867 eV (relative to internal zero) - | Occupation number: 0.00000000 - | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) - - ESTIMATED overall HOMO-LUMO gap: 0.71577973 eV between HOMO at k-point 1 and LUMO at k-point 4 - | This appears to be an indirect band gap. - | Smallest direct gap : 2.43039973 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, - this system is most likely an insulator or a semiconductor. - - Total energy components: - | Sum of eigenvalues : -328.16422814 Ha -8929.80299115 eV - | XC energy correction : -41.78940596 Ha -1137.14759372 eV - | XC potential correction : 53.96545100 Ha 1468.47463700 eV - | Free-atom electrostatic energy: -263.69998542 Ha -7175.64169592 eV - | Hartree energy correction : -0.95793492 Ha -26.06673543 eV - | Entropy correction : 0.00000000 Ha 0.00000000 eV - | --------------------------- - | Total energy : -580.64610344 Ha -15800.18437921 eV - | Total energy, T -> 0 : -580.64610344 Ha -15800.18437921 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -580.64610344 Ha -15800.18437921 eV - - Derived energy quantities: - | Kinetic energy : 582.30511417 Ha 15845.32835809 eV - | Electrostatic energy : -1121.16181165 Ha -30508.36514358 eV - | Energy correction for multipole - | error in Hartree potential : 0.02046075 Ha 0.55676534 eV - | Sum of eigenvalues per atom : -4464.90149557 eV - | Total energy (T->0) per atom : -7900.09218960 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -7900.09218960 eV - Evaluating new KS density using the density matrix - Evaluating density matrix - Time summed over all CPUs for getting density from density matrix: real work 0.878 s, elapsed 0.878 s - Integration grid: deviation in total charge ( - N_e) = 8.526513E-14 - - atomic forces [eV/Ang]: - ----------------------- - atom # 1 - Hellmann-Feynman : -0.301813E-11 0.151709E-10 -0.597160E-11 - Ionic forces : 0.000000E+00 0.000000E+00 0.000000E+00 - Multipole : -0.429915E-12 0.408843E-12 0.330797E-12 - Hartree pot. SCF incomplete : 0.774785E-11 -0.164390E-11 0.271242E-11 - Pulay + GGA : 0.000000E+00 0.000000E+00 0.000000E+00 - ---------------------------------------------------------------- - Total forces( 1) : 0.429981E-11 0.139359E-10 -0.292838E-11 - atom # 2 - Hellmann-Feynman : -0.321159E-08 -0.323502E-08 -0.271578E-08 - Ionic forces : 0.000000E+00 0.000000E+00 0.000000E+00 - Multipole : -0.381397E-12 0.994567E-13 -0.178339E-12 - Hartree pot. SCF incomplete : -0.132766E-10 -0.328139E-11 -0.147250E-10 - Pulay + GGA : 0.000000E+00 0.000000E+00 0.000000E+00 - ---------------------------------------------------------------- - Total forces( 2) : -0.322524E-08 -0.323820E-08 -0.273068E-08 - - - Self-consistency convergence accuracy: - | Change of charge density : 0.4358E-07 - | Change of sum of eigenvalues : 0.2362E-04 eV - | Change of total energy : -0.1724E-07 eV - | Change of forces : 0.3752E-08 eV/A - - ------------------------------------------------------------- - End self-consistency iteration # 13 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 3.905 s 3.926 s - | Charge density & force component update : 0.874 s 0.880 s - | Density mixing : 0.002 s 0.002 s - | Hartree multipole update : 0.001 s 0.001 s - | Hartree multipole summation : 1.652 s 1.660 s - | Hartree pot. SCF incomplete forces : 0.941 s 0.946 s - | Integration : 0.430 s 0.433 s - | Solution of K.-S. eqns. : 0.005 s 0.004 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 1.538 MB (on task 0) - | Maximum: 1.538 MB (on task 0) - | Average: 1.538 MB - | Peak value for overall tracked memory usage: - | Minimum: 7.766 MB (on task 0 after allocating gradient_basis_wave) - | Maximum: 7.766 MB (on task 0 after allocating gradient_basis_wave) - | Average: 7.766 MB - | Largest tracked array allocation so far: - | Minimum: 3.456 MB (hamiltonian_shell on task 0) - | Maximum: 3.456 MB (hamiltonian_shell on task 0) - | Average: 3.456 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - ------------------------------------------------------------- - Begin self-consistency iteration # 14 - - Date : 20230628, Time : 104151.721 ------------------------------------------------------------- - Pulay mixing of updated and previous charge densities. - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 28.0000000000 - | Integrated number of electrons on 3D grid : 28.0000000000 - | Charge integration error : 0.0000000000 - | Normalization factor for density and gradient : 1.0000000000 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = 0.270874E-12 - | Sum of charges compensated after spline to logarithmic grids = -0.122151E-03 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = 0.000000E+00 - Summing up the Hartree potential. - Time summed over all CPUs for potential: real work 1.655 s, elapsed 1.655 s - | RMS charge density error from multipole expansion : 0.151050E-01 - | Average real-space part of the electrostatic potential : 0.49365270 eV - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.432 s, elapsed 0.432 s - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.000 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -4.88675710 eV - What follows are estimated values for band gap, HOMO, LUMO, etc. - | They are estimated on a discrete k-point grid and not necessarily exact. - | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. - - Highest occupied state (VBM) at -5.30909840 eV (relative to internal zero) - | Occupation number: 2.00000000 - | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - - Lowest unoccupied state (CBM) at -4.59331867 eV (relative to internal zero) - | Occupation number: 0.00000000 - | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) - - ESTIMATED overall HOMO-LUMO gap: 0.71577973 eV between HOMO at k-point 1 and LUMO at k-point 4 - | This appears to be an indirect band gap. - | Smallest direct gap : 2.43039973 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, - this system is most likely an insulator or a semiconductor. - - Total energy components: - | Sum of eigenvalues : -328.16422814 Ha -8929.80299120 eV - | XC energy correction : -41.78940596 Ha -1137.14759372 eV - | XC potential correction : 53.96545100 Ha 1468.47463700 eV - | Free-atom electrostatic energy: -263.69998542 Ha -7175.64169592 eV - | Hartree energy correction : -0.95793492 Ha -26.06673538 eV - | Entropy correction : 0.00000000 Ha 0.00000000 eV - | --------------------------- - | Total energy : -580.64610344 Ha -15800.18437921 eV - | Total energy, T -> 0 : -580.64610344 Ha -15800.18437921 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -580.64610344 Ha -15800.18437921 eV - - Derived energy quantities: - | Kinetic energy : 582.30511417 Ha 15845.32835807 eV - | Electrostatic energy : -1121.16181165 Ha -30508.36514356 eV - | Energy correction for multipole - | error in Hartree potential : 0.02046075 Ha 0.55676534 eV - | Sum of eigenvalues per atom : -4464.90149560 eV - | Total energy (T->0) per atom : -7900.09218960 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -7900.09218960 eV - Evaluating new KS density using the density matrix - Evaluating density matrix - Time summed over all CPUs for getting density from density matrix: real work 0.880 s, elapsed 0.880 s - - Evaluating density-matrix-based force terms: batch-based integration - Evaluating density matrix - Evaluating density matrix - Integration grid: deviation in total charge ( - N_e) = 5.684342E-14 - - atomic forces [eV/Ang]: - ----------------------- - atom # 1 - Hellmann-Feynman : -0.234213E-11 0.147179E-10 -0.562263E-11 - Ionic forces : 0.000000E+00 0.000000E+00 0.000000E+00 - Multipole : -0.426895E-12 -0.442928E-12 0.739783E-12 - Hartree pot. SCF incomplete : -0.617057E-13 -0.175337E-10 -0.164096E-11 - Pulay + GGA : -0.604955E-09 -0.281370E-08 -0.508452E-08 - ---------------------------------------------------------------- - Total forces( 1) : -0.607785E-09 -0.281696E-08 -0.509104E-08 - atom # 2 - Hellmann-Feynman : -0.321355E-08 -0.323494E-08 -0.271592E-08 - Ionic forces : 0.000000E+00 0.000000E+00 0.000000E+00 - Multipole : -0.158276E-11 -0.926307E-12 0.104550E-11 - Hartree pot. SCF incomplete : -0.148700E-10 -0.116788E-10 -0.446800E-11 - Pulay + GGA : 0.123613E-07 0.681601E-08 0.315313E-08 - ---------------------------------------------------------------- - Total forces( 2) : 0.913127E-08 0.356846E-08 0.433781E-09 - - - Analytical stress tensor components [eV] xx yy zz xy xz yz - ----------------------------------------------------------------------------------------------------------------------------------------------------------- - Nuclear Hellmann-Feynman : -0.1512290147E+02 -0.1512316362E+02 -0.1512316362E+02 -0.4495744872E-13 0.2437323406E-13 0.8556343749E-13 - Multipole Hellmann-Feynman : -0.3192783535E+02 -0.3192784615E+02 -0.3192784615E+02 0.5502862228E-12 0.1763303039E-11 0.9656615355E-13 - On-site Multipole corrections : -0.2831479611E+00 -0.2831479611E+00 -0.2831479611E+00 0.5397487875E-12 -0.1675883126E-12 -0.1160859080E-11 - Strain deriv. of the orbitals : 0.4588718671E+02 0.4588745791E+02 0.4588745791E+02 -0.9985870616E-10 0.5370060305E-10 0.5631374550E-10 - ----------------------------------------------------------------------------------------------------------------------------------------------------------- - Sum of all contributions : -0.1446698077E+01 -0.1446699812E+01 -0.1446699812E+01 -0.9881362860E-10 0.5532069101E-10 0.5533501601E-10 - - +-------------------------------------------------------------------+ - | Analytical stress tensor - Symmetrized | - | Cartesian components [eV/A**3] | - +-------------------------------------------------------------------+ - | x y z | - | | - | x -0.03459259 -0.00000000 0.00000000 | - | y -0.00000000 -0.03459263 0.00000000 | - | z 0.00000000 0.00000000 -0.03459263 | - | | - | Pressure: 0.03459262 [eV/A**3] | - | | - +-------------------------------------------------------------------+ - - - Self-consistency convergence accuracy: - | Change of charge density : 0.2433E-09 - | Change of sum of eigenvalues : -0.4863E-07 eV - | Change of total energy : 0.3094E-10 eV - | Change of forces : 0.2719E-11 eV/A - - Writing Kohn-Sham eigenvalues. - K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - - State Occupation Eigenvalue [Ha] Eigenvalue [eV] - 1 2.00000 -65.742465 -1788.94348 - 2 2.00000 -65.742465 -1788.94348 - 3 2.00000 -5.103523 -138.87393 - 4 2.00000 -5.103295 -138.86771 - 5 2.00000 -3.487125 -94.88950 - 6 2.00000 -3.487125 -94.88950 - 7 2.00000 -3.487125 -94.88950 - 8 2.00000 -3.486606 -94.87537 - 9 2.00000 -3.486606 -94.87537 - 10 2.00000 -3.486606 -94.87537 - 11 2.00000 -0.626307 -17.04268 - 12 2.00000 -0.195106 -5.30910 - 13 2.00000 -0.195106 -5.30910 - 14 2.00000 -0.195106 -5.30910 - 15 0.00000 -0.105790 -2.87870 - 16 0.00000 -0.105790 -2.87870 - 17 0.00000 -0.105790 -2.87870 - 18 0.00000 -0.087344 -2.37675 - 19 0.00000 0.089813 2.44394 - 20 0.00000 0.089813 2.44394 - - What follows are estimated values for band gap, HOMO, LUMO, etc. - | They are estimated on a discrete k-point grid and not necessarily exact. - | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. - - Highest occupied state (VBM) at -5.30909840 eV (relative to internal zero) - | Occupation number: 2.00000000 - | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - - Lowest unoccupied state (CBM) at -4.59331867 eV (relative to internal zero) - | Occupation number: 0.00000000 - | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) - - ESTIMATED overall HOMO-LUMO gap: 0.71577973 eV between HOMO at k-point 1 and LUMO at k-point 4 - | This appears to be an indirect band gap. - | Smallest direct gap : 2.43039973 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, - this system is most likely an insulator or a semiconductor. - | Chemical Potential : -4.88675710 eV - - Self-consistency cycle converged. - - ------------------------------------------------------------- - End self-consistency iteration # 14 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 20.526 s 20.662 s - | Charge density & force component update : 17.497 s 17.617 s - | Density mixing : 0.002 s 0.002 s - | Hartree multipole update : 0.001 s 0.001 s - | Hartree multipole summation : 1.650 s 1.658 s - | Hartree pot. SCF incomplete forces : 0.942 s 0.947 s - | Integration : 0.430 s 0.432 s - | Solution of K.-S. eqns. : 0.005 s 0.005 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 1.538 MB (on task 0) - | Maximum: 1.538 MB (on task 0) - | Average: 1.538 MB - | Peak value for overall tracked memory usage: - | Minimum: 14.236 MB (on task 0 after allocating d_wave) - | Maximum: 14.236 MB (on task 0 after allocating d_wave) - | Average: 14.236 MB - | Largest tracked array allocation so far: - | Minimum: 3.456 MB (hamiltonian_shell on task 0) - | Maximum: 3.456 MB (hamiltonian_shell on task 0) - | Average: 3.456 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - Removing unitary transformations (pure translations, rotations) from forces on atoms. - Atomic forces before filtering: - | Net force on center of mass : 0.852349E-08 0.751505E-09 -0.465726E-08 eV/A - Atomic forces after filtering: - | Net force on center of mass : 0.199384E-23 0.000000E+00 -0.132923E-23 eV/A - - Energy and forces in a compact form: - | Total energy uncorrected : -0.158001843792097E+05 eV - | Total energy corrected : -0.158001843792097E+05 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -0.158001843792097E+05 eV - Total atomic forces (unitary forces cleaned) [eV/Ang]: - | 1 -0.486952935970507E-08 -0.319270797951684E-08 -0.276241042439398E-08 - | 2 0.486952935970508E-08 0.319270797951684E-08 0.276241042439398E-08 - - ------------------------------------ - Start decomposition of the XC Energy - ------------------------------------ - X and C from original XC functional choice - Hartree-Fock Energy : 0.000000000 Ha 0.000000000 eV - X Energy : -40.702535223 Ha -1107.572336068 eV - C Energy : -1.086870742 Ha -29.575257650 eV - XC Energy w/o HF : -41.789405964 Ha -1137.147593718 eV - Total XC Energy : -41.789405964 Ha -1137.147593718 eV - ------------------------------------ - LDA X and C from self-consistent density - X Energy LDA : -37.637384307 Ha -1024.165335950 eV - C Energy LDA : -2.146804754 Ha -58.417529610 eV - ------------------------------------ - End decomposition of the XC Energy - ------------------------------------ - ------------------------------------------------------------- - Relaxation / MD: End force evaluation. : max(cpu_time) wall_clock(cpu1) - | Time for this force evaluation : 48.916 s 49.214 s - ------------------------------------------------------------- - Geometry optimization: Attempting to predict improved coordinates. - - +-------------------------------------------------------------------+ - | Generalized derivatives on lattice vectors [eV/A] | - +-------------------------------------------------------------------+ - |lattice_vector 0.26255863 -0.26255895 -0.26255895 | - |lattice_vector -0.26255863 0.26255895 -0.26255895 | - |lattice_vector -0.26255863 -0.26255895 0.26255895 | - +-------------------------------------------------------------------+ - | Forces on lattice vectors cleaned from atomic contributions [eV/A]| - +-------------------------------------------------------------------+ - |lattice_vector -0.26255863 0.26255895 0.26255895 | - |lattice_vector 0.26255863 -0.26255895 0.26255895 | - |lattice_vector 0.26255863 0.26255895 -0.26255895 | - +-------------------------------------------------------------------+ - Removing unitary transformations (pure translations, rotations) from forces on atoms. - Atomic forces before filtering: - | Net force on center of mass : 0.199384E-23 0.000000E+00 -0.132923E-23 eV/A - Atomic forces after filtering: - | Net force on center of mass : 0.664615E-24 0.000000E+00 0.000000E+00 eV/A - Net remaining forces (excluding translations, rotations) in present geometry: - || Forces on atoms || = 0.486953E-08 eV/A. - || Forces on lattice || = 0.262559E+00 eV/A^3. - Maximum force component is 0.262559E+00 eV/A. - Present geometry is not yet converged. - - Relaxation step number 1: Predicting new coordinates. - - Advancing geometry using trust radius method. - Allocating 0.061 MB for stored_KS_eigenvector - | Hessian has 0 negative and 3 zero eigenvalues. - | Positive eigenvalues (eV/A^2): 7.54E+00 ... 3.02E+01 - | Use Quasi-Newton step of length |H^-1 F| = 4.27E-02 A. - Finished advancing geometry - | Time : 0.001 s - Updated atomic structure: - x [A] y [A] z [A] - lattice_vector 0.00000002 2.77241620 2.77241620 - lattice_vector 2.77241617 -0.00000001 2.77241618 - lattice_vector 2.77241617 2.77241618 -0.00000001 - - atom -0.00000000 -0.00000000 -0.00000000 Si - atom 1.38620809 1.38620809 1.38620809 Si - - Fractional coordinates: - L1 L2 L3 - atom_frac -0.00000000 -0.00000000 -0.00000000 Si - atom_frac 0.25000000 0.25000000 0.25000000 Si ------------------------------------------------------------- - Writing the current geometry to file "geometry.in.next_step". - Writing estimated Hessian matrix to file 'hessian.aims' - - Quantities derived from the lattice vectors: - | Reciprocal lattice vector 1: -1.133161 1.133161 1.133161 - | Reciprocal lattice vector 2: 1.133161 -1.133161 1.133161 - | Reciprocal lattice vector 3: 1.133161 1.133161 -1.133161 - | Unit cell volume : 0.426192E+02 A^3 - - Range separation radius for Ewald summation (hartree_convergence_parameter): 3.97864235 bohr. - ------------------------------------------------------------- - Begin self-consistency loop: Re-initialization. - - Date : 20230628, Time : 104212.390 ------------------------------------------------------------- - - Initializing index lists of integration centers etc. from given atomic structure: - Mapping all atomic coordinates to central unit cell. - - Initializing the k-points - Using symmetry for reducing the k-points - | k-points reduced from: 8 to 8 - | Number of k-points : 8 - The eigenvectors in the calculations are REAL. - | K-points in task 0: 8 - | Number of basis functions in the Hamiltonian integrals : 2161 - | Number of basis functions in a single unit cell : 50 - | Number of centers in hartree potential : 708 - | Number of centers in hartree multipole : 318 - | Number of centers in electron density summation: 190 - | Number of centers in basis integrals : 198 - | Number of centers in integrals : 101 - | Number of centers in hamiltonian : 190 - | Consuming 14 KiB for k_phase. - | Number of super-cells (origin) [n_cells] : 2197 - | Number of super-cells (after PM_index) [n_cells] : 112 - | Number of super-cells in hamiltonian [n_cells_in_hamiltonian]: 112 - | Size of matrix packed + index [n_hamiltonian_matrix_size] : 85499 - Partitioning the integration grid into batches with parallel hashing+maxmin method. - | Number of batches: 128 - | Maximal batch size: 90 - | Minimal batch size: 85 - | Average batch size: 87.562 - | Standard deviation of batch sizes: 1.493 - - Integration load balanced across 1 MPI tasks. - Work distribution over tasks is as follows: - Initializing partition tables, free-atom densities, potentials, etc. across the integration grid (initialize_grid_storage). - | Species 1: outer_partition_radius set to 5.000694715736543 AA . - | The sparse table of interatomic distances needs 212.76 kbyte instead of 313.63 kbyte of memory. - | Net number of integration points: 11208 - | of which are non-zero points : 9852 - | Numerical average free-atom electrostatic potential : -12.33430044 eV - Renormalizing the initial density to the exact electron count on the 3D integration grid. - | Initial density: Formal number of electrons (from input files) : 28.0000000000 - | Integrated number of electrons on 3D grid : 28.0042648595 - | Charge integration error : 0.0042648595 - | Normalization factor for density and gradient : 0.9998477068 - Renormalizing the free-atom superposition density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 28.0000000000 - | Integrated number of electrons on 3D grid : 28.0042648595 - | Charge integration error : 0.0042648595 - | Normalization factor for density and gradient : 0.9998477068 - Obtaining max. number of non-zero basis functions in each batch (get_n_compute_maxes). - Calculating total energy contributions from superposition of free atom densities. - Initialize hartree_potential_storage - Integrating overlap matrix. - Time summed over all CPUs for integration: real work 0.265 s, elapsed 0.265 s - Orthonormalizing eigenvectors - - End scf reinitialization - timings : max(cpu_time) wall_clock(cpu1) - | Time for scf. reinitialization : 0.588 s 0.592 s - | Boundary condition initialization : 0.059 s 0.059 s - | Integration : 0.264 s 0.265 s - | Grid partitioning : 0.036 s 0.036 s - | Preloading free-atom quantities on grid : 0.189 s 0.190 s - | Free-atom superposition energy : 0.027 s 0.028 s - | K.-S. eigenvector reorthonormalization : 0.001 s 0.001 s ------------------------------------------------------------- - Evaluating new KS density using the density matrix - Evaluating density matrix - Time summed over all CPUs for getting density from density matrix: real work 0.842 s, elapsed 0.842 s - Integration grid: deviation in total charge ( - N_e) = -7.105427E-15 - - Time for density update prior : max(cpu_time) wall_clock(cpu1) - | self-consistency iterative process : 0.838 s 0.844 s - ------------------------------------------------------------- - Begin self-consistency iteration # 1 - - Date : 20230628, Time : 104213.826 ------------------------------------------------------------- - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 28.0000000000 - | Integrated number of electrons on 3D grid : 28.0000000000 - | Charge integration error : -0.0000000000 - | Normalization factor for density and gradient : 1.0000000000 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = -0.941446E-13 - | Sum of charges compensated after spline to logarithmic grids = -0.109990E-03 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = 0.000000E+00 - Summing up the Hartree potential. - | Estimated reciprocal-space cutoff momentum G_max: 2.34376572 bohr^-1 . - | Reciprocal lattice points for long-range Hartree potential: 58 - Time summed over all CPUs for potential: real work 0.392 s, elapsed 0.392 s - | RMS charge density error from multipole expansion : 0.147126E-01 - | Average real-space part of the electrostatic potential : 0.47611346 eV - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.414 s, elapsed 0.414 s - Decreasing sparse matrix size: - | Tolerance: 0.1000E-12 - Hamiltonian matrix - | Array has 78708 nonzero elements out of 85499 elements - | Sparsity factor is 0.079 - Overlap matrix - | Array has 70208 nonzero elements out of 85499 elements - | Sparsity factor is 0.179 - New size of hamiltonian matrix: 78735 - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Singularity check in k-point 1, task 0 (analysis for other k-points/tasks may follow below): - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.001 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -4.92413184 eV - Writing Kohn-Sham eigenvalues. - K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - - State Occupation Eigenvalue [Ha] Eigenvalue [eV] - 1 2.00000 -65.744985 -1789.01207 - 2 2.00000 -65.744985 -1789.01207 - 3 2.00000 -5.104589 -138.90292 - 4 2.00000 -5.104381 -138.89727 - 5 2.00000 -3.488273 -94.92075 - 6 2.00000 -3.488273 -94.92075 - 7 2.00000 -3.488273 -94.92075 - 8 2.00000 -3.487794 -94.90769 - 9 2.00000 -3.487794 -94.90769 - 10 2.00000 -3.487794 -94.90769 - 11 2.00000 -0.620837 -16.89383 - 12 2.00000 -0.194307 -5.28735 - 13 2.00000 -0.194307 -5.28735 - 14 2.00000 -0.194307 -5.28735 - 15 0.00000 -0.105227 -2.86338 - 16 0.00000 -0.105227 -2.86338 - 17 0.00000 -0.105227 -2.86338 - 18 0.00000 -0.094308 -2.56625 - 19 0.00000 0.090742 2.46922 - 20 0.00000 0.090742 2.46922 - - What follows are estimated values for band gap, HOMO, LUMO, etc. - | They are estimated on a discrete k-point grid and not necessarily exact. - | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. - - Highest occupied state (VBM) at -5.28735399 eV (relative to internal zero) - | Occupation number: 2.00000000 - | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - - Lowest unoccupied state (CBM) at -4.53451456 eV (relative to internal zero) - | Occupation number: 0.00000000 - | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) - - ESTIMATED overall HOMO-LUMO gap: 0.75283943 eV between HOMO at k-point 1 and LUMO at k-point 4 - | This appears to be an indirect band gap. - | Smallest direct gap : 2.42397618 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, - this system is most likely an insulator or a semiconductor. - - Total energy components: - | Sum of eigenvalues : -328.17151144 Ha -8930.00117985 eV - | XC energy correction : -41.77616004 Ha -1136.78715377 eV - | XC potential correction : 53.94777676 Ha 1467.99369627 eV - | Free-atom electrostatic energy: -263.74356637 Ha -7176.82759392 eV - | Hartree energy correction : -0.90343740 Ha -24.58378245 eV - | Entropy correction : 0.00000000 Ha 0.00000000 eV - | --------------------------- - | Total energy : -580.64689850 Ha -15800.20601371 eV - | Total energy, T -> 0 : -580.64689850 Ha -15800.20601371 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -580.64689850 Ha -15800.20601371 eV - - Derived energy quantities: - | Kinetic energy : 582.22497978 Ha 15843.14779022 eV - | Electrostatic energy : -1121.09571823 Ha -30506.56665016 eV - | Energy correction for multipole - | error in Hartree potential : 0.01980078 Ha 0.53880656 eV - | Sum of eigenvalues per atom : -4465.00058992 eV - | Total energy (T->0) per atom : -7900.10300686 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -7900.10300686 eV - Evaluating new KS density using the density matrix - Evaluating density matrix - Time summed over all CPUs for getting density from density matrix: real work 0.843 s, elapsed 0.843 s - Integration grid: deviation in total charge ( - N_e) = 9.592327E-14 - - Self-consistency convergence accuracy: - | Change of charge density : 0.1352E+00 - | Change of sum of eigenvalues : -0.8930E+04 eV - | Change of total energy : -0.1580E+05 eV - - ------------------------------------------------------------- - End self-consistency iteration # 1 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 1.649 s 1.659 s - | Charge density update : 0.838 s 0.844 s - | Density mixing & preconditioning : 0.000 s 0.000 s - | Hartree multipole update : 0.001 s 0.001 s - | Hartree multipole summation : 0.392 s 0.394 s - | Integration : 0.412 s 0.415 s - | Solution of K.-S. eqns. : 0.005 s 0.005 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 1.632 MB (on task 0) - | Maximum: 1.632 MB (on task 0) - | Average: 1.632 MB - | Peak value for overall tracked memory usage: - | Minimum: 14.236 MB (on task 0 after allocating d_wave) - | Maximum: 14.236 MB (on task 0 after allocating d_wave) - | Average: 14.236 MB - | Largest tracked array allocation so far: - | Minimum: 3.456 MB (hamiltonian_shell on task 0) - | Maximum: 3.456 MB (hamiltonian_shell on task 0) - | Average: 3.456 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - ------------------------------------------------------------- - Begin self-consistency iteration # 2 - - Date : 20230628, Time : 104215.485 ------------------------------------------------------------- - Pulay mixing of updated and previous charge densities. - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 28.0000000000 - | Integrated number of electrons on 3D grid : 27.9999681480 - | Charge integration error : -0.0000318520 - | Normalization factor for density and gradient : 1.0000011376 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = -0.224623E-12 - | Sum of charges compensated after spline to logarithmic grids = -0.109994E-03 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = 0.000000E+00 - Summing up the Hartree potential. - Time summed over all CPUs for potential: real work 0.392 s, elapsed 0.392 s - | RMS charge density error from multipole expansion : 0.147060E-01 - | Average real-space part of the electrostatic potential : 0.47622186 eV - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.418 s, elapsed 0.418 s - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.000 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -4.92436221 eV - What follows are estimated values for band gap, HOMO, LUMO, etc. - | They are estimated on a discrete k-point grid and not necessarily exact. - | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. - - Highest occupied state (VBM) at -5.28752711 eV (relative to internal zero) - | Occupation number: 2.00000000 - | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - - Lowest unoccupied state (CBM) at -4.53462713 eV (relative to internal zero) - | Occupation number: 0.00000000 - | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) - - ESTIMATED overall HOMO-LUMO gap: 0.75289998 eV between HOMO at k-point 1 and LUMO at k-point 4 - | This appears to be an indirect band gap. - | Smallest direct gap : 2.42401123 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, - this system is most likely an insulator or a semiconductor. - - Total energy components: - | Sum of eigenvalues : -328.16927255 Ha -8929.94025655 eV - | XC energy correction : -41.77644354 Ha -1136.79486832 eV - | XC potential correction : 53.94814771 Ha 1468.00379049 eV - | Free-atom electrostatic energy: -263.74356637 Ha -7176.82759392 eV - | Hartree energy correction : -0.90576420 Ha -24.64709786 eV - | Entropy correction : 0.00000000 Ha 0.00000000 eV - | --------------------------- - | Total energy : -580.64689895 Ha -15800.20602616 eV - | Total energy, T -> 0 : -580.64689895 Ha -15800.20602616 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -580.64689895 Ha -15800.20602616 eV - - Derived energy quantities: - | Kinetic energy : 582.23052760 Ha 15843.29875414 eV - | Electrostatic energy : -1121.10098301 Ha -30506.70991198 eV - | Energy correction for multipole - | error in Hartree potential : 0.01979779 Ha 0.53872539 eV - | Sum of eigenvalues per atom : -4464.97012828 eV - | Total energy (T->0) per atom : -7900.10301308 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -7900.10301308 eV - Evaluating new KS density using the density matrix - Evaluating density matrix - Time summed over all CPUs for getting density from density matrix: real work 0.843 s, elapsed 0.843 s - Integration grid: deviation in total charge ( - N_e) = -6.039613E-14 - - Self-consistency convergence accuracy: - | Change of charge density : 0.1080E-02 - | Change of sum of eigenvalues : 0.6092E-01 eV - | Change of total energy : -0.1245E-04 eV - - ------------------------------------------------------------- - End self-consistency iteration # 2 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 1.829 s 1.840 s - | Charge density update : 0.839 s 0.845 s - | Density mixing & preconditioning : 0.176 s 0.177 s - | Hartree multipole update : 0.001 s 0.001 s - | Hartree multipole summation : 0.392 s 0.394 s - | Integration : 0.416 s 0.419 s - | Solution of K.-S. eqns. : 0.005 s 0.004 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 1.632 MB (on task 0) - | Maximum: 1.632 MB (on task 0) - | Average: 1.632 MB - | Peak value for overall tracked memory usage: - | Minimum: 14.236 MB (on task 0 after allocating d_wave) - | Maximum: 14.236 MB (on task 0 after allocating d_wave) - | Average: 14.236 MB - | Largest tracked array allocation so far: - | Minimum: 3.456 MB (hamiltonian_shell on task 0) - | Maximum: 3.456 MB (hamiltonian_shell on task 0) - | Average: 3.456 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - ------------------------------------------------------------- - Begin self-consistency iteration # 3 - - Date : 20230628, Time : 104217.325 ------------------------------------------------------------- - Pulay mixing of updated and previous charge densities. - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 28.0000000000 - | Integrated number of electrons on 3D grid : 27.9998896082 - | Charge integration error : -0.0001103918 - | Normalization factor for density and gradient : 1.0000039426 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = -0.292231E-13 - | Sum of charges compensated after spline to logarithmic grids = -0.110006E-03 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = 0.000000E+00 - Summing up the Hartree potential. - Time summed over all CPUs for potential: real work 0.392 s, elapsed 0.392 s - | RMS charge density error from multipole expansion : 0.146846E-01 - | Average real-space part of the electrostatic potential : 0.47660009 eV - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.416 s, elapsed 0.416 s - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.000 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -4.92509627 eV - What follows are estimated values for band gap, HOMO, LUMO, etc. - | They are estimated on a discrete k-point grid and not necessarily exact. - | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. - - Highest occupied state (VBM) at -5.28807241 eV (relative to internal zero) - | Occupation number: 2.00000000 - | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - - Lowest unoccupied state (CBM) at -4.53498682 eV (relative to internal zero) - | Occupation number: 0.00000000 - | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) - - ESTIMATED overall HOMO-LUMO gap: 0.75308559 eV between HOMO at k-point 1 and LUMO at k-point 4 - | This appears to be an indirect band gap. - | Smallest direct gap : 2.42411875 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, - this system is most likely an insulator or a semiconductor. - - Total energy components: - | Sum of eigenvalues : -328.16210705 Ha -8929.74527316 eV - | XC energy correction : -41.77733114 Ha -1136.81902112 eV - | XC potential correction : 53.94931109 Ha 1468.03544747 eV - | Free-atom electrostatic energy: -263.74356637 Ha -7176.82759392 eV - | Hartree energy correction : -0.91320725 Ha -24.84963361 eV - | Entropy correction : 0.00000000 Ha 0.00000000 eV - | --------------------------- - | Total energy : -580.64690072 Ha -15800.20607434 eV - | Total energy, T -> 0 : -580.64690072 Ha -15800.20607434 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -580.64690072 Ha -15800.20607434 eV - - Derived energy quantities: - | Kinetic energy : 582.24779135 Ha 15843.76852458 eV - | Electrostatic energy : -1121.11736093 Ha -30507.15557780 eV - | Energy correction for multipole - | error in Hartree potential : 0.01978805 Ha 0.53846031 eV - | Sum of eigenvalues per atom : -4464.87263658 eV - | Total energy (T->0) per atom : -7900.10303717 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -7900.10303717 eV - Evaluating new KS density using the density matrix - Evaluating density matrix - Time summed over all CPUs for getting density from density matrix: real work 0.843 s, elapsed 0.843 s - Integration grid: deviation in total charge ( - N_e) = -3.552714E-15 - - Self-consistency convergence accuracy: - | Change of charge density : 0.8212E-03 - | Change of sum of eigenvalues : 0.1950E+00 eV - | Change of total energy : -0.4817E-04 eV - - ------------------------------------------------------------- - End self-consistency iteration # 3 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 1.829 s 1.840 s - | Charge density update : 0.839 s 0.845 s - | Density mixing & preconditioning : 0.177 s 0.178 s - | Hartree multipole update : 0.001 s 0.001 s - | Hartree multipole summation : 0.392 s 0.395 s - | Integration : 0.414 s 0.416 s - | Solution of K.-S. eqns. : 0.005 s 0.005 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 1.632 MB (on task 0) - | Maximum: 1.632 MB (on task 0) - | Average: 1.632 MB - | Peak value for overall tracked memory usage: - | Minimum: 14.236 MB (on task 0 after allocating d_wave) - | Maximum: 14.236 MB (on task 0 after allocating d_wave) - | Average: 14.236 MB - | Largest tracked array allocation so far: - | Minimum: 3.456 MB (hamiltonian_shell on task 0) - | Maximum: 3.456 MB (hamiltonian_shell on task 0) - | Average: 3.456 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - ------------------------------------------------------------- - Begin self-consistency iteration # 4 - - Date : 20230628, Time : 104219.165 ------------------------------------------------------------- - Pulay mixing of updated and previous charge densities. - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 28.0000000000 - | Integrated number of electrons on 3D grid : 27.9999408726 - | Charge integration error : -0.0000591274 - | Normalization factor for density and gradient : 1.0000021117 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = -0.172218E-12 - | Sum of charges compensated after spline to logarithmic grids = -0.110001E-03 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = 0.000000E+00 - Summing up the Hartree potential. - Time summed over all CPUs for potential: real work 0.391 s, elapsed 0.391 s - | RMS charge density error from multipole expansion : 0.146807E-01 - | Average real-space part of the electrostatic potential : 0.47680126 eV - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.416 s, elapsed 0.416 s - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.001 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -4.92516045 eV - What follows are estimated values for band gap, HOMO, LUMO, etc. - | They are estimated on a discrete k-point grid and not necessarily exact. - | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. - - Highest occupied state (VBM) at -5.28809015 eV (relative to internal zero) - | Occupation number: 2.00000000 - | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - - Lowest unoccupied state (CBM) at -4.53502662 eV (relative to internal zero) - | Occupation number: 0.00000000 - | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) - - ESTIMATED overall HOMO-LUMO gap: 0.75306353 eV between HOMO at k-point 1 and LUMO at k-point 4 - | This appears to be an indirect band gap. - | Smallest direct gap : 2.42410496 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, - this system is most likely an insulator or a semiconductor. - - Total energy components: - | Sum of eigenvalues : -328.16153795 Ha -8929.72978733 eV - | XC energy correction : -41.77728814 Ha -1136.81785082 eV - | XC potential correction : 53.94926632 Ha 1468.03422934 eV - | Free-atom electrostatic energy: -263.74356637 Ha -7176.82759392 eV - | Hartree energy correction : -0.91377546 Ha -24.86509528 eV - | Entropy correction : 0.00000000 Ha 0.00000000 eV - | --------------------------- - | Total energy : -580.64690159 Ha -15800.20609801 eV - | Total energy, T -> 0 : -580.64690159 Ha -15800.20609801 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -580.64690159 Ha -15800.20609801 eV - - Derived energy quantities: - | Kinetic energy : 582.24635446 Ha 15843.72942496 eV - | Electrostatic energy : -1121.11596792 Ha -30507.11767215 eV - | Energy correction for multipole - | error in Hartree potential : 0.01978597 Ha 0.53840359 eV - | Sum of eigenvalues per atom : -4464.86489366 eV - | Total energy (T->0) per atom : -7900.10304901 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -7900.10304901 eV - Evaluating new KS density using the density matrix - Evaluating density matrix - Time summed over all CPUs for getting density from density matrix: real work 0.843 s, elapsed 0.843 s - Integration grid: deviation in total charge ( - N_e) = 7.105427E-15 - - Self-consistency convergence accuracy: - | Change of charge density : 0.1212E-03 - | Change of sum of eigenvalues : 0.1549E-01 eV - | Change of total energy : -0.2367E-04 eV - - ------------------------------------------------------------- - End self-consistency iteration # 4 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 1.829 s 1.839 s - | Charge density update : 0.839 s 0.844 s - | Density mixing & preconditioning : 0.177 s 0.178 s - | Hartree multipole update : 0.001 s 0.001 s - | Hartree multipole summation : 0.392 s 0.394 s - | Integration : 0.414 s 0.416 s - | Solution of K.-S. eqns. : 0.005 s 0.005 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 1.632 MB (on task 0) - | Maximum: 1.632 MB (on task 0) - | Average: 1.632 MB - | Peak value for overall tracked memory usage: - | Minimum: 14.236 MB (on task 0 after allocating d_wave) - | Maximum: 14.236 MB (on task 0 after allocating d_wave) - | Average: 14.236 MB - | Largest tracked array allocation so far: - | Minimum: 3.456 MB (hamiltonian_shell on task 0) - | Maximum: 3.456 MB (hamiltonian_shell on task 0) - | Average: 3.456 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - ------------------------------------------------------------- - Begin self-consistency iteration # 5 - - Date : 20230628, Time : 104221.004 ------------------------------------------------------------- - Pulay mixing of updated and previous charge densities. - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 28.0000000000 - | Integrated number of electrons on 3D grid : 28.0000009518 - | Charge integration error : 0.0000009518 - | Normalization factor for density and gradient : 0.9999999660 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = -0.573319E-13 - | Sum of charges compensated after spline to logarithmic grids = -0.110000E-03 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = 0.000000E+00 - Summing up the Hartree potential. - Time summed over all CPUs for potential: real work 0.392 s, elapsed 0.392 s - | RMS charge density error from multipole expansion : 0.146804E-01 - | Average real-space part of the electrostatic potential : 0.47674538 eV - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.417 s, elapsed 0.417 s - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.000 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -4.92521506 eV - What follows are estimated values for band gap, HOMO, LUMO, etc. - | They are estimated on a discrete k-point grid and not necessarily exact. - | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. - - Highest occupied state (VBM) at -5.28815749 eV (relative to internal zero) - | Occupation number: 2.00000000 - | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - - Lowest unoccupied state (CBM) at -4.53505514 eV (relative to internal zero) - | Occupation number: 0.00000000 - | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) - - ESTIMATED overall HOMO-LUMO gap: 0.75310235 eV between HOMO at k-point 1 and LUMO at k-point 4 - | This appears to be an indirect band gap. - | Smallest direct gap : 2.42412689 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, - this system is most likely an insulator or a semiconductor. - - Total energy components: - | Sum of eigenvalues : -328.16171552 Ha -8929.73461922 eV - | XC energy correction : -41.77728120 Ha -1136.81766215 eV - | XC potential correction : 53.94925555 Ha 1468.03393614 eV - | Free-atom electrostatic energy: -263.74356637 Ha -7176.82759392 eV - | Hartree energy correction : -0.91359388 Ha -24.86015427 eV - | Entropy correction : 0.00000000 Ha 0.00000000 eV - | --------------------------- - | Total energy : -580.64690143 Ha -15800.20609342 eV - | Total energy, T -> 0 : -580.64690143 Ha -15800.20609342 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -580.64690143 Ha -15800.20609342 eV - - Derived energy quantities: - | Kinetic energy : 582.24622913 Ha 15843.72601460 eV - | Electrostatic energy : -1121.11584936 Ha -30507.11444587 eV - | Energy correction for multipole - | error in Hartree potential : 0.01978570 Ha 0.53839640 eV - | Sum of eigenvalues per atom : -4464.86730961 eV - | Total energy (T->0) per atom : -7900.10304671 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -7900.10304671 eV - Evaluating new KS density using the density matrix - Evaluating density matrix - Time summed over all CPUs for getting density from density matrix: real work 0.846 s, elapsed 0.846 s - Integration grid: deviation in total charge ( - N_e) = -2.131628E-14 - - Self-consistency convergence accuracy: - | Change of charge density : 0.1907E-04 - | Change of sum of eigenvalues : -0.4832E-02 eV - | Change of total energy : 0.4595E-05 eV - - ------------------------------------------------------------- - End self-consistency iteration # 5 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 1.831 s 1.843 s - | Charge density update : 0.841 s 0.847 s - | Density mixing & preconditioning : 0.177 s 0.178 s - | Hartree multipole update : 0.001 s 0.001 s - | Hartree multipole summation : 0.392 s 0.395 s - | Integration : 0.414 s 0.417 s - | Solution of K.-S. eqns. : 0.005 s 0.004 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 1.632 MB (on task 0) - | Maximum: 1.632 MB (on task 0) - | Average: 1.632 MB - | Peak value for overall tracked memory usage: - | Minimum: 14.236 MB (on task 0 after allocating d_wave) - | Maximum: 14.236 MB (on task 0 after allocating d_wave) - | Average: 14.236 MB - | Largest tracked array allocation so far: - | Minimum: 3.456 MB (hamiltonian_shell on task 0) - | Maximum: 3.456 MB (hamiltonian_shell on task 0) - | Average: 3.456 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - ------------------------------------------------------------- - Begin self-consistency iteration # 6 - - Date : 20230628, Time : 104222.847 ------------------------------------------------------------- - Pulay mixing of updated and previous charge densities. - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 28.0000000000 - | Integrated number of electrons on 3D grid : 28.0000003017 - | Charge integration error : 0.0000003017 - | Normalization factor for density and gradient : 0.9999999892 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = -0.979218E-13 - | Sum of charges compensated after spline to logarithmic grids = -0.110001E-03 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = 0.000000E+00 - Summing up the Hartree potential. - Time summed over all CPUs for potential: real work 0.392 s, elapsed 0.392 s - | RMS charge density error from multipole expansion : 0.146805E-01 - | Average real-space part of the electrostatic potential : 0.47675856 eV - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.416 s, elapsed 0.416 s - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.001 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -4.92519957 eV - What follows are estimated values for band gap, HOMO, LUMO, etc. - | They are estimated on a discrete k-point grid and not necessarily exact. - | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. - - Highest occupied state (VBM) at -5.28814004 eV (relative to internal zero) - | Occupation number: 2.00000000 - | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - - Lowest unoccupied state (CBM) at -4.53504651 eV (relative to internal zero) - | Occupation number: 0.00000000 - | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) - - ESTIMATED overall HOMO-LUMO gap: 0.75309352 eV between HOMO at k-point 1 and LUMO at k-point 4 - | This appears to be an indirect band gap. - | Smallest direct gap : 2.42412063 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, - this system is most likely an insulator or a semiconductor. - - Total energy components: - | Sum of eigenvalues : -328.16169163 Ha -8929.73396917 eV - | XC energy correction : -41.77728210 Ha -1136.81768649 eV - | XC potential correction : 53.94925665 Ha 1468.03396632 eV - | Free-atom electrostatic energy: -263.74356637 Ha -7176.82759392 eV - | Hartree energy correction : -0.91361801 Ha -24.86081093 eV - | Entropy correction : 0.00000000 Ha 0.00000000 eV - | --------------------------- - | Total energy : -580.64690145 Ha -15800.20609418 eV - | Total energy, T -> 0 : -580.64690145 Ha -15800.20609418 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -580.64690145 Ha -15800.20609418 eV - - Derived energy quantities: - | Kinetic energy : 582.24620850 Ha 15843.72545323 eV - | Electrostatic energy : -1121.11582786 Ha -30507.11386092 eV - | Energy correction for multipole - | error in Hartree potential : 0.01978591 Ha 0.53840207 eV - | Sum of eigenvalues per atom : -4464.86698458 eV - | Total energy (T->0) per atom : -7900.10304709 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -7900.10304709 eV - Evaluating new KS density using the density matrix - Evaluating density matrix - Time summed over all CPUs for getting density from density matrix: real work 0.846 s, elapsed 0.846 s - Integration grid: deviation in total charge ( - N_e) = -1.421085E-14 - - Self-consistency convergence accuracy: - | Change of charge density : 0.2242E-05 - | Change of sum of eigenvalues : 0.6500E-03 eV - | Change of total energy : -0.7676E-06 eV - - ------------------------------------------------------------- - End self-consistency iteration # 6 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 1.831 s 1.842 s - | Charge density update : 0.842 s 0.847 s - | Density mixing & preconditioning : 0.177 s 0.178 s - | Hartree multipole update : 0.001 s 0.001 s - | Hartree multipole summation : 0.392 s 0.394 s - | Integration : 0.414 s 0.417 s - | Solution of K.