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Two arguments have to -be specified, POSCAR-format crystal structure and directory name that is created -where `velph.toml` is stored. The available options are explained below. Some -options can be specified in `[init.options]` section of the velph-toml template -file (see {ref}`velph-init-template`). - - -#### `--template-toml` - -Using this option, `velph.toml` like file is read as the template instead of the -template hard coded in velph code. - -#### `--tolerance` - -This is used for the symmetry check tolerance in Angstrom. Symmetry is searched -always even without `--symmetrize`. - -#### `--symmetrize` - -By default (no-symmetrize), the input POSCAR-type structure is simply used as -the unit cell. With `--symmetrize`, input POSCAR-type structure is symmetrized -and standardized conventional unit cell and primitive cell ("unitcell" and -"primitive_cell", respectively) are written in `velph.toml`. - -#### `--no-find-primitive` - -By this option, the input POSCAR-type structure is used as the primitive cell -even if it is not a primitive cell. - -#### `--kspacing` and `--kspacing-dense` - -Sampling k-point meshes are calculated from these values in the similar way to -VASP `KSPACING` definition by overwriting the template. - -#### `--max-num-atoms` - -Supercell shape is determined so that its number of atoms is equal or less than -this number respecting the crystallographic point group. - -#### `--phonopy-max-num-atoms` and `--phono3py-max-num-atoms` - -Supercell shapes for phonopy and phono3py are determined in the same manner as -`--max-num-atoms`. - -#### `--cell-for-relax` - -This chooses unit cell or primitive cell for structure optimization (`relax`). -The default is `unitcell`. Specify `primitive` to use primitive cell. - -#### `--cell-for-nac` - -This chooses unit cell or primitive cell for NAC calculation (`nac`). The -default is `primitive`. Specify `primitive` to use primitive cell. - -#### `--primitive-cell-choice` - -Primitive cell choice, "standardized" (default) or "reduced". - -#### `--use-grg` - -Use generalized regular grid. - -#### `--amplitude` - -Distance of displacements in Angstrom. - -#### `--magmom` - -String corresponding to INCAR MAGMOM tag value for unit cell, e.g., "24*1" or "0 -0 1". This is similar to `MAGMOM` tag in phonopy, see -https://phonopy.github.io/phonopy/setting-tags.html#magmom. In velph, the -asterisk symbol (`*`) is supported. - -(velph-init-template)= -## `velph init` template - -`velph init` is the command to prepare `velph.toml`. Without specifying a -velph-toml-template, the default template is used. Custom template can be -specified as follows: - -``` -% velph init [OPTIONS] CELL_FILENAME PROJECT_FOLDER --template-toml velph-tmpl.toml -``` - -The `velph-tmpl.toml` (arbitrary file name) is almost like the `velph.toml` -file. It means that the `velph-tmpl.toml` may be created modifying -`velph.toml`. The sections that exist only in the `velph-tmpl.toml` but not in -`velph.toml` is `[init.options]`. This can be used as alternatives of command -options of `velph-init`, e.g., - -```toml -[init.options] -kspacing = 0.2 -kspacing_dense = 0.1 -max_num_atoms = 120 -``` - -These `[init.options]` keywords can be found along with the list of the command -options by - -``` -% velph init --help -``` - -## Settings in sections of `velph.toml` - -Note that the same can be applied to `velph-tmpl.toml`. - -### Default INCAR settings - -The default INCAR settins are written in `[vasp.incar]`. These settings are -overwritten by `[vasp.CALC_TYPE.incar]` (`CALC_TYPE` can be `phelel`, `relax`, -`nac`, `transport`, `phono3py`, `phono3py.phonon`, etc). - -### Scheduler settings - -The parameters used for generating the job submission script are specified as -strings in `[scheduler]`. If `[vasp.CALC_TYPE.scheduler]` is -specified, `[scheduler]` settings are overwritten by the settings for -`[vasp.CALC_TYPE]`. The content in this section operates through [Python string -formatting](https://docs.python.org/3/library/stdtypes.html#str.format), using -replacement fields named after keyword arguments. Each parameter line in the -`[scheduler]` section is treated as a keyword argument, which is then inserted -into the string format. - -In the `[scheduler]` section, the parameters `scheduler_name` and -`scheduler_template` have special roles: - -- `scheduler_name`: Specifies the template type, with options `slurm`, `sge`, or - `custom`. For `slurm` and `sge`, the template string (i.e., - `scheduler_template`) is - [hard-coded](https://github.com/phonopy/phelel/blob/develop/src/phelel/velph/utils/scheduler.py). - If `custom` is selected, the string provided by `scheduler_template` is used, - into which the parameters are inserted. -- `scheduler_template`: The string template where parameters defined in this - section are inserted. - -An example is shown below. - -```toml -[scheduler] -scheduler_name = "sge" -job_name = "PbTe" -mpirun_command = "mpirun" -vasp_binary = "/usr/local/cluster-1/bin/vasp_std" -pe = "vienna 32" -prepend_text = ''' -source /opt/intel/oneapi/setvars.sh --config="/home/togo/.oneapi-config" -''' - -... -[vasp.phelel.scheduler] -pe = "paris 24" - -... -[vasp.phonopy.scheduler] -scheduler_template = '''#!/bin/bash -#QSUB2 core 192 -#QSUB2 mpi 192 -#QSUB2 smp 1 -#QSUB2 wtime 48:00:00 -#PBS -N {job_name} -cd $PBS_O_WORKDIR - -{prepend_text} -{mpirun_command} {vasp_binary} | tee vasp_output -{append_text} -''' -job_name = "PbTe" -mpirun_command = "mpijob" -vasp_binary = "/usr/local/cluster-2/bin/vasp_std" -prepend_text = ''' -. /etc/profile.d/modules.sh -module load inteloneapi22u3 -''' -append_text = "" -``` - - -## Example (NiTiSn) - -`POSCAR-unitcell`, `POTCAR`, and `velph-tmpl.toml` are located in the current directory. - -Initial `POSCAR-unitcell`, -``` -Ti4Sn4Ni4 -1.0 -5.906882041566931 0.000000000000000 0.000000000000000 -0.000000000000000 5.906882041566931 0.000000000000000 -0.000000000000000 0.000000000000000 5.906882041566931 -Ti Sn Ni -4 4 4 -Direct -0.000000000000000 0.000000000000000 0.000000000000000 -0.000000000000000 0.500000000000000 0.500000000000000 -0.500000000000000 0.000000000000000 0.500000000000000 -0.500000000000000 0.500000000000000 0.000000000000000 -0.500000000000000 0.500000000000000 0.500000000000000 -0.500000000000000 0.000000000000000 0.000000000000000 -0.000000000000000 0.500000000000000 0.000000000000000 -0.000000000000000 0.000000000000000 0.500000000000000 -0.250000000000000 0.250000000000000 0.250000000000000 -0.250000000000000 0.750000000000000 0.750000000000000 -0.750000000000000 0.250000000000000 0.750000000000000 -0.750000000000000 0.750000000000000 0.250000000000000 -``` - -`velph-tmpl.toml`, -```toml -[init.options] -kspacing = 0.1 -kspacing_dense = 0.2 -max_num_atoms = 100 - -[vasp.incar] -encut = 520 -ncore = 4 - -[vasp.phelel.incar] -kpar = 2 -[vasp.phelel.scheduler] -pe = "mpi* 48" - -[vasp.transport.scheduler] -pe = "mpi* 144" - -[scheduler] -scheduler_name = "sge" -job_name = "TiNiSn" -mpirun_command = "mpirun" -vasp_binary = "/usr/local/vasp/bin/vasp_std" -pe = "vienna 32" -prepend_text = ''' -source /opt/intel/oneapi/setvars.sh intel64 --config="/home/togo/.oneapi-config" -''' -append_text = "" -``` - -`POTCAR` choice, -``` - PAW_PBE Ti_sv 26Sep2005 - PAW_PBE Sn_d 06Sep2000 - PAW_PBE Ni 02Aug2007 -``` - -``` -% velph init POSCAR_Ti4Sn4Ni4 relax --template-toml velph-tmpl.toml -Crystal structure file: "POSCAR_Ti4Sn4Ni4". -Velph template file: "velph-tmpl.toml". -Read crystal structure file "POSCAR_Ti4Sn4Ni4". -Read velph template file "velph-tmpl.toml". -Following options were found in "velph-tmpl.toml": - kspacing = "0.1" - kspacing_dense = "0.2" - max_num_atoms = "100" -The command options were prefered to [init.options] in "velph-tmpl.toml". -Found a primitive cell whose transformation matrix is - [ 0.000 0.500 0.500] - [ 0.500 0.000 0.500] - [ 0.500 0.500 0.000] -Supercell is generated with respect to the cell below. --------------------------------------------------------------------------------- -lattice: -- [ 5.906882041566931, 0.000000000000000, 0.000000000000000 ] # a -- [ 0.000000000000000, 5.906882041566931, 0.000000000000000 ] # b -- [ 0.000000000000000, 0.000000000000000, 5.906882041566931 ] # c -points: -- symbol: Ti # 1 - coordinates: [ 0.000000000000000, 0.000000000000000, 0.000000000000000 ] - mass: 47.867000 -- symbol: Ti # 2 - coordinates: [ 0.000000000000000, 0.500000000000000, 0.500000000000000 ] - mass: 47.867000 -- symbol: Ti # 3 - coordinates: [ 0.500000000000000, 0.000000000000000, 0.500000000000000 ] - mass: 47.867000 -- symbol: Ti # 4 - coordinates: [ 0.500000000000000, 0.500000000000000, 0.000000000000000 ] - mass: 47.867000 -- symbol: Sn # 5 - coordinates: [ 0.500000000000000, 0.500000000000000, 0.500000000000000 ] - mass: 118.710000 -- symbol: Sn # 6 - coordinates: [ 0.500000000000000, 0.000000000000000, 0.000000000000000 ] - mass: 118.710000 -- symbol: Sn # 7 - coordinates: [ 0.000000000000000, 0.500000000000000, 0.000000000000000 ] - mass: 118.710000 -- symbol: Sn # 8 - coordinates: [ 0.000000000000000, 0.000000000000000, 0.500000000000000 ] - mass: 118.710000 -- symbol: Ni # 9 - coordinates: [ 0.250000000000000, 0.250000000000000, 0.250000000000000 ] - mass: 58.693400 -- symbol: Ni # 10 - coordinates: [ 0.250000000000000, 0.750000000000000, 0.750000000000000 ] - mass: 58.693400 -- symbol: Ni # 11 - coordinates: [ 0.750000000000000, 0.250000000000000, 0.750000000000000 ] - mass: 58.693400 -- symbol: Ni # 12 - coordinates: [ 0.750000000000000, 0.750000000000000, 0.250000000000000 ] - mass: 58.693400 --------------------------------------------------------------------------------- -[vasp.incar] (basic INCAR settings) - ismear = 0 - sigma = 0.01 - ediff = 1e-08 - encut = 520 - prec = accurate - lreal = False - lwave = False - lcharg = False - ncore = 4 -[phelel] - supercell_dimension: [2 2 2] -[vasp.*.kpoints.mesh] (*kspacing=0.1) - selfenergy: [18 18 18]* - el_bands: [18 18 18]* - phelel: [5 5 5]* - relax: [11 11 11]* - nac: [18 18 18]* -[vasp.*.kpoints_dense.mesh] (*kspacing_dense=0.2) - selfenergy: [9 9 9]* - el_bands: [9 9 9]* -Created new folder "relax". -Initial settings were written to "relax/velph.toml". -Found "POTCAR". - PAW_PBE Ti_sv 26Sep2005 - PAW_PBE Sn_d 06Sep2000 - PAW_PBE Ni 02Aug2007 - Max ENMAX in "POTCAR" is 274.61. -"POTCAR" was copied to "relax/POTCAR". -``` - - -A directory `relax` is created and `velph.toml` is stored in it. - -`relax/velph.toml`, -```toml -[phelel] -version = "0.6.0" -supercell_dimension = [2, 2, 2] -amplitude = 0.03 -diagonal = true -plusminus = true -fft_mesh = [32, 32, 32] - -# ... - -[vasp.relax] -cell = "unitcell" -[vasp.relax.incar] -ediffg = -1e-06 -ibrion = 2 -isif = 3 -nsw = 10 -ismear = 0 -sigma = 0.01 -ediff = 1e-08 -encut = 520 -prec = "accurate" -lreal = false -lwave = false -lcharg = false -ncore = 4 -[vasp.relax.kpoints] -mesh = [11, 11, 11] - -# ... - -[scheduler] -scheduler_name = "sge" -job_name = "TiNiSn" -mpirun_command = "mpirun" -vasp_binary = "/usr/local/vasp/bin/vasp_std" -pe = "vienna 32" -prepend_text = "source /opt/intel/oneapi/setvars.sh intel64 --config=\"/home/togo/.oneapi-config\"\n" -append_text = "" - -[symmetry] -spacegroup_type = "F-43m" -tolerance = 1e-05 -primitive_matrix = [ - [ 0.000000000000000, 0.500000000000000, 0.500000000000000 ], - [ 0.500000000000000, 0.000000000000000, 0.500000000000000 ], - [ 0.500000000000000, 0.500000000000000, 0.000000000000000 ], -] - -[unitcell] -lattice = [ - [ 5.906882041566931, 0.000000000000000, 0.000000000000000 ], # a - [ 0.000000000000000, 5.906882041566931, 0.000000000000000 ], # b - [ 0.000000000000000, 0.000000000000000, 5.906882041566931 ], # c -] -[[unitcell.points]] # 1 -symbol = "Ti" -coordinates = [ 0.000000000000000, 0.000000000000000, 0.000000000000000 ] -[[unitcell.points]] # 2 -symbol = "Ti" -coordinates = [ 0.000000000000000, 0.500000000000000, 0.500000000000000 ] -[[unitcell.points]] # 3 -symbol = "Ti" -coordinates = [ 0.500000000000000, 0.000000000000000, 0.500000000000000 ] -[[unitcell.points]] # 4 -symbol = "Ti" -coordinates = [ 0.500000000000000, 0.500000000000000, 0.000000000000000 ] -[[unitcell.points]] # 5 -symbol = "Sn" -coordinates = [ 0.500000000000000, 0.500000000000000, 0.500000000000000 ] -[[unitcell.points]] # 6 -symbol = "Sn" -coordinates = [ 0.500000000000000, 0.000000000000000, 0.000000000000000 ] -[[unitcell.points]] # 7 -symbol = "Sn" -coordinates = [ 0.000000000000000, 0.500000000000000, 0.000000000000000 ] -[[unitcell.points]] # 8 -symbol = "Sn" -coordinates = [ 0.000000000000000, 0.000000000000000, 0.500000000000000 ] -[[unitcell.points]] # 9 -symbol = "Ni" -coordinates = [ 0.250000000000000, 0.250000000000000, 0.250000000000000 ] -[[unitcell.points]] # 10 -symbol = "Ni" -coordinates = [ 0.250000000000000, 0.750000000000000, 0.750000000000000 ] -[[unitcell.points]] # 11 -symbol = "Ni" -coordinates = [ 0.750000000000000, 0.250000000000000, 0.750000000000000 ] -[[unitcell.points]] # 12 -symbol = "Ni" -coordinates = [ 0.750000000000000, 0.750000000000000, 0.250000000000000 ] -[primitive_cell] -lattice = [ - [ 0.000000000000000, 2.953441020783465, 2.953441020783465 ], # a - [ 2.953441020783465, 0.000000000000000, 2.953441020783465 ], # b - [ 2.953441020783465, 2.953441020783465, 0.000000000000000 ], # c -] -[[primitive_cell.points]] # 1 -symbol = "Ti" -coordinates = [ 0.000000000000000, 0.000000000000000, 0.000000000000000 ] -[[primitive_cell.points]] # 2 -symbol = "Sn" -coordinates = [ 0.500000000000000, 0.500000000000000, 0.500000000000000 ] -[[primitive_cell.points]] # 3 -symbol = "Ni" -coordinates = [ 0.250000000000000, 0.250000000000000, 0.250000000000000 ] -``` - -`fft_mesh` is calculated from `encut` value in the `[vasp.selfenergy.incar]` section. - -Change directory to `relax`. -``` -% velph relax generate -% cd relax/iter1 -% qsub _job.sh -``` -Structure optimization is done until stress becomes less than 0.1kB (0.01GPa). -Go back to the top directory and start supercell calculation. - -``` -% velph init --template-toml velph-tmpl.toml `ls relax/relax/iter*/CONTCAR|tail -n 1` calc -Crystal structure file: "relax/relax/iter2/CONTCAR". -Velph template file: "velph-tmpl.toml". -Read crystal structure file "relax/relax/iter2/CONTCAR". -Read velph template file "velph-tmpl.toml". -Following options were found in "velph-tmpl.toml": - kspacing = "0.1" - kspacing_dense = "0.2" - max_num_atoms = "100" -The command options were prefered to [init.options] in "velph-tmpl.toml". -Found a primitive cell whose transformation matrix is - [ 0.000 0.500 0.500] - [ 0.500 0.000 0.500] - [ 0.500 0.500 0.000] -Supercell is generated with respect to the cell below. --------------------------------------------------------------------------------- -lattice: -- [ 5.949975748250650, 0.000000000000000, 0.000000000000000 ] # a -- [ 0.000000000000000, 5.949975748250650, -0.000000000000000 ] # b -- [ 0.000000000000000, 0.000000000000000, 5.949975748250650 ] # c -points: -- symbol: Ti # 1 - coordinates: [ 0.000000000000000, 0.000000000000000, 0.000000000000000 ] - mass: 47.867000 -- symbol: Ti # 2 - coordinates: [ 0.000000000000000, 0.500000000000000, 0.500000000000000 ] - mass: 47.867000 -- symbol: Ti # 3 - coordinates: [ 0.500000000000000, 0.000000000000000, 0.500000000000000 ] - mass: 47.867000 -- symbol: Ti # 4 - coordinates: [ 0.500000000000000, 0.500000000000000, 0.000000000000000 ] - mass: 47.867000 -- symbol: Sn # 5 - coordinates: [ 0.500000000000000, 0.500000000000000, 0.500000000000000 ] - mass: 118.710000 -- symbol: Sn # 6 - coordinates: [ 0.500000000000000, 0.000000000000000, 0.000000000000000 ] - mass: 118.710000 -- symbol: Sn # 7 - coordinates: [ 0.000000000000000, 0.500000000000000, 0.000000000000000 ] - mass: 118.710000 -- symbol: Sn # 8 - coordinates: [ 0.000000000000000, 0.000000000000000, 0.500000000000000 ] - mass: 118.710000 -- symbol: Ni # 9 - coordinates: [ 0.250000000000000, 0.250000000000000, 0.250000000000000 ] - mass: 58.693400 -- symbol: Ni # 10 - coordinates: [ 0.250000000000000, 0.750000000000000, 0.750000000000000 ] - mass: 58.693400 -- symbol: Ni # 11 - coordinates: [ 0.750000000000000, 0.250000000000000, 0.750000000000000 ] - mass: 58.693400 -- symbol: Ni # 12 - coordinates: [ 0.750000000000000, 0.750000000000000, 0.250000000000000 ] - mass: 58.693400 --------------------------------------------------------------------------------- -[vasp.incar] (basic INCAR settings) - ismear = 0 - sigma = 0.01 - ediff = 1e-08 - encut = 520 - prec = accurate - lreal = False - lwave = False - lcharg = False - ncore = 4 -[phelel] - supercell_dimension: [2 2 2] -[vasp.*.kpoints.mesh] (*kspacing=0.1) - selfenergy: [18 18 18]* - el_bands: [18 18 18]* - phelel: [5 5 5]* - relax: [11 11 11]* - nac: [18 18 18]* -[vasp.*.kpoints_dense.mesh] (*kspacing_dense=0.2) - selfenergy: [9 9 9]* - el_bands: [9 9 9]* -Created new folder "calc". -Initial settings were written to "calc/velph.toml". -Found "POTCAR". - PAW_PBE Ti_sv 26Sep2005 - PAW_PBE Sn_d 06Sep2000 - PAW_PBE Ni 02Aug2007 - Max ENMAX in "POTCAR" is 274.61. -"POTCAR" was copied to "calc/POTCAR". -``` - -Change directory to `calc`. -``` -% cd calc -``` - -`velph.toml`, -``` -[phelel] -version = "0.6.0" -supercell_dimension = [2, 2, 2] -amplitude = 0.03 -diagonal = true -plusminus = true -fft_mesh = [32, 32, 32] - -[vasp.phelel.incar] -lwap = true -isym = 0 -kpar = 2 -ismear = 0 -sigma = 0.01 -ediff = 1e-08 -encut = 520 -prec = "accurate" -lreal = false -lwave = false -lcharg = false -ncore = 4 -[vasp.phelel.kpoints] -mesh = [5, 5, 5] -[vasp.phelel.scheduler] -pe = "mpi* 48" - -# ... - -[vasp.nac] -cell = "primitive" -[vasp.nac.incar] -lepsilon = true -ismear = 0 -sigma = 0.01 -ediff = 1e-08 -encut = 520 -prec = "accurate" -lreal = false -lwave = false -lcharg = false -[vasp.nac.kpoints] -mesh = [18, 18, 18] - -# ... -``` - -NAC and supercell calculations, -``` -% velph nac generate -% cd nac; qsub _job.sh; cd .. -% velph phelel init -Found "nac" directory. Read NAC params. -"phelel/phelel_disp.yaml" was generated by phelel. -VASP input files will be generated by "velph phelel generate". -% velph supercell generate -VASP input files were generated in "supercell/disp-000". -VASP input files were generated in "supercell/disp-001". -VASP input files were generated in "supercell/disp-002". -VASP input files were generated in "supercell/disp-003". -VASP input files were generated in "supercell/disp-004". -VASP input files were generated in "supercell/disp-005". -VASP input files were generated in "supercell/disp-006". -% for i in {000..006};do cd phelel/disp-$i; qsub _job.sh; cd ../..;done -``` - -Using the VASP results of the supercell calculations, derivatives of properties -are computed using the phelel code. The results are stored in a newly created -file `phelel/phelel_params.hdf5`. This process creates only -`phelel/phelel_params.hdf5` and is invoked by the following velph command: -``` -% velph phelel differentiate -Running finufft (eps=1.000e-06)... -Running finufft (eps=1.000e-06)... -Running finufft (eps=1.000e-06)... -"phelel/phelel_params.hdf5" has been made. -``` - -NAC parameters in `phelel/phelel_params.hdf5` comes from -`phelel/phelel_disp.yaml`, i.e., - -1. NAC parameters are stored in `phelel/phelel_disp.yaml` when - `phelel/phelel_disp.yaml` is created by `velph phelel init`. -2. NAC data in `phelel/phelel_disp.yaml` are transfered to - `phelel/phelel_params.hdf5` by `velph phelel differentiate`. - -Therefore, `nac` calculation has to exist in the initial step `velph phelel -init`. If the `nac` calculation is performed after the supercell calculation, -`velph phelel init` and `velph phelel differentiate` have to be re-executed to -store the NAC parameters in `phelel/phelel_params.hdf5`. diff --git a/_sources/velph-example.md b/_sources/velph-example.md new file mode 100644 index 0000000..eb9885e --- /dev/null +++ b/_sources/velph-example.md @@ -0,0 +1,468 @@ +# `velph` example + +## NiTiSn + +`POSCAR-unitcell`, `POTCAR`, and `velph-tmpl.toml` are located in the current directory. + +Initial `POSCAR-unitcell`, +``` +Ti4Sn4Ni4 +1.0 +5.906882041566931 0.000000000000000 0.000000000000000 +0.000000000000000 5.906882041566931 0.000000000000000 +0.000000000000000 0.000000000000000 5.906882041566931 +Ti Sn Ni +4 4 4 +Direct +0.000000000000000 0.000000000000000 0.000000000000000 +0.000000000000000 0.500000000000000 0.500000000000000 +0.500000000000000 0.000000000000000 0.500000000000000 +0.500000000000000 0.500000000000000 0.000000000000000 +0.500000000000000 0.500000000000000 0.500000000000000 +0.500000000000000 0.000000000000000 0.000000000000000 +0.000000000000000 