Merge pull request #1 from benrich37/input_cov

Input cov

src/pymatgen/io/jdftx/jdftxinfile.py

@@ -27,6 +27,7 @@
     get_tag_object,
 )
 from pymatgen.util.io_utils import clean_lines
+from pymatgen.util.typing import SpeciesLike
 
 if TYPE_CHECKING:
     from typing import Any
@@ -745,6 +746,22 @@ def __post_init__(self) -> None:
         Post init function for JDFTXStructure. Asserts self.structure is
         ordered, and adds selective dynamics if needed.
         """
+        # TODO: Remove integers from species name (ie convert Si0 -> Si)
+        # TODO: Test if this fix works
+        for i in range(len(self.structure.species)):
+            name = ""
+            if isinstance(self.structure.species[i], str):
+                name_str = self.structure.species[i]
+            elif isinstance(self.structure.species[i], SpeciesLike):
+                name_str = self.structure.species[i].symbol
+                if not isinstance(name_str, str):
+                    name_str = name_str.symbol
+            else:
+                raise TypeError("Species must be a string or SpeciesLike object")
+            for j in range(len(name_str)):
+                if not name_str[j].isdigit():
+                    name += name_str[j]
+            self.structure.species[i] = name
         if self.structure.is_ordered:
             site_properties = {}
             if self.selective_dynamics is not None:

src/pymatgen/io/jdftx/jdftxinfile_master_format.py

@@ -12,6 +12,7 @@
 from copy import deepcopy
 from typing import Any
 
+from pymatgen.io.jdftx.data import atom_valence_electrons
 from pymatgen.io.jdftx.generic_tags import (
     AbstractTag,
     BoolTag,
@@ -83,7 +84,11 @@
             optional=False,
             allow_list_representation=True,
             subtags={
-                "species-id": StrTag(write_tagname=False, optional=False),
+                "species-id": StrTag(
+                    write_tagname=False,
+                    optional=False,
+                    options=list(atom_valence_electrons.keys()),  # Required in case bad species names gets fed
+                ),
                 "x0": FloatTag(write_tagname=False, optional=False, prec=12),
                 "x1": FloatTag(write_tagname=False, optional=False, prec=12),
                 "x2": FloatTag(write_tagname=False, optional=False, prec=12),

src/pymatgen/io/jdftx/jdftxoutfileslice.py

@@ -146,6 +146,7 @@ class JDFTXOutfileSlice(ClassPrintFormatter):
     has_solvation: bool = False
     fluid: str | None = None
     is_gc: bool | None = None
+    is_bgw: bool = False
 
     @property
     def t_s(self) -> float | None:
@@ -632,19 +633,19 @@ def get_truncationvars(self, text: list[str]) -> tuple[str, float] | tuple[None,
         truncation_radius = None
         if line is not None:
             truncation_type = text[line].split()[1]
+            if truncation_type not in maptypes:
+                raise ValueError("Problem with this truncation!")
             truncation_type = maptypes[truncation_type]
             direc = None
             if len(text[line].split()) == 3:
                 direc = text[line].split()[2]
-            if truncation_type == "slab" and direc != "001":
-                raise ValueError("BGW slab Coulomb truncation must be along z!")
-            if truncation_type == "wire" and direc != "001":
-                raise ValueError(
-                    "BGW wire Coulomb truncation must be periodic \
-                                 in z!"
-                )
-            if truncation_type == "error":
-                raise ValueError("Problem with this truncation!")
+            if self.is_bgw:
+                if truncation_type == "slab" and direc != "001":
+                    raise ValueError("BGW slab Coulomb truncation must be along z!")
+                if truncation_type == "wire" and direc != "001":
+                    raise ValueError("BGW wire Coulomb truncation must be periodic in z!")
+            # if truncation_type == "error":
+            #     raise ValueError("Problem with this truncation!")
             if truncation_type == "spherical":
                 line = find_key("Initialized spherical truncation of radius", text)
                 truncation_radius = float(text[line].split()[5]) / ang_to_bohr
@@ -763,10 +764,7 @@ def get_eigstats_varsdict(self, text: list[str], prefix: str | None) -> dict[str
         lines2 = find_all_key("eigStats' ...", text)
         lines3 = [lines1[i] for i in range(len(lines1)) if lines1[i] in lines2]
         if not len(lines3):
-            raise ValueError(
-                'Must run DFT job with "dump End EigStats" to get summary gap\
-                      information!'
-            )
+            raise ValueError('Must run DFT job with "dump End EigStats" to get summary gap information!')
         line = lines3[-1]
         varsdict["emin"] = float(text[line + 1].split()[1]) * Ha_to_eV
         varsdict["homo"] = float(text[line + 2].split()[1]) * Ha_to_eV
@@ -811,7 +809,7 @@ def get_pp_type(self, text: list[str]) -> str:
         """
         skey = "Reading pseudopotential file"
         line = find_key(skey, text)
-        ppfile_example = text[line].split(skey)[1].split(":")[0].strip("'")
+        ppfile_example = text[line].split(skey)[1].split(":")[0].strip("'").strip()
         pptype = None
         readable = ["GBRV", "SG15"]
         for _pptype in readable:
@@ -824,10 +822,7 @@ def get_pp_type(self, text: list[str]) -> str:
                 else:
                     pptype = _pptype
         if pptype is None:
-            raise ValueError(
-                f"Could not determine pseudopotential type from file name\
-                      {ppfile_example}"
-            )
+            raise ValueError(f"Could not determine pseudopotential type from file name {ppfile_example}")
         return pptype
 
     def set_pseudo_vars(self, text: list[str]) -> None:
@@ -1070,7 +1065,7 @@ def set_orb_fillings(self) -> None:
             else:
                 self.set_orb_fillings_nobroad(self.nspin)
         else:
-            raise ValueError(" Cannot set homo/lumo filling with self.nspin as None")
+            raise ValueError("Cannot set homo/lumo filling with self.nspin as None")
 
     def set_fluid(self, text: list[str]) -> None:  # Is this redundant to the fluid settings?
         """Set the fluid class variable.
@@ -1251,7 +1246,7 @@ def determine_is_metal(self) -> bool:
                 if self.lumo_filling is not None:
                     return self._determine_is_metal(tol_partial, self.nspin, self.homo_filling, self.lumo_filling)
                 raise ValueError("Cannot determine if system is metal - self.lumo_filling undefined")
-            raise ValueError("Cannot determine if system is metal - self.homo_fillig undefined")
+            raise ValueError("Cannot determine if system is metal - self.homo_filling undefined")
         raise ValueError("Cannot determine if system is metal - self.nspin undefined")
 
     def check_solvation(self) -> bool:
@@ -1266,13 +1261,13 @@ def check_solvation(self) -> bool:
         """
         return self.fluid is not None
 
-    def write(self) -> NotImplementedError:
+    def write(self) -> None:
         """Return an error.
 
         Return an error. (pre-commit needs a docustring here)
         """
         # don't need a write method since will never do that
-        return NotImplementedError("There is no need to write a JDFTx out file")
+        raise NotImplementedError("There is no need to write a JDFTx out file")
 
     def to_dict(self) -> dict:
         """Convert dataclass to dictionary representation.

src/pymatgen/io/jdftx/jdftxoutfileslice_helpers.py

@@ -26,6 +26,10 @@ def get_start_lines(
             start_lines.append(i)
     if add_end and i is not None:
         start_lines.append(i)
+    if i is None:
+        raise ValueError("Outfile parser fed an empty file.")
+    if not len(start_lines):
+        raise ValueError("No JDFTx calculations found in file.")
     return start_lines