-S. eqns. : 0.005 s 0.005 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 1.632 MB (on task 0) - | Maximum: 1.632 MB (on task 0) - | Average: 1.632 MB - | Peak value for overall tracked memory usage: - | Minimum: 14.236 MB (on task 0 after allocating d_wave) - | Maximum: 14.236 MB (on task 0 after allocating d_wave) - | Average: 14.236 MB - | Largest tracked array allocation so far: - | Minimum: 3.456 MB (hamiltonian_shell on task 0) - | Maximum: 3.456 MB (hamiltonian_shell on task 0) - | Average: 3.456 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - ------------------------------------------------------------- - Begin self-consistency iteration # 7 - - Date : 20230628, Time : 104224.689 ------------------------------------------------------------- - Pulay mixing of updated and previous charge densities. - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 28.0000000000 - | Integrated number of electrons on 3D grid : 27.9999997341 - | Charge integration error : -0.0000002659 - | Normalization factor for density and gradient : 1.0000000095 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = -0.759542E-13 - | Sum of charges compensated after spline to logarithmic grids = -0.110001E-03 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = 0.000000E+00 - Summing up the Hartree potential. - Time summed over all CPUs for potential: real work 0.392 s, elapsed 0.392 s - | RMS charge density error from multipole expansion : 0.146805E-01 - | Average real-space part of the electrostatic potential : 0.47675972 eV - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.418 s, elapsed 0.418 s - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.000 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -4.92520057 eV - What follows are estimated values for band gap, HOMO, LUMO, etc. - | They are estimated on a discrete k-point grid and not necessarily exact. - | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. - - Highest occupied state (VBM) at -5.28814071 eV (relative to internal zero) - | Occupation number: 2.00000000 - | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - - Lowest unoccupied state (CBM) at -4.53504696 eV (relative to internal zero) - | Occupation number: 0.00000000 - | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) - - ESTIMATED overall HOMO-LUMO gap: 0.75309375 eV between HOMO at k-point 1 and LUMO at k-point 4 - | This appears to be an indirect band gap. - | Smallest direct gap : 2.42412065 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, - this system is most likely an insulator or a semiconductor. - - Total energy components: - | Sum of eigenvalues : -328.16168066 Ha -8929.73367061 eV - | XC energy correction : -41.77728329 Ha -1136.81771884 eV - | XC potential correction : 53.94925820 Ha 1468.03400849 eV - | Free-atom electrostatic energy: -263.74356637 Ha -7176.82759392 eV - | Hartree energy correction : -0.91362935 Ha -24.86111942 eV - | Entropy correction : 0.00000000 Ha 0.00000000 eV - | --------------------------- - | Total energy : -580.64690146 Ha -15800.20609430 eV - | Total energy, T -> 0 : -580.64690146 Ha -15800.20609430 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -580.64690146 Ha -15800.20609430 eV - - Derived energy quantities: - | Kinetic energy : 582.24622796 Ha 15843.72598272 eV - | Electrostatic energy : -1121.11584613 Ha -30507.11435818 eV - | Energy correction for multipole - | error in Hartree potential : 0.01978591 Ha 0.53840187 eV - | Sum of eigenvalues per atom : -4464.86683530 eV - | Total energy (T->0) per atom : -7900.10304715 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -7900.10304715 eV - Evaluating new KS density using the density matrix - Evaluating density matrix - Time summed over all CPUs for getting density from density matrix: real work 0.843 s, elapsed 0.843 s - Integration grid: deviation in total charge ( - N_e) = 2.842171E-14 - - Self-consistency convergence accuracy: - | Change of charge density : 0.1144E-05 - | Change of sum of eigenvalues : 0.2986E-03 eV - | Change of total energy : -0.1153E-06 eV - - ------------------------------------------------------------- - End self-consistency iteration # 7 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 1.831 s 1.842 s - | Charge density update : 0.839 s 0.845 s - | Density mixing & preconditioning : 0.178 s 0.179 s - | Hartree multipole update : 0.001 s 0.001 s - | Hartree multipole summation : 0.392 s 0.394 s - | Integration : 0.416 s 0.418 s - | Solution of K.-S. eqns. : 0.005 s 0.005 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 1.632 MB (on task 0) - | Maximum: 1.632 MB (on task 0) - | Average: 1.632 MB - | Peak value for overall tracked memory usage: - | Minimum: 14.236 MB (on task 0 after allocating d_wave) - | Maximum: 14.236 MB (on task 0 after allocating d_wave) - | Average: 14.236 MB - | Largest tracked array allocation so far: - | Minimum: 3.456 MB (hamiltonian_shell on task 0) - | Maximum: 3.456 MB (hamiltonian_shell on task 0) - | Average: 3.456 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - ------------------------------------------------------------- - Begin self-consistency iteration # 8 - - Date : 20230628, Time : 104226.531 ------------------------------------------------------------- - Pulay mixing of updated and previous charge densities. - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 28.0000000000 - | Integrated number of electrons on 3D grid : 28.0000000174 - | Charge integration error : 0.0000000174 - | Normalization factor for density and gradient : 0.9999999994 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = -0.172245E-12 - | Sum of charges compensated after spline to logarithmic grids = -0.110001E-03 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = 0.000000E+00 - Summing up the Hartree potential. - Time summed over all CPUs for potential: real work 0.391 s, elapsed 0.391 s - | RMS charge density error from multipole expansion : 0.146805E-01 - | Average real-space part of the electrostatic potential : 0.47675985 eV - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.417 s, elapsed 0.417 s - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.001 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -4.92520043 eV - What follows are estimated values for band gap, HOMO, LUMO, etc. - | They are estimated on a discrete k-point grid and not necessarily exact. - | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. - - Highest occupied state (VBM) at -5.28814063 eV (relative to internal zero) - | Occupation number: 2.00000000 - | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - - Lowest unoccupied state (CBM) at -4.53504686 eV (relative to internal zero) - | Occupation number: 0.00000000 - | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) - - ESTIMATED overall HOMO-LUMO gap: 0.75309377 eV between HOMO at k-point 1 and LUMO at k-point 4 - | This appears to be an indirect band gap. - | Smallest direct gap : 2.42412061 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, - this system is most likely an insulator or a semiconductor. - - Total energy components: - | Sum of eigenvalues : -328.16168179 Ha -8929.73370147 eV - | XC energy correction : -41.77728314 Ha -1136.81771479 eV - | XC potential correction : 53.94925800 Ha 1468.03400294 eV - | Free-atom electrostatic energy: -263.74356637 Ha -7176.82759392 eV - | Hartree energy correction : -0.91362816 Ha -24.86108705 eV - | Entropy correction : 0.00000000 Ha 0.00000000 eV - | --------------------------- - | Total energy : -580.64690146 Ha -15800.20609429 eV - | Total energy, T -> 0 : -580.64690146 Ha -15800.20609429 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -580.64690146 Ha -15800.20609429 eV - - Derived energy quantities: - | Kinetic energy : 582.24622659 Ha 15843.72594546 eV - | Electrostatic energy : -1121.11584491 Ha -30507.11432496 eV - | Energy correction for multipole - | error in Hartree potential : 0.01978591 Ha 0.53840201 eV - | Sum of eigenvalues per atom : -4464.86685073 eV - | Total energy (T->0) per atom : -7900.10304715 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -7900.10304715 eV - Preliminary charge convergence reached. Turning off preconditioner. - - Evaluating new KS density using the density matrix - Evaluating density matrix - Time summed over all CPUs for getting density from density matrix: real work 0.845 s, elapsed 0.845 s - Integration grid: deviation in total charge ( - N_e) = -2.131628E-14 - - Self-consistency convergence accuracy: - | Change of charge density : 0.1356E-06 - | Change of sum of eigenvalues : -0.3086E-04 eV - | Change of total energy : 0.7722E-08 eV - - Electronic self-consistency reached - switching on the force computation. - - Electronic self-consistency reached - switching on the analytical stress tensor computation. - - ------------------------------------------------------------- - End self-consistency iteration # 8 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 1.831 s 1.842 s - | Charge density & force component update : 0.841 s 0.846 s - | Density mixing : 0.178 s 0.179 s - | Hartree multipole update : 0.001 s 0.001 s - | Hartree multipole summation : 0.392 s 0.394 s - | Hartree pot. SCF incomplete forces : 0.942 s 0.947 s - | Integration : 0.414 s 0.417 s - | Solution of K.-S. eqns. : 0.005 s 0.005 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 1.632 MB (on task 0) - | Maximum: 1.632 MB (on task 0) - | Average: 1.632 MB - | Peak value for overall tracked memory usage: - | Minimum: 14.236 MB (on task 0 after allocating d_wave) - | Maximum: 14.236 MB (on task 0 after allocating d_wave) - | Average: 14.236 MB - | Largest tracked array allocation so far: - | Minimum: 3.456 MB (hamiltonian_shell on task 0) - | Maximum: 3.456 MB (hamiltonian_shell on task 0) - | Average: 3.456 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - ------------------------------------------------------------- - Begin self-consistency iteration # 9 - - Date : 20230628, Time : 104228.373 ------------------------------------------------------------- - Pulay mixing of updated and previous charge densities. - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 28.0000000000 - | Integrated number of electrons on 3D grid : 27.9999999992 - | Charge integration error : -0.0000000008 - | Normalization factor for density and gradient : 1.0000000000 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = -0.150379E-12 - | Sum of charges compensated after spline to logarithmic grids = -0.110001E-03 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = -0.150405E-12 - Summing up the Hartree potential. - Time summed over all CPUs for potential: real work 1.654 s, elapsed 1.654 s - | RMS charge density error from multipole expansion : 0.146805E-01 - | Average real-space part of the electrostatic potential : 0.47675985 eV - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.416 s, elapsed 0.416 s - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.000 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -4.92520044 eV - What follows are estimated values for band gap, HOMO, LUMO, etc. - | They are estimated on a discrete k-point grid and not necessarily exact. - | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. - - Highest occupied state (VBM) at -5.28814064 eV (relative to internal zero) - | Occupation number: 2.00000000 - | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - - Lowest unoccupied state (CBM) at -4.53504686 eV (relative to internal zero) - | Occupation number: 0.00000000 - | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) - - ESTIMATED overall HOMO-LUMO gap: 0.75309378 eV between HOMO at k-point 1 and LUMO at k-point 4 - | This appears to be an indirect band gap. - | Smallest direct gap : 2.42412061 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, - this system is most likely an insulator or a semiconductor. - - Total energy components: - | Sum of eigenvalues : -328.16168175 Ha -8929.73370032 eV - | XC energy correction : -41.77728314 Ha -1136.81771491 eV - | XC potential correction : 53.94925801 Ha 1468.03400310 eV - | Free-atom electrostatic energy: -263.74356637 Ha -7176.82759392 eV - | Hartree energy correction : -0.91362820 Ha -24.86108824 eV - | Entropy correction : 0.00000000 Ha 0.00000000 eV - | --------------------------- - | Total energy : -580.64690146 Ha -15800.20609429 eV - | Total energy, T -> 0 : -580.64690146 Ha -15800.20609429 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -580.64690146 Ha -15800.20609429 eV - - Derived energy quantities: - | Kinetic energy : 582.24622666 Ha 15843.72594733 eV - | Electrostatic energy : -1121.11584498 Ha -30507.11432671 eV - | Energy correction for multipole - | error in Hartree potential : 0.01978591 Ha 0.53840201 eV - | Sum of eigenvalues per atom : -4464.86685016 eV - | Total energy (T->0) per atom : -7900.10304715 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -7900.10304715 eV - Evaluating new KS density using the density matrix - Evaluating density matrix - Time summed over all CPUs for getting density from density matrix: real work 0.843 s, elapsed 0.843 s - Integration grid: deviation in total charge ( - N_e) = -7.460699E-14 - - atomic forces [eV/Ang]: - ----------------------- - atom # 1 - Hellmann-Feynman : -0.145696E-06 0.748304E-07 0.742362E-07 - Ionic forces : 0.000000E+00 0.000000E+00 0.000000E+00 - Multipole : 0.103356E-07 -0.366332E-08 -0.377652E-08 - Hartree pot. SCF incomplete : -0.454440E-09 0.155893E-09 0.272707E-09 - Pulay + GGA : 0.000000E+00 0.000000E+00 0.000000E+00 - ---------------------------------------------------------------- - Total forces( 1) : -0.135814E-06 0.713230E-07 0.707324E-07 - atom # 2 - Hellmann-Feynman : 0.145882E-06 -0.722275E-07 -0.731727E-07 - Ionic forces : 0.000000E+00 0.000000E+00 0.000000E+00 - Multipole : -0.103354E-07 0.366328E-08 0.377543E-08 - Hartree pot. SCF incomplete : 0.389921E-09 -0.232855E-09 -0.270420E-09 - Pulay + GGA : 0.000000E+00 0.000000E+00 0.000000E+00 - ---------------------------------------------------------------- - Total forces( 2) : 0.135936E-06 -0.687971E-07 -0.696677E-07 - - - Self-consistency convergence accuracy: - | Change of charge density : 0.4476E-08 - | Change of sum of eigenvalues : 0.1149E-05 eV - | Change of total energy : 0.1454E-09 eV - | Change of forces : 0.1677E-06 eV/A - - ------------------------------------------------------------- - End self-consistency iteration # 9 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 3.851 s 3.873 s - | Charge density & force component update : 0.839 s 0.845 s - | Density mixing : 0.002 s 0.002 s - | Hartree multipole update : 0.001 s 0.001 s - | Hartree multipole summation : 1.649 s 1.658 s - | Hartree pot. SCF incomplete forces : 0.941 s 0.946 s - | Integration : 0.414 s 0.416 s - | Solution of K.-S. eqns. : 0.005 s 0.005 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 1.632 MB (on task 0) - | Maximum: 1.632 MB (on task 0) - | Average: 1.632 MB - | Peak value for overall tracked memory usage: - | Minimum: 14.236 MB (on task 0 after allocating d_wave) - | Maximum: 14.236 MB (on task 0 after allocating d_wave) - | Average: 14.236 MB - | Largest tracked array allocation so far: - | Minimum: 3.456 MB (hamiltonian_shell on task 0) - | Maximum: 3.456 MB (hamiltonian_shell on task 0) - | Average: 3.456 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - ------------------------------------------------------------- - Begin self-consistency iteration # 10 - - Date : 20230628, Time : 104232.246 ------------------------------------------------------------- - Pulay mixing of updated and previous charge densities. - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 28.0000000000 - | Integrated number of electrons on 3D grid : 28.0000000000 - | Charge integration error : -0.0000000000 - | Normalization factor for density and gradient : 1.0000000000 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = -0.657781E-13 - | Sum of charges compensated after spline to logarithmic grids = -0.110001E-03 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = 0.000000E+00 - Summing up the Hartree potential. - Time summed over all CPUs for potential: real work 1.653 s, elapsed 1.653 s - | RMS charge density error from multipole expansion : 0.146805E-01 - | Average real-space part of the electrostatic potential : 0.47675985 eV - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.417 s, elapsed 0.417 s - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.000 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -4.92520044 eV - What follows are estimated values for band gap, HOMO, LUMO, etc. - | They are estimated on a discrete k-point grid and not necessarily exact. - | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. - - Highest occupied state (VBM) at -5.28814064 eV (relative to internal zero) - | Occupation number: 2.00000000 - | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - - Lowest unoccupied state (CBM) at -4.53504686 eV (relative to internal zero) - | Occupation number: 0.00000000 - | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) - - ESTIMATED overall HOMO-LUMO gap: 0.75309378 eV between HOMO at k-point 1 and LUMO at k-point 4 - | This appears to be an indirect band gap. - | Smallest direct gap : 2.42412061 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, - this system is most likely an insulator or a semiconductor. - - Total energy components: - | Sum of eigenvalues : -328.16168174 Ha -8929.73370007 eV - | XC energy correction : -41.77728314 Ha -1136.81771494 eV - | XC potential correction : 53.94925801 Ha 1468.03400314 eV - | Free-atom electrostatic energy: -263.74356637 Ha -7176.82759392 eV - | Hartree energy correction : -0.91362821 Ha -24.86108850 eV - | Entropy correction : 0.00000000 Ha 0.00000000 eV - | --------------------------- - | Total energy : -580.64690146 Ha -15800.20609429 eV - | Total energy, T -> 0 : -580.64690146 Ha -15800.20609429 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -580.64690146 Ha -15800.20609429 eV - - Derived energy quantities: - | Kinetic energy : 582.24622668 Ha 15843.72594782 eV - | Electrostatic energy : -1121.11584499 Ha -30507.11432716 eV - | Energy correction for multipole - | error in Hartree potential : 0.01978591 Ha 0.53840201 eV - | Sum of eigenvalues per atom : -4464.86685003 eV - | Total energy (T->0) per atom : -7900.10304715 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -7900.10304715 eV - Evaluating new KS density using the density matrix - Evaluating density matrix - Time summed over all CPUs for getting density from density matrix: real work 0.843 s, elapsed 0.843 s - - Evaluating density-matrix-based force terms: batch-based integration - Evaluating density matrix - Evaluating density matrix - Integration grid: deviation in total charge ( - N_e) = -2.486900E-14 - - atomic forces [eV/Ang]: - ----------------------- - atom # 1 - Hellmann-Feynman : -0.145995E-06 0.750543E-07 0.744960E-07 - Ionic forces : 0.000000E+00 0.000000E+00 0.000000E+00 - Multipole : 0.103364E-07 -0.366274E-08 -0.377878E-08 - Hartree pot. SCF incomplete : -0.358185E-09 0.103402E-09 0.222414E-09 - Pulay + GGA : 0.169233E-06 -0.805632E-07 -0.834521E-07 - ---------------------------------------------------------------- - Total forces( 1) : 0.332160E-07 -0.906822E-08 -0.125124E-07 - atom # 2 - Hellmann-Feynman : 0.146165E-06 -0.724696E-07 -0.734276E-07 - Ionic forces : 0.000000E+00 0.000000E+00 0.000000E+00 - Multipole : -0.103358E-07 0.366295E-08 0.377614E-08 - Hartree pot. SCF incomplete : 0.293215E-09 -0.158219E-09 -0.190451E-09 - Pulay + GGA : -0.183358E-06 0.756836E-07 0.762508E-07 - ---------------------------------------------------------------- - Total forces( 2) : -0.472358E-07 0.671870E-08 0.640891E-08 - - - Analytical stress tensor components [eV] xx yy zz xy xz yz - ----------------------------------------------------------------------------------------------------------------------------------------------------------- - Nuclear Hellmann-Feynman : -0.1414603250E+02 -0.1414626976E+02 -0.1414626973E+02 -0.2419395416E-07 -0.2344943180E-07 0.7515882712E-07 - Multipole Hellmann-Feynman : -0.3058493612E+02 -0.3058494702E+02 -0.3058494706E+02 -0.5452181630E-07 -0.5027800706E-07 0.2153701328E-06 - On-site Multipole corrections : -0.2833796336E+00 -0.2833796336E+00 -0.2833796336E+00 0.4306547092E-10 0.4092601380E-10 -0.1215927816E-09 - Strain deriv. of the orbitals : 0.4401780801E+02 0.4401805485E+02 0.4401805485E+02 0.2741294229E-07 0.2308618083E-07 -0.1752726495E-06 - ----------------------------------------------------------------------------------------------------------------------------------------------------------- - Sum of all contributions : -0.9965402449E+00 -0.9965415741E+00 -0.9965415777E+00 -0.5125976270E-07 -0.5060033201E-07 0.1151347177E-06 - - +-------------------------------------------------------------------+ - | Analytical stress tensor - Symmetrized | - | Cartesian components [eV/A**3] | - +-------------------------------------------------------------------+ - | x y z | - | | - | x -0.02338243 -0.00000000 -0.00000000 | - | y -0.00000000 -0.02338246 0.00000000 | - | z -0.00000000 0.00000000 -0.02338246 | - | | - | Pressure: 0.02338245 [eV/A**3] | - | | - +-------------------------------------------------------------------+ - - - Self-consistency convergence accuracy: - | Change of charge density : 0.1796E-09 - | Change of sum of eigenvalues : 0.2478E-06 eV - | Change of total energy : -0.4640E-10 eV - | Change of forces : 0.4524E-09 eV/A - - Writing Kohn-Sham eigenvalues. - K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - - State Occupation Eigenvalue [Ha] Eigenvalue [eV] - 1 2.00000 -65.744123 -1788.98861 - 2 2.00000 -65.744123 -1788.98861 - 3 2.00000 -5.104202 -138.89241 - 4 2.00000 -5.103995 -138.88676 - 5 2.00000 -3.487854 -94.90933 - 6 2.00000 -3.487854 -94.90933 - 7 2.00000 -3.487854 -94.90933 - 8 2.00000 -3.487374 -94.89627 - 9 2.00000 -3.487374 -94.89627 - 10 2.00000 -3.487374 -94.89627 - 11 2.00000 -0.620861 -16.89449 - 12 2.00000 -0.194336 -5.28814 - 13 2.00000 -0.194336 -5.28814 - 14 2.00000 -0.194336 -5.28814 - 15 0.00000 -0.105251 -2.86402 - 16 0.00000 -0.105251 -2.86402 - 17 0.00000 -0.105251 -2.86402 - 18 0.00000 -0.094315 -2.56644 - 19 0.00000 0.090720 2.46860 - 20 0.00000 0.090720 2.46860 - - What follows are estimated values for band gap, HOMO, LUMO, etc. - | They are estimated on a discrete k-point grid and not necessarily exact. - | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. - - Highest occupied state (VBM) at -5.28814064 eV (relative to internal zero) - | Occupation number: 2.00000000 - | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - - Lowest unoccupied state (CBM) at -4.53504686 eV (relative to internal zero) - | Occupation number: 0.00000000 - | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) - - ESTIMATED overall HOMO-LUMO gap: 0.75309378 eV between HOMO at k-point 1 and LUMO at k-point 4 - | This appears to be an indirect band gap. - | Smallest direct gap : 2.42412061 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, - this system is most likely an insulator or a semiconductor. - | Chemical Potential : -4.92520044 eV - - Self-consistency cycle converged. - - ------------------------------------------------------------- - End self-consistency iteration # 10 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 19.789 s 19.919 s - | Charge density & force component update : 16.791 s 16.906 s - | Density mixing : 0.002 s 0.002 s - | Hartree multipole update : 0.001 s 0.001 s - | Hartree multipole summation : 1.649 s 1.657 s - | Hartree pot. SCF incomplete forces : 0.926 s 0.931 s - | Integration : 0.415 s 0.417 s - | Solution of K.-S. eqns. : 0.005 s 0.005 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 1.632 MB (on task 0) - | Maximum: 1.632 MB (on task 0) - | Average: 1.632 MB - | Peak value for overall tracked memory usage: - | Minimum: 14.236 MB (on task 0 after allocating d_wave) - | Maximum: 14.236 MB (on task 0 after allocating d_wave) - | Average: 14.236 MB - | Largest tracked array allocation so far: - | Minimum: 3.456 MB (hamiltonian_shell on task 0) - | Maximum: 3.456 MB (hamiltonian_shell on task 0) - | Average: 3.456 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - Removing unitary transformations (pure translations, rotations) from forces on atoms. - Atomic forces before filtering: - | Net force on center of mass : -0.140198E-07 -0.234952E-08 -0.610350E-08 eV/A - Atomic forces after filtering: - | Net force on center of mass : -0.531692E-23 -0.132923E-23 0.000000E+00 eV/A - - Energy and forces in a compact form: - | Total energy uncorrected : -0.158002060942910E+05 eV - | Total energy corrected : -0.158002060942910E+05 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -0.158002060942910E+05 eV - Total atomic forces (unitary forces cleaned) [eV/Ang]: - | 1 0.402258645112855E-07 -0.789345665168126E-08 -0.946066143948756E-08 - | 2 -0.402258645112855E-07 0.789345665168126E-08 0.946066143948756E-08 - - ------------------------------------ - Start decomposition of the XC Energy - ------------------------------------ - X and C from original XC functional choice - Hartree-Fock Energy : 0.000000000 Ha 0.000000000 eV - X Energy : -40.691832894 Ha -1107.281110900 eV - C Energy : -1.085450248 Ha -29.536604044 eV - XC Energy w/o HF : -41.777283142 Ha -1136.817714944 eV - Total XC Energy : -41.777283142 Ha -1136.817714944 eV - ------------------------------------ - LDA X and C from self-consistent density - X Energy LDA : -37.625522323 Ha -1023.842554939 eV - C Energy LDA : -2.145950281 Ha -58.394278201 eV - ------------------------------------ - End decomposition of the XC Energy - ------------------------------------ - ------------------------------------------------------------- - Relaxation / MD: End force evaluation. : max(cpu_time) wall_clock(cpu1) - | Time for this force evaluation : 39.534 s 39.781 s - ------------------------------------------------------------- - Geometry optimization: Attempting to predict improved coordinates. - - +-------------------------------------------------------------------+ - | Generalized derivatives on lattice vectors [eV/A] | - +-------------------------------------------------------------------+ - |lattice_vector 0.17972412 -0.17972435 -0.17972435 | - |lattice_vector -0.17972414 0.17972439 -0.17972441 | - |lattice_vector -0.17972414 -0.17972441 0.17972440 | - +-------------------------------------------------------------------+ - | Forces on lattice vectors cleaned from atomic contributions [eV/A]| - +-------------------------------------------------------------------+ - |lattice_vector -0.17972412 0.17972435 0.17972435 | - |lattice_vector 0.17972414 -0.17972439 0.17972441 | - |lattice_vector 0.17972414 0.17972441 -0.17972440 | - +-------------------------------------------------------------------+ - Removing unitary transformations (pure translations, rotations) from forces on atoms. - Atomic forces before filtering: - | Net force on center of mass : -0.531692E-23 -0.132923E-23 0.000000E+00 eV/A - Atomic forces after filtering: - | Net force on center of mass : -0.531692E-23 -0.132923E-23 0.000000E+00 eV/A - Net remaining forces (excluding translations, rotations) in present geometry: - || Forces on atoms || = 0.402259E-07 eV/A. - || Forces on lattice || = 0.179724E+00 eV/A^3. - Maximum force component is 0.179724E+00 eV/A. - Present geometry is not yet converged. - - Relaxation step number 2: Predicting new coordinates. - - Advancing geometry using trust radius method. - | True / expected gain: -2.17E-02 eV / -1.37E-02 eV = 1.5829 - | Harmonic / expected gain: -2.31E-02 eV / -1.37E-02 eV = 1.6845 - | Hessian has 0 negative and 3 zero eigenvalues. - | Positive eigenvalues (eV/A^2): 3.92E+00 ... 3.02E+01 - | Use Quasi-Newton step of length |H^-1 F| = 9.26E-02 A. - Finished advancing geometry - | Time : 0.000 s - Updated atomic structure: - x [A] y [A] z [A] - lattice_vector 0.00000007 2.81020375 2.81020375 - lattice_vector 2.81020365 -0.00000003 2.81020369 - lattice_vector 2.81020365 2.81020369 -0.00000004 - - atom 0.00000001 -0.00000000 -0.00000000 Si - atom 1.40510183 1.40510185 1.40510185 Si - - Fractional coordinates: - L1 L2 L3 - atom_frac -0.00000000 0.00000000 0.00000000 Si - atom_frac 0.25000000 0.25000000 0.25000000 Si ------------------------------------------------------------- - Writing the current geometry to file "geometry.in.next_step". - Writing estimated Hessian matrix to file 'hessian.aims' - - Quantities derived from the lattice vectors: - | Reciprocal lattice vector 1: -1.117923 1.117923 1.117923 - | Reciprocal lattice vector 2: 1.117923 -1.117923 1.117923 - | Reciprocal lattice vector 3: 1.117923 1.117923 -1.117923 - | Unit cell volume : 0.443857E+02 A^3 - - Range separation radius for Ewald summation (hartree_convergence_parameter): 4.03797672 bohr. - ------------------------------------------------------------- - Begin self-consistency loop: Re-initialization. - - Date : 20230628, Time : 104252.172 ------------------------------------------------------------- - - Initializing index lists of integration centers etc. from given atomic structure: - Mapping all atomic coordinates to central unit cell. - - Initializing the k-points - Using symmetry for reducing the k-points - | k-points reduced from: 8 to 8 - | Number of k-points : 8 - The eigenvectors in the calculations are REAL. - | K-points in task 0: 8 - | Number of basis functions in the Hamiltonian integrals : 1771 - | Number of basis functions in a single unit cell : 50 - | Number of centers in hartree potential : 708 - | Number of centers in hartree multipole : 318 - | Number of centers in electron density summation: 190 - | Number of centers in basis integrals : 198 - | Number of centers in integrals : 101 - | Number of centers in hamiltonian : 190 - | Consuming 14 KiB for k_phase. - | Number of super-cells (origin) [n_cells] : 2197 - | Number of super-cells (after PM_index) [n_cells] : 112 - | Number of super-cells in hamiltonian [n_cells_in_hamiltonian]: 112 - | Size of matrix packed + index [n_hamiltonian_matrix_size] : 82595 - Partitioning the integration grid into batches with parallel hashing+maxmin method. - | Number of batches: 128 - | Maximal batch size: 90 - | Minimal batch size: 85 - | Average batch size: 87.562 - | Standard deviation of batch sizes: 1.493 - - Integration load balanced across 1 MPI tasks. - Work distribution over tasks is as follows: - Initializing partition tables, free-atom densities, potentials, etc. across the integration grid (initialize_grid_storage). - | Species 1: outer_partition_radius set to 5.000694715736543 AA . - | The sparse table of interatomic distances needs 194.62 kbyte instead of 313.63 kbyte of memory. - | Net number of integration points: 11208 - | of which are non-zero points : 9876 - | Numerical average free-atom electrostatic potential : -11.84315486 eV - Renormalizing the initial density to the exact electron count on the 3D integration grid. - | Initial density: Formal number of electrons (from input files) : 28.0000000000 - | Integrated number of electrons on 3D grid : 28.0038026450 - | Charge integration error : 0.0038026450 - | Normalization factor for density and gradient : 0.9998642097 - Renormalizing the free-atom superposition density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 28.0000000000 - | Integrated number of electrons on 3D grid : 28.0038026450 - | Charge integration error : 0.0038026450 - | Normalization factor for density and gradient : 0.9998642097 - Obtaining max. number of non-zero basis functions in each batch (get_n_compute_maxes). - Calculating total energy contributions from superposition of free atom densities. - Initialize hartree_potential_storage - Integrating overlap matrix. - Time summed over all CPUs for integration: real work 0.254 s, elapsed 0.254 s - Orthonormalizing eigenvectors - - End scf reinitialization - timings : max(cpu_time) wall_clock(cpu1) - | Time for scf. reinitialization : 0.560 s 0.563 s - | Boundary condition initialization : 0.064 s 0.064 s - | Integration : 0.252 s 0.254 s - | Grid partitioning : 0.032 s 0.032 s - | Preloading free-atom quantities on grid : 0.174 s 0.175 s - | Free-atom superposition energy : 0.027 s 0.027 s - | K.-S. eigenvector reorthonormalization : 0.001 s 0.001 s ------------------------------------------------------------- - Evaluating new KS density using the density matrix - Evaluating density matrix - Time summed over all CPUs for getting density from density matrix: real work 0.805 s, elapsed 0.805 s - Integration grid: deviation in total charge ( - N_e) = 7.105427E-15 - - Time for density update prior : max(cpu_time) wall_clock(cpu1) - | self-consistency iterative process : 0.801 s 0.807 s - ------------------------------------------------------------- - Begin self-consistency iteration # 1 - - Date : 20230628, Time : 104253.542 ------------------------------------------------------------- - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 28.0000000000 - | Integrated number of electrons on 3D grid : 28.0000000000 - | Charge integration error : 0.0000000000 - | Normalization factor for density and gradient : 1.0000000000 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = 0.158275E-12 - | Sum of charges compensated after spline to logarithmic grids = -0.694106E-04 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = 0.000000E+00 - Summing up the Hartree potential. - | Estimated reciprocal-space cutoff momentum G_max: 2.30767722 bohr^-1 . - | Reciprocal lattice points for long-range Hartree potential: 58 - Time summed over all CPUs for potential: real work 0.391 s, elapsed 0.391 s - | RMS charge density error from multipole expansion : 0.138738E-01 - | Average real-space part of the electrostatic potential : 0.43982773 eV - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.397 s, elapsed 0.397 s - Decreasing sparse matrix size: - | Tolerance: 0.1000E-12 - Hamiltonian matrix - | Array has 75370 nonzero elements out of 82595 elements - | Sparsity factor is 0.087 - Overlap matrix - | Array has 68470 nonzero elements out of 82595 elements - | Sparsity factor is 0.171 - New size of hamiltonian matrix: 75393 - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Singularity check in k-point 1, task 0 (analysis for other k-points/tasks may follow below): - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.000 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -5.00592993 eV - Writing Kohn-Sham eigenvalues. - K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - - State Occupation Eigenvalue [Ha] Eigenvalue [eV] - 1 2.00000 -65.749436 -1789.13317 - 2 2.00000 -65.749436 -1789.13317 - 3 2.00000 -5.106559 -138.95654 - 4 2.00000 -5.106390 -138.95195 - 5 2.00000 -3.490380 -94.97807 - 6 2.00000 -3.490380 -94.97807 - 7 2.00000 -3.490380 -94.97807 - 8 2.00000 -3.489976 -94.96707 - 9 2.00000 -3.489976 -94.96707 - 10 2.00000 -3.489976 -94.96707 - 11 2.00000 -0.609457 -16.58418 - 12 2.00000 -0.192712 -5.24397 - 13 2.00000 -0.192712 -5.24397 - 14 2.00000 -0.192712 -5.24397 - 15 0.00000 -0.109029 -2.96684 - 16 0.00000 -0.104086 -2.83233 - 17 0.00000 -0.104086 -2.83233 - 18 0.00000 -0.104086 -2.83233 - 19 0.00000 0.092607 2.51996 - 20 0.00000 0.092607 2.51996 - - What follows are estimated values for band gap, HOMO, LUMO, etc. - | They are estimated on a discrete k-point grid and not necessarily exact. - | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. - - Highest occupied state (VBM) at -5.24396793 eV (relative to internal zero) - | Occupation number: 2.00000000 - | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - - Lowest unoccupied state (CBM) at -4.41671413 eV (relative to internal zero) - | Occupation number: 0.00000000 - | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) - - ESTIMATED overall HOMO-LUMO gap: 0.82725381 eV between HOMO at k-point 1 and LUMO at k-point 4 - | This appears to be an indirect band gap. - | Smallest direct gap : 2.27712508 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, - this system is most likely an insulator or a semiconductor. - - Total energy components: - | Sum of eigenvalues : -328.17953753 Ha -8930.21958065 eV - | XC energy correction : -41.74961532 Ha -1136.06483528 eV - | XC potential correction : 53.91234167 Ha 1467.02945857 eV - | Free-atom electrostatic energy: -263.83177839 Ha -7179.22796514 eV - | Hartree energy correction : -0.79902556 Ha -21.74259165 eV - | Entropy correction : -0.00000000 Ha -0.00000000 eV - | --------------------------- - | Total energy : -580.64761512 Ha -15800.22551413 eV - | Total energy, T -> 0 : -580.64761512 Ha -15800.22551413 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -580.64761512 Ha -15800.22551413 eV - - Derived energy quantities: - | Kinetic energy : 582.08268557 Ha 15839.27576796 eV - | Electrostatic energy : -1120.98068538 Ha -30503.43644682 eV - | Energy correction for multipole - | error in Hartree potential : 0.01842747 Ha 0.50143705 eV - | Sum of eigenvalues per atom : -4465.10979032 eV - | Total energy (T->0) per atom : -7900.11275707 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -7900.11275707 eV - Evaluating new KS density using the density matrix - Evaluating density matrix - Time summed over all CPUs for getting density from density matrix: real work 0.809 s, elapsed 0.809 s - Integration grid: deviation in total charge ( - N_e) = 4.973799E-14 - - Self-consistency convergence accuracy: - | Change of charge density : 0.1325E+00 - | Change of sum of eigenvalues : -0.8930E+04 eV - | Change of total energy : -0.1580E+05 eV - - ------------------------------------------------------------- - End self-consistency iteration # 1 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 1.598 s 1.607 s - | Charge density update : 0.805 s 0.810 s - | Density mixing & preconditioning : 0.000 s 0.000 s - | Hartree multipole update : 0.001 s 0.001 s - | Hartree multipole summation : 0.392 s 0.394 s - | Integration : 0.395 s 0.398 s - | Solution of K.-S. eqns. : 0.005 s 0.004 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 1.569 MB (on task 0) - | Maximum: 1.569 MB (on task 0) - | Average: 1.569 MB - | Peak value for overall tracked memory usage: - | Minimum: 14.236 MB (on task 0 after allocating d_wave) - | Maximum: 14.236 MB (on task 0 after allocating d_wave) - | Average: 14.236 MB - | Largest tracked array allocation so far: - | Minimum: 3.456 MB (hamiltonian_shell on task 0) - | Maximum: 3.456 MB (hamiltonian_shell on task 0) - | Average: 3.456 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - ------------------------------------------------------------- - Begin self-consistency iteration # 2 - - Date : 20230628, Time : 104255.149 ------------------------------------------------------------- - Pulay mixing of updated and previous charge densities. - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 28.0000000000 - | Integrated number of electrons on 3D grid : 27.9999816483 - | Charge integration error : -0.0000183517 - | Normalization factor for density and gradient : 1.0000006554 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = 0.130890E-13 - | Sum of charges compensated after spline to logarithmic grids = -0.694375E-04 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = 0.000000E+00 - Summing up the Hartree potential. - Time summed over all CPUs for potential: real work 0.392 s, elapsed 0.392 s - | RMS charge density error from multipole expansion : 0.138614E-01 - | Average real-space part of the electrostatic potential : 0.43992626 eV - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.401 s, elapsed 0.401 s - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.000 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -5.00656759 eV - What follows are estimated values for band gap, HOMO, LUMO, etc. - | They are estimated on a discrete k-point grid and not necessarily exact. - | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. - - Highest occupied state (VBM) at -5.24455109 eV (relative to internal zero) - | Occupation number: 2.00000000 - | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - - Lowest unoccupied state (CBM) at -4.41699375 eV (relative to internal zero) - | Occupation number: 0.00000000 - | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) - - ESTIMATED overall HOMO-LUMO gap: 0.82755734 eV between HOMO at k-point 1 and LUMO at k-point 4 - | This appears to be an indirect band gap. - | Smallest direct gap : 2.27729154 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, - this system is most likely an insulator or a semiconductor. - - Total energy components: - | Sum of eigenvalues : -328.17620388 Ha -8930.12886748 eV - | XC energy correction : -41.75005579 Ha -1136.07682099 eV - | XC potential correction : 53.91291833 Ha 1467.04515027 eV - | Free-atom electrostatic energy: -263.83177839 Ha -7179.22796514 eV - | Hartree energy correction : -0.80249533 Ha -21.83700887 eV - | Entropy correction : -0.00000000 Ha -0.00000000 eV - | --------------------------- - | Total energy : -580.64761505 Ha -15800.22551221 eV - | Total energy, T -> 0 : -580.64761505 Ha -15800.22551221 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -580.64761505 Ha -15800.22551221 eV - - Derived energy quantities: - | Kinetic energy : 582.09177949 Ha 15839.52322595 eV - | Electrostatic energy : -1120.98933875 Ha -30503.67191717 eV - | Energy correction for multipole - | error in Hartree potential : 0.01842356 Ha 0.50133061 eV - | Sum of eigenvalues per atom : -4465.06443374 eV - | Total energy (T->0) per atom : -7900.11275611 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -7900.11275611 eV - Evaluating new KS density using the density matrix - Evaluating density matrix - Time summed over all CPUs for getting density from density matrix: real work 0.808 s, elapsed 0.808 s - Integration grid: deviation in total charge ( - N_e) = 4.973799E-14 - - Self-consistency convergence accuracy: - | Change of charge density : 0.2137E-02 - | Change of sum of eigenvalues : 0.9071E-01 eV - | Change of total energy : 0.1920E-05 eV - - ------------------------------------------------------------- - End self-consistency iteration # 2 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 1.778 s 1.789 s - | Charge density update : 0.804 s 0.809 s - | Density mixing & preconditioning : 0.177 s 0.178 s - | Hartree multipole update : 0.001 s 0.002 s - | Hartree multipole summation : 0.392 s 0.394 s - | Integration : 0.399 s 0.401 s - | Solution of K.