0.500000000000000 0.000000000000000 +0.000000000000000 0.000000000000000 0.500000000000000 +0.250000000000000 0.250000000000000 0.250000000000000 +0.250000000000000 0.750000000000000 0.750000000000000 +0.750000000000000 0.250000000000000 0.750000000000000 +0.750000000000000 0.750000000000000 0.250000000000000 +``` + +`velph-tmpl.toml`, +```toml +[init.options] +kspacing = 0.1 +kspacing_dense = 0.2 +max_num_atoms = 100 + +[vasp.incar] +encut = 520 +ncore = 4 + +[vasp.phelel.incar] +kpar = 2 +[vasp.phelel.scheduler] +pe = "mpi* 48" + +[vasp.transport.scheduler] +pe = "mpi* 144" + +[scheduler] +scheduler_name = "sge" +job_name = "TiNiSn" +mpirun_command = "mpirun" +vasp_binary = "/usr/local/vasp/bin/vasp_std" +pe = "vienna 32" +prepend_text = ''' +source /opt/intel/oneapi/setvars.sh intel64 --config="/home/togo/.oneapi-config" +''' +append_text = "" +``` + +`POTCAR` choice, +``` + PAW_PBE Ti_sv 26Sep2005 + PAW_PBE Sn_d 06Sep2000 + PAW_PBE Ni 02Aug2007 +``` + +``` +% velph init POSCAR_Ti4Sn4Ni4 relax --template-toml velph-tmpl.toml +Crystal structure file: "POSCAR_Ti4Sn4Ni4". +Velph template file: "velph-tmpl.toml". +Read crystal structure file "POSCAR_Ti4Sn4Ni4". +Read velph template file "velph-tmpl.toml". +Following options were found in "velph-tmpl.toml": + kspacing = "0.1" + kspacing_dense = "0.2" + max_num_atoms = "100" +The command options were prefered to [init.options] in "velph-tmpl.toml". +Found a primitive cell whose transformation matrix is + [ 0.000 0.500 0.500] + [ 0.500 0.000 0.500] + [ 0.500 0.500 0.000] +Supercell is generated with respect to the cell below. +-------------------------------------------------------------------------------- +lattice: +- [ 5.906882041566931, 0.000000000000000, 0.000000000000000 ] # a +- [ 0.000000000000000, 5.906882041566931, 0.000000000000000 ] # b +- [ 0.000000000000000, 0.000000000000000, 5.906882041566931 ] # c +points: +- symbol: Ti # 1 + coordinates: [ 0.000000000000000, 0.000000000000000, 0.000000000000000 ] + mass: 47.867000 +- symbol: Ti # 2 + coordinates: [ 0.000000000000000, 0.500000000000000, 0.500000000000000 ] + mass: 47.867000 +- symbol: Ti # 3 + coordinates: [ 0.500000000000000, 0.000000000000000, 0.500000000000000 ] + mass: 47.867000 +- symbol: Ti # 4 + coordinates: [ 0.500000000000000, 0.500000000000000, 0.000000000000000 ] + mass: 47.867000 +- symbol: Sn # 5 + coordinates: [ 0.500000000000000, 0.500000000000000, 0.500000000000000 ] + mass: 118.710000 +- symbol: Sn # 6 + coordinates: [ 0.500000000000000, 0.000000000000000, 0.000000000000000 ] + mass: 118.710000 +- symbol: Sn # 7 + coordinates: [ 0.000000000000000, 0.500000000000000, 0.000000000000000 ] + mass: 118.710000 +- symbol: Sn # 8 + coordinates: [ 0.000000000000000, 0.000000000000000, 0.500000000000000 ] + mass: 118.710000 +- symbol: Ni # 9 + coordinates: [ 0.250000000000000, 0.250000000000000, 0.250000000000000 ] + mass: 58.693400 +- symbol: Ni # 10 + coordinates: [ 0.250000000000000, 0.750000000000000, 0.750000000000000 ] + mass: 58.693400 +- symbol: Ni # 11 + coordinates: [ 0.750000000000000, 0.250000000000000, 0.750000000000000 ] + mass: 58.693400 +- symbol: Ni # 12 + coordinates: [ 0.750000000000000, 0.750000000000000, 0.250000000000000 ] + mass: 58.693400 +-------------------------------------------------------------------------------- +[vasp.incar] (basic INCAR settings) + ismear = 0 + sigma = 0.01 + ediff = 1e-08 + encut = 520 + prec = accurate + lreal = False + lwave = False + lcharg = False + ncore = 4 +[phelel] + supercell_dimension: [2 2 2] +[vasp.*.kpoints.mesh] (*kspacing=0.1) + selfenergy: [18 18 18]* + el_bands: [18 18 18]* + phelel: [5 5 5]* + relax: [11 11 11]* + nac: [18 18 18]* +[vasp.*.kpoints_dense.mesh] (*kspacing_dense=0.2) + selfenergy: [9 9 9]* + el_bands: [9 9 9]* +Created new folder "relax". +Initial settings were written to "relax/velph.toml". +Found "POTCAR". + PAW_PBE Ti_sv 26Sep2005 + PAW_PBE Sn_d 06Sep2000 + PAW_PBE Ni 02Aug2007 + Max ENMAX in "POTCAR" is 274.61. +"POTCAR" was copied to "relax/POTCAR". +``` + + +A directory `relax` is created and `velph.toml` is stored in it. + +`relax/velph.toml`, +```toml +[phelel] +version = "0.6.0" +supercell_dimension = [2, 2, 2] +amplitude = 0.03 +diagonal = true +plusminus = true +fft_mesh = [32, 32, 32] + +# ... + +[vasp.relax] +cell = "unitcell" +[vasp.relax.incar] +ediffg = -1e-06 +ibrion = 2 +isif = 3 +nsw = 10 +ismear = 0 +sigma = 0.01 +ediff = 1e-08 +encut = 520 +prec = "accurate" +lreal = false +lwave = false +lcharg = false +ncore = 4 +[vasp.relax.kpoints] +mesh = [11, 11, 11] + +# ... + +[scheduler] +scheduler_name = "sge" +job_name = "TiNiSn" +mpirun_command = "mpirun" +vasp_binary = "/usr/local/vasp/bin/vasp_std" +pe = "vienna 32" +prepend_text = "source /opt/intel/oneapi/setvars.sh intel64 --config=\"/home/togo/.oneapi-config\"\n" +append_text = "" + +[symmetry] +spacegroup_type = "F-43m" +tolerance = 1e-05 +primitive_matrix = [ + [ 0.000000000000000, 0.500000000000000, 0.500000000000000 ], + [ 0.500000000000000, 0.000000000000000, 0.500000000000000 ], + [ 0.500000000000000, 0.500000000000000, 0.000000000000000 ], +] + +[unitcell] +lattice = [ + [ 5.906882041566931, 0.000000000000000, 0.000000000000000 ], # a + [ 0.000000000000000, 5.906882041566931, 0.000000000000000 ], # b + [ 0.000000000000000, 0.000000000000000, 5.906882041566931 ], # c +] +[[unitcell.points]] # 1 +symbol = "Ti" +coordinates = [ 0.000000000000000, 0.000000000000000, 0.000000000000000 ] +[[unitcell.points]] # 2 +symbol = "Ti" +coordinates = [ 0.000000000000000, 0.500000000000000, 0.500000000000000 ] +[[unitcell.points]] # 3 +symbol = "Ti" +coordinates = [ 0.500000000000000, 0.000000000000000, 0.500000000000000 ] +[[unitcell.points]] # 4 +symbol = "Ti" +coordinates = [ 0.500000000000000, 0.500000000000000, 0.000000000000000 ] +[[unitcell.points]] # 5 +symbol = "Sn" +coordinates = [ 0.500000000000000, 0.500000000000000, 0.500000000000000 ] +[[unitcell.points]] # 6 +symbol = "Sn" +coordinates = [ 0.500000000000000, 0.000000000000000, 0.000000000000000 ] +[[unitcell.points]] # 7 +symbol = "Sn" +coordinates = [ 0.000000000000000, 0.500000000000000, 0.000000000000000 ] +[[unitcell.points]] # 8 +symbol = "Sn" +coordinates = [ 0.000000000000000, 0.000000000000000, 0.500000000000000 ] +[[unitcell.points]] # 9 +symbol = "Ni" +coordinates = [ 0.250000000000000, 0.250000000000000, 0.250000000000000 ] +[[unitcell.points]] # 10 +symbol = "Ni" +coordinates = [ 0.250000000000000, 0.750000000000000, 0.750000000000000 ] +[[unitcell.points]] # 11 +symbol = "Ni" +coordinates = [ 0.750000000000000, 0.250000000000000, 0.750000000000000 ] +[[unitcell.points]] # 12 +symbol = "Ni" +coordinates = [ 0.750000000000000, 0.750000000000000, 0.250000000000000 ] +[primitive_cell] +lattice = [ + [ 0.000000000000000, 2.953441020783465, 2.953441020783465 ], # a + [ 2.953441020783465, 0.000000000000000, 2.953441020783465 ], # b + [ 2.953441020783465, 