-S. eqns. : 0.005 s 0.005 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 1.569 MB (on task 0) - | Maximum: 1.569 MB (on task 0) - | Average: 1.569 MB - | Peak value for overall tracked memory usage: - | Minimum: 14.236 MB (on task 0 after allocating d_wave) - | Maximum: 14.236 MB (on task 0 after allocating d_wave) - | Average: 14.236 MB - | Largest tracked array allocation so far: - | Minimum: 3.456 MB (hamiltonian_shell on task 0) - | Maximum: 3.456 MB (hamiltonian_shell on task 0) - | Average: 3.456 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - ------------------------------------------------------------- - Begin self-consistency iteration # 3 - - Date : 20230628, Time : 104256.938 ------------------------------------------------------------- - Pulay mixing of updated and previous charge densities. - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 28.0000000000 - | Integrated number of electrons on 3D grid : 27.9998999680 - | Charge integration error : -0.0001000320 - | Normalization factor for density and gradient : 1.0000035726 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = 0.191295E-14 - | Sum of charges compensated after spline to logarithmic grids = -0.695443E-04 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = 0.000000E+00 - Summing up the Hartree potential. - Time summed over all CPUs for potential: real work 0.391 s, elapsed 0.391 s - | RMS charge density error from multipole expansion : 0.138170E-01 - | Average real-space part of the electrostatic potential : 0.44042345 eV - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.400 s, elapsed 0.400 s - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.000 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -5.00875522 eV - What follows are estimated values for band gap, HOMO, LUMO, etc. - | They are estimated on a discrete k-point grid and not necessarily exact. - | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. - - Highest occupied state (VBM) at -5.24650921 eV (relative to internal zero) - | Occupation number: 2.00000000 - | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - - Lowest unoccupied state (CBM) at -4.41793384 eV (relative to internal zero) - | Occupation number: 0.00000000 - | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) - - ESTIMATED overall HOMO-LUMO gap: 0.82857537 eV between HOMO at k-point 1 and LUMO at k-point 4 - | This appears to be an indirect band gap. - | Smallest direct gap : 2.27795944 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, - this system is most likely an insulator or a semiconductor. - - Total energy components: - | Sum of eigenvalues : -328.16359582 Ha -8929.78578471 eV - | XC energy correction : -41.75168311 Ha -1136.12110253 eV - | XC potential correction : 53.91505137 Ha 1467.10319311 eV - | Free-atom electrostatic energy: -263.83177839 Ha -7179.22796514 eV - | Hartree energy correction : -0.81561003 Ha -22.19387804 eV - | Entropy correction : -0.00000000 Ha -0.00000000 eV - | --------------------------- - | Total energy : -580.64761598 Ha -15800.22553731 eV - | Total energy, T -> 0 : -580.64761598 Ha -15800.22553731 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -580.64761598 Ha -15800.22553731 eV - - Derived energy quantities: - | Kinetic energy : 582.12506692 Ha 15840.42902298 eV - | Electrostatic energy : -1121.02099979 Ha -30504.53345776 eV - | Energy correction for multipole - | error in Hartree potential : 0.01840991 Ha 0.50095915 eV - | Sum of eigenvalues per atom : -4464.89289235 eV - | Total energy (T->0) per atom : -7900.11276865 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -7900.11276865 eV - Evaluating new KS density using the density matrix - Evaluating density matrix - Time summed over all CPUs for getting density from density matrix: real work 0.808 s, elapsed 0.808 s - Integration grid: deviation in total charge ( - N_e) = 3.907985E-14 - - Self-consistency convergence accuracy: - | Change of charge density : 0.1672E-02 - | Change of sum of eigenvalues : 0.3431E+00 eV - | Change of total energy : -0.2509E-04 eV - - ------------------------------------------------------------- - End self-consistency iteration # 3 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 1.778 s 1.788 s - | Charge density update : 0.804 s 0.809 s - | Density mixing & preconditioning : 0.178 s 0.179 s - | Hartree multipole update : 0.001 s 0.001 s - | Hartree multipole summation : 0.392 s 0.394 s - | Integration : 0.398 s 0.400 s - | Solution of K.-S. eqns. : 0.005 s 0.005 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 1.569 MB (on task 0) - | Maximum: 1.569 MB (on task 0) - | Average: 1.569 MB - | Peak value for overall tracked memory usage: - | Minimum: 14.236 MB (on task 0 after allocating d_wave) - | Maximum: 14.236 MB (on task 0 after allocating d_wave) - | Average: 14.236 MB - | Largest tracked array allocation so far: - | Minimum: 3.456 MB (hamiltonian_shell on task 0) - | Maximum: 3.456 MB (hamiltonian_shell on task 0) - | Average: 3.456 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - ------------------------------------------------------------- - Begin self-consistency iteration # 4 - - Date : 20230628, Time : 104258.726 ------------------------------------------------------------- - Pulay mixing of updated and previous charge densities. - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 28.0000000000 - | Integrated number of electrons on 3D grid : 27.9999295002 - | Charge integration error : -0.0000704998 - | Normalization factor for density and gradient : 1.0000025179 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = 0.145459E-12 - | Sum of charges compensated after spline to logarithmic grids = -0.695626E-04 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = 0.000000E+00 - Summing up the Hartree potential. - Time summed over all CPUs for potential: real work 0.391 s, elapsed 0.391 s - | RMS charge density error from multipole expansion : 0.138179E-01 - | Average real-space part of the electrostatic potential : 0.44071380 eV - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.401 s, elapsed 0.401 s - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.000 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -5.00850126 eV - What follows are estimated values for band gap, HOMO, LUMO, etc. - | They are estimated on a discrete k-point grid and not necessarily exact. - | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. - - Highest occupied state (VBM) at -5.24618997 eV (relative to internal zero) - | Occupation number: 2.00000000 - | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - - Lowest unoccupied state (CBM) at -4.41778973 eV (relative to internal zero) - | Occupation number: 0.00000000 - | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) - - ESTIMATED overall HOMO-LUMO gap: 0.82840023 eV between HOMO at k-point 1 and LUMO at k-point 4 - | This appears to be an indirect band gap. - | Smallest direct gap : 2.27808000 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, - this system is most likely an insulator or a semiconductor. - - Total energy components: - | Sum of eigenvalues : -328.16275576 Ha -8929.76292551 eV - | XC energy correction : -41.75170074 Ha -1136.12158234 eV - | XC potential correction : 53.91508115 Ha 1467.10400346 eV - | Free-atom electrostatic energy: -263.83177839 Ha -7179.22796514 eV - | Hartree energy correction : -0.81646339 Ha -22.21709927 eV - | Entropy correction : -0.00000000 Ha -0.00000000 eV - | --------------------------- - | Total energy : -580.64761713 Ha -15800.22556879 eV - | Total energy, T -> 0 : -580.64761713 Ha -15800.22556879 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -580.64761713 Ha -15800.22556879 eV - - Derived energy quantities: - | Kinetic energy : 582.12482304 Ha 15840.42238664 eV - | Electrostatic energy : -1121.02073943 Ha -30504.52637309 eV - | Energy correction for multipole - | error in Hartree potential : 0.01841088 Ha 0.50098545 eV - | Sum of eigenvalues per atom : -4464.88146276 eV - | Total energy (T->0) per atom : -7900.11278440 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -7900.11278440 eV - Evaluating new KS density using the density matrix - Evaluating density matrix - Time summed over all CPUs for getting density from density matrix: real work 0.812 s, elapsed 0.812 s - Integration grid: deviation in total charge ( - N_e) = -4.263256E-14 - - Self-consistency convergence accuracy: - | Change of charge density : 0.1558E-03 - | Change of sum of eigenvalues : 0.2286E-01 eV - | Change of total energy : -0.3149E-04 eV - - ------------------------------------------------------------- - End self-consistency iteration # 4 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 1.782 s 1.794 s - | Charge density update : 0.808 s 0.814 s - | Density mixing & preconditioning : 0.178 s 0.179 s - | Hartree multipole update : 0.001 s 0.002 s - | Hartree multipole summation : 0.392 s 0.393 s - | Integration : 0.399 s 0.401 s - | Solution of K.-S. eqns. : 0.005 s 0.005 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 1.569 MB (on task 0) - | Maximum: 1.569 MB (on task 0) - | Average: 1.569 MB - | Peak value for overall tracked memory usage: - | Minimum: 14.236 MB (on task 0 after allocating d_wave) - | Maximum: 14.236 MB (on task 0 after allocating d_wave) - | Average: 14.236 MB - | Largest tracked array allocation so far: - | Minimum: 3.456 MB (hamiltonian_shell on task 0) - | Maximum: 3.456 MB (hamiltonian_shell on task 0) - | Average: 3.456 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - ------------------------------------------------------------- - Begin self-consistency iteration # 5 - - Date : 20230628, Time : 104300.520 ------------------------------------------------------------- - Pulay mixing of updated and previous charge densities. - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 28.0000000000 - | Integrated number of electrons on 3D grid : 27.9999639037 - | Charge integration error : -0.0000360963 - | Normalization factor for density and gradient : 1.0000012892 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = 0.947663E-13 - | Sum of charges compensated after spline to logarithmic grids = -0.695766E-04 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = 0.000000E+00 - Summing up the Hartree potential. - Time summed over all CPUs for potential: real work 0.391 s, elapsed 0.391 s - | RMS charge density error from multipole expansion : 0.138146E-01 - | Average real-space part of the electrostatic potential : 0.44085511 eV - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.402 s, elapsed 0.402 s - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.000 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -5.00862633 eV - What follows are estimated values for band gap, HOMO, LUMO, etc. - | They are estimated on a discrete k-point grid and not necessarily exact. - | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. - - Highest occupied state (VBM) at -5.24629314 eV (relative to internal zero) - | Occupation number: 2.00000000 - | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - - Lowest unoccupied state (CBM) at -4.41784591 eV (relative to internal zero) - | Occupation number: 0.00000000 - | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) - - ESTIMATED overall HOMO-LUMO gap: 0.82844723 eV between HOMO at k-point 1 and LUMO at k-point 4 - | This appears to be an indirect band gap. - | Smallest direct gap : 2.27813467 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, - this system is most likely an insulator or a semiconductor. - - Total energy components: - | Sum of eigenvalues : -328.16254782 Ha -8929.75726714 eV - | XC energy correction : -41.75163465 Ha -1136.11978386 eV - | XC potential correction : 53.91500339 Ha 1467.10188744 eV - | Free-atom electrostatic energy: -263.83177839 Ha -7179.22796514 eV - | Hartree energy correction : -0.81666037 Ha -22.22245928 eV - | Entropy correction : -0.00000000 Ha -0.00000000 eV - | --------------------------- - | Total energy : -580.64761784 Ha -15800.22558798 eV - | Total energy, T -> 0 : -580.64761784 Ha -15800.22558798 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -580.64761784 Ha -15800.22558798 eV - - Derived energy quantities: - | Kinetic energy : 582.12305363 Ha 15840.37423862 eV - | Electrostatic energy : -1121.01903682 Ha -30504.48004274 eV - | Energy correction for multipole - | error in Hartree potential : 0.01840905 Ha 0.50093578 eV - | Sum of eigenvalues per atom : -4464.87863357 eV - | Total energy (T->0) per atom : -7900.11279399 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -7900.11279399 eV - Evaluating new KS density using the density matrix - Evaluating density matrix - Time summed over all CPUs for getting density from density matrix: real work 0.806 s, elapsed 0.806 s - Integration grid: deviation in total charge ( - N_e) = -2.131628E-14 - - Self-consistency convergence accuracy: - | Change of charge density : 0.1220E-03 - | Change of sum of eigenvalues : 0.5658E-02 eV - | Change of total energy : -0.1918E-04 eV - - ------------------------------------------------------------- - End self-consistency iteration # 5 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 1.777 s 1.788 s - | Charge density update : 0.802 s 0.807 s - | Density mixing & preconditioning : 0.177 s 0.178 s - | Hartree multipole update : 0.001 s 0.001 s - | Hartree multipole summation : 0.392 s 0.394 s - | Integration : 0.400 s 0.402 s - | Solution of K.-S. eqns. : 0.005 s 0.005 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 1.569 MB (on task 0) - | Maximum: 1.569 MB (on task 0) - | Average: 1.569 MB - | Peak value for overall tracked memory usage: - | Minimum: 14.236 MB (on task 0 after allocating d_wave) - | Maximum: 14.236 MB (on task 0 after allocating d_wave) - | Average: 14.236 MB - | Largest tracked array allocation so far: - | Minimum: 3.456 MB (hamiltonian_shell on task 0) - | Maximum: 3.456 MB (hamiltonian_shell on task 0) - | Average: 3.456 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - ------------------------------------------------------------- - Begin self-consistency iteration # 6 - - Date : 20230628, Time : 104302.308 ------------------------------------------------------------- - Pulay mixing of updated and previous charge densities. - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 28.0000000000 - | Integrated number of electrons on 3D grid : 28.0000002635 - | Charge integration error : 0.0000002635 - | Normalization factor for density and gradient : 0.9999999906 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = 0.134233E-13 - | Sum of charges compensated after spline to logarithmic grids = -0.695774E-04 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = 0.000000E+00 - Summing up the Hartree potential. - Time summed over all CPUs for potential: real work 0.391 s, elapsed 0.391 s - | RMS charge density error from multipole expansion : 0.138149E-01 - | Average real-space part of the electrostatic potential : 0.44087742 eV - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.400 s, elapsed 0.400 s - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.000 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -5.00859466 eV - What follows are estimated values for band gap, HOMO, LUMO, etc. - | They are estimated on a discrete k-point grid and not necessarily exact. - | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. - - Highest occupied state (VBM) at -5.24625679 eV (relative to internal zero) - | Occupation number: 2.00000000 - | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - - Lowest unoccupied state (CBM) at -4.41782701 eV (relative to internal zero) - | Occupation number: 0.00000000 - | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) - - ESTIMATED overall HOMO-LUMO gap: 0.82842977 eV between HOMO at k-point 1 and LUMO at k-point 4 - | This appears to be an indirect band gap. - | Smallest direct gap : 2.27813896 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, - this system is most likely an insulator or a semiconductor. - - Total energy components: - | Sum of eigenvalues : -328.16249298 Ha -8929.75577487 eV - | XC energy correction : -41.75163831 Ha -1136.11988366 eV - | XC potential correction : 53.91500793 Ha 1467.10201098 eV - | Free-atom electrostatic energy: -263.83177839 Ha -7179.22796514 eV - | Hartree energy correction : -0.81671611 Ha -22.22397621 eV - | Entropy correction : -0.00000000 Ha -0.00000000 eV - | --------------------------- - | Total energy : -580.64761787 Ha -15800.22558889 eV - | Total energy, T -> 0 : -580.64761787 Ha -15800.22558889 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -580.64761787 Ha -15800.22558889 eV - - Derived energy quantities: - | Kinetic energy : 582.12301570 Ha 15840.37320663 eV - | Electrostatic energy : -1121.01899526 Ha -30504.47891186 eV - | Energy correction for multipole - | error in Hartree potential : 0.01840955 Ha 0.50094923 eV - | Sum of eigenvalues per atom : -4464.87788744 eV - | Total energy (T->0) per atom : -7900.11279444 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -7900.11279444 eV - Evaluating new KS density using the density matrix - Evaluating density matrix - Time summed over all CPUs for getting density from density matrix: real work 0.805 s, elapsed 0.805 s - Integration grid: deviation in total charge ( - N_e) = 2.842171E-14 - - Self-consistency convergence accuracy: - | Change of charge density : 0.6472E-05 - | Change of sum of eigenvalues : 0.1492E-02 eV - | Change of total energy : -0.9144E-06 eV - - ------------------------------------------------------------- - End self-consistency iteration # 6 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 1.775 s 1.785 s - | Charge density update : 0.802 s 0.806 s - | Density mixing & preconditioning : 0.178 s 0.178 s - | Hartree multipole update : 0.001 s 0.001 s - | Hartree multipole summation : 0.392 s 0.394 s - | Integration : 0.398 s 0.401 s - | Solution of K.-S. eqns. : 0.005 s 0.004 s - | Total energy evaluation : 0.000 s 0.001 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 1.569 MB (on task 0) - | Maximum: 1.569 MB (on task 0) - | Average: 1.569 MB - | Peak value for overall tracked memory usage: - | Minimum: 14.236 MB (on task 0 after allocating d_wave) - | Maximum: 14.236 MB (on task 0 after allocating d_wave) - | Average: 14.236 MB - | Largest tracked array allocation so far: - | Minimum: 3.456 MB (hamiltonian_shell on task 0) - | Maximum: 3.456 MB (hamiltonian_shell on task 0) - | Average: 3.456 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - ------------------------------------------------------------- - Begin self-consistency iteration # 7 - - Date : 20230628, Time : 104304.093 ------------------------------------------------------------- - Pulay mixing of updated and previous charge densities. - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 28.0000000000 - | Integrated number of electrons on 3D grid : 28.0000000212 - | Charge integration error : 0.0000000212 - | Normalization factor for density and gradient : 0.9999999992 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = 0.804936E-13 - | Sum of charges compensated after spline to logarithmic grids = -0.695777E-04 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = 0.000000E+00 - Summing up the Hartree potential. - Time summed over all CPUs for potential: real work 0.392 s, elapsed 0.392 s - | RMS charge density error from multipole expansion : 0.138148E-01 - | Average real-space part of the electrostatic potential : 0.44087905 eV - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.401 s, elapsed 0.401 s - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.000 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -5.00860015 eV - What follows are estimated values for band gap, HOMO, LUMO, etc. - | They are estimated on a discrete k-point grid and not necessarily exact. - | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. - - Highest occupied state (VBM) at -5.24626186 eV (relative to internal zero) - | Occupation number: 2.00000000 - | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - - Lowest unoccupied state (CBM) at -4.41782925 eV (relative to internal zero) - | Occupation number: 0.00000000 - | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) - - ESTIMATED overall HOMO-LUMO gap: 0.82843261 eV between HOMO at k-point 1 and LUMO at k-point 4 - | This appears to be an indirect band gap. - | Smallest direct gap : 2.27814005 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, - this system is most likely an insulator or a semiconductor. - - Total energy components: - | Sum of eigenvalues : -328.16247288 Ha -8929.75522800 eV - | XC energy correction : -41.75164027 Ha -1136.11993695 eV - | XC potential correction : 53.91501052 Ha 1467.10208164 eV - | Free-atom electrostatic energy: -263.83177839 Ha -7179.22796514 eV - | Hartree energy correction : -0.81673685 Ha -22.22454051 eV - | Entropy correction : -0.00000000 Ha -0.00000000 eV - | --------------------------- - | Total energy : -580.64761787 Ha -15800.22558896 eV - | Total energy, T -> 0 : -580.64761787 Ha -15800.22558896 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -580.64761787 Ha -15800.22558896 eV - - Derived energy quantities: - | Kinetic energy : 582.12304709 Ha 15840.37406077 eV - | Electrostatic energy : -1121.01902469 Ha -30504.47971278 eV - | Energy correction for multipole - | error in Hartree potential : 0.01840953 Ha 0.50094889 eV - | Sum of eigenvalues per atom : -4464.87761400 eV - | Total energy (T->0) per atom : -7900.11279448 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -7900.11279448 eV - Evaluating new KS density using the density matrix - Evaluating density matrix - Time summed over all CPUs for getting density from density matrix: real work 0.807 s, elapsed 0.807 s - Integration grid: deviation in total charge ( - N_e) = 0.000000E+00 - - Self-consistency convergence accuracy: - | Change of charge density : 0.3201E-05 - | Change of sum of eigenvalues : 0.5469E-03 eV - | Change of total energy : -0.6885E-07 eV - - ------------------------------------------------------------- - End self-consistency iteration # 7 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 1.777 s 1.788 s - | Charge density update : 0.803 s 0.808 s - | Density mixing & preconditioning : 0.178 s 0.180 s - | Hartree multipole update : 0.001 s 0.001 s - | Hartree multipole summation : 0.392 s 0.394 s - | Integration : 0.398 s 0.401 s - | Solution of K.-S. eqns. : 0.005 s 0.004 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 1.569 MB (on task 0) - | Maximum: 1.569 MB (on task 0) - | Average: 1.569 MB - | Peak value for overall tracked memory usage: - | Minimum: 14.236 MB (on task 0 after allocating d_wave) - | Maximum: 14.236 MB (on task 0 after allocating d_wave) - | Average: 14.236 MB - | Largest tracked array allocation so far: - | Minimum: 3.456 MB (hamiltonian_shell on task 0) - | Maximum: 3.456 MB (hamiltonian_shell on task 0) - | Average: 3.456 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - ------------------------------------------------------------- - Begin self-consistency iteration # 8 - - Date : 20230628, Time : 104305.881 ------------------------------------------------------------- - Pulay mixing of updated and previous charge densities. - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 28.0000000000 - | Integrated number of electrons on 3D grid : 27.9999999720 - | Charge integration error : -0.0000000280 - | Normalization factor for density and gradient : 1.0000000010 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = 0.113845E-12 - | Sum of charges compensated after spline to logarithmic grids = -0.695777E-04 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = 0.000000E+00 - Summing up the Hartree potential. - Time summed over all CPUs for potential: real work 0.391 s, elapsed 0.391 s - | RMS charge density error from multipole expansion : 0.138147E-01 - | Average real-space part of the electrostatic potential : 0.44087717 eV - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.400 s, elapsed 0.400 s - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.000 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -5.00860220 eV - What follows are estimated values for band gap, HOMO, LUMO, etc. - | They are estimated on a discrete k-point grid and not necessarily exact. - | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. - - Highest occupied state (VBM) at -5.24626423 eV (relative to internal zero) - | Occupation number: 2.00000000 - | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - - Lowest unoccupied state (CBM) at -4.41783017 eV (relative to internal zero) - | Occupation number: 0.00000000 - | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) - - ESTIMATED overall HOMO-LUMO gap: 0.82843406 eV between HOMO at k-point 1 and LUMO at k-point 4 - | This appears to be an indirect band gap. - | Smallest direct gap : 2.27813974 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, - this system is most likely an insulator or a semiconductor. - - Total energy components: - | Sum of eigenvalues : -328.16247913 Ha -8929.75539800 eV - | XC energy correction : -41.75163983 Ha -1136.11992500 eV - | XC potential correction : 53.91500993 Ha 1467.10206565 eV - | Free-atom electrostatic energy: -263.83177839 Ha -7179.22796514 eV - | Hartree energy correction : -0.81673045 Ha -22.22436629 eV - | Entropy correction : -0.00000000 Ha -0.00000000 eV - | --------------------------- - | Total energy : -580.64761787 Ha -15800.22558879 eV - | Total energy, T -> 0 : -580.64761787 Ha -15800.22558879 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -580.64761787 Ha -15800.22558879 eV - - Derived energy quantities: - | Kinetic energy : 582.12304576 Ha 15840.37402446 eV - | Electrostatic energy : -1121.01902379 Ha -30504.47968825 eV - | Energy correction for multipole - | error in Hartree potential : 0.01840953 Ha 0.50094875 eV - | Sum of eigenvalues per atom : -4464.87769900 eV - | Total energy (T->0) per atom : -7900.11279439 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -7900.11279439 eV - Evaluating new KS density using the density matrix - Evaluating density matrix - Time summed over all CPUs for getting density from density matrix: real work 0.808 s, elapsed 0.808 s - Integration grid: deviation in total charge ( - N_e) = -3.907985E-14 - - Self-consistency convergence accuracy: - | Change of charge density : 0.6371E-06 - | Change of sum of eigenvalues : -0.1700E-03 eV - | Change of total energy : 0.1710E-06 eV - - ------------------------------------------------------------- - End self-consistency iteration # 8 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 1.778 s 1.789 s - | Charge density update : 0.804 s 0.809 s - | Density mixing & preconditioning : 0.178 s 0.180 s - | Hartree multipole update : 0.001 s 0.001 s - | Hartree multipole summation : 0.392 s 0.394 s - | Integration : 0.398 s 0.400 s - | Solution of K.-S. eqns. : 0.005 s 0.005 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 1.569 MB (on task 0) - | Maximum: 1.569 MB (on task 0) - | Average: 1.569 MB - | Peak value for overall tracked memory usage: - | Minimum: 14.236 MB (on task 0 after allocating d_wave) - | Maximum: 14.236 MB (on task 0 after allocating d_wave) - | Average: 14.236 MB - | Largest tracked array allocation so far: - | Minimum: 3.456 MB (hamiltonian_shell on task 0) - | Maximum: 3.456 MB (hamiltonian_shell on task 0) - | Average: 3.456 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - ------------------------------------------------------------- - Begin self-consistency iteration # 9 - - Date : 20230628, Time : 104307.670 ------------------------------------------------------------- - Pulay mixing of updated and previous charge densities. - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 28.0000000000 - | Integrated number of electrons on 3D grid : 28.0000000003 - | Charge integration error : 0.0000000003 - | Normalization factor for density and gradient : 1.0000000000 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = 0.601429E-13 - | Sum of charges compensated after spline to logarithmic grids = -0.695777E-04 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = 0.000000E+00 - Summing up the Hartree potential. - Time summed over all CPUs for potential: real work 0.391 s, elapsed 0.391 s - | RMS charge density error from multipole expansion : 0.138147E-01 - | Average real-space part of the electrostatic potential : 0.44087721 eV - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.401 s, elapsed 0.401 s - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.000 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -5.00860218 eV - What follows are estimated values for band gap, HOMO, LUMO, etc. - | They are estimated on a discrete k-point grid and not necessarily exact. - | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. - - Highest occupied state (VBM) at -5.24626421 eV (relative to internal zero) - | Occupation number: 2.00000000 - | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - - Lowest unoccupied state (CBM) at -4.41783015 eV (relative to internal zero) - | Occupation number: 0.00000000 - | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) - - ESTIMATED overall HOMO-LUMO gap: 0.82843407 eV between HOMO at k-point 1 and LUMO at k-point 4 - | This appears to be an indirect band gap. - | Smallest direct gap : 2.27813973 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, - this system is most likely an insulator or a semiconductor. - - Total energy components: - | Sum of eigenvalues : -328.16247910 Ha -8929.75539715 eV - | XC energy correction : -41.75163984 Ha -1136.11992507 eV - | XC potential correction : 53.91500994 Ha 1467.10206572 eV - | Free-atom electrostatic energy: -263.83177839 Ha -7179.22796514 eV - | Hartree energy correction : -0.81673048 Ha -22.22436715 eV - | Entropy correction : -0.00000000 Ha -0.00000000 eV - | --------------------------- - | Total energy : -580.64761787 Ha -15800.22558879 eV - | Total energy, T -> 0 : -580.64761787 Ha -15800.22558879 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -580.64761787 Ha -15800.22558879 eV - - Derived energy quantities: - | Kinetic energy : 582.12304580 Ha 15840.37402565 eV - | Electrostatic energy : -1121.01902383 Ha -30504.47968937 eV - | Energy correction for multipole - | error in Hartree potential : 0.01840953 Ha 0.50094879 eV - | Sum of eigenvalues per atom : -4464.87769858 eV - | Total energy (T->0) per atom : -7900.11279439 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -7900.11279439 eV - Preliminary charge convergence reached. Turning off preconditioner. - - Evaluating new KS density using the density matrix - Evaluating density matrix - Time summed over all CPUs for getting density from density matrix: real work 0.806 s, elapsed 0.806 s - Integration grid: deviation in total charge ( - N_e) = 7.105427E-15 - - Self-consistency convergence accuracy: - | Change of charge density : 0.1012E-07 - | Change of sum of eigenvalues : 0.8489E-06 eV - | Change of total energy : -0.1237E-10 eV - - Electronic self-consistency reached - switching on the force computation. - - Electronic self-consistency reached - switching on the analytical stress tensor computation. - - ------------------------------------------------------------- - End self-consistency iteration # 9 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 1.776 s 1.786 s - | Charge density & force component update : 0.802 s 0.807 s - | Density mixing : 0.178 s 0.179 s - | Hartree multipole update : 0.001 s 0.001 s - | Hartree multipole summation : 0.392 s 0.394 s - | Hartree pot. SCF incomplete forces : 0.926 s 0.931 s - | Integration : 0.398 s 0.401 s - | Solution of K.-S. eqns. : 0.005 s 0.004 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 1.569 MB (on task 0) - | Maximum: 1.569 MB (on task 0) - | Average: 1.569 MB - | Peak value for overall tracked memory usage: - | Minimum: 14.236 MB (on task 0 after allocating d_wave) - | Maximum: 14.236 MB (on task 0 after allocating d_wave) - | Average: 14.236 MB - | Largest tracked array allocation so far: - | Minimum: 3.456 MB (hamiltonian_shell on task 0) - | Maximum: 3.456 MB (hamiltonian_shell on task 0) - | Average: 3.456 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - ------------------------------------------------------------- - Begin self-consistency iteration # 10 - - Date : 20230628, Time : 104309.457 ------------------------------------------------------------- - Pulay mixing of updated and previous charge densities. - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 28.0000000000 - | Integrated number of electrons on 3D grid : 28.0000000000 - | Charge integration error : 0.0000000000 - | Normalization factor for density and gradient : 1.0000000000 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = 0.115654E-13 - | Sum of charges compensated after spline to logarithmic grids = -0.695777E-04 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = 0.000000E+00 - Summing up the Hartree potential. - Time summed over all CPUs for potential: real work 1.652 s, elapsed 1.652 s - | RMS charge density error from multipole expansion : 0.138147E-01 - | Average real-space part of the electrostatic potential : 0.44087721 eV - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.401 s, elapsed 0.401 s - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.000 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -5.00860218 eV - What follows are estimated values for band gap, HOMO, LUMO, etc. - | They are estimated on a discrete k-point grid and not necessarily exact. - | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. - - Highest occupied state (VBM) at -5.24626422 eV (relative to internal zero) - | Occupation number: 2.00000000 - | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - - Lowest unoccupied state (CBM) at -4.41783015 eV (relative to internal zero) - | Occupation number: 0.00000000 - | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) - - ESTIMATED overall HOMO-LUMO gap: 0.82843407 eV between HOMO at k-point 1 and LUMO at k-point 4 - | This appears to be an indirect band gap. - | Smallest direct gap : 2.27813973 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, - this system is most likely an insulator or a semiconductor. - - Total energy components: - | Sum of eigenvalues : -328.16247910 Ha -8929.75539713 eV - | XC energy correction : -41.75163984 Ha -1136.11992507 eV - | XC potential correction : 53.91500994 Ha 1467.10206572 eV - | Free-atom electrostatic energy: -263.83177839 Ha -7179.22796514 eV - | Hartree energy correction : -0.81673048 Ha -22.22436717 eV - | Entropy correction : -0.00000000 Ha -0.00000000 eV - | --------------------------- - | Total energy : -580.64761787 Ha -15800.22558879 eV - | Total energy, T -> 0 : -580.64761787 Ha -15800.22558879 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -580.64761787 Ha -15800.22558879 eV - - Derived energy quantities: - | Kinetic energy : 582.12304581 Ha 15840.37402572 eV - | Electrostatic energy : -1121.01902384 Ha -30504.47968944 eV - | Energy correction for multipole - | error in Hartree potential : 0.01840953 Ha 0.50094879 eV - | Sum of eigenvalues per atom : -4464.87769857 eV - | Total energy (T->0) per atom : -7900.11279439 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -7900.11279439 eV - Evaluating new KS density using the density matrix - Evaluating density matrix - Time summed over all CPUs for getting density from density matrix: real work 0.806 s, elapsed 0.806 s - Integration grid: deviation in total charge ( - N_e) = -1.065814E-14 - - atomic forces [eV/Ang]: - ----------------------- - atom # 1 - Hellmann-Feynman : -0.542618E-06 0.229221E-06 0.236877E-06 - Ionic forces : 0.000000E+00 0.000000E+00 0.000000E+00 - Multipole : -0.108365E-07 -0.318034E-08 -0.208258E-08 - Hartree pot. SCF incomplete : 0.256616E-09 -0.279956E-10 -0.321834E-10 - Pulay + GGA : 0.000000E+00 0.000000E+00 0.000000E+00 - ---------------------------------------------------------------- - Total forces( 1) : -0.553198E-06 0.226012E-06 0.234762E-06 - atom # 2 - Hellmann-Feynman : 0.547917E-06 -0.227080E-06 -0.236616E-06 - Ionic forces : 0.000000E+00 0.000000E+00 0.000000E+00 - Multipole : 0.108364E-07 0.317865E-08 0.208329E-08 - Hartree pot. SCF incomplete : -0.278235E-09 0.101879E-10 0.602639E-10 - Pulay + GGA : 0.000000E+00 0.000000E+00 0.000000E+00 - ---------------------------------------------------------------- - Total forces( 2) : 0.558475E-06 -0.223891E-06 -0.234472E-06 - - - Self-consistency convergence accuracy: - | Change of charge density : 0.7985E-09 - | Change of sum of eigenvalues : 0.2060E-07 eV - | Change of total energy : 0.1237E-10 eV - | Change of forces : 0.6442E-06 eV/A - - ------------------------------------------------------------- - End self-consistency iteration # 10 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 3.799 s 3.819 s - | Charge density & force component update : 0.802 s 0.807 s - | Density mixing : 0.002 s 0.002 s - | Hartree multipole update : 0.001 s 0.001 s - | Hartree multipole summation : 1.648 s 1.655 s - | Hartree pot. SCF incomplete forces : 0.943 s 0.948 s - | Integration : 0.398 s 0.401 s - | Solution of K.-S. eqns. : 0.005 s 0.005 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 1.569 MB (on task 0) - | Maximum: 1.569 MB (on task 0) - | Average: 1.569 MB - | Peak value for overall tracked memory usage: - | Minimum: 14.236 MB (on task 0 after allocating d_wave) - | Maximum: 14.236 MB (on task 0 after allocating d_wave) - | Average: 14.236 MB - | Largest tracked array allocation so far: - | Minimum: 3.456 MB (hamiltonian_shell on task 0) - | Maximum: 3.456 MB (hamiltonian_shell on task 0) - | Average: 3.456 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - ------------------------------------------------------------- - Begin self-consistency iteration # 11 - - Date : 20230628, Time : 104313.276 ------------------------------------------------------------- - Pulay mixing of updated and previous charge densities. - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 28.0000000000 - | Integrated number of electrons on 3D grid : 28.0000000000 - | Charge integration error : 0.0000000000 - | Normalization factor for density and gradient : 1.0000000000 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = -0.137138E-13 - | Sum of charges compensated after spline to logarithmic grids = -0.695777E-04 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = -0.135922E-13 - Summing up the Hartree potential. - Time summed over all CPUs for potential: real work 1.652 s, elapsed 1.652 s - | RMS charge density error from multipole expansion : 0.138147E-01 - | Average real-space part of the electrostatic potential : 0.44087721 eV - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.401 s, elapsed 0.401 s - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.000 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -5.00860218 eV - What follows are estimated values for band gap, HOMO, LUMO, etc. - | They are estimated on a discrete k-point grid and not necessarily exact. - | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. - - Highest occupied state (VBM) at -5.24626422 eV (relative to internal zero) - | Occupation number: 2.00000000 - | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - - Lowest unoccupied state (CBM) at -4.41783015 eV (relative to internal zero) - | Occupation number: 0.00000000 - | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) - - ESTIMATED overall HOMO-LUMO gap: 0.82843407 eV between HOMO at k-point 1 and LUMO at k-point 4 - | This appears to be an indirect band gap. - | Smallest direct gap : 2.27813973 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, - this system is most likely an insulator or a semiconductor. - - Total energy components: - | Sum of eigenvalues : -328.16247909 Ha -8929.75539708 eV - | XC energy correction : -41.75163984 Ha -1136.11992508 eV - | XC potential correction : 53.91500994 Ha 1467.10206573 eV - | Free-atom electrostatic energy: -263.83177839 Ha -7179.22796514 eV - | Hartree energy correction : -0.81673048 Ha -22.22436722 eV - | Entropy correction : -0.00000000 Ha -0.00000000 eV - | --------------------------- - | Total energy : -580.64761787 Ha -15800.22558879 eV - | Total energy, T -> 0 : -580.64761787 Ha -15800.22558879 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -580.64761787 Ha -15800.22558879 eV - - Derived energy quantities: - | Kinetic energy : 582.12304581 Ha 15840.37402582 eV - | Electrostatic energy : -1121.01902384 Ha -30504.47968953 eV - | Energy correction for multipole - | error in Hartree potential : 0.01840953 Ha 0.50094879 eV - | Sum of eigenvalues per atom : -4464.87769854 eV - | Total energy (T->0) per atom : -7900.11279439 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -7900.11279439 eV - Evaluating new KS density using the density matrix - Evaluating density matrix - Time summed over all CPUs for getting density from density matrix: real work 0.807 s, elapsed 0.807 s - - Evaluating density-matrix-based force terms: batch-based integration - Evaluating density matrix - Evaluating density matrix - Integration grid: deviation in total charge ( - N_e) = -3.552714E-14 - - atomic forces [eV/Ang]: - ----------------------- - atom # 1 - Hellmann-Feynman : -0.542369E-06 0.229192E-06 0.236855E-06 - Ionic forces : 0.000000E+00 0.000000E+00 0.000000E+00 - Multipole : -0.108372E-07 -0.317971E-08 -0.208314E-08 - Hartree pot. SCF incomplete : 0.204530E-09 0.426881E-11 -0.411103E-10 - Pulay + GGA : 0.332299E-06 -0.197292E-06 -0.199532E-06 - ---------------------------------------------------------------- - Total forces( 1) : -0.220703E-06 0.287241E-07 0.351991E-07 - atom # 2 - Hellmann-Feynman : 0.547666E-06 -0.227067E-06 -0.236586E-06 - Ionic forces : 0.000000E+00 0.000000E+00 0.000000E+00 - Multipole : 0.108385E-07 0.318083E-08 0.208178E-08 - Hartree pot. SCF incomplete : -0.232279E-09 0.152712E-10 0.687008E-10 - Pulay + GGA : -0.334454E-06 0.187898E-06 0.189976E-06 - ---------------------------------------------------------------- - Total forces( 2) : 0.223819E-06 -0.359731E-07 -0.444596E-07 - - - Analytical stress tensor components [eV] xx yy zz xy xz yz - ----------------------------------------------------------------------------------------------------------------------------------------------------------- - Nuclear Hellmann-Feynman : -0.1215583460E+02 -0.1215602163E+02 -0.1215602163E+02 0.1223944233E-07 0.1859811812E-08 -0.2081627194E-06 - Multipole Hellmann-Feynman : -0.2784699655E+02 -0.2784700724E+02 -0.2784700725E+02 0.1401674465E-06 0.9598284490E-07 -0.7751689496E-06 - On-site Multipole corrections : -0.2839687132E+00 -0.2839687135E+00 -0.2839687135E+00 0.3702642801E-10 0.4462349828E-10 0.5734027137E-10 - Strain deriv. of the orbitals : 0.4017672923E+02 0.4017692687E+02 0.4017692687E+02 -0.2331229685E-06 -0.1839374584E-06 0.1063722946E-05 - ----------------------------------------------------------------------------------------------------------------------------------------------------------- - Sum of all contributions : -0.1100706416E+00 -0.1100707148E+00 -0.1100707131E+00 -0.8067905325E-07 -0.8605017815E-07 0.8044861777E-07 - - +-------------------------------------------------------------------+ - | Analytical stress tensor - Symmetrized | - | Cartesian components [eV/A**3] | - +-------------------------------------------------------------------+ - | x y z | - | | - | x -0.00247987 -0.00000000 -0.00000000 | - | y -0.00000000 -0.00247987 0.00000000 | - | z -0.00000000 0.00000000 -0.00247987 | - | | - | Pressure: 0.00247987 [eV/A**3] | - | | - +-------------------------------------------------------------------+ - - - Self-consistency convergence accuracy: - | Change of charge density : 0.5403E-09 - | Change of sum of eigenvalues : 0.5458E-07 eV - | Change of total energy : -0.2166E-10 eV - | Change of forces : 0.2508E-09 eV/A - - Writing Kohn-Sham eigenvalues. - K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - - State Occupation Eigenvalue [Ha] Eigenvalue [eV] - 1 2.00000 -65.747889 -1789.09108 - 2 2.00000 -65.747889 -1789.09108 - 3 2.00000 -5.105889 -138.93830 - 4 2.00000 -5.105720 -138.93370 - 5 2.00000 -3.489648 -94.95816 - 6 2.00000 -3.489648 -94.95816 - 7 2.00000 -3.489648 -94.95816 - 8 2.00000 -3.489244 -94.94715 - 9 2.00000 -3.489244 -94.94715 - 10 2.00000 -3.489244 -94.94715 - 11 2.00000 -0.609526 -16.58603 - 12 2.00000 -0.192797 -5.24626 - 13 2.00000 -0.192797 -5.24626 - 14 2.00000 -0.192797 -5.24626 - 15 0.00000 -0.109077 -2.96812 - 16 0.00000 -0.104155 -2.83419 - 17 0.00000 -0.104155 -2.83419 - 18 0.00000 -0.104155 -2.83419 - 19 0.00000 0.092547 2.51834 - 20 0.00000 0.092547 2.51834 - - What follows are estimated values for band gap, HOMO, LUMO, etc. - | They are estimated on a discrete k-point grid and not necessarily exact. - | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. - - Highest occupied state (VBM) at -5.24626422 eV (relative to internal zero) - | Occupation number: 2.00000000 - | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - - Lowest unoccupied state (CBM) at -4.41783015 eV (relative to internal zero) - | Occupation number: 0.00000000 - | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) - - ESTIMATED overall HOMO-LUMO gap: 0.82843407 eV between HOMO at k-point 1 and LUMO at k-point 4 - | This appears to be an indirect band gap. - | Smallest direct gap : 2.27813973 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, - this system is most likely an insulator or a semiconductor. - | Chemical Potential : -5.00860218 eV - - Self-consistency cycle converged. - - ------------------------------------------------------------- - End self-consistency iteration # 11 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 19.043 s 19.167 s - | Charge density & force component update : 16.048 s 16.157 s - | Density mixing : 0.002 s 0.002 s - | Hartree multipole update : 0.001 s 0.001 s - | Hartree multipole summation : 1.648 s 1.656 s - | Hartree pot. SCF incomplete forces : 0.941 s 0.946 s - | Integration : 0.398 s 0.401 s - | Solution of K.-S. eqns. : 0.005 s 0.004 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 1.569 MB (on task 0) - | Maximum: 1.569 MB (on task 0) - | Average: 1.569 MB - | Peak value for overall tracked memory usage: - | Minimum: 14.236 MB (on task 0 after allocating d_wave) - | Maximum: 14.236 MB (on task 0 after allocating d_wave) - | Average: 14.236 MB - | Largest tracked array allocation so far: - | Minimum: 3.456 MB (hamiltonian_shell on task 0) - | Maximum: 3.456 MB (hamiltonian_shell on task 0) - | Average: 3.456 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - Removing unitary transformations (pure translations, rotations) from forces on atoms. - Atomic forces before filtering: - | Net force on center of mass : 0.311585E-08 -0.724909E-08 -0.926049E-08 eV/A - Atomic forces after filtering: - | Net force on center of mass : 0.000000E+00 0.000000E+00 0.000000E+00 eV/A - - Energy and forces in a compact form: - | Total energy uncorrected : -0.158002255887876E+05 eV - | Total energy corrected : -0.158002255887876E+05 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -0.158002255887876E+05 eV - Total atomic forces (unitary forces cleaned) [eV/Ang]: - | 1 -0.222260903726852E-06 0.323486013650826E-07 0.398293064328442E-07 - | 2 0.222260903726852E-06 -0.323486013650826E-07 -0.398293064328442E-07 - - ------------------------------------ - Start decomposition of the XC Energy - ------------------------------------ - X and C from original XC functional choice - Hartree-Fock Energy : 0.000000000 Ha 0.000000000 eV - X Energy : -40.669204423 Ha -1106.665358876 eV - C Energy : -1.082435412 Ha -29.454566200 eV - XC Energy w/o HF : -41.751639836 Ha -1136.119925076 eV - Total XC Energy : -41.751639836 Ha -1136.119925076 eV - ------------------------------------ - LDA X and C from self-consistent density - X Energy LDA : -37.600440540 Ha -1023.160044893 eV - C Energy LDA : -2.144134624 Ha -58.344871663 eV - ------------------------------------ - End decomposition of the XC Energy - ------------------------------------ - ------------------------------------------------------------- - Relaxation / MD: End force evaluation. : max(cpu_time) wall_clock(cpu1) - | Time for this force evaluation : 40.030 s 40.277 s - ------------------------------------------------------------- - Geometry optimization: Attempting to predict improved coordinates. - - +-------------------------------------------------------------------+ - | Generalized derivatives on lattice vectors [eV/A] | - +-------------------------------------------------------------------+ - |lattice_vector 0.01958407 -0.01958409 -0.01958409 | - |lattice_vector -0.01958411 0.01958412 -0.01958415 | - |lattice_vector -0.01958410 -0.01958415 0.01958412 | - +-------------------------------------------------------------------+ - | Forces on lattice vectors cleaned from atomic contributions [eV/A]| - +-------------------------------------------------------------------+ - |lattice_vector -0.01958407 0.01958409 0.01958409 | - |lattice_vector 0.01958411 -0.01958412 0.01958415 | - |lattice_vector 0.01958410 0.01958415 -0.01958412 | - +-------------------------------------------------------------------+ - Removing unitary transformations (pure translations, rotations) from forces on atoms. - Atomic forces before filtering: - | Net force on center of mass : 0.000000E+00 0.000000E+00 0.000000E+00 eV/A - Atomic forces after filtering: - | Net force on center of mass : 0.000000E+00 0.000000E+00 0.000000E+00 eV/A - Net remaining forces (excluding translations, rotations) in present geometry: - || Forces on atoms || = 0.222261E-06 eV/A. - || Forces on lattice || = 0.195841E-01 eV/A^3. - Maximum force component is 0.195841E-01 eV/A. - Present geometry is not yet converged. - - Relaxation step number 3: Predicting new coordinates. - - Advancing geometry using trust radius method. - | True / expected gain: -1.95E-02 eV / -2.04E-02 eV = 0.9568 - | Harmonic / expected gain: -2.26E-02 eV / -2.04E-02 eV = 1.1090 - | Hessian has 0 negative and 3 zero eigenvalues. - | Positive eigenvalues (eV/A^2): 3.58E+00 ... 3.02E+01 - | Use Quasi-Newton step of length |H^-1 F| = 1.13E-02 A. - Finished advancing geometry - | Time : 0.000 s - Updated atomic structure: - x [A] y [A] z [A] - lattice_vector 0.00000007 2.81482492 2.81482492 - lattice_vector 2.81482482 -0.00000004 2.81482486 - lattice_vector 2.81482482 2.81482486 -0.00000004 - - atom -0.00000001 0.00000000 0.00000000 Si - atom 1.40741244 1.40741244 1.40741244 Si - - Fractional coordinates: - L1 L2 L3 - atom_frac 0.00000000 -0.00000000 -0.00000000 Si - atom_frac 0.25000000 0.25000000 0.25000000 Si ------------------------------------------------------------- - Writing the current geometry to file "geometry.in.next_step". - Writing estimated Hessian matrix to file 'hessian.aims' - - Quantities derived from the lattice vectors: - | Reciprocal lattice vector 1: -1.116088 1.116088 1.116088 - | Reciprocal lattice vector 2: 1.116088 -1.116088 1.116088 - | Reciprocal lattice vector 3: 1.116088 1.116088 -1.116088 - | Unit cell volume : 0.446051E+02 A^3 - - Range separation radius for Ewald summation (hartree_convergence_parameter): 4.04522276 bohr. - ------------------------------------------------------------- - Begin self-consistency loop: Re-initialization. - - Date : 20230628, Time : 104332.450 ------------------------------------------------------------- - - Initializing index lists of integration centers etc. from given atomic structure: - Mapping all atomic coordinates to central unit cell. - - Initializing the k-points - Using symmetry for reducing the k-points - | k-points reduced from: 8 to 8 - | Number of k-points : 8 - The eigenvectors in the calculations are REAL. - | K-points in task 0: 8 - | Number of basis functions in the Hamiltonian integrals : 1771 - | Number of basis functions in a single unit cell : 50 - | Number of centers in hartree potential : 708 - | Number of centers in hartree multipole : 318 - | Number of centers in electron density summation: 190 - | Number of centers in basis integrals : 198 - | Number of centers in integrals : 101 - | Number of centers in hamiltonian : 190 - | Consuming 14 KiB for k_phase. - | Number of super-cells (origin) [n_cells] : 2197 - | Number of super-cells (after PM_index) [n_cells] : 112 - | Number of super-cells in hamiltonian [n_cells_in_hamiltonian]: 112 - | Size of matrix packed + index [n_hamiltonian_matrix_size] : 82583 - Partitioning the integration grid into batches with parallel hashing+maxmin method. - | Number of batches: 128 - | Maximal batch size: 90 - | Minimal batch size: 85 - | Average batch size: 87.562 - | Standard deviation of batch sizes: 1.493 - - Integration load balanced across 1 MPI tasks. - Work distribution over tasks is as follows: - Initializing partition tables, free-atom densities, potentials, etc. across the integration grid (initialize_grid_storage). - | Species 1: outer_partition_radius set to 5.000694715736543 AA . - | The sparse table of interatomic distances needs 194.62 kbyte instead of 313.63 kbyte of memory. - | Net number of integration points: 11208 - | of which are non-zero points : 9876 - | Numerical average free-atom electrostatic potential : -11.78489284 eV - Renormalizing the initial density to the exact electron count on the 3D integration grid. - | Initial density: Formal number of electrons (from input files) : 28.0000000000 - | Integrated number of electrons on 3D grid : 28.0037489641 - | Charge integration error : 0.0037489641 - | Normalization factor for density and gradient : 0.9998661263 - Renormalizing the free-atom superposition density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 28.0000000000 - | Integrated number of electrons on 3D grid : 28.0037489641 - | Charge integration error : 0.0037489641 - | Normalization factor for density and gradient : 0.9998661263 - Obtaining max. number of non-zero basis functions in each batch (get_n_compute_maxes). - Calculating total energy contributions from superposition of free atom densities. - Initialize hartree_potential_storage - Integrating overlap matrix. - Time summed over all CPUs for integration: real work 0.254 s, elapsed 0.254 s - Orthonormalizing eigenvectors - - End scf reinitialization - timings : max(cpu_time) wall_clock(cpu1) - | Time for scf. reinitialization : 0.561 s 0.564 s - | Boundary condition initialization : 0.064 s 0.065 s - | Integration : 0.252 s 0.254 s - | Grid partitioning : 0.032 s 0.032 s - | Preloading free-atom quantities on grid : 0.174 s 0.175 s - | Free-atom superposition energy : 0.027 s 0.027 s - | K.-S. eigenvector reorthonormalization : 0.001 s 0.001 s ------------------------------------------------------------- - Evaluating new KS density using the density matrix - Evaluating density matrix - Time summed over all CPUs for getting density from density matrix: real work 0.802 s, elapsed 0.802 s - Integration grid: deviation in total charge ( - N_e) = -1.776357E-14 - - Time for density update prior : max(cpu_time) wall_clock(cpu1) - | self-consistency iterative process : 0.798 s 0.804 s - ------------------------------------------------------------- - Begin self-consistency iteration # 1 - - Date : 20230628, Time : 104333.818 ------------------------------------------------------------- - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 28.0000000000 - | Integrated number of electrons on 3D grid : 28.0000000000 - | Charge integration error : 0.0000000000 - | Normalization factor for density and gradient : 1.0000000000 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = 0.281885E-13 - | Sum of charges compensated after spline to logarithmic grids = -0.634484E-04 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = 0.281375E-13 - Summing up the Hartree potential. - | Estimated reciprocal-space cutoff momentum G_max: 2.30334413 bohr^-1 . - | Reciprocal lattice points for long-range Hartree potential: 58 - Time summed over all CPUs for potential: real work 0.393 s, elapsed 0.393 s - | RMS charge density error from multipole expansion : 0.137198E-01 - | Average real-space part of the electrostatic potential : 0.43641905 eV - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.398 s, elapsed 0.398 s - Decreasing sparse matrix size: - | Tolerance: 0.1000E-12 - Hamiltonian matrix - | Array has 74604 nonzero elements out of 82583 elements - | Sparsity factor is 0.097 - Overlap matrix - | Array has 68322 nonzero elements out of 82583 elements - | Sparsity factor is 0.173 - New size of hamiltonian matrix: 74633 - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Singularity check in k-point 1, task 0 (analysis for other k-points/tasks may follow below): - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.001 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -5.01844054 eV - Writing Kohn-Sham eigenvalues. - K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - - State Occupation Eigenvalue [Ha] Eigenvalue [eV] - 1 2.00000 -65.748529 -1789.10850 - 2 2.00000 -65.748529 -1789.10850 - 3 2.00000 -5.106185 -138.94637 - 4 2.00000 -5.106020 -138.94188 - 5 2.00000 -3.489964 -94.96676 - 6 2.00000 -3.489964 -94.96676 - 7 2.00000 -3.489964 -94.96676 - 8 2.00000 -3.489568 -94.95598 - 9 2.00000 -3.489568 -94.95598 - 10 2.00000 -3.489568 -94.95598 - 11 2.00000 -0.608175 -16.54927 - 12 2.00000 -0.192610 -5.24119 - 13 2.00000 -0.192610 -5.24119 - 14 2.00000 -0.192610 -5.24119 - 15 0.00000 -0.110839 -3.01608 - 16 0.00000 -0.104019 -2.83051 - 17 0.00000 -0.104019 -2.83051 - 18 0.00000 -0.104019 -2.83051 - 19 0.00000 0.092765 2.52427 - 20 0.00000 0.092765 2.52427 - - What follows are estimated values for band gap, HOMO, LUMO, etc. - | They are estimated on a discrete k-point grid and not necessarily exact. - | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. - - Highest occupied state (VBM) at -5.24118513 eV (relative to internal zero) - | Occupation number: 2.00000000 - | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - - Lowest unoccupied state (CBM) at -4.40418353 eV (relative to internal zero) - | Occupation number: 0.00000000 - | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) - - ESTIMATED overall HOMO-LUMO gap: 0.83700160 eV between HOMO at k-point 1 and LUMO at k-point 4 - | This appears to be an indirect band gap. - | Smallest direct gap : 2.22510843 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, - this system is most likely an insulator or a semiconductor. - - Total energy components: - | Sum of eigenvalues : -328.16494985 Ha -8929.82262971 eV - | XC energy correction : -41.74834478 Ha -1136.03026208 eV - | XC potential correction : 53.91061389 Ha 1466.98244316 eV - | Free-atom electrostatic energy: -263.84200016 Ha -7179.50611365 eV - | Hartree energy correction : -0.80293588 Ha -21.84899693 eV - | Entropy correction : -0.00000000 Ha -0.00000000 eV - | --------------------------- - | Total energy : -580.64761678 Ha -15800.22555921 eV - | Total energy, T -> 0 : -580.64761678 Ha -15800.22555921 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -580.64761678 Ha -15800.22555921 eV - - Derived energy quantities: - | Kinetic energy : 582.10394346 Ha 15839.85422458 eV - | Electrostatic energy : -1121.00321546 Ha -30504.04952171 eV - | Energy correction for multipole - | error in Hartree potential : 0.01825064 Ha 0.49662528 eV - | Sum of eigenvalues per atom : -4464.91131485 eV - | Total energy (T->0) per atom : -7900.11277960 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -7900.11277960 eV - Evaluating new KS density using the density matrix - Evaluating density matrix - Time summed over all CPUs for getting density from density matrix: real work 0.800 s, elapsed 0.800 s - Integration grid: deviation in total charge ( - N_e) = 6.039613E-14 - - Self-consistency convergence accuracy: - | Change of charge density : 0.1310E+00 - | Change of sum of eigenvalues : -0.8930E+04 eV - | Change of total energy : -0.1580E+05 eV - - ------------------------------------------------------------- - End self-consistency iteration # 1 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 1.595 s 1.601 s - | Charge density update : 0.800 s 0.801 s - | Density mixing & preconditioning : 0.000 s 0.000 s - | Hartree multipole update : 0.001 s 0.001 s - | Hartree multipole summation : 0.393 s 0.395 s - | Integration : 0.396 s 0.399 s - | Solution of K.-S. eqns. : 0.005 s 0.005 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 1.554 MB (on task 0) - | Maximum: 1.554 MB (on task 0) - | Average: 1.554 MB - | Peak value for overall tracked memory usage: - | Minimum: 14.236 MB (on task 0 after allocating d_wave) - | Maximum: 14.236 MB (on task 0 after allocating d_wave) - | Average: 14.236 MB - | Largest tracked array allocation so far: - | Minimum: 3.456 MB (hamiltonian_shell on task 0) - | Maximum: 3.456 MB (hamiltonian_shell on task 0) - | Average: 3.456 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - ------------------------------------------------------------- - Begin self-consistency iteration # 2 - - Date : 20230628, Time : 104335.419 ------------------------------------------------------------- - Pulay mixing of updated and previous charge densities. - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 28.0000000000 - | Integrated number of electrons on 3D grid : 27.9999917916 - | Charge integration error : -0.0000082084 - | Normalization factor for density and gradient : 1.0000002932 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = -0.429136E-13 - | Sum of charges compensated after spline to logarithmic grids = -0.634540E-04 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = 0.000000E+00 - Summing up the Hartree potential. - Time summed over all CPUs for potential: real work 0.390 s, elapsed 0.390 s - | RMS charge density error from multipole expansion : 0.137185E-01 - | Average real-space part of the electrostatic potential : 0.43644029 eV - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.396 s, elapsed 0.396 s - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.001 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -5.01850965 eV - What follows are estimated values for band gap, HOMO, LUMO, etc. - | They are estimated on a discrete k-point grid and not necessarily exact. - | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. - - Highest occupied state (VBM) at -5.24124683 eV (relative to internal zero) - | Occupation number: 2.00000000 - | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - - Lowest unoccupied state (CBM) at -4.40420932 eV (relative to internal zero) - | Occupation number: 0.00000000 - | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) - - ESTIMATED overall HOMO-LUMO gap: 0.83703751 eV between HOMO at k-point 1 and LUMO at k-point 4 - | This appears to be an indirect band gap. - | Smallest direct gap : 2.22513239 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, - this system is most likely an insulator or a semiconductor. - - Total energy components: - | Sum of eigenvalues : -328.16451174 Ha -8929.81070830 eV - | XC energy correction : -41.74840253 Ha -1136.03183343 eV - | XC potential correction : 53.91068936 Ha 1466.98449680 eV - | Free-atom electrostatic energy: -263.84200016 Ha -7179.50611365 eV - | Hartree energy correction : -0.80339175 Ha -21.86140183 eV - | Entropy correction : -0.00000000 Ha -0.00000000 eV - | --------------------------- - | Total energy : -580.64761682 Ha -15800.22556040 eV - | Total energy, T -> 0 : -580.64761682 Ha -15800.22556040 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -580.64761682 Ha -15800.22556040 eV - - Derived energy quantities: - | Kinetic energy : 582.10515597 Ha 15839.88721854 eV - | Electrostatic energy : -1121.00437027 Ha -30504.08094552 eV - | Energy correction for multipole - | error in Hartree potential : 0.01825039 Ha 0.49661835 eV - | Sum of eigenvalues per atom : -4464.90535415 eV - | Total energy (T->0) per atom : -7900.11278020 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -7900.11278020 eV - Evaluating new KS density using the density matrix - Evaluating density matrix - Time summed over all CPUs for getting density from density matrix: real work 0.798 s, elapsed 0.798 s - Integration grid: deviation in total charge ( - N_e) = -3.552714E-14 - - Self-consistency convergence accuracy: - | Change of charge density : 0.2454E-03 - | Change of sum of eigenvalues : 0.1192E-01 eV - | Change of total energy : -0.1196E-05 eV - - ------------------------------------------------------------- - End self-consistency iteration # 2 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 1.771 s 1.771 s - | Charge density update : 0.799 s 0.799 s - | Density mixing & preconditioning : 0.177 s 0.177 s - | Hartree multipole update : 0.001 s 0.001 s - | Hartree multipole summation : 0.393 s 0.392 s - | Integration : 0.396 s 0.397 s - | Solution of K.-S. eqns. : 0.005 s 0.005 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 1.554 MB (on task 0) - | Maximum: 1.554 MB (on task 0) - | Average: 1.554 MB - | Peak value for overall tracked memory usage: - | Minimum: 14.236 MB (on task 0 after allocating d_wave) - | Maximum: 14.236 MB (on task 0 after allocating d_wave) - | Average: 14.236 MB - | Largest tracked array allocation so far: - | Minimum: 3.456 MB (hamiltonian_shell on task 0) - | Maximum: 3.456 MB (hamiltonian_shell on task 0) - | Average: 3.456 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - ------------------------------------------------------------- - Begin self-consistency iteration # 3 - - Date : 20230628, Time : 104337.190 ------------------------------------------------------------- - Pulay mixing of updated and previous charge densities. - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 28.0000000000 - | Integrated number of electrons on 3D grid : 27.9999746841 - | Charge integration error : -0.0000253159 - | Normalization factor for density and gradient : 1.0000009041 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = -0.383018E-13 - | Sum of charges compensated after spline to logarithmic grids = -0.634724E-04 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = -0.383621E-13 - Summing up the Hartree potential. - Time summed over all CPUs for potential: real work 0.391 s, elapsed 0.391 s - | RMS charge density error from multipole expansion : 0.137142E-01 - | Average real-space part of the electrostatic potential : 0.43651485 eV - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.396 s, elapsed 0.396 s - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.001 s - Finished solving standard eigenproblem - | Time : 0.000 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -5.01873043 eV - What follows are estimated values for band gap, HOMO, LUMO, etc. - | They are estimated on a discrete k-point grid and not necessarily exact. - | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. - - Highest occupied state (VBM) at -5.24144412 eV (relative to internal zero) - | Occupation number: 2.00000000 - | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - - Lowest unoccupied state (CBM) at -4.40429028 eV (relative to internal zero) - | Occupation number: 0.00000000 - | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) - - ESTIMATED overall HOMO-LUMO gap: 0.83715384 eV between HOMO at k-point 1 and LUMO at k-point 4 - | This appears to be an indirect band gap. - | Smallest direct gap : 2.22520734 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, - this system is most likely an insulator or a semiconductor. - - Total energy components: - | Sum of eigenvalues : -328.16315258 Ha -8929.77372365 eV - | XC energy correction : -41.74857787 Ha -1136.03660464 eV - | XC potential correction : 53.91091893 Ha 1466.99074380 eV - | Free-atom electrostatic energy: -263.84200016 Ha -7179.50611365 eV - | Hartree energy correction : -0.80480531 Ha -21.89986660 eV - | Entropy correction : -0.00000000 Ha -0.00000000 eV - | --------------------------- - | Total energy : -580.64761698 Ha -15800.22556475 eV - | Total energy, T -> 0 : -580.64761698 Ha -15800.22556475 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -580.64761698 Ha -15800.22556475 eV - - Derived energy quantities: - | Kinetic energy : 582.10881200 Ha 15839.98670431 eV - | Electrostatic energy : -1121.00785112 Ha -30504.17566441 eV - | Energy correction for multipole - | error in Hartree potential : 0.01824968 Ha 0.49659904 eV - | Sum of eigenvalues per atom : -4464.88686183 eV - | Total energy (T->0) per atom : -7900.11278237 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -7900.11278237 eV - Evaluating new KS density using the density matrix - Evaluating density matrix - Time summed over all CPUs for getting density from density matrix: real work 0.799 s, elapsed 0.799 s - Integration grid: deviation in total charge ( - N_e) = -7.105427E-15 - - Self-consistency convergence accuracy: - | Change of charge density : 0.1866E-03 - | Change of sum of eigenvalues : 0.3698E-01 eV - | Change of total energy : -0.4348E-05 eV - - ------------------------------------------------------------- - End self-consistency iteration # 3 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 1.773 s 1.773 s - | Charge density update : 0.800 s 0.800 s - | Density mixing & preconditioning : 0.178 s 0.178 s - | Hartree multipole update : 0.001 s 0.001 s - | Hartree multipole summation : 0.393 s 0.393 s - | Integration : 0.396 s 0.396 s - | Solution of K.-S. eqns. : 0.005 s 0.005 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 1.554 MB (on task 0) - | Maximum: 1.554 MB (on task 0) - | Average: 1.554 MB - | Peak value for overall tracked memory usage: - | Minimum: 14.236 MB (on task 0 after allocating d_wave) - | Maximum: 14.236 MB (on task 0 after allocating d_wave) - | Average: 14.236 MB - | Largest tracked array allocation so far: - | Minimum: 3.456 MB (hamiltonian_shell on task 0) - | Maximum: 3.456 MB (hamiltonian_shell on task 0) - | Average: 3.456 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - ------------------------------------------------------------- - Begin self-consistency iteration # 4 - - Date : 20230628, Time : 104338.963 ------------------------------------------------------------- - Pulay mixing of updated and previous charge densities. - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 28.0000000000 - | Integrated number of electrons on 3D grid : 28.0000001275 - | Charge integration error : 0.0000001275 - | Normalization factor for density and gradient : 0.9999999954 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = -0.356423E-13 - | Sum of charges compensated after spline to logarithmic grids = -0.634774E-04 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = -0.355182E-13 - Summing up the Hartree potential. - Time summed over all CPUs for potential: real work 0.391 s, elapsed 0.391 s - | RMS charge density error from multipole expansion : 0.137135E-01 - | Average real-space part of the electrostatic potential : 0.43655206 eV - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.396 s, elapsed 0.396 s - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.001 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -5.01875904 eV - What follows are estimated values for band gap, HOMO, LUMO, etc. - | They are estimated on a discrete k-point grid and not necessarily exact. - | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. - - Highest occupied state (VBM) at -5.24147007 eV (relative to internal zero) - | Occupation number: 2.00000000 - | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - - Lowest unoccupied state (CBM) at -4.40429494 eV (relative to internal zero) - | Occupation number: 0.00000000 - | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) - - ESTIMATED overall HOMO-LUMO gap: 0.83717513 eV between HOMO at k-point 1 and LUMO at k-point 4 - | This appears to be an indirect band gap. - | Smallest direct gap : 2.22521115 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, - this system is most likely an insulator or a semiconductor. - - Total energy components: - | Sum of eigenvalues : -328.16312551 Ha -8929.77298693 eV - | XC energy correction : -41.74856597 Ha -1136.03628091 eV - | XC potential correction : 53.91090505 Ha 1466.99036601 eV - | Free-atom electrostatic energy: -263.84200016 Ha -7179.50611365 eV - | Hartree energy correction : -0.80483046 Ha -21.90055117 eV - | Entropy correction : -0.00000000 Ha -0.00000000 eV - | --------------------------- - | Total energy : -580.64761705 Ha -15800.22556665 eV - | Total energy, T -> 0 : -580.64761705 Ha -15800.22556665 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -580.64761705 Ha -15800.22556665 eV - - Derived energy quantities: - | Kinetic energy : 582.10845902 Ha 15839.97709920 eV - | Electrostatic energy : -1121.00751011 Ha -30504.16638494 eV - | Energy correction for multipole - | error in Hartree potential : 0.01825001 Ha 0.49660813 eV - | Sum of eigenvalues per atom : -4464.88649346 eV - | Total energy (T->0) per atom : -7900.11278332 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -7900.11278332 eV - Evaluating new KS density using the density matrix - Evaluating density matrix - Time summed over all CPUs for getting density from density matrix: real work 0.800 s, elapsed 0.800 s - Integration grid: deviation in total charge ( - N_e) = -7.105427E-15 - - Self-consistency convergence accuracy: - | Change of charge density : 0.2666E-04 - | Change of sum of eigenvalues : 0.7367E-03 eV - | Change of total energy : -0.1898E-05 eV - - ------------------------------------------------------------- - End self-consistency iteration # 4 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 1.773 s 1.774 s - | Charge density update : 0.801 s 0.801 s - | Density mixing & preconditioning : 0.178 s 0.178 s - | Hartree multipole update : 0.001 s 0.001 s - | Hartree multipole summation : 0.393 s 0.393 s - | Integration : 0.396 s 0.396 s - | Solution of K.-S. eqns. : 0.005 s 0.005 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 1.554 MB (on task 0) - | Maximum: 1.554 MB (on task 0) - | Average: 1.554 MB - | Peak value for overall tracked memory usage: - | Minimum: 14.236 MB (on task 0 after allocating d_wave) - | Maximum: 14.236 MB (on task 0 after allocating d_wave) - | Average: 14.236 MB - | Largest tracked array allocation so far: - | Minimum: 3.456 MB (hamiltonian_shell on task 0) - | Maximum: 3.456 MB (hamiltonian_shell on task 0) - | Average: 3.456 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - ------------------------------------------------------------- - Begin self-consistency iteration # 5 - - Date : 20230628, Time : 104340.737 ------------------------------------------------------------- - Pulay mixing of updated and previous charge densities. - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 28.0000000000 - | Integrated number of electrons on 3D grid : 27.9999999970 - | Charge integration error : -0.0000000030 - | Normalization factor for density and gradient : 1.0000000001 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = -0.408762E-13 - | Sum of charges compensated after spline to logarithmic grids = -0.634778E-04 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = -0.407702E-13 - Summing up the Hartree potential. - Time summed over all CPUs for potential: real work 0.391 s, elapsed 0.391 s - | RMS charge density error from multipole expansion : 0.137135E-01 - | Average real-space part of the electrostatic potential : 0.43655673 eV - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.396 s, elapsed 0.396 s - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.000 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -5.01875552 eV - What follows are estimated values for band gap, HOMO, LUMO, etc. - | They are estimated on a discrete k-point grid and not necessarily exact. - | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. - - Highest occupied state (VBM) at -5.24146591 eV (relative to internal zero) - | Occupation number: 2.00000000 - | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - - Lowest unoccupied state (CBM) at -4.40429219 eV (relative to internal zero) - | Occupation number: 0.00000000 - | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) - - ESTIMATED overall HOMO-LUMO gap: 0.83717372 eV between HOMO at k-point 1 and LUMO at k-point 4 - | This appears to be an indirect band gap. - | Smallest direct gap : 2.22521117 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, - this system is most likely an insulator or a semiconductor. - - Total energy components: - | Sum of eigenvalues : -328.16311891 Ha -8929.77280749 eV - | XC energy correction : -41.74856632 Ha -1136.03629037 eV - | XC potential correction : 53.91090547 Ha 1466.99037744 eV - | Free-atom electrostatic energy: -263.84200016 Ha -7179.50611365 eV - | Hartree energy correction : -0.80483714 Ha -21.90073277 eV - | Entropy correction : -0.00000000 Ha -0.00000000 eV - | --------------------------- - | Total energy : -580.64761706 Ha -15800.22556684 eV - | Total energy, T -> 0 : -580.64761706 Ha -15800.22556684 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -580.64761706 Ha -15800.22556684 eV - - Derived energy quantities: - | Kinetic energy : 582.10845957 Ha 15839.97711419 eV - | Electrostatic energy : -1121.00751032 Ha -30504.16639066 eV - | Energy correction for multipole - | error in Hartree potential : 0.01825010 Ha 0.49661059 eV - | Sum of eigenvalues per atom : -4464.88640374 eV - | Total energy (T->0) per atom : -7900.11278342 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -7900.11278342 eV - Evaluating new KS density using the density matrix - Evaluating density matrix - Time summed over all CPUs for getting density from density matrix: real work 0.798 s, elapsed 0.798 s - Integration grid: deviation in total charge ( - N_e) = 0.000000E+00 - - Self-consistency convergence accuracy: - | Change of charge density : 0.5995E-06 - | Change of sum of eigenvalues : 0.1794E-03 eV - | Change of total energy : -0.1944E-06 eV - - ------------------------------------------------------------- - End self-consistency iteration # 5 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 1.772 s 1.772 s - | Charge density update : 0.799 s 0.800 s - | Density mixing & preconditioning : 0.177 s 0.177 s - | Hartree multipole update : 0.001 s 0.001 s - | Hartree multipole summation : 0.393 s 0.393 s - | Integration : 0.396 s 0.397 s - | Solution of K.-S. eqns. : 0.005 s 0.004 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 1.554 MB (on task 0) - | Maximum: 1.554 MB (on task 0) - | Average: 1.554 MB - | Peak value for overall tracked memory usage: - | Minimum: 14.236 MB (on task 0 after allocating d_wave) - | Maximum: 14.236 MB (on task 0 after allocating d_wave) - | Average: 14.236 MB - | Largest tracked array allocation so far: - | Minimum: 3.456 MB (hamiltonian_shell on task 0) - | Maximum: 3.456 MB (hamiltonian_shell on task 0) - | Average: 3.456 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - ------------------------------------------------------------- - Begin self-consistency iteration # 6 - - Date : 20230628, Time : 104342.509 ------------------------------------------------------------- - Pulay mixing of updated and previous charge densities. - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 28.0000000000 - | Integrated number of electrons on 3D grid : 28.0000000042 - | Charge integration error : 0.0000000042 - | Normalization factor for density and gradient : 0.9999999998 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = 0.678360E-13 - | Sum of charges compensated after spline to logarithmic grids = -0.634779E-04 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = 0.679112E-13 - Summing up the Hartree potential. - Time summed over all CPUs for potential: real work 0.390 s, elapsed 0.390 s - | RMS charge density error from multipole expansion : 0.137135E-01 - | Average real-space part of the electrostatic potential : 0.43655657 eV - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.396 s, elapsed 0.396 s - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.001 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -5.01875563 eV - What follows are estimated values for band gap, HOMO, LUMO, etc. - | They are estimated on a discrete k-point grid and not necessarily exact. - | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. - - Highest occupied state (VBM) at -5.24146606 eV (relative to internal zero) - | Occupation number: 2.00000000 - | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - - Lowest unoccupied state (CBM) at -4.40429220 eV (relative to internal zero) - | Occupation number: 0.00000000 - | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) - - ESTIMATED overall HOMO-LUMO gap: 0.83717386 eV between HOMO at k-point 1 and LUMO at k-point 4 - | This appears to be an indirect band gap. - | Smallest direct gap : 2.22521105 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, - this system is most likely an insulator or a semiconductor. - - Total energy components: - | Sum of eigenvalues : -328.16312017 Ha -8929.77284167 eV - | XC energy correction : -41.74856622 Ha -1136.03628782 eV - | XC potential correction : 53.91090534 Ha 1466.99037394 eV - | Free-atom electrostatic energy: -263.84200016 Ha -7179.50611365 eV - | Hartree energy correction : -0.80483584 Ha -21.90069763 eV - | Entropy correction : -0.00000000 Ha -0.00000000 eV - | --------------------------- - | Total energy : -580.64761706 Ha -15800.22556682 eV - | Total energy, T -> 0 : -580.64761706 Ha -15800.22556682 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -580.64761706 Ha -15800.22556682 eV - - Derived energy quantities: - | Kinetic energy : 582.10845878 Ha 15839.97709252 eV - | Electrostatic energy : -1121.00750962 Ha -30504.16637153 eV - | Energy correction for multipole - | error in Hartree potential : 0.01825011 Ha 0.49661067 eV - | Sum of eigenvalues per atom : -4464.88642083 eV - | Total energy (T->0) per atom : -7900.11278341 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -7900.11278341 eV - Preliminary charge convergence reached. Turning off preconditioner. - - Evaluating new KS density using the density matrix - Evaluating density matrix - Time summed over all CPUs for getting density from density matrix: real work 0.800 s, elapsed 0.800 s - Integration grid: deviation in total charge ( - N_e) = -1.065814E-14 - - Self-consistency convergence accuracy: - | Change of charge density : 0.6807E-07 - | Change of sum of eigenvalues : -0.3418E-04 eV - | Change of total energy : 0.2030E-07 eV - - Electronic self-consistency reached - switching on the force computation. - - Electronic self-consistency reached - switching on the analytical stress tensor computation. - - ------------------------------------------------------------- - End self-consistency iteration # 6 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 1.774 s 1.774 s - | Charge density & force component update : 0.801 s 0.801 s - | Density mixing : 0.177 s 0.177 s - | Hartree multipole update : 0.001 s 0.002 s - | Hartree multipole summation : 0.393 s 0.393 s - | Hartree pot. SCF incomplete forces : 0.941 s 0.946 s - | Integration : 0.396 s 0.396 s - | Solution of K.-S. eqns. : 0.005 s 0.004 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 1.554 MB (on task 0) - | Maximum: 1.554 MB (on task 0) - | Average: 1.554 MB - | Peak value for overall tracked memory usage: - | Minimum: 14.236 MB (on task 0 after allocating d_wave) - | Maximum: 14.236 MB (on task 0 after allocating d_wave) - | Average: 14.236 MB - | Largest tracked array allocation so far: - | Minimum: 3.456 MB (hamiltonian_shell on task 0) - | Maximum: 3.456 MB (hamiltonian_shell on task 0) - | Average: 3.456 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - ------------------------------------------------------------- - Begin self-consistency iteration # 7 - - Date : 20230628, Time : 104344.283 ------------------------------------------------------------- - Pulay mixing of updated and previous charge densities. - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 28.0000000000 - | Integrated number of electrons on 3D grid : 27.9999999961 - | Charge integration error : -0.0000000039 - | Normalization factor for density and gradient : 1.0000000001 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = 0.380846E-13 - | Sum of charges compensated after spline to logarithmic grids = -0.634779E-04 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = 0.379498E-13 - Summing up the Hartree potential. - Time summed over all CPUs for potential: real work 1.649 s, elapsed 1.649 s - | RMS charge density error from multipole expansion : 0.137135E-01 - | Average real-space part of the electrostatic potential : 0.43655657 eV - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.396 s, elapsed 0.396 s - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.000 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -5.01875572 eV - What follows are estimated values for band gap, HOMO, LUMO, etc. - | They are estimated on a discrete k-point grid and not necessarily exact. - | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. - - Highest occupied state (VBM) at -5.24146615 eV (relative to internal zero) - | Occupation number: 2.00000000 - | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - - Lowest unoccupied state (CBM) at -4.40429223 eV (relative to internal zero) - | Occupation number: 0.00000000 - | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) - - ESTIMATED overall HOMO-LUMO gap: 0.83717392 eV between HOMO at k-point 1 and LUMO at k-point 4 - | This appears to be an indirect band gap. - | Smallest direct gap : 2.22521105 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, - this system is most likely an insulator or a semiconductor. - - Total energy components: - | Sum of eigenvalues : -328.16312012 Ha -8929.77284040 eV - | XC energy correction : -41.74856623 Ha -1136.03628808 eV - | XC potential correction : 53.91090535 Ha 1466.99037429 eV - | Free-atom electrostatic energy: -263.84200016 Ha -7179.50611365 eV - | Hartree energy correction : -0.80483589 Ha -21.90069898 eV - | Entropy correction : -0.00000000 Ha -0.00000000 eV - | --------------------------- - | Total energy : -580.64761706 Ha -15800.22556682 eV - | Total energy, T -> 0 : -580.64761706 Ha -15800.22556682 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -580.64761706 Ha -15800.22556682 eV - - Derived energy quantities: - | Kinetic energy : 582.10845912 Ha 15839.97710180 eV - | Electrostatic energy : -1121.00750995 Ha -30504.16638054 eV - | Energy correction for multipole - | error in Hartree potential : 0.01825011 Ha 0.49661067 eV - | Sum of eigenvalues per atom : -4464.88642020 eV - | Total energy (T->0) per atom : -7900.11278341 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -7900.11278341 eV - Evaluating new KS density using the density matrix - Evaluating density matrix - Time summed over all CPUs for getting density from density matrix: real work 0.801 s, elapsed 0.801 s - Integration grid: deviation in total charge ( - N_e) = -1.065814E-14 - - atomic forces [eV/Ang]: - ----------------------- - atom # 1 - Hellmann-Feynman : -0.174533E-06 0.132859E-06 0.162610E-06 - Ionic forces : 0.000000E+00 0.000000E+00 0.000000E+00 - Multipole : 0.458049E-07 -0.978235E-08 -0.108478E-07 - Hartree pot. SCF incomplete : 0.122555E-08 0.445755E-08 -0.423237E-08 - Pulay + GGA : 0.000000E+00 0.000000E+00 0.000000E+00 - ---------------------------------------------------------------- - Total forces( 1) : -0.127502E-06 0.127534E-06 0.147530E-06 - atom # 2 - Hellmann-Feynman : 0.175265E-06 -0.122017E-06 -0.156383E-06 - Ionic forces : 0.000000E+00 0.000000E+00 0.000000E+00 - Multipole : -0.458035E-07 0.978442E-08 0.108489E-07 - Hartree pot. SCF incomplete : -0.119578E-08 -0.463144E-08 0.434145E-08 - Pulay + GGA : 0.000000E+00 0.000000E+00 0.000000E+00 - ---------------------------------------------------------------- - Total forces( 2) : 0.128266E-06 -0.116864E-06 -0.141192E-06 - - - Self-consistency convergence accuracy: - | Change of charge density : 0.3795E-07 - | Change of sum of eigenvalues : 0.1262E-05 eV - | Change of total energy : 0.1893E-08 eV - | Change of forces : 0.2294E-06 eV/A - - ------------------------------------------------------------- - End self-consistency iteration # 7 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 3.799 s 3.799 s - | Charge density & force component update : 0.802 s 0.802 s - | Density mixing : 0.001 s 0.001 s - | Hartree multipole update : 0.001 s 0.001 s - | Hartree multipole summation : 1.652 s 1.653 s - | Hartree pot. SCF incomplete forces : 0.942 s 0.942 s - | Integration : 0.396 s 0.396 s - | Solution of K.-S. eqns. : 0.005 s 0.004 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 1.554 MB (on task 0) - | Maximum: 1.554 MB (on task 0) - | Average: 1.554 MB - | Peak value for overall tracked memory usage: - | Minimum: 14.236 MB (on task 0 after allocating d_wave) - | Maximum: 14.236 MB (on task 0 after allocating d_wave) - | Average: 14.236 MB - | Largest tracked array allocation so far: - | Minimum: 3.456 MB (hamiltonian_shell on task 0) - | Maximum: 3.456 MB (hamiltonian_shell on task 0) - | Average: 3.456 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - ------------------------------------------------------------- - Begin self-consistency iteration # 8 - - Date : 20230628, Time : 104348.082 ------------------------------------------------------------- - Pulay mixing of updated and previous charge densities. - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 28.0000000000 - | Integrated number of electrons on 3D grid : 28.0000000009 - | Charge integration error : 0.0000000009 - | Normalization factor for density and gradient : 1.0000000000 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = -0.853832E-13 - | Sum of charges compensated after spline to logarithmic grids = -0.634779E-04 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = -0.853537E-13 - Summing up the Hartree potential. - Time summed over all CPUs for potential: real work 1.645 s, elapsed 1.645 s - | RMS charge density error from multipole expansion : 0.137135E-01 - | Average real-space part of the electrostatic potential : 0.43655656 eV - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.396 s, elapsed 0.396 s - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.001 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -5.01875570 eV - What follows are estimated values for band gap, HOMO, LUMO, etc. - | They are estimated on a discrete k-point grid and not necessarily exact. - | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. - - Highest occupied state (VBM) at -5.24146614 eV (relative to internal zero) - | Occupation number: 2.00000000 - | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - - Lowest unoccupied state (CBM) at -4.40429223 eV (relative to internal zero) - | Occupation number: 0.00000000 - | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) - - ESTIMATED overall HOMO-LUMO gap: 0.83717391 eV between HOMO at k-point 1 and LUMO at k-point 4 - | This appears to be an indirect band gap. - | Smallest direct gap : 2.22521105 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, - this system is most likely an insulator or a semiconductor. - - Total energy components: - | Sum of eigenvalues : -328.16312017 Ha -8929.77284175 eV - | XC energy correction : -41.74856623 Ha -1136.03628793 eV - | XC potential correction : 53.91090535 Ha 1466.99037409 eV - | Free-atom electrostatic energy: -263.84200016 Ha -7179.50611365 eV - | Hartree energy correction : -0.80483584 Ha -21.90069758 eV - | Entropy correction : -0.00000000 Ha -0.00000000 eV - | --------------------------- - | Total energy : -580.64761706 Ha -15800.22556682 eV - | Total energy, T -> 0 : -580.64761706 Ha -15800.22556682 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -580.64761706 Ha -15800.22556682 eV - - Derived energy quantities: - | Kinetic energy : 582.10845902 Ha 15839.97709910 eV - | Electrostatic energy : -1121.00750985 Ha -30504.16637799 eV - | Energy correction for multipole - | error in Hartree potential : 0.01825011 Ha 0.49661066 eV - | Sum of eigenvalues per atom : -4464.88642088 eV - | Total energy (T->0) per atom : -7900.11278341 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -7900.11278341 eV - Evaluating new KS density using the density matrix - Evaluating density matrix - Time summed over all CPUs for getting density from density matrix: real work 0.797 s, elapsed 0.797 s - - Evaluating density-matrix-based force terms: batch-based integration - Evaluating density matrix - Evaluating density matrix - Integration grid: deviation in total charge ( - N_e) = 2.131628E-14 - - atomic forces [eV/Ang]: - ----------------------- - atom # 1 - Hellmann-Feynman : -0.133256E-06 0.186553E-06 0.959840E-07 - Ionic forces : 0.000000E+00 0.000000E+00 0.000000E+00 - Multipole : 0.458312E-07 -0.990532E-08 -0.106989E-07 - Hartree pot. SCF incomplete : -0.149097E-07 -0.997635E-08 0.151466E-07 - Pulay + GGA : 0.444819E-06 -0.209681E-06 -0.166655E-06 - ---------------------------------------------------------------- - Total forces( 1) : 0.342484E-06 -0.430094E-07 -0.662230E-07 - atom # 2 - Hellmann-Feynman : 0.134051E-06 -0.176390E-06 -0.894499E-07 - Ionic forces : 0.000000E+00 0.000000E+00 0.000000E+00 - Multipole : -0.458309E-07 0.990579E-08 0.106979E-07 - Hartree pot. SCF incomplete : 0.148654E-07 0.105211E-07 -0.153964E-07 - Pulay + GGA : -0.443163E-06 0.186049E-06 0.141031E-06 - ---------------------------------------------------------------- - Total forces( 2) : -0.340078E-06 0.300861E-07 0.468829E-07 - - - Analytical stress tensor components [eV] xx yy zz xy xz yz - ----------------------------------------------------------------------------------------------------------------------------------------------------------- - Nuclear Hellmann-Feynman : -0.1192389456E+02 -0.1192407593E+02 -0.1192407593E+02 -0.7957847272E-07 -0.5039490827E-07 0.4410918514E-06 - Multipole Hellmann-Feynman : -0.2752793058E+02 -0.2752794118E+02 -0.2752794118E+02 -0.2504360107E-06 -0.1946134947E-06 0.1412451753E-05 - On-site Multipole corrections : -0.2840312241E+00 -0.2840312244E+00 -0.2840312245E+00 0.9961793290E-10 0.8914761865E-10 -0.3776534998E-09 - Strain deriv. of the orbitals : 0.3972740784E+02 0.3972759987E+02 0.3972759987E+02 0.2202138934E-06 0.1385950070E-06 -0.1507222448E-05 - ----------------------------------------------------------------------------------------------------------------------------------------------------------- - Sum of all contributions : -0.8448519987E-02 -0.8448470439E-02 -0.8448469456E-02 -0.1097009721E-06 -0.1063242483E-06 0.3459435029E-06 - - +-------------------------------------------------------------------+ - | Analytical stress tensor - Symmetrized | - | Cartesian components [eV/A**3] | - +-------------------------------------------------------------------+ - | x y z | - | | - | x -0.00018941 -0.00000000 -0.00000000 | - | y -0.00000000 -0.00018941 0.00000001 | - | z -0.00000000 0.00000001 -0.00018941 | - | | - | Pressure: 0.00018941 [eV/A**3] | - | | - +-------------------------------------------------------------------+ - - * Warning: Stress tensor is anisotropic. Be aware that pressure is an isotropic quantity. - - - Self-consistency convergence accuracy: - | Change of charge density : 0.8719E-08 - | Change of sum of eigenvalues : -0.1351E-05 eV - | Change of total energy : 0.4053E-09 eV - | Change of forces : 0.9513E-07 eV/A - - Writing Kohn-Sham eigenvalues. - K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - - State Occupation Eigenvalue [Ha] Eigenvalue [eV] - 1 2.00000 -65.748361 -1789.10394 - 2 2.00000 -65.748361 -1789.10394 - 3 2.00000 -5.106113 -138.94441 - 4 2.00000 -5.105948 -138.93992 - 5 2.00000 -3.489886 -94.96462 - 6 2.00000 -3.489886 -94.96462 - 7 2.00000 -3.489886 -94.96462 - 8 2.00000 -3.489489 -94.95384 - 9 2.00000 -3.489489 -94.95384 - 10 2.00000 -3.489489 -94.95384 - 11 2.00000 -0.608183 -16.54950 - 12 2.00000 -0.192620 -5.24147 - 13 2.00000 -0.192620 -5.24147 - 14 2.00000 -0.192620 -5.24147 - 15 0.00000 -0.110845 -3.01626 - 16 0.00000 -0.104028 -2.83075 - 17 0.00000 -0.104028 -2.83075 - 18 0.00000 -0.104028 -2.83075 - 19 0.00000 0.092758 2.52407 - 20 0.00000 0.092758 2.52407 - - What follows are estimated values for band gap, HOMO, LUMO, etc. - | They are estimated on a discrete k-point grid and not necessarily exact. - | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. - - Highest occupied state (VBM) at -5.24146614 eV (relative to internal zero) - | Occupation number: 2.00000000 - | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - - Lowest unoccupied state (CBM) at -4.40429223 eV (relative to internal zero) - | Occupation number: 0.00000000 - | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) - - ESTIMATED overall HOMO-LUMO gap: 0.83717391 eV between HOMO at k-point 1 and LUMO at k-point 4 - | This appears to be an indirect band gap. - | Smallest direct gap : 2.22521105 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, - this system is most likely an insulator or a semiconductor. - | Chemical Potential : -5.01875570 eV - - Self-consistency cycle converged. - - ------------------------------------------------------------- - End self-consistency iteration # 8 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 19.041 s 19.042 s - | Charge density & force component update : 16.053 s 16.053 s - | Density mixing : 0.002 s 0.002 s - | Hartree multipole update : 0.001 s 0.001 s - | Hartree multipole summation : 1.648 s 1.648 s - | Hartree pot. SCF incomplete forces : 0.935 s 0.935 s - | Integration : 0.396 s 0.397 s - | Solution of K.