2.953441020783465, 0.000000000000000 ], # c +] +[[primitive_cell.points]] # 1 +symbol = "Ti" +coordinates = [ 0.000000000000000, 0.000000000000000, 0.000000000000000 ] +[[primitive_cell.points]] # 2 +symbol = "Sn" +coordinates = [ 0.500000000000000, 0.500000000000000, 0.500000000000000 ] +[[primitive_cell.points]] # 3 +symbol = "Ni" +coordinates = [ 0.250000000000000, 0.250000000000000, 0.250000000000000 ] +``` + +`fft_mesh` is calculated from `encut` value in the `[vasp.selfenergy.incar]` section. + +Change directory to `relax`. +``` +% velph relax generate +% cd relax/iter1 +% qsub _job.sh +``` +Structure optimization is done until stress becomes less than 0.1kB (0.01GPa). +Go back to the top directory and start supercell calculation. + +``` +% velph init --template-toml velph-tmpl.toml `ls relax/relax/iter*/CONTCAR|tail -n 1` calc +Crystal structure file: "relax/relax/iter2/CONTCAR". +Velph template file: "velph-tmpl.toml". +Read crystal structure file "relax/relax/iter2/CONTCAR". +Read velph template file "velph-tmpl.toml". +Following options were found in "velph-tmpl.toml": + kspacing = "0.1" + kspacing_dense = "0.2" + max_num_atoms = "100" +The command options were prefered to [init.options] in "velph-tmpl.toml". +Found a primitive cell whose transformation matrix is + [ 0.000 0.500 0.500] + [ 0.500 0.000 0.500] + [ 0.500 0.500 0.000] +Supercell is generated with respect to the cell below. +-------------------------------------------------------------------------------- +lattice: +- [ 5.949975748250650, 0.000000000000000, 0.000000000000000 ] # a +- [ 0.000000000000000, 5.949975748250650, -0.000000000000000 ] # b +- [ 0.000000000000000, 0.000000000000000, 5.949975748250650 ] # c +points: +- symbol: Ti # 1 + coordinates: [ 0.000000000000000, 0.000000000000000, 0.000000000000000 ] + mass: 47.867000 +- symbol: Ti # 2 + coordinates: [ 0.000000000000000, 0.500000000000000, 0.500000000000000 ] + mass: 47.867000 +- symbol: Ti # 3 + coordinates: [ 0.500000000000000, 0.000000000000000, 0.500000000000000 ] + mass: 47.867000 +- symbol: Ti # 4 + coordinates: [ 0.500000000000000, 0.500000000000000, 0.000000000000000 ] + mass: 47.867000 +- symbol: Sn # 5 + coordinates: [ 0.500000000000000, 0.500000000000000, 0.500000000000000 ] + mass: 118.710000 +- symbol: Sn # 6 + coordinates: [ 0.500000000000000, 0.000000000000000, 0.000000000000000 ] + mass: 118.710000 +- symbol: Sn # 7 + coordinates: [ 0.000000000000000, 0.500000000000000, 0.000000000000000 ] + mass: 118.710000 +- symbol: Sn # 8 + coordinates: [ 0.000000000000000, 0.000000000000000, 0.500000000000000 ] + mass: 118.710000 +- symbol: Ni # 9 + coordinates: [ 0.250000000000000, 0.250000000000000, 0.250000000000000 ] + mass: 58.693400 +- symbol: Ni # 10 + coordinates: [ 0.250000000000000, 0.750000000000000, 0.750000000000000 ] + mass: 58.693400 +- symbol: Ni # 11 + coordinates: [ 0.750000000000000, 0.250000000000000, 0.750000000000000 ] + mass: 58.693400 +- symbol: Ni # 12 + coordinates: [ 0.750000000000000, 0.750000000000000, 0.250000000000000 ] + mass: 58.693400 +-------------------------------------------------------------------------------- +[vasp.incar] (basic INCAR settings) + ismear = 0 + sigma = 0.01 + ediff = 1e-08 + encut = 520 + prec = accurate + lreal = False + lwave = False + lcharg = False + ncore = 4 +[phelel] + supercell_dimension: [2 2 2] +[vasp.*.kpoints.mesh] (*kspacing=0.1) + selfenergy: [18 18 18]* + el_bands: [18 18 18]* + phelel: [5 5 5]* + relax: [11 11 11]* + nac: [18 18 18]* +[vasp.*.kpoints_dense.mesh] (*kspacing_dense=0.2) + selfenergy: [9 9 9]* + el_bands: [9 9 9]* +Created new folder "calc". +Initial settings were written to "calc/velph.toml". +Found "POTCAR". + PAW_PBE Ti_sv 26Sep2005 + PAW_PBE Sn_d 06Sep2000 + PAW_PBE Ni 02Aug2007 + Max ENMAX in "POTCAR" is 274.61. +"POTCAR" was copied to "calc/POTCAR". +``` + +Change directory to `calc`. +``` +% cd calc +``` + +`velph.toml`, +``` +[phelel] +version = "0.6.0" +supercell_dimension = [2, 2, 2] +amplitude = 0.03 +diagonal = true +plusminus = true +fft_mesh = [32, 32, 32] + +[vasp.phelel.incar] +lwap = true +isym = 0 +kpar = 2 +ismear = 0 +sigma = 0.01 +ediff = 1e-08 +encut = 520 +prec = "accurate" +lreal = false +lwave = false +lcharg = false +ncore = 4 +[vasp.phelel.kpoints] +mesh = [5, 5, 5] +[vasp.phelel.scheduler] +pe = "mpi* 48" + +# ... + +[vasp.nac] +cell = "primitive" +[vasp.nac.incar] +lepsilon = true +ismear = 0 +sigma = 0.01 +ediff = 1e-08 +encut = 520 +prec = "accurate" +lreal = false +lwave = false +lcharg = false +[vasp.nac.kpoints] +mesh = [18, 18, 18] + +# ... +``` + +NAC and supercell calculations, +``` +% velph nac generate +% cd nac; qsub _job.sh; cd .. +% velph phelel init +Found "nac" directory. Read NAC params. +"phelel/phelel_disp.yaml" was generated by phelel. +VASP input files will be generated by "velph phelel generate". +% velph supercell generate +VASP input files were generated in "supercell/disp-000". +VASP input files were generated in "supercell/disp-001". +VASP input files were generated in "supercell/disp-002". +VASP input files were generated in "supercell/disp-003". +VASP input files were generated in "supercell/disp-004". +VASP input files were generated in "supercell/disp-005". +VASP input files were generated in "supercell/disp-006". +% for i in {000..006};do cd phelel/disp-$i; qsub _job.sh; cd ../..;done +``` + +Using the VASP results of the supercell calculations, derivatives of properties +are computed using the phelel code. The results are stored in a newly created +file `phelel/phelel_params.hdf5`. This process creates only +`phelel/phelel_params.hdf5` and is invoked by the following velph command: +``` +% velph phelel differentiate +Running finufft (eps=1.000e-06)... +Running finufft (eps=1.000e-06)... +Running finufft (eps=1.000e-06)... +"phelel/phelel_params.hdf5" has been made. +``` + +NAC parameters in `phelel/phelel_params.hdf5` comes from +`phelel/phelel_disp.yaml`, i.e., + +1. NAC parameters are stored in `phelel/phelel_disp.yaml` when + `phelel/phelel_disp.yaml` is created by `velph phelel init`. +2. NAC data in `phelel/phelel_disp.yaml` are transfered to + `phelel/phelel_params.hdf5` by `velph phelel differentiate`. + +Therefore, `nac` calculation has to exist in the initial step `velph phelel +init`. If the `nac` calculation is performed after the supercell calculation, +`velph phelel init` and `velph phelel differentiate` have to be re-executed to +store the NAC parameters in `phelel/phelel_params.hdf5`. diff --git a/_sources/velph-init.md b/_sources/velph-init.md new file mode 100644 index 0000000..96a2a99 --- /dev/null +++ b/_sources/velph-init.md @@ -0,0 +1,187 @@ +# `velph init` + +`velph init` with command options will generate modified `velph.toml` from the +template. +``` +% velph init [OPTIONS] CELL_FILENAME PROJECT_FOLDER +``` + +`velph init --help` shows short documents of the options. Two