-S. eqns. : 0.005 s 0.004 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 1.554 MB (on task 0) - | Maximum: 1.554 MB (on task 0) - | Average: 1.554 MB - | Peak value for overall tracked memory usage: - | Minimum: 14.236 MB (on task 0 after allocating d_wave) - | Maximum: 14.236 MB (on task 0 after allocating d_wave) - | Average: 14.236 MB - | Largest tracked array allocation so far: - | Minimum: 3.456 MB (hamiltonian_shell on task 0) - | Maximum: 3.456 MB (hamiltonian_shell on task 0) - | Average: 3.456 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - Removing unitary transformations (pure translations, rotations) from forces on atoms. - Atomic forces before filtering: - | Net force on center of mass : 0.240662E-08 -0.129234E-07 -0.193401E-07 eV/A - Atomic forces after filtering: - | Net force on center of mass : 0.000000E+00 -0.106338E-22 0.000000E+00 eV/A - - Energy and forces in a compact form: - | Total energy uncorrected : -0.158002255668194E+05 eV - | Total energy corrected : -0.158002255668194E+05 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -0.158002255668194E+05 eV - Total atomic forces (unitary forces cleaned) [eV/Ang]: - | 1 0.341280940656103E-06 -0.365477601296885E-07 -0.565529618943033E-07 - | 2 -0.341280940656103E-06 0.365477601296885E-07 0.565529618943033E-07 - - ------------------------------------ - Start decomposition of the XC Energy - ------------------------------------ - X and C from original XC functional choice - Hartree-Fock Energy : 0.000000000 Ha 0.000000000 eV - X Energy : -40.666493062 Ha -1106.591578968 eV - C Energy : -1.082073165 Ha -29.444708963 eV - XC Energy w/o HF : -41.748566227 Ha -1136.036287931 eV - Total XC Energy : -41.748566227 Ha -1136.036287931 eV - ------------------------------------ - LDA X and C from self-consistent density - X Energy LDA : -37.597435086 Ha -1023.078262336 eV - C Energy LDA : -2.143916094 Ha -58.338925176 eV - ------------------------------------ - End decomposition of the XC Energy - ------------------------------------ - ------------------------------------------------------------- - Relaxation / MD: End force evaluation. : max(cpu_time) wall_clock(cpu1) - | Time for this force evaluation : 34.665 s 34.680 s - ------------------------------------------------------------- - Geometry optimization: Attempting to predict improved coordinates. - - +-------------------------------------------------------------------+ - | Generalized derivatives on lattice vectors [eV/A] | - +-------------------------------------------------------------------+ - |lattice_vector 0.00150068 -0.00150063 -0.00150063 | - |lattice_vector -0.00150072 0.00150075 -0.00150079 | - |lattice_vector -0.00150072 -0.00150079 0.00150075 | - +-------------------------------------------------------------------+ - | Forces on lattice vectors cleaned from atomic contributions [eV/A]| - +-------------------------------------------------------------------+ - |lattice_vector -0.00150068 0.00150063 0.00150063 | - |lattice_vector 0.00150072 -0.00150075 0.00150079 | - |lattice_vector 0.00150072 0.00150079 -0.00150075 | - +-------------------------------------------------------------------+ - Removing unitary transformations (pure translations, rotations) from forces on atoms. - Atomic forces before filtering: - | Net force on center of mass : 0.000000E+00 -0.106338E-22 0.000000E+00 eV/A - Atomic forces after filtering: - | Net force on center of mass : 0.000000E+00 0.000000E+00 0.000000E+00 eV/A - Net remaining forces (excluding translations, rotations) in present geometry: - || Forces on atoms || = 0.341281E-06 eV/A. - || Forces on lattice || = 0.150079E-02 eV/A^3. - Maximum force component is 0.150079E-02 eV/A. - Present geometry is not yet converged. - - Relaxation step number 4: Predicting new coordinates. - - Advancing geometry using trust radius method. - | True / expected gain: 2.20E-05 eV / -2.72E-04 eV = -0.0809 - | Harmonic / expected gain: -2.92E-04 eV / -2.72E-04 eV = 1.0766 - | Using harmonic gain instead of DE to judge step. - | Hessian has 0 negative and 3 zero eigenvalues. - | Positive eigenvalues (eV/A^2): 3.35E+00 ... 3.02E+01 - | Use Quasi-Newton step of length |H^-1 F| = 9.39E-04 A. - Finished advancing geometry - | Time : 0.000 s - Updated atomic structure: - x [A] y [A] z [A] - lattice_vector 0.00000007 2.81520842 2.81520842 - lattice_vector 2.81520832 -0.00000004 2.81520837 - lattice_vector 2.81520832 2.81520837 -0.00000004 - - atom 0.00000002 -0.00000000 -0.00000000 Si - atom 1.40760416 1.40760419 1.40760419 Si - - Fractional coordinates: - L1 L2 L3 - atom_frac -0.00000000 0.00000000 0.00000000 Si - atom_frac 0.25000000 0.25000000 0.25000000 Si ------------------------------------------------------------- - Writing the current geometry to file "geometry.in.next_step". - Writing estimated Hessian matrix to file 'hessian.aims' - - Quantities derived from the lattice vectors: - | Reciprocal lattice vector 1: -1.115936 1.115936 1.115936 - | Reciprocal lattice vector 2: 1.115936 -1.115936 1.115936 - | Reciprocal lattice vector 3: 1.115936 1.115936 -1.115936 - | Unit cell volume : 0.446233E+02 A^3 - - Range separation radius for Ewald summation (hartree_convergence_parameter): 4.04582400 bohr. - ------------------------------------------------------------- - Begin self-consistency loop: Re-initialization. - - Date : 20230628, Time : 104407.131 ------------------------------------------------------------- - - Initializing index lists of integration centers etc. from given atomic structure: - Mapping all atomic coordinates to central unit cell. - - Initializing the k-points - Using symmetry for reducing the k-points - | k-points reduced from: 8 to 8 - | Number of k-points : 8 - The eigenvectors in the calculations are REAL. - | K-points in task 0: 8 - | Number of basis functions in the Hamiltonian integrals : 1771 - | Number of basis functions in a single unit cell : 50 - | Number of centers in hartree potential : 708 - | Number of centers in hartree multipole : 318 - | Number of centers in electron density summation: 190 - | Number of centers in basis integrals : 198 - | Number of centers in integrals : 101 - | Number of centers in hamiltonian : 190 - | Consuming 14 KiB for k_phase. - | Number of super-cells (origin) [n_cells] : 2197 - | Number of super-cells (after PM_index) [n_cells] : 112 - | Number of super-cells in hamiltonian [n_cells_in_hamiltonian]: 112 - | Size of matrix packed + index [n_hamiltonian_matrix_size] : 82583 - Partitioning the integration grid into batches with parallel hashing+maxmin method. - | Number of batches: 128 - | Maximal batch size: 90 - | Minimal batch size: 85 - | Average batch size: 87.562 - | Standard deviation of batch sizes: 1.493 - - Integration load balanced across 1 MPI tasks. - Work distribution over tasks is as follows: - Initializing partition tables, free-atom densities, potentials, etc. across the integration grid (initialize_grid_storage). - | Species 1: outer_partition_radius set to 5.000694715736543 AA . - | The sparse table of interatomic distances needs 194.62 kbyte instead of 313.63 kbyte of memory. - | Net number of integration points: 11208 - | of which are non-zero points : 9876 - | Numerical average free-atom electrostatic potential : -11.78007497 eV - Renormalizing the initial density to the exact electron count on the 3D integration grid. - | Initial density: Formal number of electrons (from input files) : 28.0000000000 - | Integrated number of electrons on 3D grid : 28.0037445357 - | Charge integration error : 0.0037445357 - | Normalization factor for density and gradient : 0.9998662845 - Renormalizing the free-atom superposition density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 28.0000000000 - | Integrated number of electrons on 3D grid : 28.0037445357 - | Charge integration error : 0.0037445357 - | Normalization factor for density and gradient : 0.9998662845 - Obtaining max. number of non-zero basis functions in each batch (get_n_compute_maxes). - Calculating total energy contributions from superposition of free atom densities. - Initialize hartree_potential_storage - Integrating overlap matrix. - Time summed over all CPUs for integration: real work 0.253 s, elapsed 0.253 s - Orthonormalizing eigenvectors - - End scf reinitialization - timings : max(cpu_time) wall_clock(cpu1) - | Time for scf. reinitialization : 0.562 s 0.561 s - | Boundary condition initialization : 0.064 s 0.064 s - | Integration : 0.253 s 0.253 s - | Grid partitioning : 0.032 s 0.032 s - | Preloading free-atom quantities on grid : 0.174 s 0.174 s - | Free-atom superposition energy : 0.027 s 0.027 s - | K.-S. eigenvector reorthonormalization : 0.001 s 0.000 s ------------------------------------------------------------- - Evaluating new KS density using the density matrix - Evaluating density matrix - Time summed over all CPUs for getting density from density matrix: real work 0.796 s, elapsed 0.796 s - Integration grid: deviation in total charge ( - N_e) = -7.105427E-15 - - Time for density update prior : max(cpu_time) wall_clock(cpu1) - | self-consistency iterative process : 0.797 s 0.798 s - ------------------------------------------------------------- - Begin self-consistency iteration # 1 - - Date : 20230628, Time : 104408.490 ------------------------------------------------------------- - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 28.0000000000 - | Integrated number of electrons on 3D grid : 28.0000000000 - | Charge integration error : 0.0000000000 - | Normalization factor for density and gradient : 1.0000000000 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = -0.296378E-13 - | Sum of charges compensated after spline to logarithmic grids = -0.629591E-04 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = -0.296722E-13 - Summing up the Hartree potential. - | Estimated reciprocal-space cutoff momentum G_max: 2.30298530 bohr^-1 . - | Reciprocal lattice points for long-range Hartree potential: 58 - Time summed over all CPUs for potential: real work 0.390 s, elapsed 0.390 s - | RMS charge density error from multipole expansion : 0.137057E-01 - | Average real-space part of the electrostatic potential : 0.43618715 eV - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.393 s, elapsed 0.393 s - Decreasing sparse matrix size: - | Tolerance: 0.1000E-12 - Hamiltonian matrix - | Array has 74550 nonzero elements out of 82583 elements - | Sparsity factor is 0.097 - Overlap matrix - | Array has 68306 nonzero elements out of 82583 elements - | Sparsity factor is 0.173 - New size of hamiltonian matrix: 74577 - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Singularity check in k-point 1, task 0 (analysis for other k-points/tasks may follow below): - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.001 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.000 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -5.01957146 eV - Writing Kohn-Sham eigenvalues. - K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - - State Occupation Eigenvalue [Ha] Eigenvalue [eV] - 1 2.00000 -65.748414 -1789.10539 - 2 2.00000 -65.748414 -1789.10539 - 3 2.00000 -5.106138 -138.94508 - 4 2.00000 -5.105973 -138.94060 - 5 2.00000 -3.489912 -94.96534 - 6 2.00000 -3.489912 -94.96534 - 7 2.00000 -3.489912 -94.96534 - 8 2.00000 -3.489516 -94.95457 - 9 2.00000 -3.489516 -94.95457 - 10 2.00000 -3.489516 -94.95457 - 11 2.00000 -0.608071 -16.54646 - 12 2.00000 -0.192605 -5.24105 - 13 2.00000 -0.192605 -5.24105 - 14 2.00000 -0.192605 -5.24105 - 15 0.00000 -0.110991 -3.02022 - 16 0.00000 -0.104017 -2.83044 - 17 0.00000 -0.104017 -2.83044 - 18 0.00000 -0.104017 -2.83044 - 19 0.00000 0.092776 2.52456 - 20 0.00000 0.092776 2.52456 - - What follows are estimated values for band gap, HOMO, LUMO, etc. - | They are estimated on a discrete k-point grid and not necessarily exact. - | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. - - Highest occupied state (VBM) at -5.24104779 eV (relative to internal zero) - | Occupation number: 2.00000000 - | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - - Lowest unoccupied state (CBM) at -4.40316738 eV (relative to internal zero) - | Occupation number: 0.00000000 - | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) - - ESTIMATED overall HOMO-LUMO gap: 0.83788041 eV between HOMO at k-point 1 and LUMO at k-point 4 - | This appears to be an indirect band gap. - | Smallest direct gap : 2.22082344 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, - this system is most likely an insulator or a semiconductor. - - Total energy components: - | Sum of eigenvalues : -328.16332796 Ha -8929.77849588 eV - | XC energy correction : -41.74829363 Ha -1136.02887010 eV - | XC potential correction : 53.91054166 Ha 1466.98047781 eV - | Free-atom electrostatic energy: -263.84284311 Ha -7179.52905141 eV - | Hartree energy correction : -0.80369312 Ha -21.86960252 eV - | Entropy correction : -0.00000000 Ha -0.00000000 eV - | --------------------------- - | Total energy : -580.64761615 Ha -15800.22554210 eV - | Total energy, T -> 0 : -580.64761615 Ha -15800.22554210 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -580.64761615 Ha -15800.22554210 eV - - Derived energy quantities: - | Kinetic energy : 582.10688240 Ha 15839.93419700 eV - | Electrostatic energy : -1121.00620492 Ha -30504.13086900 eV - | Energy correction for multipole - | error in Hartree potential : 0.01823700 Ha 0.49625397 eV - | Sum of eigenvalues per atom : -4464.88924794 eV - | Total energy (T->0) per atom : -7900.11277105 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -7900.11277105 eV - Evaluating new KS density using the density matrix - Evaluating density matrix - Time summed over all CPUs for getting density from density matrix: real work 0.798 s, elapsed 0.798 s - Integration grid: deviation in total charge ( - N_e) = 2.842171E-14 - - Self-consistency convergence accuracy: - | Change of charge density : 0.1308E+00 - | Change of sum of eigenvalues : -0.8930E+04 eV - | Change of total energy : -0.1580E+05 eV - - ------------------------------------------------------------- - End self-consistency iteration # 1 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 1.592 s 1.592 s - | Charge density update : 0.799 s 0.799 s - | Density mixing & preconditioning : 0.000 s 0.000 s - | Hartree multipole update : 0.001 s 0.001 s - | Hartree multipole summation : 0.393 s 0.393 s - | Integration : 0.394 s 0.394 s - | Solution of K.-S. eqns. : 0.005 s 0.005 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 1.553 MB (on task 0) - | Maximum: 1.553 MB (on task 0) - | Average: 1.553 MB - | Peak value for overall tracked memory usage: - | Minimum: 14.236 MB (on task 0 after allocating d_wave) - | Maximum: 14.236 MB (on task 0 after allocating d_wave) - | Average: 14.236 MB - | Largest tracked array allocation so far: - | Minimum: 3.456 MB (hamiltonian_shell on task 0) - | Maximum: 3.456 MB (hamiltonian_shell on task 0) - | Average: 3.456 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - ------------------------------------------------------------- - Begin self-consistency iteration # 2 - - Date : 20230628, Time : 104410.082 ------------------------------------------------------------- - Pulay mixing of updated and previous charge densities. - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 28.0000000000 - | Integrated number of electrons on 3D grid : 27.9999998182 - | Charge integration error : -0.0000001818 - | Normalization factor for density and gradient : 1.0000000065 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = -0.102120E-12 - | Sum of charges compensated after spline to logarithmic grids = -0.629596E-04 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = -0.102153E-12 - Summing up the Hartree potential. - Time summed over all CPUs for potential: real work 0.391 s, elapsed 0.391 s - | RMS charge density error from multipole expansion : 0.137056E-01 - | Average real-space part of the electrostatic potential : 0.43618904 eV - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.397 s, elapsed 0.397 s - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.000 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -5.01957712 eV - What follows are estimated values for band gap, HOMO, LUMO, etc. - | They are estimated on a discrete k-point grid and not necessarily exact. - | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. - - Highest occupied state (VBM) at -5.24105283 eV (relative to internal zero) - | Occupation number: 2.00000000 - | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - - Lowest unoccupied state (CBM) at -4.40316944 eV (relative to internal zero) - | Occupation number: 0.00000000 - | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) - - ESTIMATED overall HOMO-LUMO gap: 0.83788339 eV between HOMO at k-point 1 and LUMO at k-point 4 - | This appears to be an indirect band gap. - | Smallest direct gap : 2.22082548 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, - this system is most likely an insulator or a semiconductor. - - Total energy components: - | Sum of eigenvalues : -328.16329335 Ha -8929.77755408 eV - | XC energy correction : -41.74829799 Ha -1136.02898875 eV - | XC potential correction : 53.91054739 Ha 1466.98063355 eV - | Free-atom electrostatic energy: -263.84284311 Ha -7179.52905141 eV - | Hartree energy correction : -0.80372910 Ha -21.87058153 eV - | Entropy correction : -0.00000000 Ha -0.00000000 eV - | --------------------------- - | Total energy : -580.64761616 Ha -15800.22554222 eV - | Total energy, T -> 0 : -580.64761616 Ha -15800.22554222 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -580.64761616 Ha -15800.22554222 eV - - Derived energy quantities: - | Kinetic energy : 582.10696926 Ha 15839.93656074 eV - | Electrostatic energy : -1121.00628743 Ha -30504.13311421 eV - | Energy correction for multipole - | error in Hartree potential : 0.01823698 Ha 0.49625347 eV - | Sum of eigenvalues per atom : -4464.88877704 eV - | Total energy (T->0) per atom : -7900.11277111 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -7900.11277111 eV - Evaluating new KS density using the density matrix - Evaluating density matrix - Time summed over all CPUs for getting density from density matrix: real work 0.797 s, elapsed 0.797 s - Integration grid: deviation in total charge ( - N_e) = 2.131628E-14 - - Self-consistency convergence accuracy: - | Change of charge density : 0.2024E-04 - | Change of sum of eigenvalues : 0.9418E-03 eV - | Change of total energy : -0.1217E-06 eV - - ------------------------------------------------------------- - End self-consistency iteration # 2 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 1.771 s 1.771 s - | Charge density update : 0.799 s 0.799 s - | Density mixing & preconditioning : 0.177 s 0.177 s - | Hartree multipole update : 0.001 s 0.001 s - | Hartree multipole summation : 0.393 s 0.393 s - | Integration : 0.397 s 0.397 s - | Solution of K.-S. eqns. : 0.005 s 0.004 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 1.553 MB (on task 0) - | Maximum: 1.553 MB (on task 0) - | Average: 1.553 MB - | Peak value for overall tracked memory usage: - | Minimum: 14.236 MB (on task 0 after allocating d_wave) - | Maximum: 14.236 MB (on task 0 after allocating d_wave) - | Average: 14.236 MB - | Largest tracked array allocation so far: - | Minimum: 3.456 MB (hamiltonian_shell on task 0) - | Maximum: 3.456 MB (hamiltonian_shell on task 0) - | Average: 3.456 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - ------------------------------------------------------------- - Begin self-consistency iteration # 3 - - Date : 20230628, Time : 104411.853 ------------------------------------------------------------- - Pulay mixing of updated and previous charge densities. - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 28.0000000000 - | Integrated number of electrons on 3D grid : 27.9999993680 - | Charge integration error : -0.0000006320 - | Normalization factor for density and gradient : 1.0000000226 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = -0.198103E-12 - | Sum of charges compensated after spline to logarithmic grids = -0.629613E-04 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = -0.198260E-12 - Summing up the Hartree potential. - Time summed over all CPUs for potential: real work 0.390 s, elapsed 0.390 s - | RMS charge density error from multipole expansion : 0.137052E-01 - | Average real-space part of the electrostatic potential : 0.43619612 eV - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.397 s, elapsed 0.397 s - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.000 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -5.01959701 eV - What follows are estimated values for band gap, HOMO, LUMO, etc. - | They are estimated on a discrete k-point grid and not necessarily exact. - | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. - - Highest occupied state (VBM) at -5.24107060 eV (relative to internal zero) - | Occupation number: 2.00000000 - | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - - Lowest unoccupied state (CBM) at -4.40317657 eV (relative to internal zero) - | Occupation number: 0.00000000 - | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) - - ESTIMATED overall HOMO-LUMO gap: 0.83789403 eV between HOMO at k-point 1 and LUMO at k-point 4 - | This appears to be an indirect band gap. - | Smallest direct gap : 2.22083239 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, - this system is most likely an insulator or a semiconductor. - - Total energy components: - | Sum of eigenvalues : -328.16317457 Ha -8929.77432201 eV - | XC energy correction : -41.74831282 Ha -1136.02939240 eV - | XC potential correction : 53.91056687 Ha 1466.98116369 eV - | Free-atom electrostatic energy: -263.84284311 Ha -7179.52905141 eV - | Hartree energy correction : -0.80385254 Ha -21.87394053 eV - | Entropy correction : -0.00000000 Ha -0.00000000 eV - | --------------------------- - | Total energy : -580.64761617 Ha -15800.22554266 eV - | Total energy, T -> 0 : -580.64761617 Ha -15800.22554266 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -580.64761617 Ha -15800.22554266 eV - - Derived energy quantities: - | Kinetic energy : 582.10726704 Ha 15839.94466374 eV - | Electrostatic energy : -1121.00657039 Ha -30504.14081400 eV - | Energy correction for multipole - | error in Hartree potential : 0.01823692 Ha 0.49625195 eV - | Sum of eigenvalues per atom : -4464.88716101 eV - | Total energy (T->0) per atom : -7900.11277133 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -7900.11277133 eV - Evaluating new KS density using the density matrix - Evaluating density matrix - Time summed over all CPUs for getting density from density matrix: real work 0.798 s, elapsed 0.798 s - Integration grid: deviation in total charge ( - N_e) = 5.329071E-14 - - Self-consistency convergence accuracy: - | Change of charge density : 0.1574E-04 - | Change of sum of eigenvalues : 0.3232E-02 eV - | Change of total energy : -0.4336E-06 eV - - ------------------------------------------------------------- - End self-consistency iteration # 3 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 1.773 s 1.773 s - | Charge density update : 0.800 s 0.799 s - | Density mixing & preconditioning : 0.178 s 0.178 s - | Hartree multipole update : 0.001 s 0.001 s - | Hartree multipole summation : 0.393 s 0.393 s - | Integration : 0.397 s 0.397 s - | Solution of K.-S. eqns. : 0.005 s 0.004 s - | Total energy evaluation : 0.000 s 0.001 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 1.553 MB (on task 0) - | Maximum: 1.553 MB (on task 0) - | Average: 1.553 MB - | Peak value for overall tracked memory usage: - | Minimum: 14.236 MB (on task 0 after allocating d_wave) - | Maximum: 14.236 MB (on task 0 after allocating d_wave) - | Average: 14.236 MB - | Largest tracked array allocation so far: - | Minimum: 3.456 MB (hamiltonian_shell on task 0) - | Maximum: 3.456 MB (hamiltonian_shell on task 0) - | Average: 3.456 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - ------------------------------------------------------------- - Begin self-consistency iteration # 4 - - Date : 20230628, Time : 104413.626 ------------------------------------------------------------- - Pulay mixing of updated and previous charge densities. - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 28.0000000000 - | Integrated number of electrons on 3D grid : 27.9999999956 - | Charge integration error : -0.0000000044 - | Normalization factor for density and gradient : 1.0000000002 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = 0.862839E-14 - | Sum of charges compensated after spline to logarithmic grids = -0.629616E-04 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = 0.874725E-14 - Summing up the Hartree potential. - Time summed over all CPUs for potential: real work 0.390 s, elapsed 0.390 s - | RMS charge density error from multipole expansion : 0.137051E-01 - | Average real-space part of the electrostatic potential : 0.43619824 eV - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.397 s, elapsed 0.397 s - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.000 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -5.01959782 eV - What follows are estimated values for band gap, HOMO, LUMO, etc. - | They are estimated on a discrete k-point grid and not necessarily exact. - | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. - - Highest occupied state (VBM) at -5.24107146 eV (relative to internal zero) - | Occupation number: 2.00000000 - | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - - Lowest unoccupied state (CBM) at -4.40317637 eV (relative to internal zero) - | Occupation number: 0.00000000 - | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) - - ESTIMATED overall HOMO-LUMO gap: 0.83789509 eV between HOMO at k-point 1 and LUMO at k-point 4 - | This appears to be an indirect band gap. - | Smallest direct gap : 2.22083176 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, - this system is most likely an insulator or a semiconductor. - - Total energy components: - | Sum of eigenvalues : -328.16317903 Ha -8929.77444340 eV - | XC energy correction : -41.74831175 Ha -1136.02936317 eV - | XC potential correction : 53.91056551 Ha 1466.98112663 eV - | Free-atom electrostatic energy: -263.84284311 Ha -7179.52905141 eV - | Hartree energy correction : -0.80384779 Ha -21.87381136 eV - | Entropy correction : -0.00000000 Ha -0.00000000 eV - | --------------------------- - | Total energy : -580.64761617 Ha -15800.22554270 eV - | Total energy, T -> 0 : -580.64761617 Ha -15800.22554270 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -580.64761617 Ha -15800.22554270 eV - - Derived energy quantities: - | Kinetic energy : 582.10725382 Ha 15839.94430404 eV - | Electrostatic energy : -1121.00655825 Ha -30504.14048358 eV - | Energy correction for multipole - | error in Hartree potential : 0.01823696 Ha 0.49625293 eV - | Sum of eigenvalues per atom : -4464.88722170 eV - | Total energy (T->0) per atom : -7900.11277135 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -7900.11277135 eV - Evaluating new KS density using the density matrix - Evaluating density matrix - Time summed over all CPUs for getting density from density matrix: real work 0.799 s, elapsed 0.799 s - Integration grid: deviation in total charge ( - N_e) = 8.526513E-14 - - Self-consistency convergence accuracy: - | Change of charge density : 0.1066E-05 - | Change of sum of eigenvalues : -0.1214E-03 eV - | Change of total energy : -0.4500E-07 eV - - ------------------------------------------------------------- - End self-consistency iteration # 4 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 1.774 s 1.774 s - | Charge density update : 0.800 s 0.800 s - | Density mixing & preconditioning : 0.178 s 0.178 s - | Hartree multipole update : 0.001 s 0.002 s - | Hartree multipole summation : 0.393 s 0.392 s - | Integration : 0.397 s 0.398 s - | Solution of K.-S. eqns. : 0.005 s 0.004 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 1.553 MB (on task 0) - | Maximum: 1.553 MB (on task 0) - | Average: 1.553 MB - | Peak value for overall tracked memory usage: - | Minimum: 14.236 MB (on task 0 after allocating d_wave) - | Maximum: 14.236 MB (on task 0 after allocating d_wave) - | Average: 14.236 MB - | Largest tracked array allocation so far: - | Minimum: 3.456 MB (hamiltonian_shell on task 0) - | Maximum: 3.456 MB (hamiltonian_shell on task 0) - | Average: 3.456 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - ------------------------------------------------------------- - Begin self-consistency iteration # 5 - - Date : 20230628, Time : 104415.400 ------------------------------------------------------------- - Pulay mixing of updated and previous charge densities. - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 28.0000000000 - | Integrated number of electrons on 3D grid : 28.0000000003 - | Charge integration error : 0.0000000003 - | Normalization factor for density and gradient : 1.0000000000 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = 0.946356E-14 - | Sum of charges compensated after spline to logarithmic grids = -0.629616E-04 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = 0.934464E-14 - Summing up the Hartree potential. - Time summed over all CPUs for potential: real work 0.390 s, elapsed 0.390 s - | RMS charge density error from multipole expansion : 0.137051E-01 - | Average real-space part of the electrostatic potential : 0.43619869 eV - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.397 s, elapsed 0.397 s - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.001 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -5.01959745 eV - What follows are estimated values for band gap, HOMO, LUMO, etc. - | They are estimated on a discrete k-point grid and not necessarily exact. - | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. - - Highest occupied state (VBM) at -5.24107102 eV (relative to internal zero) - | Occupation number: 2.00000000 - | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - - Lowest unoccupied state (CBM) at -4.40317611 eV (relative to internal zero) - | Occupation number: 0.00000000 - | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) - - ESTIMATED overall HOMO-LUMO gap: 0.83789491 eV between HOMO at k-point 1 and LUMO at k-point 4 - | This appears to be an indirect band gap. - | Smallest direct gap : 2.22083180 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, - this system is most likely an insulator or a semiconductor. - - Total energy components: - | Sum of eigenvalues : -328.16317801 Ha -8929.77441560 eV - | XC energy correction : -41.74831181 Ha -1136.02936478 eV - | XC potential correction : 53.91056559 Ha 1466.98112877 eV - | Free-atom electrostatic energy: -263.84284311 Ha -7179.52905141 eV - | Hartree energy correction : -0.80384883 Ha -21.87383971 eV - | Entropy correction : -0.00000000 Ha -0.00000000 eV - | --------------------------- - | Total energy : -580.64761617 Ha -15800.22554272 eV - | Total energy, T -> 0 : -580.64761617 Ha -15800.22554272 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -580.64761617 Ha -15800.22554272 eV - - Derived energy quantities: - | Kinetic energy : 582.10725387 Ha 15839.94430542 eV - | Electrostatic energy : -1121.00655824 Ha -30504.14048337 eV - | Energy correction for multipole - | error in Hartree potential : 0.01823697 Ha 0.49625314 eV - | Sum of eigenvalues per atom : -4464.88720780 eV - | Total energy (T->0) per atom : -7900.11277136 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -7900.11277136 eV - Preliminary charge convergence reached. Turning off preconditioner. - - Evaluating new KS density using the density matrix - Evaluating density matrix - Time summed over all CPUs for getting density from density matrix: real work 0.801 s, elapsed 0.801 s - Integration grid: deviation in total charge ( - N_e) = 1.065814E-14 - - Self-consistency convergence accuracy: - | Change of charge density : 0.6149E-07 - | Change of sum of eigenvalues : 0.2780E-04 eV - | Change of total energy : -0.2328E-07 eV - - Electronic self-consistency reached - switching on the force computation. - - Electronic self-consistency reached - switching on the analytical stress tensor computation. - - ------------------------------------------------------------- - End self-consistency iteration # 5 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 1.775 s 1.776 s - | Charge density & force component update : 0.802 s 0.802 s - | Density mixing : 0.178 s 0.178 s - | Hartree multipole update : 0.001 s 0.001 s - | Hartree multipole summation : 0.393 s 0.393 s - | Hartree pot. SCF incomplete forces : 0.935 s 0.935 s - | Integration : 0.397 s 0.397 s - | Solution of K.-S. eqns. : 0.005 s 0.005 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 1.553 MB (on task 0) - | Maximum: 1.553 MB (on task 0) - | Average: 1.553 MB - | Peak value for overall tracked memory usage: - | Minimum: 14.236 MB (on task 0 after allocating d_wave) - | Maximum: 14.236 MB (on task 0 after allocating d_wave) - | Average: 14.236 MB - | Largest tracked array allocation so far: - | Minimum: 3.456 MB (hamiltonian_shell on task 0) - | Maximum: 3.456 MB (hamiltonian_shell on task 0) - | Average: 3.456 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - ------------------------------------------------------------- - Begin self-consistency iteration # 6 - - Date : 20230628, Time : 104417.176 ------------------------------------------------------------- - Pulay mixing of updated and previous charge densities. - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 28.0000000000 - | Integrated number of electrons on 3D grid : 28.0000000000 - | Charge integration error : 0.0000000000 - | Normalization factor for density and gradient : 1.0000000000 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = 0.772723E-14 - | Sum of charges compensated after spline to logarithmic grids = -0.629616E-04 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = 0.763731E-14 - Summing up the Hartree potential. - Time summed over all CPUs for potential: real work 1.644 s, elapsed 1.644 s - | RMS charge density error from multipole expansion : 0.137051E-01 - | Average real-space part of the electrostatic potential : 0.43619869 eV - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.397 s, elapsed 0.397 s - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.000 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -5.01959745 eV - What follows are estimated values for band gap, HOMO, LUMO, etc. - | They are estimated on a discrete k-point grid and not necessarily exact. - | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. - - Highest occupied state (VBM) at -5.24107102 eV (relative to internal zero) - | Occupation number: 2.00000000 - | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - - Lowest unoccupied state (CBM) at -4.40317611 eV (relative to internal zero) - | Occupation number: 0.00000000 - | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) - - ESTIMATED overall HOMO-LUMO gap: 0.83789491 eV between HOMO at k-point 1 and LUMO at k-point 4 - | This appears to be an indirect band gap. - | Smallest direct gap : 2.22083180 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, - this system is most likely an insulator or a semiconductor. - - Total energy components: - | Sum of eigenvalues : -328.16317801 Ha -8929.77441570 eV - | XC energy correction : -41.74831181 Ha -1136.02936478 eV - | XC potential correction : 53.91056559 Ha 1466.98112877 eV - | Free-atom electrostatic energy: -263.84284311 Ha -7179.52905141 eV - | Hartree energy correction : -0.80384883 Ha -21.87383961 eV - | Entropy correction : -0.00000000 Ha -0.00000000 eV - | --------------------------- - | Total energy : -580.64761617 Ha -15800.22554272 eV - | Total energy, T -> 0 : -580.64761617 Ha -15800.22554272 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -580.64761617 Ha -15800.22554272 eV - - Derived energy quantities: - | Kinetic energy : 582.10725386 Ha 15839.94430505 eV - | Electrostatic energy : -1121.00655823 Ha -30504.14048300 eV - | Energy correction for multipole - | error in Hartree potential : 0.01823697 Ha 0.49625314 eV - | Sum of eigenvalues per atom : -4464.88720785 eV - | Total energy (T->0) per atom : -7900.11277136 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -7900.11277136 eV - Evaluating new KS density using the density matrix - Evaluating density matrix - Time summed over all CPUs for getting density from density matrix: real work 0.799 s, elapsed 0.799 s - Integration grid: deviation in total charge ( - N_e) = 0.000000E+00 - - atomic forces [eV/Ang]: - ----------------------- - atom # 1 - Hellmann-Feynman : -0.591784E-06 0.154593E-06 0.163668E-06 - Ionic forces : 0.000000E+00 0.000000E+00 0.000000E+00 - Multipole : -0.528189E-07 0.315861E-08 0.748176E-08 - Hartree pot. SCF incomplete : 0.105940E-07 -0.281635E-08 0.592908E-08 - Pulay + GGA : 0.000000E+00 0.000000E+00 0.000000E+00 - ---------------------------------------------------------------- - Total forces( 1) : -0.634009E-06 0.154935E-06 0.177079E-06 - atom # 2 - Hellmann-Feynman : 0.596618E-06 -0.152609E-06 -0.157106E-06 - Ionic forces : 0.000000E+00 0.000000E+00 0.000000E+00 - Multipole : 0.528178E-07 -0.315954E-08 -0.748044E-08 - Hartree pot. SCF incomplete : -0.109746E-07 0.239156E-08 -0.598959E-08 - Pulay + GGA : 0.000000E+00 0.000000E+00 0.000000E+00 - ---------------------------------------------------------------- - Total forces( 2) : 0.638461E-06 -0.153376E-06 -0.170576E-06 - - - Self-consistency convergence accuracy: - | Change of charge density : 0.6540E-08 - | Change of sum of eigenvalues : -0.9572E-07 eV - | Change of total energy : 0.3496E-09 eV - | Change of forces : 0.6866E-06 eV/A - - ------------------------------------------------------------- - End self-consistency iteration # 6 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 3.795 s 3.795 s - | Charge density & force component update : 0.801 s 0.801 s - | Density mixing : 0.001 s 0.001 s - | Hartree multipole update : 0.001 s 0.002 s - | Hartree multipole summation : 1.648 s 1.647 s - | Hartree pot. SCF incomplete forces : 0.942 s 0.942 s - | Integration : 0.397 s 0.398 s - | Solution of K.-S. eqns. : 0.005 s 0.004 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 1.553 MB (on task 0) - | Maximum: 1.553 MB (on task 0) - | Average: 1.553 MB - | Peak value for overall tracked memory usage: - | Minimum: 14.236 MB (on task 0 after allocating d_wave) - | Maximum: 14.236 MB (on task 0 after allocating d_wave) - | Average: 14.236 MB - | Largest tracked array allocation so far: - | Minimum: 3.456 MB (hamiltonian_shell on task 0) - | Maximum: 3.456 MB (hamiltonian_shell on task 0) - | Average: 3.456 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - ------------------------------------------------------------- - Begin self-consistency iteration # 7 - - Date : 20230628, Time : 104420.971 ------------------------------------------------------------- - Pulay mixing of updated and previous charge densities. - Renormalizing the density to the exact electron count on the 3D integration grid. - | Formal number of electrons (from input files) : 28.0000000000 - | Integrated number of electrons on 3D grid : 28.0000000000 - | Charge integration error : -0.0000000000 - | Normalization factor for density and gradient : 1.0000000000 - - Evaluating partitioned Hartree potential by multipole expansion. - | Original multipole sum: apparent total charge = -0.690394E-13 - | Sum of charges compensated after spline to logarithmic grids = -0.629616E-04 - | Analytical far-field extrapolation by fixed multipoles: - | Hartree multipole sum: apparent total charge = -0.690219E-13 - Summing up the Hartree potential. - Time summed over all CPUs for potential: real work 1.647 s, elapsed 1.647 s - | RMS charge density error from multipole expansion : 0.137051E-01 - | Average real-space part of the electrostatic potential : 0.43619869 eV - - Integrating Hamiltonian matrix: batch-based integration. - Time summed over all CPUs for integration: real work 0.398 s, elapsed 0.398 s - - Updating Kohn-Sham eigenvalues and eigenvectors using ELSI and the (modified) LAPACK eigensolver. - Starting LAPACK eigensolver - Finished Cholesky decomposition - | Time : 0.000 s - Finished transformation to standard eigenproblem - | Time : 0.000 s - Finished solving standard eigenproblem - | Time : 0.001 s - Finished back-transformation of eigenvectors - | Time : 0.000 s - - Obtaining occupation numbers and chemical potential using ELSI. - | Chemical potential (Fermi level): -5.01959746 eV - What follows are estimated values for band gap, HOMO, LUMO, etc. - | They are estimated on a discrete k-point grid and not necessarily exact. - | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. - - Highest occupied state (VBM) at -5.24107103 eV (relative to internal zero) - | Occupation number: 2.00000000 - | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - - Lowest unoccupied state (CBM) at -4.40317611 eV (relative to internal zero) - | Occupation number: 0.00000000 - | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) - - ESTIMATED overall HOMO-LUMO gap: 0.83789492 eV between HOMO at k-point 1 and LUMO at k-point 4 - | This appears to be an indirect band gap. - | Smallest direct gap : 2.22083180 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, - this system is most likely an insulator or a semiconductor. - - Total energy components: - | Sum of eigenvalues : -328.16317802 Ha -8929.77441578 eV - | XC energy correction : -41.74831181 Ha -1136.02936478 eV - | XC potential correction : 53.91056559 Ha 1466.98112878 eV - | Free-atom electrostatic energy: -263.84284311 Ha -7179.52905141 eV - | Hartree energy correction : -0.80384883 Ha -21.87383953 eV - | Entropy correction : -0.00000000 Ha -0.00000000 eV - | --------------------------- - | Total energy : -580.64761617 Ha -15800.22554272 eV - | Total energy, T -> 0 : -580.64761617 Ha -15800.22554272 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -580.64761617 Ha -15800.22554272 eV - - Derived energy quantities: - | Kinetic energy : 582.10725386 Ha 15839.94430512 eV - | Electrostatic energy : -1121.00655823 Ha -30504.14048306 eV - | Energy correction for multipole - | error in Hartree potential : 0.01823697 Ha 0.49625314 eV - | Sum of eigenvalues per atom : -4464.88720789 eV - | Total energy (T->0) per atom : -7900.11277136 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy per atom : -7900.11277136 eV - Evaluating new KS density using the density matrix - Evaluating density matrix - Time summed over all CPUs for getting density from density matrix: real work 0.800 s, elapsed 0.800 s - - Evaluating density-matrix-based force terms: batch-based integration - Evaluating density matrix - Evaluating density matrix - Integration grid: deviation in total charge ( - N_e) = 4.263256E-14 - - atomic forces [eV/Ang]: - ----------------------- - atom # 1 - Hellmann-Feynman : -0.593616E-06 0.154244E-06 0.167646E-06 - Ionic forces : 0.000000E+00 0.000000E+00 0.000000E+00 - Multipole : -0.528170E-07 0.316161E-08 0.747925E-08 - Hartree pot. SCF incomplete : 0.113701E-07 -0.273145E-08 0.453902E-08 - Pulay + GGA : 0.511538E-07 -0.880170E-07 -0.703409E-07 - ---------------------------------------------------------------- - Total forces( 1) : -0.583909E-06 0.666570E-07 0.109323E-06 - atom # 2 - Hellmann-Feynman : 0.598422E-06 -0.152266E-06 -0.161091E-06 - Ionic forces : 0.000000E+00 0.000000E+00 0.000000E+00 - Multipole : 0.528195E-07 -0.315968E-08 -0.747820E-08 - Hartree pot. SCF incomplete : -0.117211E-07 0.229555E-08 -0.457792E-08 - Pulay + GGA : -0.678800E-07 0.867322E-07 0.606676E-07 - ---------------------------------------------------------------- - Total forces( 2) : 0.571641E-06 -0.663978E-07 -0.112479E-06 - - - Analytical stress tensor components [eV] xx yy zz xy xz yz - ----------------------------------------------------------------------------------------------------------------------------------------------------------- - Nuclear Hellmann-Feynman : -0.1190475719E+02 -0.1190493809E+02 -0.1190493809E+02 0.1216492596E-06 0.5622001483E-07 -0.6683101677E-06 - Multipole Hellmann-Feynman : -0.2750159986E+02 -0.2750161039E+02 -0.2750161039E+02 0.3888406713E-06 0.2448907761E-06 -0.2201423316E-05 - On-site Multipole corrections : -0.2840362645E+00 -0.2840362649E+00 -0.2840362649E+00 -0.4332915843E-10 -0.1151778884E-10 0.3636389044E-09 - Strain deriv. of the orbitals : 0.3969034003E+02 0.3969053146E+02 0.3969053146E+02 -0.5077012238E-06 -0.3198719154E-06 0.2664048369E-05 - ----------------------------------------------------------------------------------------------------------------------------------------------------------- - Sum of all contributions : -0.5328603275E-04 -0.5328338212E-04 -0.5328212227E-04 0.2745377944E-08 -0.1877264225E-07 -0.2053214757E-06 - - +-------------------------------------------------------------------+ - | Analytical stress tensor - Symmetrized | - | Cartesian components [eV/A**3] | - +-------------------------------------------------------------------+ - | x y z | - | | - | x -0.00000119 0.00000000 -0.00000000 | - | y 0.00000000 -0.00000119 -0.00000000 | - | z -0.00000000 -0.00000000 -0.00000119 | - | | - | Pressure: 0.00000119 [eV/A**3] | - | | - +-------------------------------------------------------------------+ - - * Warning: Stress tensor is anisotropic. Be aware that pressure is an isotropic quantity. - - - Self-consistency convergence accuracy: - | Change of charge density : 0.3462E-08 - | Change of sum of eigenvalues : -0.8864E-07 eV - | Change of total energy : 0.2227E-09 eV - | Change of forces : 0.4388E-08 eV/A - - Writing Kohn-Sham eigenvalues. - K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - - State Occupation Eigenvalue [Ha] Eigenvalue [eV] - 1 2.00000 -65.748401 -1789.10501 - 2 2.00000 -65.748401 -1789.10501 - 3 2.00000 -5.106132 -138.94492 - 4 2.00000 -5.105967 -138.94044 - 5 2.00000 -3.489905 -94.96516 - 6 2.00000 -3.489905 -94.96516 - 7 2.00000 -3.489905 -94.96516 - 8 2.00000 -3.489510 -94.95440 - 9 2.00000 -3.489510 -94.95440 - 10 2.00000 -3.489510 -94.95440 - 11 2.00000 -0.608072 -16.54648 - 12 2.00000 -0.192606 -5.24107 - 13 2.00000 -0.192606 -5.24107 - 14 2.00000 -0.192606 -5.24107 - 15 0.00000 -0.110992 -3.02024 - 16 0.00000 -0.104018 -2.83046 - 17 0.00000 -0.104018 -2.83046 - 18 0.00000 -0.104018 -2.83046 - 19 0.00000 0.092775 2.52455 - 20 0.00000 0.092775 2.52455 - - What follows are estimated values for band gap, HOMO, LUMO, etc. - | They are estimated on a discrete k-point grid and not necessarily exact. - | For converged numbers, create a DOS and/or band structure plot on a denser k-grid. - - Highest occupied state (VBM) at -5.24107103 eV (relative to internal zero) - | Occupation number: 2.00000000 - | K-point: 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - - Lowest unoccupied state (CBM) at -4.40317611 eV (relative to internal zero) - | Occupation number: 0.00000000 - | K-point: 4 at 0.000000 0.500000 0.500000 (in units of recip. lattice) - - ESTIMATED overall HOMO-LUMO gap: 0.83789492 eV between HOMO at k-point 1 and LUMO at k-point 4 - | This appears to be an indirect band gap. - | Smallest direct gap : 2.22083180 eV for k_point 1 at 0.000000 0.000000 0.000000 (in units of recip. lattice) - The gap value is above 0.2 eV. Unless you are using a very sparse k-point grid, - this system is most likely an insulator or a semiconductor. - | Chemical Potential : -5.01959746 eV - - Self-consistency cycle converged. - - ------------------------------------------------------------- - End self-consistency iteration # 7 : max(cpu_time) wall_clock(cpu1) - | Time for this iteration : 18.939 s 19.008 s - | Charge density & force component update : 15.942 s 16.006 s - | Density mixing : 0.001 s 0.001 s - | Hartree multipole update : 0.001 s 0.002 s - | Hartree multipole summation : 1.651 s 1.650 s - | Hartree pot. SCF incomplete forces : 0.941 s 0.946 s - | Integration : 0.398 s 0.398 s - | Solution of K.-S. eqns. : 0.005 s 0.005 s - | Total energy evaluation : 0.000 s 0.000 s - - Partial memory accounting: - | Current value for overall tracked memory usage: - | Minimum: 1.553 MB (on task 0) - | Maximum: 1.553 MB (on task 0) - | Average: 1.553 MB - | Peak value for overall tracked memory usage: - | Minimum: 14.236 MB (on task 0 after allocating d_wave) - | Maximum: 14.236 MB (on task 0 after allocating d_wave) - | Average: 14.236 MB - | Largest tracked array allocation so far: - | Minimum: 3.456 MB (hamiltonian_shell on task 0) - | Maximum: 3.456 MB (hamiltonian_shell on task 0) - | Average: 3.456 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. ------------------------------------------------------------- - Removing unitary transformations (pure translations, rotations) from forces on atoms. - Atomic forces before filtering: - | Net force on center of mass : -0.122682E-07 0.259215E-09 -0.315608E-08 eV/A - Atomic forces after filtering: - | Net force on center of mass : -0.850707E-22 0.000000E+00 -0.212677E-22 eV/A - - Energy and forces in a compact form: - | Total energy uncorrected : -0.158002255427229E+05 eV - | Total energy corrected : -0.158002255427229E+05 eV <-- do not rely on this value for anything but (periodic) metals - | Electronic free energy : -0.158002255427229E+05 eV - Total atomic forces (unitary forces cleaned) [eV/Ang]: - | 1 -0.577774893695394E-06 0.665273903016273E-07 0.110901338442392E-06 - | 2 0.577774893695393E-06 -0.665273903016273E-07 -0.110901338442392E-06 - - ------------------------------------ - Start decomposition of the XC Energy - ------------------------------------ - X and C from original XC functional choice - Hartree-Fock Energy : 0.000000000 Ha 0.000000000 eV - X Energy : -40.666268639 Ha -1106.585472109 eV - C Energy : -1.082043167 Ha -29.443892673 eV - XC Energy w/o HF : -41.748311806 Ha -1136.029364783 eV - Total XC Energy : -41.748311806 Ha -1136.029364783 eV - ------------------------------------ - LDA X and C from self-consistent density - X Energy LDA : -37.597186314 Ha -1023.071492920 eV - C Energy LDA : -2.143897994 Ha -58.338432637 eV - ------------------------------------ - End decomposition of the XC Energy - ------------------------------------ - ------------------------------------------------------------- - Relaxation / MD: End force evaluation. : max(cpu_time) wall_clock(cpu1) - | Time for this force evaluation : 32.785 s 32.854 s - ------------------------------------------------------------- - Geometry optimization: Attempting to predict improved coordinates. - - +-------------------------------------------------------------------+ - | Generalized derivatives on lattice vectors [eV/A] | - +-------------------------------------------------------------------+ - |lattice_vector 0.00000946 -0.00000950 -0.00000950 | - |lattice_vector -0.00000947 0.00000943 -0.00000943 | - |lattice_vector -0.00000946 -0.00000943 0.00000942 | - +-------------------------------------------------------------------+ - | Forces on lattice vectors cleaned from atomic contributions [eV/A]| - +-------------------------------------------------------------------+ - |lattice_vector -0.00000946 0.00000950 0.00000950 | - |lattice_vector 0.00000947 -0.00000943 0.00000943 | - |lattice_vector 0.00000946 0.00000943 -0.00000942 | - +-------------------------------------------------------------------+ - Removing unitary transformations (pure translations, rotations) from forces on atoms. - Atomic forces before filtering: - | Net force on center of mass : -0.850707E-22 0.000000E+00 -0.212677E-22 eV/A - Atomic forces after filtering: - | Net force on center of mass : 0.850707E-22 0.000000E+00 0.212677E-22 eV/A - Net remaining forces (excluding translations, rotations) in present geometry: - || Forces on atoms || = 0.577775E-06 eV/A. - || Forces on lattice || = 0.950044E-05 eV/A^3. - Maximum force component is 0.950044E-05 eV/A. - Present geometry is converged. - ------------------------------------------------------------- - Final atomic structure: - x [A] y [A] z [A] - lattice_vector 0.00000007 2.81520842 2.81520842 - lattice_vector 2.81520832 -0.00000004 2.81520837 - lattice_vector 2.81520832 2.81520837 -0.00000004 - - atom 0.00000002 -0.00000000 -0.00000000 Si - atom 1.40760416 1.40760419 1.40760419 Si - - Fractional coordinates: - L1 L2 L3 - atom_frac -0.00000000 0.00000000 0.00000000 Si - atom_frac 0.25000000 0.25000000 0.25000000 Si ------------------------------------------------------------- - ------------------------------------------------------------------------------- - Final output of selected total energy values: - - The following output summarizes some interesting total energy values - at the end of a run (AFTER all relaxation, molecular dynamics, etc.). - - | Total energy of the DFT / Hartree-Fock s.c.f. calculation : -15800.225542723 eV - | Final zero-broadening corrected energy (caution - metals only) : -15800.225542723 eV - | For reference only, the value of 1 Hartree used in FHI-aims is : 27.211384500 eV - | For reference only, the overall average (free atom contribution - | + realspace contribution) of the electrostatic potential after - | s.c.f. convergence is : -11.343876278 eV - - Before relying on these values, please be sure to understand exactly which - total energy value is referred to by a given number. Different objects may - all carry the same name 'total energy'. Definitions: - - Total energy of the DFT / Hartree-Fock s.c.f. calculation: - | Note that this energy does not include ANY quantities calculated after the - | s.c.f. cycle, in particular not ANY RPA, MP2, etc. many-body perturbation terms. - - Final zero-broadening corrected energy: - | For metallic systems only, a broadening of the occupation numbers at the Fermi - | level can be extrapolated back to zero broadening by an electron-gas inspired - | formula. For all systems that are not real metals, this value can be - | meaningless and should be avoided. - ------------------------------------------------------------------------------- - Methods described in the following list of references were used in this FHI-aims run. - If you publish the results, please make sure to cite these reference if they apply. - FHI-aims is an academic code, and for our developers (often, Ph.D. students - and postdocs), scientific credit in the community is essential. - Thank you for helping us! - - For any use of FHI-aims, please cite: - - Volker Blum, Ralf Gehrke, Felix Hanke, Paula Havu, Ville Havu, - Xinguo Ren, Karsten Reuter, and Matthias Scheffler - 'Ab initio molecular simulations with numeric atom-centered orbitals' - Computer Physics Communications 180, 2175-2196 (2009) - http://doi.org/10.1016/j.cpc.2009.06.022 - - - For the analytical stress tensor used in your run, please cite: - - Franz Knuth, Christian Carbogno, Viktor Atalla, Volker Blum, Matthias Scheffler - 'All-electron formalism for total energy strain derivatives and - stress tensor components for numeric atom-centered orbitals' - Computer Physics Communications 190, 33-50 (2015). - http://doi.org/10.1016/j.cpc.2015.01.003 - - - The provided symmetry information was generated with SPGlib: - - Atsushi Togo, Yusuke Seto, Dimitar Pashov - SPGlib 1.7.3 obtained from http://spglib.sourceforge.net - Copyright (C) 2008 Atsushi Togo - - - The ELSI infrastructure was used in your run to solve the Kohn-Sham electronic structure. - Please check out http://elsi-interchange.org to learn more. - If scalability is important for your project, please acknowledge ELSI by citing: - - V. W-z. Yu, F. Corsetti, A. Garcia, W. P. Huhn, M. Jacquelin, W. Jia, - B. Lange, L. Lin, J. Lu, W. Mi, A. Seifitokaldani, A. Vazquez-Mayagoitia, - C. Yang, H. Yang, and V. Blum - 'ELSI: A unified software interface for Kohn-Sham electronic structure solvers' - Computer Physics Communications 222, 267-285 (2018). - http://doi.org/10.1016/j.cpc.2017.09.007 - - - For the real-space grid partitioning and parallelization used in this calculation, please cite: - - Ville Havu, Volker Blum, Paula Havu, and Matthias Scheffler, - 'Efficient O(N) integration for all-electron electronic structure calculation' - 'using numerically tabulated basis functions' - Journal of Computational Physics 228, 8367-8379 (2009). - http://doi.org/10.1016/j.jcp.2009.08.008 - - Of course, there are many other important community references, e.g., those cited in the - above references. Our list is limited to references that describe implementations in the - FHI-aims code. The reason is purely practical (length of this list) - please credit others as well. - ------------------------------------------------------------- - Leaving FHI-aims. - Date : 20230628, Time : 104439.986 - - Computational steps: - | Number of self-consistency cycles : 50 - | Number of SCF (re)initializations : 5 - | Number of relaxation steps : 4 - - Detailed time accounting : max(cpu_time) wall_clock(cpu1) - | Total time : 196.060 s 196.938 s - | Preparation time : 0.110 s 0.111 s - | Boundary condition initialization : 0.313 s 0.313 s - | Grid partitioning : 0.169 s 0.168 s - | Preloading free-atom quantities on grid : 0.908 s 0.911 s - | Free-atom superposition energy : 0.137 s 0.137 s - | Total time for integrations : 22.234 s 22.335 s - | Total time for solution of K.-S. equations : 0.238 s 0.235 s - | Total time for EV reorthonormalization : 0.003 s 0.003 s - | Total time for density & force components : 123.835 s 124.446 s - | Total time for mixing & preconditioning : 6.421 s 6.446 s - | Total time for Hartree multipole update : 0.059 s 0.059 s - | Total time for Hartree multipole sum : 32.131 s 32.238 s - | Total time for total energy evaluation : 0.002 s 0.002 s - | Total time NSC force correction : 9.394 s 9.429 s - | Total time for scaled ZORA corrections : 0.000 s 0.000 s - - Partial memory accounting: - | Residual value for overall tracked memory usage across tasks: 0.000000 MB (should be 0.000000 MB) - | Peak values for overall tracked memory usage: - | Minimum: 14.236 MB (on task 0 after allocating d_wave) - | Maximum: 14.236 MB (on task 0 after allocating d_wave) - | Average: 14.236 MB - | Largest tracked array allocation: - | Minimum: 3.456 MB (hamiltonian_shell on task 0) - | Maximum: 3.456 MB (hamiltonian_shell on task 0) - | Average: 3.456 MB - Note: These values currently only include a subset of arrays which are explicitly tracked. - The "true" memory usage will be greater. - - Have a nice day. 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a/tests/io/aims/test_aims_outputs.py +++ b/tests/io/aims/test_aims_outputs.py @@ -1,5 +1,6 @@ from __future__ import annotations +import gzip import json from pathlib import Path @@ -26,8 +27,8 @@ def comp_images(test, ref): def test_aims_output_si(): - si = AimsOutput.from_outfile(f"{outfile_dir}/si.out") - with open(f"{outfile_dir}/si_ref.json") as ref_file: + si = AimsOutput.from_outfile(f"{outfile_dir}/si.out.gz") + with gzip.open(f"{outfile_dir}/si_ref.json.gz") as ref_file: si_ref = json.load(ref_file, cls=MontyDecoder) assert si_ref.metadata == si.metadata @@ -41,8 +42,8 @@ def test_aims_output_si(): def test_aims_output_h2o(): - h2o = AimsOutput.from_outfile(f"{outfile_dir}/h2o.out") - with open(f"{outfile_dir}/h2o_ref.json") as ref_file: + h2o = AimsOutput.from_outfile(f"{outfile_dir}/h2o.out.gz") + with gzip.open(f"{outfile_dir}/h2o_ref.json.gz", "rt") as ref_file: h2o_ref = json.load(ref_file, cls=MontyDecoder) assert h2o_ref.metadata == h2o.metadata @@ -56,9 +57,10 @@ def test_aims_output_h2o(): def test_aims_output_si_str(): - with open(f"{outfile_dir}/si.out") as si_out: + with gzip.open(f"{outfile_dir}/si.out.gz", "rt") as si_out: si = AimsOutput.from_str(si_out.read()) - with open(f"{outfile_dir}/si_ref.json") as ref_file: + + with gzip.open(f"{outfile_dir}/si_ref.json.gz", "rt") as ref_file: si_ref = json.load(ref_file, cls=MontyDecoder) assert si_ref.metadata == si.metadata @@ -72,10 +74,10 @@ def test_aims_output_si_str(): def test_aims_output_h2o_str(): - with open(f"{outfile_dir}/h2o.out") as h2o_out: + with gzip.open(f"{outfile_dir}/h2o.out.gz", "rt") as h2o_out: h2o = AimsOutput.from_str(h2o_out.read()) - with open(f"{outfile_dir}/h2o_ref.json") as ref_file: + with gzip.open(f"{outfile_dir}/h2o_ref.json.gz", "rt") as ref_file: h2o_ref = json.load(ref_file, cls=MontyDecoder) assert h2o_ref.metadata == h2o.metadata From e633e6f38e46c6e0e5650d4c268c834decb5d399 Mon Sep 17 00:00:00 2001 From: Thomas Purcell Date: Tue, 31 Oct 2023 21:25:58 +0100 Subject: [PATCH 10/30] Gzip all refrence files 1) Species blocks can now read from gzipped file 2) geometry.in can now read a gzip file --- pymatgen/io/aims/inputs.py | 20 ++- tests/io/aims/aims_input_files/control.in.h2o | 170 ------------------ .../aims/aims_input_files/control.in.h2o.gz | Bin 0 -> 1384 bytes tests/io/aims/aims_input_files/control.in.si | 126 ------------- .../io/aims/aims_input_files/control.in.si.gz | Bin 0 -> 1579 bytes .../io/aims/aims_input_files/geometry.in.h2o | 8 - .../aims/aims_input_files/geometry.in.h2o.gz | Bin 0 -> 197 bytes .../aims/aims_input_files/geometry.in.h2o.ref | 8 - .../aims_input_files/geometry.in.h2o.ref.gz | Bin 0 -> 212 bytes tests/io/aims/aims_input_files/geometry.in.si | 10 -- .../aims/aims_input_files/geometry.in.si.gz | Bin 0 -> 222 bytes .../aims/aims_input_files/geometry.in.si.ref | 10 -- .../aims_input_files/geometry.in.si.ref.gz | Bin 0 -> 243 bytes tests/io/aims/aims_input_files/h2o_ref.json | 72 -------- .../io/aims/aims_input_files/h2o_ref.json.gz | Bin 0 -> 382 bytes tests/io/aims/aims_input_files/si_ref.json | 91 ---------- tests/io/aims/aims_input_files/si_ref.json.gz | Bin 0 -> 570 bytes .../aims/species_directory/light/01_H_default | 64 ------- .../species_directory/light/01_H_default.gz | Bin 0 -> 781 bytes .../aims/species_directory/light/08_O_default | 80 --------- .../species_directory/light/08_O_default.gz | Bin 0 -> 902 bytes .../species_directory/light/14_Si_default | 87 --------- .../species_directory/light/14_Si_default.gz | Bin 0 -> 1109 bytes tests/io/aims/test_aims_inputs.py | 20 ++- 24 files changed, 28 insertions(+), 738 deletions(-) delete mode 100644 tests/io/aims/aims_input_files/control.in.h2o create mode 100644 tests/io/aims/aims_input_files/control.in.h2o.gz delete mode 100644 tests/io/aims/aims_input_files/control.in.si create mode 100644 tests/io/aims/aims_input_files/control.in.si.gz delete mode 100644 tests/io/aims/aims_input_files/geometry.in.h2o create mode 100644 tests/io/aims/aims_input_files/geometry.in.h2o.gz delete mode 100644 tests/io/aims/aims_input_files/geometry.in.h2o.ref create mode 100644 tests/io/aims/aims_input_files/geometry.in.h2o.ref.gz delete mode 100644 tests/io/aims/aims_input_files/geometry.in.si create mode 100644 tests/io/aims/aims_input_files/geometry.in.si.gz delete mode 100644 tests/io/aims/aims_input_files/geometry.in.si.ref create mode 100644 tests/io/aims/aims_input_files/geometry.in.si.ref.gz delete mode 100644 tests/io/aims/aims_input_files/h2o_ref.json create mode 100644 tests/io/aims/aims_input_files/h2o_ref.json.gz delete mode 100644 tests/io/aims/aims_input_files/si_ref.json create mode 100644 tests/io/aims/aims_input_files/si_ref.json.gz delete mode 100644 tests/io/aims/species_directory/light/01_H_default create mode 100644 tests/io/aims/species_directory/light/01_H_default.gz delete mode 100644 tests/io/aims/species_directory/light/08_O_default create mode 100644 tests/io/aims/species_directory/light/08_O_default.gz delete mode 100644 tests/io/aims/species_directory/light/14_Si_default create mode 100644 tests/io/aims/species_directory/light/14_Si_default.gz diff --git a/pymatgen/io/aims/inputs.py b/pymatgen/io/aims/inputs.py index feb48e8e0a7..767bdd8fccd 100644 --- a/pymatgen/io/aims/inputs.py +++ b/pymatgen/io/aims/inputs.py @@ -5,6 +5,7 @@ from __future__ import annotations +import gzip import time from copy import deepcopy from dataclasses import dataclass, field @@ -101,8 +102,12 @@ def from_str(cls, contents: str): @classmethod def from_file(cls, filepath: str | Path): - with open(filepath) as infile: - content = infile.read() + if str(filepath).endswith(".gz"): + with gzip.open(filepath, "rt") as infile: + content = infile.read() + else: + with open(filepath) as infile: + content = infile.read() return cls.from_str(content) @classmethod @@ -520,8 +525,15 @@ def get_species_block(self, structure, species_dir): species = np.unique(structure.species) for sp in species: filename = f"{species_dir}/{sp.Z:02d}_{sp.symbol}_default" - with open(filename) as sf: - sb += "".join(sf.readlines()) + if Path(filename).exists(): + with open(filename) as sf: + sb += "".join(sf.readlines()) + elif Path(f"{filename}.gz").exists(): + with gzip.open(f"{filename}.gz", "rt") as sf: + sb += "".join(sf.readlines()) + else: + raise ValueError("Species file for {sp.symbol} not found.") + return sb def as_dict(self) -> dict[str, Any]: diff --git a/tests/io/aims/aims_input_files/control.in.h2o b/tests/io/aims/aims_input_files/control.in.h2o deleted file mode 100644 index 057c24be7fb..00000000000 --- a/tests/io/aims/aims_input_files/control.in.h2o +++ /dev/null @@ -1,170 +0,0 @@ -#======================================================================== -# FHI-aims geometry file: /home/tpurcell/git/pymatgen/tests/io/aims/testing/geometry.in -# File generated from pymatgen -# Mon Oct 30 20:29:48 2023 -#======================================================================== -#=============================================================================== -xc pw-lda -occupation_type fermi 0.010000 -vdw_correction_hirshfeld -compute_forces .true. -relax_geometry trm 1e-3 -batch_size_limit 200 -output cube eigenstate 1 - cube origin 0.000000000000e+00 0.000000000000e+00 0.000000000000e+00 - cube edge 10 1.000000000000e-01 0.000000000000e+00 0.000000000000e+00 - cube edge 10 0.000000000000e+00 1.000000000000e-01 0.000000000000e+00 - cube edge 10 0.000000000000e+00 0.000000000000e+00 1.000000000000e-01 - cube format cube -output cube total_density - cube origin 0.000000000000e+00 0.000000000000e+00 0.000000000000e+00 - cube edge 10 1.000000000000e-01 0.000000000000e+00 0.000000000000e+00 - cube edge 10 0.000000000000e+00 1.000000000000e-01 0.000000000000e+00 - cube edge 10 0.000000000000e+00 0.000000000000e+00 1.000000000000e-01 - cube format cube -#=============================================================================== - -################################################################################ -# -# FHI-aims code project -# VB, Fritz-Haber Institut, 2009 -# -# Suggested "light" defaults for H atom (to be pasted into control.in file) -# Be sure to double-check any results obtained with these settings for post-processing, -# e.g., with the "tight" defaults and larger basis sets. -# -################################################################################ - species H -# global species definitions - nucleus 1 - mass 1.00794 -# - l_hartree 4 -# - cut_pot 3.5 1.5 1.0 - basis_dep_cutoff 1e-4 -# - radial_base 24 5.0 - radial_multiplier 1 - angular_grids specified - division 0.2421 50 - division 0.3822 110 - division 0.4799 194 - division 0.5341 302 -# division 0.5626 434 -# division 0.5922 590 -# division 0.6542 770 -# division 0.6868 1202 -# outer_grid 770 - outer_grid 302 -################################################################################ -# -# Definition of "minimal" basis -# -################################################################################ -# valence basis states - valence 1 s 1. -# ion occupancy - ion_occ 1 s 0.5 -################################################################################ -# -# Suggested additional basis functions. For production calculations, -# uncomment them one after another (the most important basis functions are -# listed first). -# -# Basis constructed for dimers: 0.5 A, 0.7 A, 1.0 A, 1.5 A, 2.5 A -# -################################################################################ -# "First tier" - improvements: -1014.90 meV to -62.69 meV - hydro 2 s 2.1 - hydro 2 p 3.5 -# "Second tier" - improvements: -12.89 meV to -1.83 meV -# hydro 1 s 0.85 -# hydro 2 p 3.7 -# hydro 2 s 1.2 -# hydro 3 d 7 -# "Third tier" - improvements: -0.25 meV to -0.12 meV -# hydro 4 f 11.2 -# hydro 3 p 4.8 -# hydro 4 d 9 -# hydro 3 s 3.2 -################################################################################ -# -# FHI-aims code project -# VB, Fritz-Haber Institut, 2009 -# -# Suggested "light" defaults for O atom (to be pasted into control.in file) -# Be sure to double-check any results obtained with these settings for post-processing, -# e.g., with the "tight" defaults and larger basis sets. -# -################################################################################ - species O -# global species definitions - nucleus 8 - mass 15.9994 -# - l_hartree 4 -# - cut_pot 3.5 1.5 1.0 - basis_dep_cutoff 1e-4 -# - radial_base 36 5.0 - radial_multiplier 1 - angular_grids specified - division 0.2659 50 - division 0.4451 110 - division 0.6052 194 - division 0.7543 302 -# division 0.8014 434 -# division 0.8507 590 -# division 0.8762 770 -# division 0.9023 974 -# division 1.2339 1202 -# outer_grid 974 - outer_grid 302 -################################################################################ -# -# Definition of "minimal" basis -# -################################################################################ -# valence basis states - valence 2 s 2. - valence 2 p 4. -# ion occupancy - ion_occ 2 s 1. - ion_occ 2 p 3. -################################################################################ -# -# Suggested additional basis functions. For production calculations, -# uncomment them one after another (the most important basis functions are -# listed first). -# -# Constructed for dimers: 1.0 A, 1.208 A, 1.5 A, 2.0 A, 3.0 A -# -################################################################################ -# "First tier" - improvements: -699.05 meV to -159.38 meV - hydro 2 p 1.8 - hydro 3 d 7.6 - hydro 3 s 6.4 -# "Second tier" - improvements: -49.91 meV to -5.39 meV -# hydro 4 f 11.6 -# hydro 3 p 6.2 -# hydro 3 d 5.6 -# hydro 5 g 17.6 -# hydro 1 s 0.75 -# "Third tier" - improvements: -2.83 meV to -0.50 meV -# ionic 2 p auto -# hydro 4 f 10.8 -# hydro 4 d 4.7 -# hydro 2 s 6.8 -# "Fourth tier" - improvements: -0.40 meV to -0.12 meV -# hydro 3 p 5 -# hydro 3 s 3.3 -# hydro 5 g 15.6 -# hydro 4 f 17.6 -# hydro 4 d 14 -# Further basis functions - -0.08 meV and below -# hydro 3 s 2.1 -# hydro 4 d 11.6 -# hydro 3 p 16 -# hydro 2 s 17.2 diff --git a/tests/io/aims/aims_input_files/control.in.h2o.gz b/tests/io/aims/aims_input_files/control.in.h2o.gz new file mode 100644 index 0000000000000000000000000000000000000000..208aa4ce02d44cc7c8d457b44a6cee9c51124e58 GIT binary patch literal 1384 zcmV-u1(*6CiwFozUqNL6|6^}%baHQOE@^HqXfkgA?N?22+c*%t>sJh%%N85U67^vz zz#g`{Fw(;!hZemWv_#3=l|+H0lDfZshg59GmXsR14ti)6Ac|&&kHg{c@#W^XD?QE) ztnNR|DX$fjOw>%v9TdD`cd*#v=R&ug%ve<|O0E~}uBN(V%|bJ!)q;zK8EC(FQ!e%Z zE^iDjq9A6&B-Jd3LW&yp0O-io&&SUw;B2VQwrj<|vUSC4u18`CW+ggo01a8UVZb=_K#x8{VV{os#XSt1J~&(11dZuJauR?x1}%G3hxfoi1RU$g+MPD^bhZ}2k{jh3Q9 z%C@xs&VapVpgL*#5pvOODmKryEc*v&vjfSLMHL%Od4niVTyH^dnZiL#n|q+2vK30t zaTUl}3XQi0n7O5Udl&&TeU>V1a;T^*agiIUxH5>!H7mS!#Q{{yGJfRKdy^kNWhFMW zI(RWP-f+Xn%63=NWfkjAS-9`JnyLXgn-*QBp>ty+s`ZviE!oT4VDHO1y>7)R3kPmw zAndRHpxB}yL9}a(7e!&`VDmkQq&Y_d!KmXDB!uXB^s~FhQuDUrSmb@~v?)8R`?{1o z-!H;epx`Wb`tO`Sa)osOa~erV@Hj){jX8sa5JdJzo#8S~(TPPFaYjLiuz^ROH{;A3 zlNc)&gyY`S%o?TMs5g#6^e&eZ-Xu=IC&zh_m04eoe$dcrle~6U+N1pEq2)jnFst#S zrq!(9{I@s@{hA+X#hQ%m51zT^`avql?QszEdiXn}i;2ScDm zB5@*J)yQbT>sCljG4yN}ppqG^iraJw)NlHo+h_USh9cD}6l$4uV@5fznN)YCI`I1~ zzLw^NXT5(}BQdWx+Vt7VU$IRkN%^nmZXNnqh`UV!YLV_uc!Ei9ujm{to3^4GLl zNFr}Jtrn7H{EAvgJ%aP5%Q0kRi6BU)w1gQmF#e!Qg7ngWxTCJtH2Q@igB&!;n5(tN z;)j+We@qCEgVZ2ia-un`IWVv9B0b_Xb-m-A>_;j7Pcf7pEhe12G}#N^jZaMqVmG`% zjfAP2`iD6qH%O;+Ks?X^@rd$>&f+2{!C#&kdwsKvzO7QovpjlMDUtUgJKTSs*@95y z_+iT4h)fAb1XSF|%~qn5=DwZMOQH9=UNR+#&MZa-1;c`zSIOpkUL}*SZ}xCy@;cn~ q$KIctL_FIfRuF7hC7uQe7@<0V9otSn9+U=iBF?{2N7ngv7XSdWF|R}b literal 0 HcmV?d00001 diff --git a/tests/io/aims/aims_input_files/control.in.si b/tests/io/aims/aims_input_files/control.in.si deleted file mode 100644 index 5d086ac5880..00000000000 --- a/tests/io/aims/aims_input_files/control.in.si +++ /dev/null @@ -1,126 +0,0 @@ -#======================================================================== -# FHI-aims geometry file: /home/tpurcell/git/pymatgen/tests/io/aims/testing/geometry.in -# File generated from pymatgen -# Mon Oct 30 20:47:24 2023 -#======================================================================== -# -# List of parameters used to initialize the calculator:# xc:pw-lda -# smearing:['fermi-dirac', 0.01] -# vdw_correction_hirshfeld:True -# compute_forces:True -# relax_geometry:['trm', '1e-3'] -# batch_size_limit:200 -# species_dir:/home/tpurcell/git/pymatgen/tests/io/aims/species_directory/light -# output:['band 0 0 0 0.5 0 0.5 10 G X', 'band 0 0 0 0.5 0.5 0.5 10 G L'] -# k_grid:[1, 1, 1] -#=============================================================================== -xc pw-lda -occupation_type fermi 0.010000 -vdw_correction_hirshfeld -compute_forces .true. -relax_geometry trm 1e-3 -batch_size_limit 200 -output band 0 0 0 0.5 0 0.5 10 G X -output band 0 0 0 0.5 0.5 0.5 10 G L -k_grid 1 1 1 -output cube eigenstate 1 - cube origin 0.000000000000e+00 0.000000000000e+00 0.000000000000e+00 - cube edge 10 1.000000000000e-01 0.000000000000e+00 0.000000000000e+00 - cube edge 10 0.000000000000e+00 1.000000000000e-01 0.000000000000e+00 - cube edge 10 0.000000000000e+00 0.000000000000e+00 1.000000000000e-01 - cube format cube -output cube total_density - cube origin 0.000000000000e+00 0.000000000000e+00 0.000000000000e+00 - cube edge 10 1.000000000000e-01 0.000000000000e+00 0.000000000000e+00 - cube edge 10 0.000000000000e+00 1.000000000000e-01 0.000000000000e+00 - cube edge 10 0.000000000000e+00 0.000000000000e+00 1.000000000000e-01 - cube format cube -#=============================================================================== - -################################################################################ -# -# FHI-aims code project -# VB, Fritz-Haber Institut, 2009 -# -# Suggested "light" defaults for Si atom (to be pasted into control.in file) -# Be sure to double-check any results obtained with these settings for post-processing, -# e.g., with the "tight" defaults and larger basis sets. -# -# 2020/09/08 Added f function to "light" after reinspection of Delta test outcomes. -# This was done for all of Al-Cl and is a tricky decision since it makes -# "light" calculations measurably more expensive for these elements. -# Nevertheless, outcomes for P, S, Cl (and to some extent, Si) appear -# to justify this choice. -# -################################################################################ - species Si -# global species definitions - nucleus 14 - mass 28.0855 -# - l_hartree 4 -# - cut_pot 3.5 1.5 1.0 - basis_dep_cutoff 1e-4 -# - radial_base 42 5.0 - radial_multiplier 1 - angular_grids specified - division 0.5866 50 - division 0.9616 110 - division 1.2249 194 - division 1.3795 302 -# division 1.4810 434 -# division 1.5529 590 -# division 1.6284 770 -# division 1.7077 974 -# division 2.4068 1202 -# outer_grid 974 - outer_grid 302 -################################################################################ -# -# Definition of "minimal" basis -# -################################################################################ -# valence basis states - valence 3 s 2. - valence 3 p 2. -# ion occupancy - ion_occ 3 s 1. - ion_occ 3 p 1. -################################################################################ -# -# Suggested additional basis functions. For production calculations, -# uncomment them one after another (the most important basis functions are -# listed first). -# -# Constructed for dimers: 1.75 A, 2.0 A, 2.25 A, 2.75 A, 3.75 A -# -################################################################################ -# "First tier" - improvements: -571.96 meV to -37.03 meV - hydro 3 d 4.2 - hydro 2 p 1.4 - hydro 4 f 6.2 - ionic 3 s auto -# "Second tier" - improvements: -16.76 meV to -3.03 meV -# hydro 3 d 9 -# hydro 5 g 9.4 -# hydro 4 p 4 -# hydro 1 s 0.65 -# "Third tier" - improvements: -3.89 meV to -0.60 meV -# ionic 3 d auto -# hydro 3 s 2.6 -# hydro 4 f 8.4 -# hydro 3 d 3.4 -# hydro 3 p 7.8 -# "Fourth tier" - improvements: -0.33 meV to -0.11 meV -# hydro 2 p 1.6 -# hydro 5 g 10.8 -# hydro 5 f 11.2 -# hydro 3 d 1 -# hydro 4 s 4.5 -# Further basis functions that fell out of the optimization - noise -# level... < -0.08 meV -# hydro 4 d 6.6 -# hydro 5 g 16.4 -# hydro 4 d 9 diff --git 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- basis_dep_cutoff 1e-4 -# - radial_base 24 5.0 - radial_multiplier 1 - angular_grids specified - division 0.2421 50 - division 0.3822 110 - division 0.4799 194 - division 0.5341 302 -# division 0.5626 434 -# division 0.5922 590 -# division 0.6542 770 -# division 0.6868 1202 -# outer_grid 770 - outer_grid 302 -################################################################################ -# -# Definition of "minimal" basis -# -################################################################################ -# valence basis states - valence 1 s 1. -# ion occupancy - ion_occ 1 s 0.5 -################################################################################ -# -# Suggested additional basis functions. 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For production calculations, -# uncomment them one after another (the most important basis functions are -# listed first). -# -# Constructed for dimers: 1.75 A, 2.0 A, 2.25 A, 2.75 A, 3.75 A -# -################################################################################ -# "First tier" - improvements: -571.96 meV to -37.03 meV - hydro 3 d 4.2 - hydro 2 p 1.4 - hydro 4 f 6.2 - ionic 3 s auto -# "Second tier" - improvements: -16.76 meV to -3.03 meV -# hydro 3 d 9 -# hydro 5 g 9.4 -# hydro 4 p 4 -# hydro 1 s 0.65 -# "Third tier" - improvements: -3.89 meV to -0.60 meV -# ionic 3 d auto -# hydro 3 s 2.6 -# hydro 4 f 8.4 -# hydro 3 d 3.4 -# hydro 3 p 7.8 -# "Fourth tier" - improvements: -0.33 meV to -0.11 meV -# hydro 2 p 1.6 -# hydro 5 g 10.8 -# hydro 5 f 11.2 -# hydro 3 d 1 -# hydro 4 s 4.5 -# Further basis functions that fell out of the optimization - noise -# level... < -0.08 meV -# hydro 4 d 6.6 -# hydro 5 g 16.4 -# hydro 4 d 9 diff --git a/tests/io/aims/species_directory/light/14_Si_default.gz b/tests/io/aims/species_directory/light/14_Si_default.gz new file mode 100644 index 0000000000000000000000000000000000000000..c60e230eeab4fa29c8277848fd8b96ff46acd23b GIT binary patch literal 1109 zcmV-b1giTViwFp1VnJm9|1mUQQ)yphWoBV@Y;*v%R?BYNIuPCaD+bP{0c=)pS;gI? zErND)ae-WPYtYijW^Uf7mn5S`W5~F0fst+5;^YByd%>0W4M?uHq;kWJ zFfO8DL1Gdm(fg=+AFbe_X=vjX+Oe;#P`x91)XiH<-Wo-31`Mcb;WJ9h!BUDqjkZ=D zy09>P{@>AlKe!>uJ$eOPO6U6^m!G7kMhhs27WMO3s=p?R25EeTAjOHTfkyXuQ zJxcEA80e5wdih4~p;MG*{5fE6#7o#Uq!J}|*xM_X|Kba3S|TZ{i<1`b_}>Da7C=x+oA@cT#=)$VC)QdsYlsL?0=t?L}Xorxg6hv!Kg$ZVzB zaCw5MAVe>Gwq_3Q$6DfO&UnX}hdOS~?eruo7OnDpcIQ{f^^R++5hp9M16GfAJt%wT zow9tgi+hP#t+UKpo8}5Z$1(<+Su-7vLIQEGaylR%m1I57X!q;a1b` z4j?X#=un#vu9$OppwY~t@RJ-~gE{rTf2mI9kB%W&YAthEI$c`5gfa2~mU$UdYoOut z&9(exTCym0Z{har_Kj9_whd$~nVJ$hZMyqYQ%0k=IIf~ZiJBZKThtRhjVGj!isnx| z;)0bE8b=m)7c{CfOAcG8SaxR1h}pR%CKeGZa?gV1x&9-Gl&z{02Xcuf9FB^blcEVR zLq}O$&}d#Msg#V96D` z_(FrBbN6|Bbj(iQU$1w;?zn{(-6zp#UGH=EM-5hV;+Ma7q@!2Dgd0O&DUvY;|2P5k b#dawmBMQYW0maoJyHfZK6D5qMati Date: Tue, 31 Oct 2023 22:19:31 +0100 Subject: [PATCH 11/30] Remove json dict comparision Error in the Actions from rounding errors, do more explicit test for as_dict --- tests/io/aims/test_aims_outputs.py | 36 ++++++++++++++++++++++++------ 1 file changed, 29 insertions(+), 7 deletions(-) diff --git a/tests/io/aims/test_aims_outputs.py b/tests/io/aims/test_aims_outputs.py index 257df760893..82962cdb415 100644 --- a/tests/io/aims/test_aims_outputs.py +++ b/tests/io/aims/test_aims_outputs.py @@ -38,8 +38,6 @@ def test_aims_output_si(): for ii in range(si.n_images): comp_images(si.get_results_for_image(ii), si_ref.get_results_for_image(ii)) - assert json.dumps(si.as_dict(), cls=MontyEncoder) == json.dumps(si_ref.as_dict(), cls=MontyEncoder) - def test_aims_output_h2o(): h2o = AimsOutput.from_outfile(f"{outfile_dir}/h2o.out.gz") @@ -53,8 +51,6 @@ def test_aims_output_h2o(): for ii in range(h2o.n_images): comp_images(h2o.get_results_for_image(ii), h2o_ref.get_results_for_image(ii)) - assert json.dumps(h2o.as_dict(), cls=MontyEncoder) == json.dumps(h2o_ref.as_dict(), cls=MontyEncoder) - def test_aims_output_si_str(): with gzip.open(f"{outfile_dir}/si.out.gz", "rt") as si_out: @@ -70,8 +66,6 @@ def test_aims_output_si_str(): for ii in range(si.n_images): comp_images(si.get_results_for_image(ii), si_ref.get_results_for_image(ii)) - assert json.dumps(si.as_dict(), cls=MontyEncoder) == json.dumps(si_ref.as_dict(), cls=MontyEncoder) - def test_aims_output_h2o_str(): with gzip.open(f"{outfile_dir}/h2o.out.gz", "rt") as h2o_out: @@ -87,4 +81,32 @@ def test_aims_output_h2o_str(): for ii in range(h2o.n_images): comp_images(h2o.get_results_for_image(ii), h2o_ref.get_results_for_image(ii)) - assert json.dumps(h2o.as_dict(), cls=MontyEncoder) == json.dumps(h2o_ref.as_dict(), cls=MontyEncoder) + +def test_aims_output_si_dict(): + si = AimsOutput.from_outfile(f"{outfile_dir}/si.out.gz") + si = json.loads(json.dumps(si.as_dict(), cls=MontyEncoder), cls=MontyDecoder) + + with gzip.open(f"{outfile_dir}/si_ref.json.gz") as ref_file: + si_ref = json.load(ref_file, cls=MontyDecoder) + + assert si_ref.metadata == si.metadata + assert si_ref.structure_summary == si.structure_summary + + assert si_ref.n_images == si.n_images + for ii in range(si.n_images): + comp_images(si.get_results_for_image(ii), si_ref.get_results_for_image(ii)) + + +def test_aims_output_h2o_dict(): + h2o = AimsOutput.from_outfile(f"{outfile_dir}/h2o.out.gz") + h2o = json.loads(json.dumps(h2o.as_dict(), cls=MontyEncoder), cls=MontyDecoder) + + with gzip.open(f"{outfile_dir}/h2o_ref.json.gz", "rt") as ref_file: + h2o_ref = json.load(ref_file, cls=MontyDecoder) + + assert h2o_ref.metadata == h2o.metadata + assert h2o_ref.structure_summary == h2o.structure_summary + + assert h2o_ref.n_images == h2o.n_images + for ii in range(h2o.n_images): + comp_images(h2o.get_results_for_image(ii), h2o_ref.get_results_for_image(ii)) From 7d85afd2cf7cc540909e8a0adef21014cd0b7e1f Mon Sep 17 00:00:00 2001 From: Thomas Purcell Date: Wed, 1 Nov 2023 17:00:01 +0100 Subject: [PATCH 12/30] Add full type hinting for inputs.py and convert docstrings 1) Docstrings are googledoc format 2) All type hinting is done --- pymatgen/io/aims/inputs.py | 285 ++++++++++++++++++++++--------------- 1 file changed, 172 insertions(+), 113 deletions(-) diff --git a/pymatgen/io/aims/inputs.py b/pymatgen/io/aims/inputs.py index 767bdd8fccd..beef726d860 100644 --- a/pymatgen/io/aims/inputs.py +++ b/pymatgen/io/aims/inputs.py @@ -1,6 +1,6 @@ """Classes for reading/manipulating/writing FHI-aims input files. -Works for geometry.in and control.in +Works for aims cube objects, geometry.in and control.in """ from __future__ import annotations @@ -23,19 +23,28 @@ @dataclass class AimsGeometryIn(MSONable): - """Class representing an aims geometry.in file""" + """Representation of an aims geometry.in file + + Attributes: + _content (str): The content of the input file + _structure (Structure or Molecule): The structure or molecule + representation of the file + + """ _content: str _structure: Structure | Molecule @classmethod - def from_str(cls, contents: str): - """The contents of the input file + def from_str(cls, contents: str) -> AimsGeometryIn: + """Create an input from the content of an input file + + Args: + contents (str): The content of the file + + Returns: + The AimsGeometryIn file for the string contents - self.__dict__ - ---------- - contents: str - The content of the string """ content_lines = [ line.strip() for line in contents.split("\n") if len(line.strip()) > 0 and line.strip()[0] != "#" @@ -101,7 +110,16 @@ def from_str(cls, contents: str): return cls(_content="\n".join(content_lines), _structure=structure) @classmethod - def from_file(cls, filepath: str | Path): + def from_file(cls, filepath: str | Path) -> AimsGeometryIn: + """Create an AimsGeometryIn from an input file + + Args: + filepath (str): The path to the input file (either plain text of gzipped) + + Returns: + The input object represented in the file + + """ if str(filepath).endswith(".gz"): with gzip.open(filepath, "rt") as infile: content = infile.read() @@ -111,13 +129,15 @@ def from_file(cls, filepath: str | Path): return cls.from_str(content) @classmethod - def from_structure(cls, structure: Structure): - """The contents of the input file + def from_structure(cls, structure: Structure | Molecule) -> AimsGeometryIn: + """Construct an input file from an input structure + + Args: + structure (Structure or Molecule): The structure for the file + + Returns: + The input object for the structure - self.__dict__ - ---------- - structure: Structure - The structure for the file """ content_lines = [] @@ -143,18 +163,16 @@ def structure(self) -> Structure | Molecule: @property def content(self) -> str: - """Accses structure for the file""" + """Accses the contents of the file""" return self._content - def write_file(self, directory: str | Path | None = None, overwrite: bool = False): + def write_file(self, directory: str | Path | None = None, overwrite: bool = False) -> None: """Writes the geometry.in file - self.__dict__ - ---------- - directory: str or Path - The directory to write the geometry.in file - overwrite: bool - If True allow to overwrite existing files + Args: + directory (str | Path | None): The directory to write the geometry.in file + overwrite (bool): If True allow to overwrite existing files + """ if directory is None: directory = Path.cwd() @@ -172,12 +190,7 @@ def write_file(self, directory: str | Path | None = None, overwrite: bool = Fals fd.write("\n") def as_dict(self) -> dict[str, Any]: - """Get a dictionary representation of the geometry.in file. - - Returns - ------- - The dictionary representation of the input file - """ + """Get a dictionary representation of the geometry.in file.""" dct = {} dct["@module"] = type(self).__module__ dct["@class"] = type(self).__name__ @@ -186,13 +199,15 @@ def as_dict(self) -> dict[str, Any]: return dct @classmethod - def from_dict(cls, d: dict[str, Any]): + def from_dict(cls, d: dict[str, Any]) -> AimsGeometryIn: """Initialize from dictionary. - self.__dict__ - ---------- - d: dict[str, Any] - The MontyEncoded dictionary + Args: + d (dict[str, Any]): The MontyEncoded dictionary of the AimsGeometryIn object + + Returns: + The input object represented by the dict + """ decoded = {k: MontyDecoder().process_decoded(v) for k, v in d.items() if not k.startswith("@")} @@ -235,29 +250,22 @@ def from_dict(cls, d: dict[str, Any]): class AimsCube(MSONable): """Class representing the FHI-aims cubes - Parameters - ---------- - type: str - The value to be outputted as a cube file - origin: Sequence[float] | tuple[float, float, float] - The origin of the cube - edges: Sequence[Sequence[float]] - Specifies the edges of a cube: dx, dy, dz - dx (float): The length of the step in the x direction - dy (float): The length of the step in the y direction - dx (float): The length of the step in the x direction - points: Sequence[int] | tuple[int, int, int] - The number of points along each edge - spinstate: int - The spin-channel to use either 1 or 2 - kpoint: int - The k-point to use (the index of the list printed from `output k_point_list`) - filename: str - The filename to use - format: str - The format to output the cube file in: cube, gOpenMol, or xsf - elf_type: int - The type of electron localization function to use (see FHI-aims manual) + Attributes: + type (str): The value to be outputted as a cube file + origin (Sequence[float] or tuple[float, float, float]): The origin of the cube + edges (Sequence[Sequence[float]]): Specifies the edges of a cube: dx, dy, dz + dx (float): The length of the step in the x direction + dy (float): The length of the step in the y direction + dx (float): The length of the step in the x direction + points (Sequence[int] or tuple[int, int, int]): The number of points + along each edge + spinstate (int): The spin-channel to use either 1 or 2 + kpoint (int): The k-point to use (the index of the list printed from + `output k_point_list`) + filename (str): The filename to use + format (str): The format to output the cube file in: cube, gOpenMol, or xsf + elf_type (int): The type of electron localization function to use ( + see FHI-aims manual) """ type: str = field(default_factory=str) @@ -276,8 +284,12 @@ class AimsCube(MSONable): filename: str | None = None elf_type: int | None = None - def __post_init__(self): - """Check the inputted variables to make sure they are correct""" + def __post_init__(self) -> None: + """Check the inputted variables to make sure they are correct + + Raises: + ValueError: If any of the inputs is invalid + """ split_type = self.type.split() if split_type[0] in ALLOWED_AIMS_CUBE_TYPES: if len(split_type) > 1: @@ -313,7 +325,8 @@ def __post_init__(self): raise ValueError("elf_type only used when the cube type is elf") @property - def control_block(self): + def control_block(self) -> str: + """Get the block of text for the control.in file of the Cube""" cb = f"output cube {self.type}\n" cb += f" cube origin {self.origin[0]: .12e} {self.origin[1]: .12e} {self.origin[2]: .12e}\n" for ii in range(3): @@ -334,12 +347,7 @@ def control_block(self): return cb def as_dict(self) -> dict[str, Any]: - """Get a dictionary representation of the geometry.in file. - - Returns - ------- - The dictionary representation of the input file - """ + """Get a dictionary representation of the geometry.in file.""" dct: dict[str, Any] = {} dct["@module"] = type(self).__module__ dct["@class"] = type(self).__name__ @@ -355,13 +363,15 @@ def as_dict(self) -> dict[str, Any]: return dct @classmethod - def from_dict(cls, d: dict[str, Any]): + def from_dict(cls, d: dict[str, Any]) -> AimsCube: """Initialize from dictionary. - self.