arguments have to +be specified, POSCAR-format crystal structure and directory name that is created +where `velph.toml` is stored. The available options are explained below. Some +options can be specified in `[init.options]` section of the velph-toml template +file (see {ref}`velph-init-template`). + +## `velph init` options + +### `--template-toml` + +Using this option, `velph.toml` like file is read as the template instead of the +template hard coded in velph code. + +### `--tolerance` + +This is used for the symmetry check tolerance in Angstrom. Symmetry is searched +always even without `--symmetrize`. + +### `--symmetrize` + +By default (no-symmetrize), the input POSCAR-type structure is simply used as +the unit cell. With `--symmetrize`, input POSCAR-type structure is symmetrized +and standardized conventional unit cell and primitive cell ("unitcell" and +"primitive_cell", respectively) are written in `velph.toml`. + +### `--no-find-primitive` + +By this option, the input POSCAR-type structure is used as the primitive cell +even if it is not a primitive cell. + +### `--kspacing` and `--kspacing-dense` + +Sampling k-point meshes are calculated from these values in the similar way to +VASP `KSPACING` definition by overwriting the template. + +### `--max-num-atoms` + +Supercell shape is determined so that its number of atoms is equal or less than +this number respecting the crystallographic point group. + +### `--phonopy-max-num-atoms` and `--phono3py-max-num-atoms` + +Supercell shapes for phonopy and phono3py are determined in the same manner as +`--max-num-atoms`. + +### `--cell-for-relax` + +This chooses unit cell or primitive cell for structure optimization (`relax`). +The default is `unitcell`. Specify `primitive` to use primitive cell. + +### `--cell-for-nac` + +This chooses unit cell or primitive cell for NAC calculation (`nac`). The +default is `primitive`. Specify `primitive` to use primitive cell. + +### `--primitive-cell-choice` + +Primitive cell choice, "standardized" (default) or "reduced". + +### `--use-grg` + +Use generalized regular grid. + +### `--amplitude` + +Distance of displacements in Angstrom. + +### `--magmom` + +String corresponding to INCAR MAGMOM tag value for unit cell, e.g., "24*1" or "0 +0 1". This is similar to `MAGMOM` tag in phonopy, see +https://phonopy.github.io/phonopy/setting-tags.html#magmom. In velph, the +asterisk symbol (`*`) is supported. + + +(velph-init-template)= +## `velph init` template + +`velph init` is the command to prepare `velph.toml`. Without specifying a +velph-toml-template, the default template is used. Custom template can be +specified as follows: + +``` +% velph init [OPTIONS] CELL_FILENAME PROJECT_FOLDER --template-toml velph-tmpl.toml +``` + +The `velph-tmpl.toml` (arbitrary file name) is almost like the `velph.toml` +file. It means that the `velph-tmpl.toml` may be created modifying +`velph.toml`. The sections that exist only in the `velph-tmpl.toml` but not in +`velph.toml` is `[init.options]`. This can be used as alternatives of command +options of `velph-init`, e.g., + +```toml +[init.options] +kspacing = 0.2 +kspacing_dense = 0.1 +max_num_atoms = 120 +``` + +These `[init.options]` keywords can be found along with the list of the command +options by + +``` +% velph init --help +``` + +## Settings in sections of `velph.toml` + +Note that the same can be applied to `velph-tmpl.toml`. + +### Default INCAR settings + +The default INCAR settins are written in `[vasp.incar]`. These settings are +overwritten by `[vasp.CALC_TYPE.incar]` (`CALC_TYPE` can be `phelel`, `relax`, +`nac`, `transport`, `phono3py`, `phono3py.phonon`, etc). + +### Scheduler settings + +The parameters used for generating the job submission script are specified as +strings in `[scheduler]`. If `[vasp.CALC_TYPE.scheduler]` is +specified, `[scheduler]` settings are overwritten by the settings for +`[vasp.CALC_TYPE]`. The content in this section operates through [Python string +formatting](https://docs.python.org/3/library/stdtypes.html#str.format), using +replacement fields named after keyword arguments. Each parameter line in the +`[scheduler]` section is treated as a keyword argument, which is then inserted +into the string format. + +In the `[scheduler]` section, the parameters `scheduler_name` and +`scheduler_template` have special roles: + +- `scheduler_name`: Specifies the template type, with options `slurm`, `sge`, or + `custom`. For `slurm` and `sge`, the template string (i.e., + `scheduler_template`) is + [hard-coded](https://github.com/phonopy/phelel/blob/develop/src/phelel/velph/utils/scheduler.py). + If `custom` is selected, the string provided by `scheduler_template` is used, + into which the parameters are inserted. +- `scheduler_template`: The string template where parameters defined in this + section are inserted. + +An example is shown below. + +```toml +[scheduler] +scheduler_name = "sge" +job_name = "PbTe" +mpirun_command = "mpirun" +vasp_binary = "/usr/local/cluster-1/bin/vasp_std" +pe = "vienna 32" +prepend_text = ''' +source /opt/intel/oneapi/setvars.sh --config="/home/togo/.oneapi-config" +''' + +... +[vasp.phelel.scheduler] +pe = "paris 24" + +... +[vasp.phonopy.scheduler] +scheduler_template = '''#!/bin/bash +#QSUB2 core 192 +#QSUB2 mpi 192 +#QSUB2 smp 1 +#QSUB2 wtime 48:00:00 +#PBS -N {job_name} +cd $PBS_O_WORKDIR + +{prepend_text} +{mpirun_command} {vasp_binary} | tee vasp_output +{append_text} +''' +job_name = "PbTe" +mpirun_command = "mpijob" +vasp_binary = "/usr/local/cluster-2/bin/vasp_std" +prepend_text = ''' +. /etc/profile.d/modules.sh +module load inteloneapi22u3 +''' +append_text = "" +``` diff --git a/_sources/velph-subcommands.md b/_sources/velph-subcommands.md new file mode 100644 index 0000000..1287cd4 --- /dev/null +++ b/_sources/velph-subcommands.md @@ -0,0 +1,52 @@ +# `velph` subcommands + +## `velph phelel` + +This command calculates the derivatives of local potentials and PAW strengths +with respect to displacement, performing similar operations as steps 1 and 3 +carried out by the `phelel` command in the {ref}`workflow `. + +### `velph phelel init` + +### `velph phelel generate` + +### `velph phelel differentiate` + +### `velph phelel phonopy` + +## `velph transport` + +### `velph transport generate` + +### `velph transport plot` + +## `velph relax` + +### `velph relax generate` + +## `velph nac` + +### `velph nac generate` + +## `velph el_bands` + +### `velph el_bands generate` +### `velph el_bands plot` + +## `velph ph_bands` + +### `velph ph_bands generate` + +### `velph ph_bands plot` + +## `velph phono3py` + +### `velph phono3py init` + +### `velph phono3py generate` + +## `velph phonopy` + +### `velph phonopy init` + +### `velph phonopy generate` diff --git a/changelog.html b/changelog.html index 8ec9713..ef729a8 100644 --- a/changelog.html +++ b/changelog.html @@ -46,7 +46,7 @@ - + @@ -141,6 +141,9 @@