__dict__ - ---------- - d: dict[str, Any] - The MontyEncoded dictionary + Args: + d(dict[str, Any]): The MontyEncoded dictionary + + Returns: + The AimsCube for d + """ decoded = {k: MontyDecoder().process_decoded(v) for k, v in d.items() if not k.startswith("@")} @@ -380,22 +390,43 @@ def from_dict(cls, d: dict[str, Any]): @dataclass class AimsControlIn(MSONable): - """Class representing and FHI-aims control.in file""" + """Class representing and FHI-aims control.in file + + Attributes: + _parameters (dict[str, Any]): The parameters dictionary conataining all input + flags (key) and values for the control.in file + """ _parameters: dict[str, Any] = field(default_factory=dict) - def __post_init__(self): + def __post_init__(self) -> None: + """Initialize the output list of _parameters""" if "output" not in self._parameters: self._parameters["output"] = [] def __getitem__(self, key: str) -> Any: - """Get an attribute of the class""" + """Get an input parameter + + Args: + key (str): The parameter to get + + Returns: + The setting for that parameter + + Raises: + KeyError: If the key is not in self._parameters + """ if key not in self._parameters: - raise AttributeError(f"{key} not set in AimsControlIn") + raise KeyError(f"{key} not set in AimsControlIn") return self._parameters[key] - def __setitem__(self, key: str, value: Any): - """set an attribute of the class""" + def __setitem__(self, key: str, value: Any) -> None: + """Set an attribute of the class + + Args: + key (str): The parameter to get + value (Any): The value for that parameter + """ if key == "output": if isinstance(value, str): value = [value] @@ -406,46 +437,66 @@ def __setitem__(self, key: str, value: Any): def __delitem__(self, key: str) -> Any: """Delete a parameter from the input object - Parameters - ---------- - key: str - The key in the parameter to remove + Args: + key (str): The key in the parameter to remove + + Returns: + Either the value of the deleted parameter or None if key is + not in self._parameters """ return self._parameters.pop(key, None) @property - def parameters(self): + def parameters(self) -> dict[str, Any]: + """The dictionary of input parameters for control.in""" return self._parameters @parameters.setter - def parameters(self, parameters: dict[str, Any]): - """reload a control.in inputs from a parameters dictionary""" + def parameters(self, parameters: dict[str, Any]) -> None: + """Reset a control.in inputs from a parameters dictionary + + Args: + parameters (dict[str, Any]): The new set of parameters to use + + """ self._parameters = parameters if "output" not in self._parameters: self._parameters["output"] = [] - def get_aims_control_parameter_str(self, key, value, format): + def get_aims_control_parameter_str(self, key: str, value: Any, format: str) -> str: + """Get the string needed to add a parameter to the control.in file + + Args: + key(str): The name of the input flag + value(Any): The value to be set for the flag + format(str): The format string to apply to the value + + Returns: + The line to add to the control.in file + + """ return f"{key :35s}" + (format % value) + "\n" def write_file( self, - structure: Structure, + structure: Structure | Molecule, directory: str | Path | None = None, verbose_header: bool = False, overwrite: bool = False, - ): - """Writes the geometry.in file - - Parameters - ---------- - structure: Structure - The structure to write the input file for - directory: str or Path - The directory to write the geometry.in file - verbose_header: bool - If True print the input option dictionary - overwrite: bool - If True allow to overwrite existing files + ) -> None: + """Writes the control.in file + + Args: + structure (Structure or Molecule): The structure to write the input + file for + directory (str or Path): The directory to write the control.in file. + If None use cwd + verbose_header (bool): If True print the input option dictionary + overwrite (bool): If True allow to overwrite existing files + + Raises: + ValueError: If a file must be overwritten and overwrite is False + ValueError: If k-grid is not provided for the periodic structures """ if directory is None: directory = Path.cwd() @@ -519,8 +570,19 @@ def write_file( fd.write(lim + "\n\n") fd.write(self.get_species_block(structure, self._parameters["species_dir"])) - def get_species_block(self, structure, species_dir): - """Get the basis set information for a structure""" + def get_species_block(self, structure: Structure | Molecule, species_dir: str | Path) -> str: + """Get the basis set information for a structure + + Args: + structure (Molecule or Structure): The structure to get the basis set information for + species_dir (str or Pat:): The directory to find the species files in + + Returns: + The block to add to the control.in file for the species + + Raises: + ValueError: If a file for the species is not found + """ sb = "" species = np.unique(structure.species) for sp in species: @@ -537,26 +599,23 @@ def get_species_block(self, structure, species_dir): return sb def as_dict(self) -> dict[str, Any]: - """Get a dictionary representation of the geometry.in file. - - Returns - ------- - The dictionary representation of the input file - """ - dct = {} + """Get a dictionary representation of the geometry.in file.""" + dct: dict[str, Any] = {} dct["@module"] = type(self).__module__ dct["@class"] = type(self).__name__ dct["parameters"] = self.parameters return dct @classmethod - def from_dict(cls, d: dict[str, Any]): + def from_dict(cls, d: dict[str, Any]) -> AimsControlIn: """Initialize from dictionary. - self.__dict__ - ---------- - d: dict[str, Any] - The MontyEncoded dictionary + Args: + d(dict[str, Any]): The MontyEncoded dictionary + + Returns: + The AimsControlIn for d + """ decoded = {k: MontyDecoder().process_decoded(v) for k, v in d.items() if not k.startswith("@")} From 168babacb27b3a1a871a54d9047151ddfe0bf65c Mon Sep 17 00:00:00 2001 From: Thomas Purcell Date: Wed, 1 Nov 2023 17:09:33 +0100 Subject: [PATCH 13/30] Convert all AimsOutput docstrings to google doc Everything is also type hintted now --- pymatgen/io/aims/output.py | 71 +++++++++++++++++++++----------------- 1 file changed, 39 insertions(+), 32 deletions(-) diff --git a/pymatgen/io/aims/output.py b/pymatgen/io/aims/output.py index b5c802a3d2a..270f92dc379 100644 --- a/pymatgen/io/aims/output.py +++ b/pymatgen/io/aims/output.py @@ -30,17 +30,16 @@ def __init__( results: Molecule | Structure | Sequence[Molecule | Structure], metadata: dict[str, Any], structure_summary: dict[str, Any], - ): + ) -> None: """AimsOutput object constructor. - Parameters - ---------- - results: Sequence[.MSONableAtoms] - A list of all images in an output file - metadata: Dict[str, Any] - The metadata of the executable used to perform the calculation - structure_summary: Dict[str, Any] - The summary of the starting atomic structure + Args: + results (Molecule or Structure or Sequence[Molecule or Structure]): A list + of all images in an output file + metadata (Dict[str, Any]): The metadata of the executable used to perform + the calculation + structure_summary (Dict[str, Any]): The summary of the starting + atomic structure """ self._results = results self._metadata = metadata @@ -59,13 +58,15 @@ def as_dict(self) -> dict[str, Any]: return d @classmethod - def from_outfile(cls, outfile: str | Path): + def from_outfile(cls, outfile: str | Path) -> AimsOutput: """Construct an AimsOutput from an output file. - Parameters - ---------- - outfile: str or Path - The aims.out file to parse + Args: + outfile: str | Path: The aims.out file to parse + + Returns: + The AimsOutput object for the output file + """ metadata, structure_summary = read_aims_header_info(outfile) results = read_aims_output(outfile, index=slice(0, None)) @@ -73,13 +74,15 @@ def from_outfile(cls, outfile: str | Path): return cls(results, metadata, structure_summary) @classmethod - def from_str(cls, content: str): + def from_str(cls, content: str) -> AimsOutput: """Construct an AimsOutput from an output file. - Parameters - ---------- - outfile: str - The content of the aims.out file + Args: + content (str): The content of the aims.out file + + Returns: + The AimsOutput for the output file content + """ metadata, structure_summary = read_aims_header_info_from_content(content) results = read_aims_output_from_content(content, index=slice(0, None)) @@ -87,31 +90,35 @@ def from_str(cls, content: str): return cls(results, metadata, structure_summary) @classmethod - def from_dict(cls, d: dict[str, Any]): + def from_dict(cls, d: dict[str, Any]) -> AimsOutput: """Construct an AimsOutput from a dictionary. - Parameters - ---------- - d: Dict[str, Any] - The dictionary used to create AimsOutput + Args: + d (dict[str, Any]): The dictionary used to create AimsOutput + + Returns: + The AimsOutput for d + """ decoded = {k: MontyDecoder().process_decoded(v) for k, v in d.items() if not k.startswith("@")} for struct in decoded["results"]: struct.properties = {k: MontyDecoder().process_decoded(v) for k, v in struct.properties.items()} - return cls(decoded["results"], decoded["metadata"], decoded["structure_summary"]) + return cls( + decoded["results"], + decoded["metadata"], + decoded["structure_summary"], + ) def get_results_for_image(self, image_ind: int) -> Structure | Molecule: """Get the results dictionary for a particular image or slice of images. - Parameters - ---------- - image_ind: int - The index of the image to get the results for + Args: + image_ind (int): The index of the image to get the results for + + Returns: + The results of the image with index images_ind - Returns - ------- - The results for that image """ return self._results[image_ind] From 0406a95d8a01f5382bdb16daffc2879464fc3858 Mon Sep 17 00:00:00 2001 From: Thomas Purcell Date: Thu, 2 Nov 2023 07:29:21 +0100 Subject: [PATCH 14/30] Add type hining and google doc strings to parsers --- pymatgen/io/aims/parsers.py | 509 +++++++++++++++++++----------------- 1 file changed, 263 insertions(+), 246 deletions(-) diff --git a/pymatgen/io/aims/parsers.py b/pymatgen/io/aims/parsers.py index b33ca1d51ef..21cc34d9cb9 100644 --- a/pymatgen/io/aims/parsers.py +++ b/pymatgen/io/aims/parsers.py @@ -11,10 +11,10 @@ from pymatgen.core import Lattice, Molecule, Structure if TYPE_CHECKING: - from collections.abc import Sequence - - from emmet.core.math import Vector3D + from collections.abc import Generator, Sequence + from io import TextIOWrapper + from emmet.core.math import Matrix3D, Vector3D # TARP: Originally an object, but type hinting needs this to be an int LINE_NOT_FOUND = -1000 @@ -28,7 +28,8 @@ class ParseError(Exception): class AimsParseError(Exception): """Exception raised if an error occurs when parsing an Aims output file.""" - def __init__(self, message): + def __init__(self, message: str) -> None: + """Initialize the error with the message, message""" self.message = message super().__init__(self.message) @@ -56,10 +57,8 @@ def __init__(self, message): class AimsOutChunk: """Base class for AimsOutChunks. - Parameters - ---------- - lines: list[str] - The list of all lines in the aims.out file + Attributes: + lines (list[str]): The list of all lines in the chunk """ lines: list[str] = field(default_factory=list) @@ -67,17 +66,13 @@ class AimsOutChunk: def reverse_search_for(self, keys: list[str], line_start: int = 0) -> int: """Find the last time one of the keys appears in self.lines. - Parameters - ---------- - keys: list[str] - The key strings to search for in self.lines - line_start: int - The lowest index to search for in self.lines + Args: + keys (list[str]): The key strings to search for in self.lines + line_start (int): The lowest index to search for in self.lines - Returns - ------- - int + Returns: The last time one of the keys appears in self.lines + """ for ll, line in enumerate(self.lines[line_start:][::-1]): if any(key in line for key in keys): @@ -88,19 +83,14 @@ def reverse_search_for(self, keys: list[str], line_start: int = 0) -> int: def search_for_all(self, key: str, line_start: int = 0, line_end: int = -1) -> list[int]: """Find the all times the key appears in self.lines. - Parameters - ---------- - key: str - The key string to search for in self.lines - line_start: int - The first line to start the search from - line_end: int - The last line to end the search at - - Returns - ------- - list[ints] + Args: + key (str): The key string to search for in self.lines + line_start (int): The first line to start the search from + line_end (int): The last line to end the search at + + Returns: All times the key appears in the lines + """ line_index = [] for ll, line in enumerate(self.lines[line_start:line_end]): @@ -111,15 +101,12 @@ def search_for_all(self, key: str, line_start: int = 0, line_end: int = -1) -> l def parse_scalar(self, property: str) -> float | None: """Parse a scalar property from the chunk. - Parameters - ---------- - property: str - The property key to parse + Args: + property (str): The property key to parse + + Returns: + The scalar value of the property or None if not found - Returns - ------- - float - The scalar value of the property """ line_start = self.reverse_search_for(scalar_property_to_line_key[property]) @@ -132,22 +119,14 @@ def parse_scalar(self, property: str) -> float | None: @dataclass class AimsOutHeaderChunk(AimsOutChunk): - """The header of the aims.out file containing general information. - - Parameters - ---------- - lines: list[str] - The list of all lines in the aims.out file - _cache: dict[str, Any] - The cache storing previously calculated results - """ + """The header of the aims.out file containing general information.""" lines: list[str] = field(default_factory=list) _cache: dict[str, Any] = field(default_factory=dict) @property - def commit_hash(self): - """Get the commit hash for the FHI-aims version.""" + def commit_hash(self) -> str: + """The commit hash for the FHI-aims version.""" line_start = self.reverse_search_for(["Commit number"]) if line_start == LINE_NOT_FOUND: raise AimsParseError("This file does not appear to be an aims-output file") @@ -155,8 +134,8 @@ def commit_hash(self): return self.lines[line_start].split(":")[1].strip() @property - def aims_uuid(self): - """Get the aims-uuid for the calculation.""" + def aims_uuid(self) -> str: + """The aims-uuid for the calculation.""" line_start = self.reverse_search_for(["aims_uuid"]) if line_start == LINE_NOT_FOUND: raise AimsParseError("This file does not appear to be an aims-output file") @@ -164,8 +143,8 @@ def aims_uuid(self): return self.lines[line_start].split(":")[1].strip() @property - def version_number(self): - """Get the commit hash for the FHI-aims version.""" + def version_number(self) -> str: + """The commit hash for the FHI-aims version.""" line_start = self.reverse_search_for(["FHI-aims version"]) if line_start == LINE_NOT_FOUND: raise AimsParseError("This file does not appear to be an aims-output file") @@ -173,8 +152,8 @@ def version_number(self): return self.lines[line_start].split(":")[1].strip() @property - def fortran_compiler(self): - """Get the fortran compiler used to make FHI-aims.""" + def fortran_compiler(self) -> str | None: + """The fortran compiler used to make FHI-aims.""" line_start = self.reverse_search_for(["Fortran compiler :"]) if line_start == LINE_NOT_FOUND: raise AimsParseError("This file does not appear to be an aims-output file") @@ -182,8 +161,8 @@ def fortran_compiler(self): return self.lines[line_start].split(":")[1].split("/")[-1].strip() @property - def c_compiler(self): - """Get the C compiler used to make FHI-aims.""" + def c_compiler(self) -> str | None: + """The C compiler used to make FHI-aims.""" line_start = self.reverse_search_for(["C compiler :"]) if line_start == LINE_NOT_FOUND: return None @@ -191,8 +170,8 @@ def c_compiler(self): return self.lines[line_start].split(":")[1].split("/")[-1].strip() @property - def fortran_compiler_flags(self): - """Get the fortran compiler flags used to make FHI-aims.""" + def fortran_compiler_flags(self) -> str | None: + """The fortran compiler flags used to make FHI-aims.""" line_start = self.reverse_search_for(["Fortran compiler flags"]) if line_start == LINE_NOT_FOUND: raise AimsParseError("This file does not appear to be an aims-output file") @@ -200,8 +179,8 @@ def fortran_compiler_flags(self): return self.lines[line_start].split(":")[1].strip() @property - def c_compiler_flags(self): - """Get the C compiler flags used to make FHI-aims.""" + def c_compiler_flags(self) -> str | None: + """The C compiler flags used to make FHI-aims.""" line_start = self.reverse_search_for(["C compiler flags"]) if line_start == LINE_NOT_FOUND: return None @@ -209,15 +188,15 @@ def c_compiler_flags(self): return self.lines[line_start].split(":")[1].strip() @property - def build_type(self): - """Get the optional build flags passed to cmake.""" + def build_type(self) -> list[str]: + """The optional build flags passed to cmake.""" line_end = self.reverse_search_for(["Linking against:"]) line_inds = self.search_for_all("Using", line_end=line_end) return [" ".join(self.lines[ind].split()[1:]).strip() for ind in line_inds] @property - def linked_against(self): + def linked_against(self) -> list[str]: """Get all libraries used to link the FHI-aims executable.""" line_start = self.reverse_search_for(["Linking against:"]) if line_start == LINE_NOT_FOUND: @@ -232,8 +211,8 @@ def linked_against(self): return linked_libs @property - def initial_lattice(self): - """Parse the initial lattice vectors from the aims.out file.""" + def initial_lattice(self) -> Lattice | None: + """The initial lattice vectors from the aims.out file.""" line_start = self.reverse_search_for(["| Unit cell:"]) if line_start == LINE_NOT_FOUND: return None @@ -245,8 +224,8 @@ def initial_lattice(self): ) @property - def initial_structure(self): - """Create an SiteCollection object for the initial structure. + def initial_structure(self) -> Structure | Molecule: + """The initial structure Using the FHI-aims output file recreate the initial structure for the calculation. @@ -280,25 +259,29 @@ def initial_structure(self): site_properties=site_properties, ) - return Molecule(species, coords, np.sum(self.initial_charges), site_properties=site_properties) + return Molecule( + species, + coords, + np.sum(self.initial_charges), + site_properties=site_properties, + ) @property - def initial_charges(self): + def initial_charges(self) -> Sequence[float]: + """The initial charges for the structure""" if "initial_charges" not in self._cache: self._parse_initial_charges_and_moments() return self._cache["initial_charges"] @property - def initial_magnetic_moments(self): + def initial_magnetic_moments(self) -> Sequence[float]: + """The initial magnetic Moments""" if "initial_magnetic_moments" not in self._cache: self._parse_initial_charges_and_moments() return self._cache["initial_magnetic_moments"] - def _parse_initial_charges_and_moments(self): - """Parse the initial charges and magnetic moments - - Once parsed store them in the cache - """ + def _parse_initial_charges_and_moments(self) -> None: + """Parse the initial charges and magnetic moments from a file""" charges = np.zeros(self.n_atoms) magmoms = None line_start = self.reverse_search_for(["Initial charges", "Initial moments and charges"]) @@ -318,17 +301,17 @@ def _parse_initial_charges_and_moments(self): self._cache["initial_magnetic_moments"] = magmoms @property - def is_md(self): - """Determine if calculation is a molecular dynamics calculation.""" + def is_md(self) -> bool: + """Is the output for a molecular dynamics calculation?""" return self.reverse_search_for(["Complete information for previous time-step:"]) != LINE_NOT_FOUND @property - def is_relaxation(self): - """Determine if the calculation is a geometry optimization or not.""" + def is_relaxation(self) -> bool: + """Is the output for a relaxation?""" return self.reverse_search_for(["Geometry relaxation:"]) != LINE_NOT_FOUND - def _parse_k_points(self): - """Get the list of k-points used in the calculation.""" + def _parse_k_points(self) -> None: + """Parse the list of k-points used in the calculation.""" n_kpts = self.parse_scalar("n_kpts") if n_kpts is None: self._cache.update( @@ -363,7 +346,6 @@ def _parse_k_points(self): "k_point_weights": k_point_weights, } ) - return @property def n_atoms(self) -> int: @@ -374,7 +356,7 @@ def n_atoms(self) -> int: return int(n_atoms) @property - def n_bands(self): + def n_bands(self) -> int | None: """The number of Kohn-Sham states for the chunk.""" line_start = self.reverse_search_for(scalar_property_to_line_key["n_bands"]) @@ -388,7 +370,7 @@ def n_bands(self): return int(line.split()[-1].strip()[:-1]) @property - def n_electrons(self): + def n_electrons(self) -> int | None: """The number of electrons for the chunk.""" line_start = self.reverse_search_for(scalar_property_to_line_key["n_electrons"]) @@ -399,7 +381,7 @@ def n_electrons(self): return int(float(line.split()[-2])) @property - def n_k_points(self): + def n_k_points(self) -> int | None: """The number of k_ppoints for the calculation.""" n_kpts = self.parse_scalar("n_kpts") if n_kpts is None: @@ -408,7 +390,7 @@ def n_k_points(self): return int(n_kpts) @property - def n_spins(self): + def n_spins(self) -> int | None: """The number of spin channels for the chunk.""" n_spins = self.parse_scalar("n_spins") if n_spins is None: @@ -416,17 +398,18 @@ def n_spins(self): return int(n_spins) @property - def electronic_temperature(self): + def electronic_temperature(self) -> float: """The electronic temperature for the chunk.""" line_start = self.reverse_search_for(scalar_property_to_line_key["electronic_temp"]) + # TARP: Default FHI-aims value if line_start == LINE_NOT_FOUND: - return 0.10 + return 0.00 line = self.lines[line_start] return float(line.split("=")[-1].strip().split()[0]) @property - def k_points(self): + def k_points(self) -> Sequence[Vector3D]: """All k-points listed in the calculation.""" if "k_points" not in self._cache: self._parse_k_points() @@ -434,7 +417,7 @@ def k_points(self): return self._cache["k_points"] @property - def k_point_weights(self): + def k_point_weights(self) -> Sequence[float]: """The k-point weights for the calculation.""" if "k_point_weights" not in self._cache: self._parse_k_points() @@ -442,7 +425,7 @@ def k_point_weights(self): return self._cache["k_point_weights"] @property - def header_summary(self): + def header_summary(self) -> dict[str, Any]: """Dictionary summarizing the information inside the header.""" return { "initial_structure": self.initial_structure, @@ -460,7 +443,7 @@ def header_summary(self): } @property - def metadata_summary(self) -> dict[str, str]: + def metadata_summary(self) -> dict[str, list[str] | str | None]: """Dictionary containing all metadata for FHI-aims build.""" return { "commit_hash": self.commit_hash, @@ -478,29 +461,30 @@ def metadata_summary(self) -> dict[str, str]: class AimsOutCalcChunk(AimsOutChunk): """A part of the aims.out file corresponding to a single structure.""" - def __init__(self, lines, header): + def __init__(self, lines: list[str], header: AimsOutHeaderChunk) -> None: """Construct the AimsOutCalcChunk. - Parameters - ---------- - lines: list[str] - The lines used for the structure - header: .AimsOutHeaderChunk - A summary of the relevant information from the aims.out header + Args: + lines (list[str]): The lines used for the structure + header (.AimsOutHeaderChunk): A summary of the relevant information from + the aims.out header """ super().__init__(lines) self._header = header.header_summary - self._cache = {} + self._cache: dict[str, Any] = {} - def _parse_structure(self): + def _parse_structure(self) -> Structure | Molecule: """Parse a structure object from the file. For the given section of the aims output file generate the calculated structure. + + Returns: + The structure or molecule for the calculation """ species, coords, velocities, lattice = self._parse_lattice_atom_pos() - site_properties = dict() + site_properties: dict[str, Sequence[Any]] = dict() if len(velocities) > 0: site_properties["velocity"] = np.array(velocities) @@ -517,9 +501,6 @@ def _parse_structure(self): if prop in results: site_properties[site_key] = results[prop] - if len(site_properties.keys()) == 0: - site_properties = None - if lattice is not None: return Structure( lattice, @@ -529,21 +510,23 @@ def _parse_structure(self): properties=properties, coords_are_cartesian=True, ) - return Molecule(species, coords, site_properties=site_properties, properties=properties) - - def _parse_lattice_atom_pos(self) -> tuple[list[str], list[Vector3D], list[Vector3D], Lattice | None]: - """Get the lattice of the structure - - Returns - ------- - species: list[str] - The species of all atoms - coords: list[Vector3D] - The cartesian coordinates of the atoms - velocities: list[Vector3D] - The velocities of all atoms - lattice: Lattice or None - The lattice of the system + return Molecule( + species, + coords, + site_properties=site_properties, + properties=properties, + ) + + def _parse_lattice_atom_pos( + self, + ) -> tuple[list[str], list[Vector3D], list[Vector3D], Lattice | None]: + """Parse the lattice and atomic positions of the structure + + Returns: + list[str]: The species symbols for the atoms in the structure + list[Vector3D]: The Cartesian coordinates of the atoms + list[Vector3D]: The velocities of the atoms + Lattice or None: The Lattice for the structure """ lattice_vectors = [] velocities: list[Vector3D] = [] @@ -566,7 +549,10 @@ def _parse_lattice_atom_pos(self) -> tuple[list[str], list[Vector3D], list[Vecto line_start += 1 - line_end = self.reverse_search_for(['Writing the current geometry to file "geometry.in.next_step"'], line_start) + line_end = self.reverse_search_for( + ['Writing the current geometry to file "geometry.in.next_step"'], + line_start, + ) if line_end == LINE_NOT_FOUND: line_end = len(self.lines) @@ -584,7 +570,8 @@ def _parse_lattice_atom_pos(self) -> tuple[list[str], list[Vector3D], list[Vecto return species, coords, velocities, lattice @property - def species(self): + def species(self) -> list[str]: + """The list of atomic symbols for all atoms in the structure""" if "species" not in self._cache: ( self._cache["species"], @@ -595,7 +582,8 @@ def species(self): return self._cache["species"] @property - def coords(self): + def coords(self) -> list[Vector3D]: + """The cartesian coordinates of the atoms""" if "coords" not in self._cache: ( self._cache["species"], @@ -606,7 +594,8 @@ def coords(self): return self._cache["coords"] @property - def velocities(self): + def velocities(self) -> list[Vector3D]: + """The velocities of the atoms""" if "velocities" not in self._cache: ( self._cache["species"], @@ -617,7 +606,8 @@ def velocities(self): return self._cache["velocities"] @property - def lattice(self): + def lattice(self) -> Lattice: + """The Lattice object for the structure""" if "lattice" not in self._cache: ( self._cache["species"], @@ -628,8 +618,8 @@ def lattice(self): return self._cache["lattice"] @property - def forces(self): - """Parse the forces from the aims.out file.""" + def forces(self) -> list[Vector3D] | None: + """The forces from the aims.out file.""" line_start = self.reverse_search_for(["Total atomic forces"]) if line_start == LINE_NOT_FOUND: return None @@ -641,8 +631,8 @@ def forces(self): ) @property - def stresses(self): - """Parse the stresses from the aims.out file and convert to kbar.""" + def stresses(self) -> list[Matrix3D] | None: + """The stresses from the aims.out file and convert to kbar.""" line_start = self.reverse_search_for(["Per atom stress (eV) used for heat flux calculation"]) if line_start == LINE_NOT_FOUND: return None @@ -655,8 +645,8 @@ def stresses(self): return np.array(stresses) * EV_PER_A3_TO_KBAR @property - def stress(self): - """Parse the stress from the aims.out file and convert to kbar.""" + def stress(self) -> Matrix3D | None: + """The stress from the aims.out file and convert to kbar.""" from ase.stress import full_3x3_to_voigt_6_stress line_start = self.reverse_search_for( @@ -672,16 +662,16 @@ def stress(self): return full_3x3_to_voigt_6_stress(stress) * EV_PER_A3_TO_KBAR @property - def is_metallic(self): - """Checks if the system is metallic.""" + def is_metallic(self) -> bool: + """Is the system is metallic.""" line_start = self.reverse_search_for( ["material is metallic within the approximate finite broadening function (occupation_type)"] ) return line_start != LINE_NOT_FOUND @property - def energy(self): - """Parse the energy from the aims.out file.""" + def energy(self) -> float: + """The energy from the aims.out file.""" if self.initial_lattice is not None and self.is_metallic: line_ind = self.reverse_search_for(["Total energy corrected"]) else: @@ -692,8 +682,8 @@ def energy(self): return float(self.lines[line_ind].split()[5]) @property - def dipole(self): - """Parse the electric dipole moment from the aims.out file.""" + def dipole(self) -> Vector3D | None: + """The electric dipole moment from the aims.out file.""" line_start = self.reverse_search_for(["Total dipole moment [eAng]"]) if line_start == LINE_NOT_FOUND: return None @@ -702,8 +692,8 @@ def dipole(self): return np.array([float(inp) for inp in line.split()[6:9]]) @property - def dielectric_tensor(self): - """Parse the dielectric tensor from the aims.out file.""" + def dielectric_tensor(self) -> Matrix3D | None: + """The dielectric tensor from the aims.out file.""" line_start = self.reverse_search_for(["PARSE DFPT_dielectric_tensor"]) if line_start == LINE_NOT_FOUND: return None @@ -715,15 +705,15 @@ def dielectric_tensor(self): return np.array([np.fromstring(line, sep=" ") for line in lines]) @property - def polarization(self): - """Parse the polarization vector from the aims.out file.""" + def polarization(self) -> Vector3D | None: + """The polarization vector from the aims.out file.""" line_start = self.reverse_search_for(["| Cartesian Polarization"]) if line_start == LINE_NOT_FOUND: return None line = self.lines[line_start] return np.array([float(s) for s in line.split()[-3:]]) - def _parse_homo_lumo(self): + def _parse_homo_lumo(self) -> dict[str, float]: """Parse the HOMO/LUMO values and get band gap if periodic.""" line_start = self.reverse_search_for(["Highest occupied state (VBM)"]) homo = float(self.lines[line_start].split(" at ")[1].split("eV")[0].strip()) @@ -751,16 +741,13 @@ def _parse_homo_lumo(self): "direct_gap": direct_gap, } - def _parse_hirshfeld(self): + def _parse_hirshfeld( + self, + ) -> tuple[Sequence[float] | None, Sequence[float] | None, Sequence[Vector3D] | None, Vector3D | None]: """Parse the Hirshfled charges volumes, and dipole moments.""" line_start = self.reverse_search_for(["Performing Hirshfeld analysis of fragment charges and moments."]) if line_start == LINE_NOT_FOUND: - return { - "charges": None, - "volumes": None, - "atomic_dipoles": None, - "dipole": None, - } + return (None, None, None, None) line_inds = self.search_for_all("Hirshfeld charge", line_start, -1) hirshfeld_charges = np.array([float(self.lines[ind].split(":")[1]) for ind in line_inds]) @@ -780,22 +767,17 @@ def _parse_hirshfeld(self): ) else: hirshfeld_dipole = None - return { - "charges": hirshfeld_charges, - "volumes": hirshfeld_volumes, - "atomic_dipoles": hirshfeld_atomic_dipoles, - "dipole": hirshfeld_dipole, - } + return (hirshfeld_charges, hirshfeld_volumes, hirshfeld_atomic_dipoles, hirshfeld_dipole) @property def structure(self) -> Structure | Molecule: - """The pytmagen SiteCollection of the output file.""" + """The pytmagen SiteCollection of the chunk.""" if "structure" not in self._cache: self._cache["structure"] = self._parse_structure() return self._cache["structure"] @property - def results(self): + def results(self) -> dict[str, Any]: """Convert an AimsOutChunk to a Results Dictionary.""" results = { "energy": self.energy, @@ -824,135 +806,151 @@ def results(self): # Properties from the aims.out header @property def initial_structure(self) -> Structure | Molecule: - """Return the initial structure of the calculation.""" + """The initial structure for the calculation""" return self._header["initial_structure"] @property def initial_lattice(self) -> Lattice | None: - """Return the initial lattice vectors for the structure.""" + """The initial Lattice of the structure""" return self._header["initial_lattice"] @property - def n_atoms(self): - """Return the number of atoms for the material.""" + def n_atoms(self) -> int: + """The number of atoms in the structure""" return self._header["n_atoms"] @property - def n_bands(self): - """Return the number of Kohn-Sham states for the chunk.""" + def n_bands(self) -> int: + """The number of Kohn-Sham states for the chunk.""" return self._header["n_bands"] @property - def n_electrons(self): - """Return the number of electrons for the chunk.""" + def n_electrons(self) -> int: + """The number of electrons for the chunk.""" return self._header["n_electrons"] @property - def n_spins(self): - """Return the number of spin channels for the chunk.""" + def n_spins(self) -> int: + """The number of spin channels for the chunk.""" return self._header["n_spins"] @property - def electronic_temperature(self): - """Return the electronic temperature for the chunk.""" + def electronic_temperature(self) -> float: + """The electronic temperature for the chunk.""" return self._header["electronic_temperature"] @property - def n_k_points(self): - """Return the number of electrons for the chunk.""" + def n_k_points(self) -> int: + """The number of k_ppoints for the calculation.""" return self._header["n_k_points"] @property - def k_points(self): - """Return the number of spin channels for the chunk.""" + def k_points(self) -> Sequence[Vector3D]: + """All k-points listed in the calculation.""" return self._header["k_points"] @property - def k_point_weights(self): - """Return tk_point_weights electronic temperature for the chunk.""" + def k_point_weights(self) -> Sequence[float]: + """The k-point weights for the calculation.""" return self._header["k_point_weights"] @property - def free_energy(self): - """Return the free energy for the chunk.""" + def free_energy(self) -> float | None: + """The free energy of the calculation""" return self.parse_scalar("free_energy") @property - def n_iter(self): - """Return the number of SCF iterations. - - The number of steps needed to converge the SCF cycle for the chunk. - """ - return self.parse_scalar("number_of_iterations") + def n_iter(self) -> int | None: + """The number of steps needed to converge the SCF cycle for the chunk.""" + val = self.parse_scalar("number_of_iterations") + if val is not None: + return int(val) + return None @property - def magmom(self): - """Return the magnetic moment for the chunk.""" + def magmom(self) -> float | None: + """The magnetic moment of the structure""" return self.parse_scalar("magnetic_moment") @property - def E_f(self): - """Return he Fermi energy for the chunk.""" + def E_f(self) -> float | None: + """The Fermi energy""" return self.parse_scalar("fermi_energy") @property - def converged(self): - """Return True if the chunk is a fully converged final structure.""" + def converged(self) -> bool: + """True if the calculation is converged""" return (len(self.lines) > 0) and ("Have a nice day." in self.lines[-5:]) @property - def hirshfeld_charges(self): - """Return the Hirshfeld charges for the chunk.""" - return self._parse_hirshfeld()["charges"] + def hirshfeld_charges(self) -> Sequence[float] | None: + """The Hirshfeld charges of the system""" + return self._parse_hirshfeld()[0] @property - def hirshfeld_atomic_dipoles(self): - """Return the Hirshfeld atomic dipole moments for the chunk.""" - return self._parse_hirshfeld()["atomic_dipoles"] + def hirshfeld_atomic_dipoles(self) -> Sequence[Vector3D] | None: + """The Hirshfeld atomic dipoles of the system""" + return self._parse_hirshfeld()[1] @property - def hirshfeld_volumes(self): - """Return the Hirshfeld volume for the chunk.""" - return self._parse_hirshfeld()["volumes"] + def hirshfeld_volumes(self) -> Sequence[float] | None: + """The Hirshfeld atomic dipoles of the system""" + return self._parse_hirshfeld()[2] @property - def hirshfeld_dipole(self): - """Return the Hirshfeld systematic dipole moment for the chunk.""" + def hirshfeld_dipole(self) -> None | Vector3D: + """The Hirshfeld dipole of the system""" if self.lattice is None: - return self._parse_hirshfeld()["dipole"] + return self._parse_hirshfeld()[3] return None @property - def vbm(self): - """Return the HOMO (VBM) of the calculation.""" + def vbm(self) -> float: + """The valance band maximum""" return self._parse_homo_lumo()["vbm"] @property - def cbm(self): - """Return the LUMO (CBM) of the calculation.""" + def cbm(self) -> float: + """The conduction band minimnum""" return self._parse_homo_lumo()["cbm"] @property - def gap(self): - """Return the HOMO-LUMO gap (band gap) of the calculation.""" + def gap(self) -> float: + """The band gap""" return self._parse_homo_lumo()["gap"] @property - def direct_gap(self): - """Return the direct band gap of the calculation.""" + def direct_gap(self) -> float: + """The direct bandgap""" return self._parse_homo_lumo()["direct_gap"] -def get_lines(content) -> list[str]: - """Get a list of lines from a str or file of content""" +def get_lines(content: str | TextIOWrapper) -> list[str]: + """Get a list of lines from a str or file of content + + Args: + content: the content of the file to parse + + Returns: + The list of lines + + """ if isinstance(content, str): return [line.strip() for line in content.split("\n")] return [line.strip() for line in content.readlines()] -def get_header_chunk(content) -> AimsOutHeaderChunk: - """Return the header information from the aims.out file.""" +def get_header_chunk(content: str | TextIOWrapper) -> AimsOutHeaderChunk: + """Get the header chunk for an output + + Args: + content (str or TextIOWrapper): the content to parse + + Returns: + The AimsHeaderChunk of the file + + """ lines = get_lines(content) header = [] stopped = False @@ -972,8 +970,16 @@ def get_header_chunk(content) -> AimsOutHeaderChunk: return AimsOutHeaderChunk(header) -def get_aims_out_chunks(content, header_chunk): - """Yield unprocessed chunks (header, lines) for each AimsOutChunk image.""" +def get_aims_out_chunks(content: str | TextIOWrapper, header_chunk: AimsOutHeaderChunk) -> Generator: + """Yield unprocessed chunks (header, lines) for each AimsOutChunk image. + + Args: + content (str or TextIOWrapper): the content to parse + header_chunk (AimsOutHeaderChunk): The AimsOutHeader for the calculation + + Yields: + The next AimsOutChunk + """ lines = list(filter(lambda x: x not in header_chunk.lines, get_lines(content))) if len(lines) == 0: return @@ -1023,41 +1029,47 @@ def get_aims_out_chunks(content, header_chunk): def check_convergence(chunks: list[AimsOutCalcChunk], non_convergence_ok: bool = False) -> bool: """Check if the aims output file is for a converged calculation. - Parameters - ---------- - chunks: list[.AimsOutCalcChunk] - The list of chunks for the aims calculations - non_convergence_ok: bool - True if it is okay for the calculation to not be converged + Args: + chunks(list[.AimsOutCalcChunk]): The list of chunks for the aims calculations + non_convergence_ok(bool): True if it is okay for the calculation to not be converged + chunks: list[AimsOutCalcChunk]: + non_convergence_ok: bool: (Default value = False) - Returns - ------- - bool + Returns: True if the calculation is converged + """ if not non_convergence_ok and not chunks[-1].converged: raise ParseError("The calculation did not complete successfully") return True -def read_aims_header_info_from_content(content: str) -> tuple[dict[str, str], dict[str, Any]]: +def read_aims_header_info_from_content( + content: str, +) -> tuple[dict[str, list[str] | None | str], dict[str, Any]]: + """Read the FHI-aims header information. + + Args: + content (str): The content of the output file to check + + Returns: + The metadata for the header of the aims calculation + """ header_chunk = get_header_chunk(content) return header_chunk.metadata_summary, header_chunk.header_summary def read_aims_header_info( filename: str | Path, -) -> tuple[dict[str, str], dict[str, Any]]: +) -> tuple[dict[str, None | list[str] | str], dict[str, Any]]: """Read the FHI-aims header information. - Parameters - ---------- - filename: str or Path - The file to read + Args: + filename(str or Path): The file to read + + Returns: + The metadata for the header of the aims calculation - Returns - ------- - The calculation metadata and the system summary """ content = None for path in [Path(filename), Path(f"{filename}.gz")]: @@ -1079,7 +1091,16 @@ def read_aims_header_info( def read_aims_output_from_content( content: str, index: int | slice = -1, non_convergence_ok: bool = False ) -> Structure | Molecule | Sequence[Structure | Molecule]: - """Read and aims output file from the content of a file""" + """Read and aims output file from the content of a file + + Args: + content (str): The content of the file to read + index: int | slice: (Default value = -1) + non_convergence_ok: bool: (Default value = False) + + Returns: + The list of images to get + """ header_chunk = get_header_chunk(content) chunks = list(get_aims_out_chunks(content, header_chunk)) @@ -1100,18 +1121,14 @@ def read_aims_output( Includes all structures for relaxations and MD runs with FHI-aims - Parameters - ---------- - filename: str or Path - The file to read - index: int or slice - The index of the images to read - non_convergence_ok: bool - True if the calculations do not have to be converged - - Returns - ------- - The selected atoms + Args: + filename(str or Path): The file to read + index(int or slice): The index of the images to read + non_convergence_ok(bool): True if the calculations do not have to be converged + + Returns: + The list of images to get + """ content = None for path in [Path(filename), Path(f"{filename}.gz")]: From 0d368cd4ec5a46e4f8d0746ffc9e8112bf89d1cc Mon Sep 17 00:00:00 2001 From: Thomas Purcell Date: Fri, 3 Nov 2023 08:37:30 +0100 Subject: [PATCH 15/30] Fix tests Forgot pip install in the last commit --- pymatgen/io/aims/parsers.py | 40 ++++++++++++++---- tests/io/aims/aims_output_files/h2o.out.gz | Bin 27959 -> 27959 bytes .../io/aims/aims_output_files/h2o_ref.json.gz | Bin 1415 -> 1415 bytes tests/io/aims/aims_output_files/si.out.gz | Bin 49958 -> 49958 bytes .../io/aims/aims_output_files/si_ref.json.gz | Bin 2518 -> 2518 bytes tests/io/aims/test_aims_parsers.py | 2 +- 6 files changed, 32 insertions(+), 10 deletions(-) diff --git a/pymatgen/io/aims/parsers.py b/pymatgen/io/aims/parsers.py index 21cc34d9cb9..a0428c89a1f 100644 --- a/pymatgen/io/aims/parsers.py +++ b/pymatgen/io/aims/parsers.py @@ -743,11 +743,19 @@ def _parse_homo_lumo(self) -> dict[str, float]: def _parse_hirshfeld( self, - ) -> tuple[Sequence[float] | None, Sequence[float] | None, Sequence[Vector3D] | None, Vector3D | None]: + ) -> None: """Parse the Hirshfled charges volumes, and dipole moments.""" line_start = self.reverse_search_for(["Performing Hirshfeld analysis of fragment charges and moments."]) if line_start == LINE_NOT_FOUND: - return (None, None, None, None) + self._cache.update( + { + "hirshfeld_charges": None, + "hirshfeld_volumes": None, + "hirshfeld_atomic_dipoles": None, + "hirshfeld_dipole": None, + } + ) + return line_inds = self.search_for_all("Hirshfeld charge", line_start, -1) hirshfeld_charges = np.array([float(self.lines[ind].split(":")[1]) for ind in line_inds]) @@ -767,7 +775,15 @@ def _parse_hirshfeld( ) else: hirshfeld_dipole = None - return (hirshfeld_charges, hirshfeld_volumes, hirshfeld_atomic_dipoles, hirshfeld_dipole) + + self._cache.update( + { + "hirshfeld_charges": hirshfeld_charges, + "hirshfeld_volumes": hirshfeld_volumes, + "hirshfeld_atomic_dipoles": hirshfeld_atomic_dipoles, + "hirshfeld_dipole": hirshfeld_dipole, + } + ) @property def structure(self) -> Structure | Molecule: @@ -885,25 +901,31 @@ def converged(self) -> bool: @property def hirshfeld_charges(self) -> Sequence[float] | None: """The Hirshfeld charges of the system""" - return self._parse_hirshfeld()[0] + if "hirshfeld_charges" not in self._cache: + self._parse_hirshfeld() + return self._cache["hirshfeld_charges"] @property def hirshfeld_atomic_dipoles(self) -> Sequence[Vector3D] | None: """The Hirshfeld atomic dipoles of the system""" - return self._parse_hirshfeld()[1] + if "hirshfeld_atomic_dipoles" not in self._cache: + self._parse_hirshfeld() + return self._cache["hirshfeld_atomic_dipoles"] @property def hirshfeld_volumes(self) -> Sequence[float] | None: """The Hirshfeld atomic dipoles of the system""" - return self._parse_hirshfeld()[2] + if "hirshfeld_volumes" not in self._cache: + self._parse_hirshfeld() + return self._cache["hirshfeld_volumes"] @property def hirshfeld_dipole(self) -> None | Vector3D: """The Hirshfeld dipole of the system""" - if self.lattice is None: - return self._parse_hirshfeld()[3] + if "hirshfeld_dipole" not in self._cache: + self._parse_hirshfeld() - return None + return self._cache["hirshfeld_dipole"] @property def vbm(self) -> float: diff --git a/tests/io/aims/aims_output_files/h2o.out.gz b/tests/io/aims/aims_output_files/h2o.out.gz index 6ecf027a56e291c58ec8c4354c90d01db6984def..f4e8ba9ca0fa610999e811c5e6c3c148785fce2f 100644 GIT binary patch delta 18 acmdmfi*frcMt1pb4vu&8TsE>BXozm?Di;s(c M003F>a<3!+0BkZC6#xJL delta 54 zcmV-60LlM{3x^8_ABzYGNR>db2U`UtP#t!SZsM|lLSOHX`;*f6FJsr&JEhwR79SV? 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test_default_header_electronic_temperature(empty_header_chunk): - assert empty_header_chunk.electronic_temperature == 0.1 + assert empty_header_chunk.electronic_temperature == 0.0 # def test_default_header_constraints(empty_header_chunk): From ed4e09c3596fb41f68b6d97cf449046d9e9a939a Mon Sep 17 00:00:00 2001 From: Thomas Purcell Date: Tue, 7 Nov 2023 11:03:59 +0100 Subject: [PATCH 16/30] Requested changes to tests 1) Moved lines objects to seperate files 2) inline k_point_weights 3) Remove trailing comma 4) tmpdir -> tmp_path --- .../aims/aims_parser_checks/calc_chunk.out.gz | Bin 0 -> 2132 bytes .../aims_parser_checks/header_chunk.out.gz | Bin 0 -> 661 bytes .../molecular_calc_chunk.out.gz | Bin 0 -> 1267 bytes .../molecular_header_chunk.out.gz | Bin 0 -> 373 bytes .../numerical_stress.out.gz | Bin 0 -> 1845 bytes tests/io/aims/test_aims_inputs.py | 12 +- tests/io/aims/test_aims_parsers.py | 644 ++---------------- 7 files changed, 46 insertions(+), 610 deletions(-) create mode 100644 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j4X^%cS4&*(7y6n2wz&2%)2r~CuB86~< Date: Tue, 7 Nov 2023 16:04:29 +0100 Subject: [PATCH 17/30] Update pymatgen/io/aims/inputs.py use numpy eye instead of a full list Co-authored-by: Janosh Riebesell Signed-off-by: Thomas Purcell --- pymatgen/io/aims/inputs.py | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/pymatgen/io/aims/inputs.py b/pymatgen/io/aims/inputs.py index beef726d860..fc916201575 100644 --- a/pymatgen/io/aims/inputs.py +++ b/pymatgen/io/aims/inputs.py @@ -271,11 +271,7 @@ class AimsCube(MSONable): type: str = field(default_factory=str) origin: Sequence[float] | tuple[float, float, float] = field(default_factory=lambda: [0.0, 0.0, 0.0]) edges: Sequence[Sequence[float]] = field( - default_factory=lambda: [ - [0.1, 0.0, 0.0], - [0.0, 0.1, 0.0], - [0.0, 0.0, 0.1], - ] + default_factory=lambda: 0.1 * np.eye(3) ) points: Sequence[int] | tuple[int, int, int] = field(default_factory=lambda: [0, 0, 0]) format: str = "cube" From a5823bb69faf3e003dda1c752a627e398574a684 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 7 Nov 2023 15:06:09 +0000 Subject: [PATCH 18/30] pre-commit auto-fixes --- pymatgen/io/aims/inputs.py | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/pymatgen/io/aims/inputs.py b/pymatgen/io/aims/inputs.py index fc916201575..49b2ac8bc93 100644 --- a/pymatgen/io/aims/inputs.py +++ b/pymatgen/io/aims/inputs.py @@ -270,9 +270,7 @@ class AimsCube(MSONable): type: str = field(default_factory=str) origin: Sequence[float] | tuple[float, float, float] = field(default_factory=lambda: [0.0, 0.0, 0.0]) - edges: Sequence[Sequence[float]] = field( - default_factory=lambda: 0.1 * np.eye(3) - ) + edges: Sequence[Sequence[float]] = field(default_factory=lambda: 0.1 * np.eye(3)) points: Sequence[int] | tuple[int, int, int] = field(default_factory=lambda: [0, 0, 0]) format: str = "cube" spinstate: int | None = None From 6da5e9debbedc2eef371dcaa8948c99aeb22ffdb Mon Sep 17 00:00:00 2001 From: Thomas Purcell Date: Tue, 7 Nov 2023 16:16:41 +0100 Subject: [PATCH 19/30] Make more changes requested --- pymatgen/io/aims/inputs.py | 23 +++++++---------------- pymatgen/io/aims/output.py | 4 ---- pymatgen/io/aims/parsers.py | 8 -------- 3 files changed, 7 insertions(+), 28 deletions(-) diff --git a/pymatgen/io/aims/inputs.py b/pymatgen/io/aims/inputs.py index 49b2ac8bc93..5d9429bbe81 100644 --- a/pymatgen/io/aims/inputs.py +++ b/pymatgen/io/aims/inputs.py @@ -29,7 +29,6 @@ class AimsGeometryIn(MSONable): _content (str): The content of the input file _structure (Structure or Molecule): The structure or molecule representation of the file - """ _content: str @@ -44,7 +43,6 @@ def from_str(cls, contents: str) -> AimsGeometryIn: Returns: The AimsGeometryIn file for the string contents - """ content_lines = [ line.strip() for line in contents.split("\n") if len(line.strip()) > 0 and line.strip()[0] != "#" @@ -118,7 +116,6 @@ def from_file(cls, filepath: str | Path) -> AimsGeometryIn: Returns: The input object represented in the file - """ if str(filepath).endswith(".gz"): with gzip.open(filepath, "rt") as infile: @@ -137,7 +134,6 @@ def from_structure(cls, structure: Structure | Molecule) -> AimsGeometryIn: Returns: The input object for the structure - """ content_lines = [] @@ -172,7 +168,6 @@ def write_file(self, directory: str | Path | None = None, overwrite: bool = Fals Args: directory (str | Path | None): The directory to write the geometry.in file overwrite (bool): If True allow to overwrite existing files - """ if directory is None: directory = Path.cwd() @@ -207,7 +202,6 @@ def from_dict(cls, d: dict[str, Any]) -> AimsGeometryIn: Returns: The input object represented by the dict - """ decoded = {k: MontyDecoder().process_decoded(v) for k, v in d.items() if not k.startswith("@")} @@ -217,7 +211,7 @@ def from_dict(cls, d: dict[str, Any]) -> AimsGeometryIn: ) -ALLOWED_AIMS_CUBE_TYPES = [ +ALLOWED_AIMS_CUBE_TYPES = ( "delta_density", "spin_density", "stm", @@ -230,20 +224,20 @@ def from_dict(cls, d: dict[str, Any]) -> AimsGeometryIn: "ion_dens", "dielec_func", "elf", -] +) -ALLOWED_AIMS_CUBE_TYPES_STATE = [ +ALLOWED_AIMS_CUBE_TYPES_STATE = ( "first_order_density", "eigenstate", "eigenstate_imag", "eigenstate_density", -] +) -ALLOWED_AIMS_CUBE_FORMATS = [ +ALLOWED_AIMS_CUBE_FORMATS = ( "cube", "gOpenMol", "xsf", -] +) @dataclass @@ -297,7 +291,7 @@ def __post_init__(self) -> None: raise ValueError("Cube type undefined") if self.format not in ALLOWED_AIMS_CUBE_FORMATS: - raise ValueError("Cube file must have a format of cube, gOpenMol, or xsf") + raise ValueError(f"{self.format} is invalid. Cube files must have a format of {ALLOWED_AIMS_CUBE_FORMATS}") if self.spinstate is not None and (self.spinstate not in [1, 2]): raise ValueError("Spin state must be 1 or 2") @@ -365,7 +359,6 @@ def from_dict(cls, d: dict[str, Any]) -> AimsCube: Returns: The AimsCube for d - """ decoded = {k: MontyDecoder().process_decoded(v) for k, v in d.items() if not k.startswith("@")} @@ -467,7 +460,6 @@ def get_aims_control_parameter_str(self, key: str, value: Any, format: str) -> s Returns: The line to add to the control.in file - """ return f"{key :35s}" + (format % value) + "\n" @@ -609,7 +601,6 @@ def from_dict(cls, d: dict[str, Any]) -> AimsControlIn: Returns: The AimsControlIn for d - """ decoded = {k: MontyDecoder().process_decoded(v) for k, v in d.items() if not k.startswith("@")} diff --git a/pymatgen/io/aims/output.py b/pymatgen/io/aims/output.py index 270f92dc379..b07cea8a33c 100644 --- a/pymatgen/io/aims/output.py +++ b/pymatgen/io/aims/output.py @@ -66,7 +66,6 @@ def from_outfile(cls, outfile: str | Path) -> AimsOutput: Returns: The AimsOutput object for the output file - """ metadata, structure_summary = read_aims_header_info(outfile) results = read_aims_output(outfile, index=slice(0, None)) @@ -82,7 +81,6 @@ def from_str(cls, content: str) -> AimsOutput: Returns: The AimsOutput for the output file content - """ metadata, structure_summary = read_aims_header_info_from_content(content) results = read_aims_output_from_content(content, index=slice(0, None)) @@ -98,7 +96,6 @@ def from_dict(cls, d: dict[str, Any]) -> AimsOutput: Returns: The AimsOutput for d - """ decoded = {k: MontyDecoder().process_decoded(v) for k, v in d.items() if not k.startswith("@")} for struct in decoded["results"]: @@ -118,7 +115,6 @@ def get_results_for_image(self, image_ind: int) -> Structure | Molecule: Returns: The results of the image with index images_ind - """ return self._results[image_ind] diff --git a/pymatgen/io/aims/parsers.py b/pymatgen/io/aims/parsers.py index a0428c89a1f..c35d4874cba 100644 --- a/pymatgen/io/aims/parsers.py +++ b/pymatgen/io/aims/parsers.py @@ -72,7 +72,6 @@ def reverse_search_for(self, keys: list[str], line_start: int = 0) -> int: Returns: The last time one of the keys appears in self.lines - """ for ll, line in enumerate(self.lines[line_start:][::-1]): if any(key in line for key in keys): @@ -90,7 +89,6 @@ def search_for_all(self, key: str, line_start: int = 0, line_end: int = -1) -> l Returns: All times the key appears in the lines - """ line_index = [] for ll, line in enumerate(self.lines[line_start:line_end]): @@ -106,7 +104,6 @@ def parse_scalar(self, property: str) -> float | None: Returns: The scalar value of the property or None if not found - """ line_start = self.reverse_search_for(scalar_property_to_line_key[property]) @@ -956,7 +953,6 @@ def get_lines(content: str | TextIOWrapper) -> list[str]: Returns: The list of lines - """ if isinstance(content, str): return [line.strip() for line in content.split("\n")] @@ -971,7 +967,6 @@ def get_header_chunk(content: str | TextIOWrapper) -> AimsOutHeaderChunk: Returns: The AimsHeaderChunk of the file - """ lines = get_lines(content) header = [] @@ -1059,7 +1054,6 @@ def check_convergence(chunks: list[AimsOutCalcChunk], non_convergence_ok: bool = Returns: True if the calculation is converged - """ if not non_convergence_ok and not chunks[-1].converged: raise ParseError("The calculation did not complete successfully") @@ -1091,7 +1085,6 @@ def read_aims_header_info( Returns: The metadata for the header of the aims calculation - """ content = None for path in [Path(filename), Path(f"{filename}.gz")]: @@ -1150,7 +1143,6 @@ def read_aims_output( Returns: The list of images to get - """ content = None for path in [Path(filename), Path(f"{filename}.gz")]: From bc0b4d68cf1893c5f215448a9ee9bf2e83e4451d Mon Sep 17 00:00:00 2001 From: Thomas Purcell Date: Wed, 8 Nov 2023 10:38:36 +0100 Subject: [PATCH 20/30] Rename io.aims.output to io.aims.outputs Keep it consistent with inputs naming scheme --- pymatgen/io/aims/{output.py => outputs.py} | 0 tests/io/aims/test_aims_outputs.py | 2 +- 2 files changed, 1 insertion(+), 1 deletion(-) rename pymatgen/io/aims/{output.py => outputs.py} (100%) diff --git a/pymatgen/io/aims/output.py b/pymatgen/io/aims/outputs.py similarity index 100% rename from pymatgen/io/aims/output.py rename to pymatgen/io/aims/outputs.py diff --git a/tests/io/aims/test_aims_outputs.py b/tests/io/aims/test_aims_outputs.py index 82962cdb415..e91a91213ef 100644 --- a/tests/io/aims/test_aims_outputs.py +++ b/tests/io/aims/test_aims_outputs.py @@ -8,7 +8,7 @@ from monty.json import MontyDecoder, MontyEncoder from pymatgen.core import Structure -from pymatgen.io.aims.output import AimsOutput +from pymatgen.io.aims.outputs import AimsOutput outfile_dir = Path(__file__).parent / "aims_output_files" From c82cd43936ac2422e05c220bdff951988cb954a8 Mon Sep 17 00:00:00 2001 From: Thomas Purcell Date: Wed, 8 Nov 2023 13:42:28 +0100 Subject: [PATCH 21/30] Add example for FHI-aims io --- examples/aims_io/FHI-aims-example.ipynb | 168 ++++++++++++++++++ examples/aims_io/species_dir/14_Si_default.gz | Bin 0 -> 1110 bytes 2 files changed, 168 insertions(+) create mode 100644 examples/aims_io/FHI-aims-example.ipynb create mode 100644 examples/aims_io/species_dir/14_Si_default.gz diff --git a/examples/aims_io/FHI-aims-example.ipynb b/examples/aims_io/FHI-aims-example.ipynb new file mode 100644 index 00000000000..1af8ec557a1 --- /dev/null +++ b/examples/aims_io/FHI-aims-example.ipynb @@ -0,0 +1,168 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": null, + "id": "8e09cccf-4335-4c59-bfa7-d3e3caeef404", + "metadata": {}, + "outputs": [], + "source": [ + "from pymatgen.io.aims.inputs import AimsGeometryIn, AimsCube, AimsControlIn\n", + "from pymatgen.io.aims.outputs import AimsOutput\n", + "\n", + "from pymatgen.core import Structure, Lattice\n", + "\n", + "import numpy as np\n", + "\n", + "from pathlib import Path\n", + "from subprocess import check_call" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "536af143-f892-4549-86d7-ff426ba265ed", + "metadata": {}, + "outputs": [], + "source": [ + "# AIMS_CMD should be modified to match your system\n", + "AIMS_CMD = \"aims.x\"\n", + "AIMS_OUTPUT = \"aims.out\"\n", + "AIMS_SD = \"species_dir\"" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "4d8d9fda-af37-45eb-971c-56fed59f3a27", + "metadata": {}, + "outputs": [], + "source": [ + "# Create test structure\n", + "structure = Structure(\n", + " lattice=Lattice(\n", + " np.array([[0, 2.715, 2.715],[2.715, 0, 2.715], [2.715, 2.715, 0]])\n", + " ),\n", + " species=[\"Si\", \"Si\"],\n", + " coords=np.array([np.zeros(3), np.ones(3) * 0.25])\n", + ")" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "8e67e134-84f8-4c35-afe4-87cd66e2e781", + "metadata": {}, + "outputs": [], + "source": [ + "# Create the geometry file from the structure\n", + "geo_in = AimsGeometryIn.from_structure(structure)\n", + "\n", + "# Create the control.in file\n", + "cont_in = AimsControlIn(\n", + " {\n", + " \"xc\": \"pw-lda\",\n", + " \"relax_geometry\": \"trm 0.01\",\n", + " \"relax_unit_cell\": \"full\",\n", + " \"species_dir\": AIMS_SD,\n", + " }\n", + ")\n", + "\n", + "# Add new parameters as if AimsControl\n", + "cont_in[\"k_grid\"] = [1, 1, 1]\n", + "\n", + "# Output options to control in automatically append the list\n", + "cont_in[\"output\"] = \"hirshfeld\"\n", + "cont_in[\"output\"] = [\"eigenvectors\"]\n", + "\n", + "# Cube file output controlled by the AimsCube class\n", + "cont_in[\"cubes\"] = [\n", + " AimsCube(\"total_density\", origin=[0,0,0], points=[11, 11, 11]),\n", + " AimsCube(\"eigenstate_density 1\", origin=[0, 0, 0], points=[11, 11, 11]),\n", + "]" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "096337d6-871a-48dc-b4b3-a3c7c6fd812e", + "metadata": {}, + "outputs": [], + "source": [ + "# Write the input files\n", + "workdir = Path.cwd() / \"workdir/\"\n", + "workdir.mkdir(exist_ok=True)\n", + "\n", + "geo_in.write_file(workdir, overwrite=True)\n", + "cont_in.write_file(structure, workdir, overwrite=True)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "c9994cd2-5e45-4071-ab87-b6b3e3af1174", + "metadata": {}, + "outputs": [], + "source": [ + "# Run the calculation\n", + "with open(f\"{workdir}/{AIMS_OUTPUT}\", \"w\") as outfile:\n", + " aims_run = check_call([AIMS_CMD], cwd=workdir, stdout=outfile)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "0c42a6c6-bb45-472f-a2cb-190cdd922047", + "metadata": {}, + "outputs": [], + "source": [ + "# Read the aims output file and the final relaxed geometry\n", + "outputs = AimsOutput.from_outfile(f\"{workdir}/{AIMS_OUTPUT}\")\n", + "relaxed_structure = AimsGeometryIn.from_file(f\"{workdir}/geometry.in.next_step\")\n", + "\n", + "# Check the results\n", + "assert outputs.get_results_for_image(-1).lattice == relaxed_structure.structure.lattice\n", + "assert np.all(outputs.get_results_for_image(-1).frac_coords == relaxed_structure.structure.frac_coords)\n", + "\n", + "assert np.allclose(\n", + " outputs.get_results_for_image(-1).properties[\"stress\"],\n", + " outputs.stress\n", + ")\n", + "\n", + "assert np.allclose(\n", + " outputs.get_results_for_image(-1).site_properties[\"force\"],\n", + " outputs.forces\n", + ")" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "e7505c66-4a2d-40ad-b248-71582674d34f", + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3 (ipykernel)", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.9.16" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/examples/aims_io/species_dir/14_Si_default.gz b/examples/aims_io/species_dir/14_Si_default.gz new file mode 100644 index 0000000000000000000000000000000000000000..9a80f272559abf029843b6dc07d109fa11fbc50f GIT binary patch literal 1110 zcmV-c1gZNUiwFpLflFlo|1mUQQ)yphWoBV@Y;*v%R?BYNIuPCaD+bP{0c=)pS;gI? zErND)ae-WPYtYijW^Uf7mn5S`W5~F0fst+5;^YByd%>0W4M?uHq;kWJ zFfO8DL1Gdm(fg=+AFbe_X=vjX+Oe;#P`x91)XiH<-Wo-31`Mcb;WJ9h!BUDqjkZ=D zy09>P{@>AlKe!>uJ$eOPO6U6^m!G7kMhhs27WMO3s=p?R25EeTAjOHTfkyXuQ zJxcEA80e5wdih4~p;MG*{5fE6#7o#Uq!J}|*xM_X|Kba3S|TZ{i<1`b_}>Da7C=x+oA@cT#=)$VC)QdsYlsL?0=t?L}Xorxg6hv!Kg$ZVzB zaCw5MAVe>Gwq_3Q$6DfO&UnX}hdOS~?eruo7OnDpcIQ{f^^R++5hp9M16GfAJt%wT zow9tgi+hP#tBcKb#vI@|^_mP}0v9XDP6sVSq`TO3zWqC`!Olr3tCp2ic>S4HzD z9&y3S35_F*y9*lCnI(rUR4hBQWyI{<5)+Gv6}e|Y16}`-M9Nmxi37Pr6Anj3%}LRO zn4zOAE@-r{x}fHq(<|EmC0m7qQloYsLAS|8EKMim;`k~-;ZTaJ6va{4U}9`(6tLuq zU3{Uz(7F4(JvwHm53tv}V0YX?i|(6fw66KN`=bUcI`PY2JkrrCVZx1}&lJfRgMXX= c`eeHlkP(IAmVn~wkX Date: Wed, 8 Nov 2023 20:08:56 +0100 Subject: [PATCH 22/30] Make corrections suggested by @janosh 1) Remove copy of species file in examples 2) Typo corrections in docstrings 3) d -> dct for `from_dict` methods 4) error mesages for AimsCube 5) Shortened default checks in Inputs 6) Removal of chdir in tests --- examples/aims_io/FHI-aims-example.ipynb | 3 +- examples/aims_io/species_dir/14_Si_default.gz | Bin 1110 -> 0 bytes pymatgen/io/aims/inputs.py | 66 +++++++++++++----- tests/io/aims/test_aims_inputs.py | 44 +++++------- 4 files changed, 68 insertions(+), 45 deletions(-) delete mode 100644 examples/aims_io/species_dir/14_Si_default.gz diff --git a/examples/aims_io/FHI-aims-example.ipynb b/examples/aims_io/FHI-aims-example.ipynb index 1af8ec557a1..ea223b2c317 100644 --- a/examples/aims_io/FHI-aims-example.ipynb +++ b/examples/aims_io/FHI-aims-example.ipynb @@ -28,7 +28,8 @@ "# AIMS_CMD should be modified to match your system\n", "AIMS_CMD = \"aims.x\"\n", "AIMS_OUTPUT = \"aims.out\"\n", - "AIMS_SD = \"species_dir\"" + "AIMS_SD = \"species_dir\"\n", + "AIMS_TEST_DIR = \"../../tests/io/aims/species_directory/light/\"" ] }, { diff --git a/examples/aims_io/species_dir/14_Si_default.gz b/examples/aims_io/species_dir/14_Si_default.gz deleted file mode 100644 index 9a80f272559abf029843b6dc07d109fa11fbc50f..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 1110 zcmV-c1gZNUiwFpLflFlo|1mUQQ)yphWoBV@Y;*v%R?BYNIuPCaD+bP{0c=)pS;gI? zErND)ae-WPYtYijW^Uf7mn5S`W5~F0fst+5;^YByd%>0W4M?uHq;kWJ zFfO8DL1Gdm(fg=+AFbe_X=vjX+Oe;#P`x91)XiH<-Wo-31`Mcb;WJ9h!BUDqjkZ=D zy09>P{@>AlKe!>uJ$eOPO6U6^m!G7kMhhs27WMO3s=p?R25EeTAjOHTfkyXuQ zJxcEA80e5wdih4~p;MG*{5fE6#7o#Uq!J}|*xM_X|Kba3S|TZ{i<1`b_}>Da7C=x+oA@cT#=)$VC)QdsYlsL?0=t?L}Xorxg6hv!Kg$ZVzB zaCw5MAVe>Gwq_3Q$6DfO&UnX}hdOS~?eruo7OnDpcIQ{f^^R++5hp9M16GfAJt%wT zow9tgi+hP#tBcKb#vI@|^_mP}0v9XDP6sVSq`TO3zWqC`!Olr3tCp2ic>S4HzD z9&y3S35_F*y9*lCnI(rUR4hBQWyI{<5)+Gv6}e|Y16}`-M9Nmxi37Pr6Anj3%}LRO zn4zOAE@-r{x}fHq(<|EmC0m7qQloYsLAS|8EKMim;`k~-;ZTaJ6va{4U}9`(6tLuq zU3{Uz(7F4(JvwHm53tv}V0YX?i|(6fw66KN`=bUcI`PY2JkrrCVZx1}&lJfRgMXX= c`eeHlkP(IAmVn~wkX AimsGeometryIn: @property def structure(self) -> Structure | Molecule: - """Accses structure for the file""" + """Access structure for the file""" return self._structure @property def content(self) -> str: - """Accses the contents of the file""" + """Access the contents of the file""" return self._content def write_file(self, directory: str | Path | None = None, overwrite: bool = False) -> None: - """Writes the geometry.in file + """Write the geometry.in file Args: directory (str | Path | None): The directory to write the geometry.in file overwrite (bool): If True allow to overwrite existing files """ - if directory is None: - directory = Path.cwd() + directory = directory or Path.cwd() if not overwrite and (Path(directory) / "geometry.in").exists(): raise ValueError(f"geometry.in file exists in {directory}") @@ -194,16 +193,16 @@ def as_dict(self) -> dict[str, Any]: return dct @classmethod - def from_dict(cls, d: dict[str, Any]) -> AimsGeometryIn: + def from_dict(cls, dct: dict[str, Any]) -> AimsGeometryIn: """Initialize from dictionary. Args: - d (dict[str, Any]): The MontyEncoded dictionary of the AimsGeometryIn object + dct (dict[str, Any]): The MontyEncoded dictionary of the AimsGeometryIn object Returns: The input object represented by the dict """ - decoded = {k: MontyDecoder().process_decoded(v) for k, v in d.items() if not k.startswith("@")} + decoded = {key: MontyDecoder().process_decoded(val) for key, val in dct.items() if not key.startswith("@")} return cls( _content=decoded["content"], @@ -272,6 +271,40 @@ class AimsCube(MSONable): filename: str | None = None elf_type: int | None = None + def __eq__(self, other: object) -> bool: + """Check if two cubes are equal to each other""" + if not isinstance(other, AimsCube): + return NotImplemented + + if self.type != other.type: + return False + + if not np.allclose(self.origin, other.origin): + return False + + if not np.allclose(self.edges, other.edges): + return False + + if not np.allclose(self.points, other.points): + return False + + if self.format != other.format: + return False + + if self.spinstate != other.spinstate: + return False + + if self.kpoint != other.kpoint: + return False + + if self.filename != other.filename: + return False + + if self.elf_type != other.elf_type: + return False + + return True + def __post_init__(self) -> None: """Check the inputted variables to make sure they are correct @@ -293,8 +326,8 @@ def __post_init__(self) -> None: if self.format not in ALLOWED_AIMS_CUBE_FORMATS: raise ValueError(f"{self.format} is invalid. Cube files must have a format of {ALLOWED_AIMS_CUBE_FORMATS}") - if self.spinstate is not None and (self.spinstate not in [1, 2]): - raise ValueError("Spin state must be 1 or 2") + if self.spinstate not in (None, 1, 2): + raise ValueError("Spin state must be 1, 2, or None") if len(self.origin) != 3: raise ValueError("The cube origin must have 3 components") @@ -310,7 +343,7 @@ def __post_init__(self) -> None: raise ValueError("Each cube edge must have 3 components") if self.elf_type is not None and self.type != "elf": - raise ValueError("elf_type only used when the cube type is elf") + raise ValueError("elf_type is only used when the cube type is elf. Otherwise it must be None") @property def control_block(self) -> str: @@ -484,8 +517,7 @@ def write_file( ValueError: If a file must be overwritten and overwrite is False ValueError: If k-grid is not provided for the periodic structures """ - if directory is None: - directory = Path.cwd() + directory = directory or Path.cwd() if (Path(directory) / "control.in").exists() and not overwrite: raise ValueError(f"control.in file already in {directory}") @@ -593,16 +625,16 @@ def as_dict(self) -> dict[str, Any]: return dct @classmethod - def from_dict(cls, d: dict[str, Any]) -> AimsControlIn: + def from_dict(cls, dct: dict[str, Any]) -> AimsControlIn: """Initialize from dictionary. Args: - d(dict[str, Any]): The MontyEncoded dictionary + dct (dict[str, Any]): The MontyEncoded dictionary Returns: - The AimsControlIn for d + The AimsControlIn for dct """ - decoded = {k: MontyDecoder().process_decoded(v) for k, v in d.items() if not k.startswith("@")} + decoded = {key: MontyDecoder().process_decoded(val) for key, val in dct.items() if not key.startswith("@")} return cls( _parameters=decoded["parameters"], diff --git a/tests/io/aims/test_aims_inputs.py b/tests/io/aims/test_aims_inputs.py index 11523c45a7c..f56c3cb9b9f 100644 --- a/tests/io/aims/test_aims_inputs.py +++ b/tests/io/aims/test_aims_inputs.py @@ -2,7 +2,6 @@ import gzip import json -import os from pathlib import Path import numpy as np @@ -47,18 +46,14 @@ def test_read_write_si_in(tmp_path): si_test_from_struct = AimsGeometryIn.from_structure(si.structure) assert si.structure == si_test_from_struct.structure - workdir = Path.cwd() - os.chdir(tmp_path) - si_test_from_struct.write_file(overwrite=True) + si_test_from_struct.write_file(directory=tmp_path, overwrite=True) with pytest.raises( ValueError, match="geometry.in file exists in ", ): - si_test_from_struct.write_file(overwrite=False) + si_test_from_struct.write_file(directory=tmp_path, overwrite=False) - compare_files(infile_dir / "geometry.in.si.ref", "geometry.in") - - os.chdir(workdir) + compare_files(infile_dir / "geometry.in.si.ref", f"{tmp_path}/geometry.in") with gzip.open(f"{infile_dir}/si_ref.json.gz", "rt") as si_ref_json: si_from_dct = json.load(si_ref_json, cls=MontyDecoder) @@ -83,19 +78,15 @@ def test_read_h2o_in(tmp_path): h2o_test_from_struct = AimsGeometryIn.from_structure(h2o.structure) assert h2o.structure == h2o_test_from_struct.structure - workdir = Path.cwd() - os.chdir(tmp_path) - h2o_test_from_struct.write_file(overwrite=True) + h2o_test_from_struct.write_file(directory=tmp_path, overwrite=True) with pytest.raises( ValueError, match="geometry.in file exists in ", ): - h2o_test_from_struct.write_file(overwrite=False) - - compare_files(infile_dir / "geometry.in.h2o.ref", "geometry.in") + h2o_test_from_struct.write_file(directory=tmp_path, overwrite=False) - os.chdir(workdir) + compare_files(infile_dir / "geometry.in.h2o.ref", f"{tmp_path}/geometry.in") with gzip.open(f"{infile_dir}/h2o_ref.json.gz", "rt") as h2o_ref_json: h2o_from_dct = json.load(h2o_ref_json, cls=MontyDecoder) @@ -125,7 +116,7 @@ def test_aims_cube(): with pytest.raises( ValueError, - match="Cube file must have a format of cube, gOpenMol, or xsf", + match="TEST_ERR is invalid. Cube files must have a format of", ): AimsCube(type=ALLOWED_AIMS_CUBE_TYPES[0], format="TEST_ERR") @@ -144,7 +135,7 @@ def test_aims_cube(): edges=[[0.0, 0.0, 0.1], [0.1, 0.0, 0.0], [0.1, 0.0]], ) - with pytest.raises(ValueError, match="elf_type only used when the cube type is elf"): + with pytest.raises(ValueError, match="elf_type is only used when the cube type is elf. Otherwise it must be None"): AimsCube(type=ALLOWED_AIMS_CUBE_TYPES[0], elf_type=1) with pytest.raises(ValueError, match="The number of points per edge must have 3 components"): @@ -196,7 +187,6 @@ def test_aims_control_in(tmp_path): "species_dir": str(infile_dir.parent / "species_directory/light"), } - workdir = Path.cwd() aims_control = AimsControlIn(parameters.copy()) for key, val in parameters.items(): @@ -206,35 +196,35 @@ def test_aims_control_in(tmp_path): assert "xc" not in aims_control.parameters aims_control.parameters = parameters - os.chdir(tmp_path) h2o = AimsGeometryIn.from_file(infile_dir / "geometry.in.h2o.gz").structure si = AimsGeometryIn.from_file(infile_dir / "geometry.in.si.gz").structure - aims_control.write_file(h2o, overwrite=True) + aims_control.write_file(h2o, directory=tmp_path, overwrite=True) - compare_files(infile_dir / "control.in.h2o", "control.in") + compare_files(infile_dir / "control.in.h2o", f"{tmp_path}/control.in") with pytest.raises( ValueError, match="k-grid must be defined for periodic systems", ): - aims_control.write_file(si, overwrite=True) + aims_control.write_file(si, directory=tmp_path, overwrite=True) aims_control["k_grid"] = [1, 1, 1] with pytest.raises( ValueError, match="control.in file already in ", ): - aims_control.write_file(si, overwrite=False) + aims_control.write_file(si, directory=tmp_path, overwrite=False) aims_control["output"] = "band 0 0 0 0.5 0 0.5 10 G X" aims_control["output"] = "band 0 0 0 0.5 0.5 0.5 10 G L" aims_control_from_dict = json.loads(json.dumps(aims_control.as_dict(), cls=MontyEncoder), cls=MontyDecoder) for key, val in aims_control.parameters.items(): + print("\n\n", key, "\n", val, "\n", aims_control_from_dict[key], "\n\n") + if key in ["output", "cubes"]: + np.all(aims_control_from_dict[key] == val) assert aims_control_from_dict[key] == val - aims_control_from_dict.write_file(si, verbose_header=True, overwrite=True) - compare_files(infile_dir / "control.in.si", "control.in") - - os.chdir(workdir) + aims_control_from_dict.write_file(si, directory=tmp_path, verbose_header=True, overwrite=True) + compare_files(infile_dir / "control.in.si", f"{tmp_path}/control.in") From 7761e4ae5b799d07344406a4ae8ea481afd98058 Mon Sep 17 00:00:00 2001 From: Janosh Riebesell Date: Wed, 8 Nov 2023 11:20:05 -0800 Subject: [PATCH 23/30] add nbstripout to pre-commit hooks apply to FHI-aims-example.ipynb --- .pre-commit-config.yaml | 6 ++++++ examples/aims_io/FHI-aims-example.ipynb | 22 +++++++--------------- 2 files changed, 13 insertions(+), 15 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 90b2bbfd3a6..762fc45e001 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -56,3 +56,9 @@ repos: # MD041: first line in a file should be a top-level heading # MD025: single title args: [--disable, MD013, MD024, MD025, MD033, MD041, "--"] + + - repo: https://github.com/kynan/nbstripout + rev: 0.6.1 + hooks: + - id: nbstripout + args: [--drop-empty-cells, --keep-output] diff --git a/examples/aims_io/FHI-aims-example.ipynb b/examples/aims_io/FHI-aims-example.ipynb index ea223b2c317..af4d207dc30 100644 --- a/examples/aims_io/FHI-aims-example.ipynb +++ b/examples/aims_io/FHI-aims-example.ipynb @@ -15,7 +15,7 @@ "import numpy as np\n", "\n", "from pathlib import Path\n", - "from subprocess import check_call" + "from subprocess import check_call\n" ] }, { @@ -29,7 +29,7 @@ "AIMS_CMD = \"aims.x\"\n", "AIMS_OUTPUT = \"aims.out\"\n", "AIMS_SD = \"species_dir\"\n", - "AIMS_TEST_DIR = \"../../tests/io/aims/species_directory/light/\"" + "AIMS_TEST_DIR = \"../../tests/io/aims/species_directory/light/\"\n" ] }, { @@ -46,7 +46,7 @@ " ),\n", " species=[\"Si\", \"Si\"],\n", " coords=np.array([np.zeros(3), np.ones(3) * 0.25])\n", - ")" + ")\n" ] }, { @@ -80,7 +80,7 @@ "cont_in[\"cubes\"] = [\n", " AimsCube(\"total_density\", origin=[0,0,0], points=[11, 11, 11]),\n", " AimsCube(\"eigenstate_density 1\", origin=[0, 0, 0], points=[11, 11, 11]),\n", - "]" + "]\n" ] }, { @@ -95,7 +95,7 @@ "workdir.mkdir(exist_ok=True)\n", "\n", "geo_in.write_file(workdir, overwrite=True)\n", - "cont_in.write_file(structure, workdir, overwrite=True)" + "cont_in.write_file(structure, workdir, overwrite=True)\n" ] }, { @@ -107,7 +107,7 @@ "source": [ "# Run the calculation\n", "with open(f\"{workdir}/{AIMS_OUTPUT}\", \"w\") as outfile:\n", - " aims_run = check_call([AIMS_CMD], cwd=workdir, stdout=outfile)" + " aims_run = check_call([AIMS_CMD], cwd=workdir, stdout=outfile)\n" ] }, { @@ -133,16 +133,8 @@ "assert np.allclose(\n", " outputs.get_results_for_image(-1).site_properties[\"force\"],\n", " outputs.forces\n", - ")" + ")\n" ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "e7505c66-4a2d-40ad-b248-71582674d34f", - "metadata": {}, - "outputs": [], - "source": [] } ], "metadata": { From d4573934a4c31c2db0e74b0dd12202e3e88360ca Mon Sep 17 00:00:00 2001 From: Janosh Riebesell Date: Wed, 8 Nov 2023 11:26:58 -0800 Subject: [PATCH 24/30] class AimsCube snake_case spin_state --- pymatgen/io/aims/inputs.py | 24 ++++++++++++------------ tests/io/aims/test_aims_inputs.py | 4 ++-- 2 files changed, 14 insertions(+), 14 deletions(-) diff --git a/pymatgen/io/aims/inputs.py b/pymatgen/io/aims/inputs.py index 77eb8cdb427..27b6f13190f 100644 --- a/pymatgen/io/aims/inputs.py +++ b/pymatgen/io/aims/inputs.py @@ -252,7 +252,7 @@ class AimsCube(MSONable): dx (float): The length of the step in the x direction points (Sequence[int] or tuple[int, int, int]): The number of points along each edge - spinstate (int): The spin-channel to use either 1 or 2 + spin_state (int): The spin-channel to use either 1 or 2 kpoint (int): The k-point to use (the index of the list printed from `output k_point_list`) filename (str): The filename to use @@ -266,7 +266,7 @@ class AimsCube(MSONable): edges: Sequence[Sequence[float]] = field(default_factory=lambda: 0.1 * np.eye(3)) points: Sequence[int] | tuple[int, int, int] = field(default_factory=lambda: [0, 0, 0]) format: str = "cube" - spinstate: int | None = None + spin_state: int | None = None kpoint: int | None = None filename: str | None = None elf_type: int | None = None @@ -291,7 +291,7 @@ def __eq__(self, other: object) -> bool: if self.format != other.format: return False - if self.spinstate != other.spinstate: + if self.spin_state != other.spin_state: return False if self.kpoint != other.kpoint: @@ -326,7 +326,7 @@ def __post_init__(self) -> None: if self.format not in ALLOWED_AIMS_CUBE_FORMATS: raise ValueError(f"{self.format} is invalid. Cube files must have a format of {ALLOWED_AIMS_CUBE_FORMATS}") - if self.spinstate not in (None, 1, 2): + if self.spin_state not in (None, 1, 2): raise ValueError("Spin state must be 1, 2, or None") if len(self.origin) != 3: @@ -350,14 +350,14 @@ def control_block(self) -> str: """Get the block of text for the control.in file of the Cube""" cb = f"output cube {self.type}\n" cb += f" cube origin {self.origin[0]: .12e} {self.origin[1]: .12e} {self.origin[2]: .12e}\n" - for ii in range(3): - cb += f" cube edge {self.points[ii]} " - cb += f"{self.edges[ii][0]: .12e} " - cb += f"{self.edges[ii][1]: .12e} " - cb += f"{self.edges[ii][2]: .12e}\n" + for idx in range(3): + cb += f" cube edge {self.points[idx]} " + cb += f"{self.edges[idx][0]: .12e} " + cb += f"{self.edges[idx][1]: .12e} " + cb += f"{self.edges[idx][2]: .12e}\n" cb += f" cube format {self.format}\n" - if self.spinstate is not None: - cb += f" cube spinstate {self.spinstate}\n" + if self.spin_state is not None: + cb += f" cube spin_state {self.spin_state}\n" if self.kpoint is not None: cb += f" cube kpoint {self.kpoint}\n" if self.filename is not None: @@ -377,7 +377,7 @@ def as_dict(self) -> dict[str, Any]: dct["edges"] = self.edges dct["points"] = self.points dct["format"] = self.format - dct["spinstate"] = self.spinstate + dct["spin_state"] = self.spin_state dct["kpoint"] = self.kpoint dct["filename"] = self.filename dct["elf_type"] = self.elf_type diff --git a/tests/io/aims/test_aims_inputs.py b/tests/io/aims/test_aims_inputs.py index f56c3cb9b9f..1a106428cdd 100644 --- a/tests/io/aims/test_aims_inputs.py +++ b/tests/io/aims/test_aims_inputs.py @@ -121,7 +121,7 @@ def test_aims_cube(): AimsCube(type=ALLOWED_AIMS_CUBE_TYPES[0], format="TEST_ERR") with pytest.raises(ValueError, match="Spin state must be 1 or 2"): - AimsCube(type=ALLOWED_AIMS_CUBE_TYPES[0], spinstate=3) + AimsCube(type=ALLOWED_AIMS_CUBE_TYPES[0], spin_state=3) with pytest.raises(ValueError, match="The cube origin must have 3 components"): AimsCube(type=ALLOWED_AIMS_CUBE_TYPES[0], origin=[0]) @@ -146,7 +146,7 @@ def test_aims_cube(): origin=[0, 0, 0], edges=[[0.01, 0, 0], [0.0, 0.01, 0], [0.0, 0, 0.01]], points=[100, 100, 100], - spinstate=1, + spin_state=1, kpoint=1, filename="test.cube", format="cube", From 5c2e354e0acaa5c48333d18a148151154a20bcbe Mon Sep 17 00:00:00 2001 From: Janosh Riebesell Date: Wed, 8 Nov 2023 11:27:20 -0800 Subject: [PATCH 25/30] fix doc str --- pymatgen/io/aims/inputs.py | 30 +++++++++--------------------- 1 file changed, 9 insertions(+), 21 deletions(-) diff --git a/pymatgen/io/aims/inputs.py b/pymatgen/io/aims/inputs.py index 27b6f13190f..11fb4553f95 100644 --- a/pymatgen/io/aims/inputs.py +++ b/pymatgen/io/aims/inputs.py @@ -88,34 +88,25 @@ def from_str(cls, contents: str) -> AimsGeometryIn: else: raise ValueError("Incorrect number of lattice vectors passed.") + site_props = {"magmom": magmom, "charge": charge} if lattice is None: - structure = Molecule( - species, - coords, - np.sum(charge), - site_properties={"magmom": magmom, "charge": charge}, - ) + structure = Molecule(species, coords, np.sum(charge), site_properties=site_props) else: structure = Structure( - lattice, - species, - coords, - np.sum(charge), - coords_are_cartesian=True, - site_properties={"magmom": magmom, "charge": charge}, + lattice, species, coords, np.sum(charge), coords_are_cartesian=True, site_properties=site_props ) return cls(_content="\n".join(content_lines), _structure=structure) @classmethod def from_file(cls, filepath: str | Path) -> AimsGeometryIn: - """Create an AimsGeometryIn from an input file + """Create an AimsGeometryIn from an input file. Args: - filepath (str): The path to the input file (either plain text of gzipped) + filepath (str | Path): The path to the input file (either plain text of gzipped) Returns: - The input object represented in the file + AimsGeometryIn: The input object represented in the file """ if str(filepath).endswith(".gz"): with gzip.open(filepath, "rt") as infile: @@ -127,13 +118,13 @@ def from_file(cls, filepath: str | Path) -> AimsGeometryIn: @classmethod def from_structure(cls, structure: Structure | Molecule) -> AimsGeometryIn: - """Construct an input file from an input structure + """Construct an input file from an input structure. Args: structure (Structure or Molecule): The structure for the file Returns: - The input object for the structure + AimsGeometryIn: The input object for the structure """ content_lines = [] @@ -204,10 +195,7 @@ def from_dict(cls, dct: dict[str, Any]) -> AimsGeometryIn: """ decoded = {key: MontyDecoder().process_decoded(val) for key, val in dct.items() if not key.startswith("@")} - return cls( - _content=decoded["content"], - _structure=decoded["structure"], - ) + return cls(_content=decoded["content"], _structure=decoded["structure"]) ALLOWED_AIMS_CUBE_TYPES = ( From ad242610c7317e8a7b008cfbab3a11a49c222b99 Mon Sep 17 00:00:00 2001 From: Janosh Riebesell Date: Wed, 8 Nov 2023 11:27:45 -0800 Subject: [PATCH 26/30] refactor AimsCube.from_dict --- pymatgen/io/aims/inputs.py | 21 ++++++--------------- 1 file changed, 6 insertions(+), 15 deletions(-) diff --git a/pymatgen/io/aims/inputs.py b/pymatgen/io/aims/inputs.py index 11fb4553f95..81c0b2c9608 100644 --- a/pymatgen/io/aims/inputs.py +++ b/pymatgen/io/aims/inputs.py @@ -372,28 +372,19 @@ def as_dict(self) -> dict[str, Any]: return dct @classmethod - def from_dict(cls, d: dict[str, Any]) -> AimsCube: + def from_dict(cls, dct: dict[str, Any]) -> AimsCube: """Initialize from dictionary. Args: - d(dict[str, Any]): The MontyEncoded dictionary + dct (dict[str, Any]): The MontyEncoded dictionary Returns: - The AimsCube for d + AimsCube """ - decoded = {k: MontyDecoder().process_decoded(v) for k, v in d.items() if not k.startswith("@")} + attrs = ("type", "origin", "edges", "points", "format", "spin_state", "kpoint", "filename", "elf_type") + decoded = {key: MontyDecoder().process_decoded(dct[key]) for key in attrs} - return cls( - type=decoded["type"], - origin=decoded["origin"], - edges=decoded["edges"], - points=decoded["points"], - format=decoded["format"], - spinstate=decoded["spinstate"], - kpoint=decoded["kpoint"], - filename=decoded["filename"], - elf_type=decoded["elf_type"], - ) + return cls(**decoded) @dataclass From 27564677fa7f4d3cb6d6cc2d89904d8d7827bef8 Mon Sep 17 00:00:00 2001 From: Janosh Riebesell Date: Wed, 8 Nov 2023 11:28:35 -0800 Subject: [PATCH 27/30] fix typo --- pymatgen/io/aims/inputs.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pymatgen/io/aims/inputs.py b/pymatgen/io/aims/inputs.py index 81c0b2c9608..5fcbd638af4 100644 --- a/pymatgen/io/aims/inputs.py +++ b/pymatgen/io/aims/inputs.py @@ -392,7 +392,7 @@ class AimsControlIn(MSONable): """Class representing and FHI-aims control.in file Attributes: - _parameters (dict[str, Any]): The parameters dictionary conataining all input + _parameters (dict[str, Any]): The parameters dictionary containing all input flags (key) and values for the control.in file """ From b45b71f43ce35fd839917ec7a66abd72100e8880 Mon Sep 17 00:00:00 2001 From: Janosh Riebesell Date: Wed, 8 Nov 2023 11:32:29 -0800 Subject: [PATCH 28/30] fix tests --- pymatgen/io/aims/inputs.py | 11 +++++------ tests/io/aims/test_aims_inputs.py | 2 +- 2 files changed, 6 insertions(+), 7 deletions(-) diff --git a/pymatgen/io/aims/inputs.py b/pymatgen/io/aims/inputs.py index 5fcbd638af4..209a3a7498a 100644 --- a/pymatgen/io/aims/inputs.py +++ b/pymatgen/io/aims/inputs.py @@ -314,8 +314,9 @@ def __post_init__(self) -> None: if self.format not in ALLOWED_AIMS_CUBE_FORMATS: raise ValueError(f"{self.format} is invalid. Cube files must have a format of {ALLOWED_AIMS_CUBE_FORMATS}") - if self.spin_state not in (None, 1, 2): - raise ValueError("Spin state must be 1, 2, or None") + valid_spins = (1, 2, None) + if self.spin_state not in valid_spins: + raise ValueError(f"Spin state must be one of {valid_spins}") if len(self.origin) != 3: raise ValueError("The cube origin must have 3 components") @@ -345,7 +346,7 @@ def control_block(self) -> str: cb += f"{self.edges[idx][2]: .12e}\n" cb += f" cube format {self.format}\n" if self.spin_state is not None: - cb += f" cube spin_state {self.spin_state}\n" + cb += f" cube spinstate {self.spin_state}\n" if self.kpoint is not None: cb += f" cube kpoint {self.kpoint}\n" if self.filename is not None: @@ -615,6 +616,4 @@ def from_dict(cls, dct: dict[str, Any]) -> AimsControlIn: """ decoded = {key: MontyDecoder().process_decoded(val) for key, val in dct.items() if not key.startswith("@")} - return cls( - _parameters=decoded["parameters"], - ) + return cls(_parameters=decoded["parameters"]) diff --git a/tests/io/aims/test_aims_inputs.py b/tests/io/aims/test_aims_inputs.py index 1a106428cdd..cadecf84e67 100644 --- a/tests/io/aims/test_aims_inputs.py +++ b/tests/io/aims/test_aims_inputs.py @@ -120,7 +120,7 @@ def test_aims_cube(): ): AimsCube(type=ALLOWED_AIMS_CUBE_TYPES[0], format="TEST_ERR") - with pytest.raises(ValueError, match="Spin state must be 1 or 2"): + with pytest.raises(ValueError, match=r"Spin state must be one of \(1, 2, None\)"): AimsCube(type=ALLOWED_AIMS_CUBE_TYPES[0], spin_state=3) with pytest.raises(ValueError, match="The cube origin must have 3 components"): From 1563c82e2a974d46ad14c489dfb8f68292dfa51a Mon Sep 17 00:00:00 2001 From: Janosh Riebesell Date: Wed, 8 Nov 2023 11:37:43 -0800 Subject: [PATCH 29/30] mv tests/io/aims/(aims_->'')input_files tests/io/aims/(aims_->'')output_files tests/io/aims/(aims_->'')parser_checks --- .../control.in.h2o.gz | Bin .../control.in.si.gz | Bin .../geometry.in.h2o.gz | Bin .../geometry.in.h2o.ref.gz | Bin .../geometry.in.si.gz | Bin .../geometry.in.si.ref.gz | Bin .../h2o_ref.json.gz | Bin .../si_ref.json.gz | Bin .../{aims_output_files => output_files}/h2o.out.gz | Bin .../h2o_ref.json.gz | Bin .../{aims_output_files => output_files}/si.out.gz | Bin .../si_ref.json.gz | Bin .../calc_chunk.out.gz | Bin .../header_chunk.out.gz | Bin .../molecular_calc_chunk.out.gz | Bin .../molecular_header_chunk.out.gz | Bin .../numerical_stress.out.gz | Bin tests/io/aims/test_aims_inputs.py | 2 +- tests/io/aims/test_aims_outputs.py | 2 +- tests/io/aims/test_aims_parsers.py | 2 +- 20 files changed, 3 insertions(+), 3 deletions(-) rename tests/io/aims/{aims_input_files => input_files}/control.in.h2o.gz (100%) rename tests/io/aims/{aims_input_files => input_files}/control.in.si.gz (100%) rename tests/io/aims/{aims_input_files => input_files}/geometry.in.h2o.gz (100%) rename tests/io/aims/{aims_input_files => input_files}/geometry.in.h2o.ref.gz (100%) rename tests/io/aims/{aims_input_files => input_files}/geometry.in.si.gz (100%) rename tests/io/aims/{aims_input_files => input_files}/geometry.in.si.ref.gz (100%) rename tests/io/aims/{aims_input_files => input_files}/h2o_ref.json.gz (100%) rename tests/io/aims/{aims_input_files => input_files}/si_ref.json.gz (100%) rename tests/io/aims/{aims_output_files => output_files}/h2o.out.gz (100%) rename tests/io/aims/{aims_output_files => output_files}/h2o_ref.json.gz (100%) rename tests/io/aims/{aims_output_files => output_files}/si.out.gz (100%) rename tests/io/aims/{aims_output_files => output_files}/si_ref.json.gz (100%) rename tests/io/aims/{aims_parser_checks => parser_checks}/calc_chunk.out.gz (100%) rename tests/io/aims/{aims_parser_checks => parser_checks}/header_chunk.out.gz (100%) rename tests/io/aims/{aims_parser_checks => parser_checks}/molecular_calc_chunk.out.gz (100%) rename tests/io/aims/{aims_parser_checks => parser_checks}/molecular_header_chunk.out.gz (100%) rename tests/io/aims/{aims_parser_checks => parser_checks}/numerical_stress.out.gz (100%) diff --git a/tests/io/aims/aims_input_files/control.in.h2o.gz b/tests/io/aims/input_files/control.in.h2o.gz similarity index 100% rename from tests/io/aims/aims_input_files/control.in.h2o.gz rename to tests/io/aims/input_files/control.in.h2o.gz diff --git a/tests/io/aims/aims_input_files/control.in.si.gz b/tests/io/aims/input_files/control.in.si.gz similarity index 100% rename from tests/io/aims/aims_input_files/control.in.si.gz rename to tests/io/aims/input_files/control.in.si.gz diff --git a/tests/io/aims/aims_input_files/geometry.in.h2o.gz b/tests/io/aims/input_files/geometry.in.h2o.gz similarity index 100% rename from tests/io/aims/aims_input_files/geometry.in.h2o.gz rename to tests/io/aims/input_files/geometry.in.h2o.gz diff --git a/tests/io/aims/aims_input_files/geometry.in.h2o.ref.gz b/tests/io/aims/input_files/geometry.in.h2o.ref.gz similarity index 100% rename from tests/io/aims/aims_input_files/geometry.in.h2o.ref.gz rename to tests/io/aims/input_files/geometry.in.h2o.ref.gz diff --git a/tests/io/aims/aims_input_files/geometry.in.si.gz b/tests/io/aims/input_files/geometry.in.si.gz similarity index 100% rename from tests/io/aims/aims_input_files/geometry.in.si.gz rename to tests/io/aims/input_files/geometry.in.si.gz diff --git a/tests/io/aims/aims_input_files/geometry.in.si.ref.gz b/tests/io/aims/input_files/geometry.in.si.ref.gz similarity index 100% rename from tests/io/aims/aims_input_files/geometry.in.si.ref.gz rename to tests/io/aims/input_files/geometry.in.si.ref.gz diff --git a/tests/io/aims/aims_input_files/h2o_ref.json.gz b/tests/io/aims/input_files/h2o_ref.json.gz similarity index 100% rename from tests/io/aims/aims_input_files/h2o_ref.json.gz rename to tests/io/aims/input_files/h2o_ref.json.gz diff --git a/tests/io/aims/aims_input_files/si_ref.json.gz b/tests/io/aims/input_files/si_ref.json.gz similarity index 100% rename from tests/io/aims/aims_input_files/si_ref.json.gz rename to tests/io/aims/input_files/si_ref.json.gz diff --git a/tests/io/aims/aims_output_files/h2o.out.gz b/tests/io/aims/output_files/h2o.out.gz similarity index 100% rename from tests/io/aims/aims_output_files/h2o.out.gz rename to tests/io/aims/output_files/h2o.out.gz diff --git a/tests/io/aims/aims_output_files/h2o_ref.json.gz b/tests/io/aims/output_files/h2o_ref.json.gz similarity index 100% rename from tests/io/aims/aims_output_files/h2o_ref.json.gz rename to tests/io/aims/output_files/h2o_ref.json.gz diff --git a/tests/io/aims/aims_output_files/si.out.gz b/tests/io/aims/output_files/si.out.gz similarity index 100% rename from tests/io/aims/aims_output_files/si.out.gz rename to tests/io/aims/output_files/si.out.gz diff --git a/tests/io/aims/aims_output_files/si_ref.json.gz b/tests/io/aims/output_files/si_ref.json.gz similarity index 100% rename from tests/io/aims/aims_output_files/si_ref.json.gz rename to tests/io/aims/output_files/si_ref.json.gz diff --git a/tests/io/aims/aims_parser_checks/calc_chunk.out.gz b/tests/io/aims/parser_checks/calc_chunk.out.gz similarity index 100% rename from tests/io/aims/aims_parser_checks/calc_chunk.out.gz rename to tests/io/aims/parser_checks/calc_chunk.out.gz diff --git a/tests/io/aims/aims_parser_checks/header_chunk.out.gz b/tests/io/aims/parser_checks/header_chunk.out.gz similarity index 100% rename from tests/io/aims/aims_parser_checks/header_chunk.out.gz rename to tests/io/aims/parser_checks/header_chunk.out.gz diff --git a/tests/io/aims/aims_parser_checks/molecular_calc_chunk.out.gz b/tests/io/aims/parser_checks/molecular_calc_chunk.out.gz similarity index 100% rename from tests/io/aims/aims_parser_checks/molecular_calc_chunk.out.gz rename to tests/io/aims/parser_checks/molecular_calc_chunk.out.gz diff --git a/tests/io/aims/aims_parser_checks/molecular_header_chunk.out.gz b/tests/io/aims/parser_checks/molecular_header_chunk.out.gz similarity index 100% rename from tests/io/aims/aims_parser_checks/molecular_header_chunk.out.gz rename to tests/io/aims/parser_checks/molecular_header_chunk.out.gz diff --git a/tests/io/aims/aims_parser_checks/numerical_stress.out.gz b/tests/io/aims/parser_checks/numerical_stress.out.gz similarity index 100% rename from tests/io/aims/aims_parser_checks/numerical_stress.out.gz rename to tests/io/aims/parser_checks/numerical_stress.out.gz diff --git a/tests/io/aims/test_aims_inputs.py b/tests/io/aims/test_aims_inputs.py index cadecf84e67..9725d870d37 100644 --- a/tests/io/aims/test_aims_inputs.py +++ b/tests/io/aims/test_aims_inputs.py @@ -16,7 +16,7 @@ AimsGeometryIn, ) -infile_dir = Path(__file__).parent / "aims_input_files" +infile_dir = Path(__file__).parent / "input_files" def compare_files(ref_file, test_file): diff --git a/tests/io/aims/test_aims_outputs.py b/tests/io/aims/test_aims_outputs.py index e91a91213ef..7c174f09e1f 100644 --- a/tests/io/aims/test_aims_outputs.py +++ b/tests/io/aims/test_aims_outputs.py @@ -10,7 +10,7 @@ from pymatgen.core import Structure from pymatgen.io.aims.outputs import AimsOutput -outfile_dir = Path(__file__).parent / "aims_output_files" +outfile_dir = Path(__file__).parent / "output_files" def comp_images(test, ref): diff --git a/tests/io/aims/test_aims_parsers.py b/tests/io/aims/test_aims_parsers.py index b361fc98264..9916eca1feb 100644 --- a/tests/io/aims/test_aims_parsers.py +++ b/tests/io/aims/test_aims_parsers.py @@ -17,7 +17,7 @@ eps_hp = 1e-15 # The espsilon value used to compare numbers that are high-precision eps_lp = 1e-7 # The espsilon value used to compare numbers that are low-precision -parser_file_dir = Path(__file__).parent / "aims_parser_checks" +parser_file_dir = Path(__file__).parent / "parser_checks" @pytest.fixture From 89c29a9b349f30c5b4215befce24d555a3e0c76d Mon Sep 17 00:00:00 2001 From: Thomas Purcell Date: Wed, 8 Nov 2023 20:55:30 +0100 Subject: [PATCH 30/30] Correct refrence json files for 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