  • Workflow of el-ph calculation
  • phelel command
  • velph command
    • +
  • velph init
    • +
  • velph subcommands
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  • velph example
  • Change Log
    • @@ -338,12 +341,12 @@

    Dec-9-2024: Version 0.6.6

    previous

    -

    velph command

    +

    velph example

     diff --git a/genindex.html b/genindex.html index 1b4a73b..752e2ad 100644 --- a/genindex.html +++ b/genindex.html @@ -141,6 +141,9 @@
  • Workflow of el-ph calculation
  • phelel command
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    • diff --git a/index.html b/index.html index 1368953..cd54089 100644 --- a/index.html +++ b/index.html @@ -143,6 +143,9 @@
  • Workflow of el-ph calculation
  • phelel command
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    • diff --git a/install.html b/install.html index 174d122..2789634 100644 --- a/install.html +++ b/install.html @@ -142,6 +142,9 @@
  • Workflow of el-ph calculation
  • phelel command
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    • diff --git a/objects.inv b/objects.inv index 673e4fe5b38c8c38b81c8d0f3cf216b60d83f6b8..ccd3edcd84e77e101eeb72efb8ada6a194d94442 100644 GIT binary patch delta 331 zcmV-R0kr;^1G@u|d4D}`!ypibcmE2cbakb!Svyr~BugDSMg%U#>H${3P4e%H4aA3S zwVmR7@1FNQf>7MFfVO4M%e}OM)h|qB@mYC|>~#v+yKO5`lp{X@u7TYXMOrYOk#H-C zti}#+<7YLOr8!7NqW}RziSrz>ESjWjGzHvu)>PWcjn4hO&VPx>9IPA=(hU97rxsRg zZY1qfW+ECjmb3&PDLl7bVuZbY77uLCGW~vNN4uW1~u$F(yFmAy{w^<#r1;yuz7g8AIHeWb zx;;tKDTo|hwnYEv_04wWeaj18?d9u?_DaXdTI~LrE9{wt*D|sk#gHC(!9Rv59Kt33 d=W*2GR+{5)UOB3B?IHaV!@xuDsvrGhlb2;UqQn3I delta 297 zcmV+^0oMMz1DOMmd4Dl)!ypiacmE2cbakb!Su<5?BugDSMief_>H$_vn&jUX`yl3G ztL5Xwl`0{T`AL2tEJqJ9x7i_a!l6uapt-h5jrW=Hu6xCAy&CDMZHoQ5kW zvPvCZ$KPtUr8x>mV*ml8We5_HnVA v5$}IwC8~3JHX@9_55W@R4*$zI*tn&Y_*+&!)!DmG-y$&b&=1uQ0FzVqRmhJE diff --git a/phelel-command.html b/phelel-command.html index d8f2f09..93740ff 100644 --- a/phelel-command.html +++ b/phelel-command.html @@ -142,6 +142,9 @@
  • Workflow of el-ph calculation
  • phelel command
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  • velph subcommands
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    • diff --git a/search.html b/search.html index 3f94988..a216bf7 100644 --- a/search.html +++ b/search.html @@ -143,6 +143,9 @@
  • Workflow of el-ph calculation
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    • diff --git a/searchindex.js b/searchindex.js index 25ecb33..1cdc855 100644 --- a/searchindex.js +++ b/searchindex.js @@ -1 +1 @@ -Search.setIndex({"alltitles": {"--amplitude": [[4, "amplitude"]], "--cd, --create-derivatives": [[3, "cd-create-derivatives"]], "--cell-for-nac": [[4, "cell-for-nac"]], "--cell-for-relax": [[4, "cell-for-relax"]], "--dim": [[3, "dim"]], "--kspacing and --kspacing-dense": [[4, "kspacing-and-kspacing-dense"]], "--magmom": [[4, "magmom"]], "--max-num-atoms": [[4, "max-num-atoms"]], "--no-find-primitive": [[4, "no-find-primitive"]], "--phonopy-max-num-atoms and --phono3py-max-num-atoms": [[4, "phonopy-max-num-atoms-and-phono3py-max-num-atoms"]], "--pm": [[3, "pm"]], "--primitive-cell-choice": [[4, "primitive-cell-choice"]], "--symmetrize": [[4, "symmetrize"]], "--template-toml": [[4, "template-toml"]], "--tolerance": [[4, "tolerance"]], "--use-grg": [[4, "use-grg"]], "-c, --cell": [[3, "c-cell"]], "-d": [[3, "d"]], "Additional steps (Optional)": [[5, 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"incorpor": 8, "indic": 3, "inform": 3, "init": [2, 4, 5], "initi": [2, 4, 5, 8], "input": [3, 4, 5, 6, 8], "insert": 6, "instanc": 8, "instead": [0, 6], "institut": 1, "integ": 3, "intel": [5, 6], "intel64": 5, "inteloneapi22u3": 6, "interact": [1, 4, 8], "introduc": 3, "invok": 5, "io": 6, "isao": 1, "isif": 5, "ismear": 5, "isym": 5, "iter": 5, "iter1": 5, "iter2": 5, "its": 6, "job": 6, "job_nam": [5, 6], "k": 6, "kei": 2, "keyword": 6, "kpar": 5, "kpoint": 5, "kpoints_dens": 5, "kress": 1, "kspace": 5, "kspacing_dens": [5, 6], "l": 5, "lattic": [4, 5, 8], "laurent": 1, "lcharg": 5, "lepsilon": 5, "less": [5, 6], "like": 6, "line": [2, 3, 4, 6], "list": [2, 6], "load": 6, "local": [3, 5, 6, 7, 8], "locat": 5, "long": 8, "lreal": 5, "lwap": 5, "lwave": 5, "made": 5, "mai": 6, "mainten": 0, "major": 0, "make": 2, "manag": 8, "manner": 6, "manuel": 1, "marsman": 1, "martijn": 1, "mass": 5, "materi": 1, "matrix": [3, 5], "max": 5, "max_num_atom": [5, 6], "mean": [3, 6], "merit": 8, "mesh": [5, 6], "messag": 4, "method": 1, "minor": 0, "miranda": 1, "mode": [0, 3], "modifi": 6, "modul": 6, "monitor": 8, "mpi": [5, 6], "mpijob": 6, "mpirun": [5, 6], "mpirun_command": [5, 6], "n": [2, 5, 6], "nac": [2, 4, 5], "name": [3, 6], "nation": 1, "ncore": 5, "necessari": 3, "need": 8, "new": 5, "newli": 5, "next": [2, 3], "ni": 5, "nine": 3, "note": 6, "nsw": 5, "number": 6, "obtain": [3, 8], "one": 3, "oneapi": [5, 6], "onli": [1, 3, 5, 6], "oper": [3, 6, 7], "opposit": 3, "opt": [5, 6], "optim": [5, 6], "option": [2, 3, 4, 5], "orchestr": 4, "order": 3, "out": 7, "overwrit": 6, "overwritten": 6, "pa": 3, "packag": 2, "parallel": 3, "param": 5, "paramet": [5, 6, 8], "pari": 6, "particularli": 8, "paw": [3, 7, 8], "paw_pb": 5, "pb": 6, "pbs_o_workdir": 6, "pbte": 6, "pe": [5, 6], "perform": [3, 4, 5, 7, 8], "ph": [3, 4], "ph_band": [2, 4], "phelel": [0, 4, 5, 6, 8], "phelel_disp": [3, 5], "phelel_param": [3, 5], "phono3pi": [2, 4], "phonon": [1, 2, 3, 4, 6, 8], "phonopi": [0, 2, 3, 4], "phy": 1, "pip": 2, "plusminu": 5, "point": [5, 6], "popular": 2, "poscar": [2, 3, 4, 5, 6], "poscar_ti4sn4ni4": 5, "potcar": 5, "potenti": [7, 8], "prec": 5, "prefer": 5, "prepar": 6, "prepend_text": [5, 6], "primit": [2, 4, 5], "primitive_cel": [5, 6], "primitive_matrix": 5, "process": 5, "profil": 6, "project": 4, "project_fold": 6, "properti": [1, 5, 8], "provid": [1, 2, 3, 4, 6], "push": 2, "pypi": 2, "python": 6, "qsub": 5, "qsub2": 6, "quantiti": 8, "quick": 4, "rang": 8, "re": 5, "read": [3, 5, 6], "recommend": 3, "reduc": 6, "refactor": 0, "refer": 4, "regular": 6, "relat": [1, 8], "relax": [2, 4, 5], "releas": 0, "reli": 2, "reload": 2, "renorm": 1, "replac": 6, "report": 1, "repres": 3, "requir": [4, 8], "respect": [2, 3, 5, 6, 7, 8], "result": [3, 4, 5, 8], "rev": 1, "role": 6, "run": [3, 4, 5], "same": 6, "sampl": 6, "schedul": 5, "scheduler_nam": [5, 6], "scheduler_templ": 6, "scienc": 1, "script": 6, "search": 6, "section": [2, 5], "see": [2, 4, 6], "seebeck": 8, "seekpath": 2, "select": [3, 6], "selfenergi": [2, 4, 5], "sequenc": 4, "sequenti": 3, "seri": 4, "set": [2, 5], "settin": 6, "setvar": [5, 6], "sge": [5, 6], "sh": [2, 5, 6], "shape": [3, 6], "short": 6, "show": [2, 4, 6], "shown": 6, "sigma": 5, "similar": [6, 7], "simplest": 2, "simpli": [3, 4, 6], "slurm": 6, "smp": 6, "sn": 5, "sn_d": 5, "so": [3, 6], "some": 6, "sourc": [5, 6], "spacegroup_typ": 5, "special": 6, "specif": 4, "specifi": [3, 6], "spglib": 2, "sposcar": 3, "standard": 6, "start": 5, "state": [4, 8], "step": [3, 4, 5, 7], "store": [3, 5, 6], "strenght": 3, "strength": [3, 7, 8], "stress": 5, "string": 6, "structur": [2, 3, 4, 5, 6, 8], "sub": 2, "submiss": 6, "subsequ": 4, "supercel": [2, 4, 5, 6, 8], "supercell_dimens": 5, "support": [2, 4, 6], "symbol": [5, 6], "symmetr": 3, "symmetri": [3, 5, 6], "systemat": [3, 4], "tab": 2, "tag": 6, "tail": 5, "tanaka": 1, "tee": 6, "templat": 5, "than": [5, 6], "thei": 3, "therefor": 5, "thermal": [4, 8], "thermoelectr": [1, 8], "thi": [1, 3, 4, 5, 6, 7], "those": 3, "three": 3, "through": 6, "ti": 5, "ti4sn4ni4": 5, "ti_sv": 5, "tinisn": 5, "tmpl": [5, 6], "togo": [1, 5, 6], "toler": 5, "toml": 5, "tomli": 2, "tool": [3, 4], "top": 5, "transfer": 5, "transform": 5, "transport": [0, 2, 4, 5, 6], "treat": 6, "trigger": 3, "true": 5, "two": [3, 6], "type": [4, 6], "under": [3, 8], "unit": [3, 6, 8], "unitcel": [2, 3, 4, 5, 6], "unless": 3, "until": 5, "updat": 0, "us": [1, 2, 3, 4, 5, 8], "usag": [2, 3, 4], "usr": [5, 6], "util": 4, "valu": [3, 5, 6], "vasp": [1, 3, 4, 5, 6, 8], "vasp_binari": [5, 6], "vasp_output": 6, "vasp_std": [5, 6], "velph": [0, 8], "verdi": 1, "version": 5, "vienna": [5, 6], "w": 2, "wa": 5, "wai": 6, "well": 8, "were": [3, 5], "when": 5, "where": 6, "which": [2, 3, 4, 6], "whose": 5, "without": 6, "workflow": [3, 4, 7], "write": [2, 4], "written": [5, 6], "wtime": 6, "yaml": [3, 5], "you": 4, "zsh": 2, "zsh_sourc": 2, "zshrc": 2}, "titles": ["Change Log", "Phelel", "Installation", "phelel command", "velph command", "velph example", "velph init", "velph subcommands", "Workflow of el-ph calculation"], "titleterms": {"0": 0, "2024": 0, "2025": 0, "31": 0, "5": 0, "6": 0, "7": 0, "8": 0, "9": 0, "addit": 8, "amplitud": 6, "atom": 6, "c": 3, "calcul": [3, 8], "cd": 3, "cell": [3, 6], "chang": 0, "choic": 6, "code": 2, "command": [2, 3, 4], "complet": 2, "contributor": 1, "creat": 3, "d": 3, "dec": 0, "default": 6, "dens": 6, "deriv": 3, "differenti": 7, "dim": 3, "displac": 3, "do": 4, "doe": 4, "el": 8, "el_band": 7, "exampl": 5, "find": 6, "from": 2, "gener": [3, 7], "grg": 6, "hint": 4, "incar": 6, "init": [6, 7], "instal": 2, "jan": 0, "kspace": 6, "licens": 1, "list": 4, "log": 0, "magmom": 6, "max": 6, "minim": 8, "nac": [6, 7], "nitisn": 5, "num": 6, "option": [6, 8], "ph": 8, "ph_band": 7, "phelel": [1, 2, 3, 7], "phono3pi": [6, 7], "phonopi": [6, 7], "plot": 7, "pm": 3, "potenti": 3, "primit": 6, "relax": [6, 7], "requir": 2, "schedul": 6, "section": 6, "set": 6, "shell": 2, "sourc": 2, "step": 8, "subcommand": [4, 7], "supercel": 3, "symmetr": 6, "templat": 6, "toler": 6, "toml": 6, "transport": 7, "us": 6, "velph": [2, 4, 5, 6, 7], "version": 0, "what": 4, "workflow": 8}}) \ No newline at end of file diff --git a/velph-command.html b/velph-command.html index feab71e..4eb7efd 100644 --- a/velph-command.html +++ b/velph-command.html @@ -46,7 +46,7 @@ - + @@ -142,6 +142,9 @@
  • Workflow of el-ph calculation
  • phelel command
  • velph command
    • +
  • velph init
    • +
  • velph subcommands
    • +
  • velph example
  • Change Log
    • @@ -290,33 +293,7 @@

    Contents

    @@ -378,643 +355,13 @@

    Listing velph -
    -

    velph command operations#

    -

    velph hints#

    +

    velph hints#

    This command provides a quick reference of calculation steps.

    % velph hints
    -
    -

    velph init#

    -

    velph init with command options will generate modified velph.toml from the -template.

    -
    % velph init [OPTIONS] CELL_FILENAME PROJECT_FOLDER
-
    -
    -

    velph init --help shows short documents of the options. Two arguments have to -be specified, POSCAR-format crystal structure and directory name that is created -where velph.toml is stored. The available options are explained below. Some -options can be specified in [init.options] section of the velph-toml template -file (see velph init template).

    -
    -

    --template-toml#

    -

    Using this option, velph.toml like file is read as the template instead of the -template hard coded in velph code.

    -
    -
    -

    --tolerance#

    -

    This is used for the symmetry check tolerance in Angstrom. Symmetry is searched -always even without --symmetrize.

    -
    -
    -

    --symmetrize#

    -

    By default (no-symmetrize), the input POSCAR-type structure is simply used as -the unit cell. With --symmetrize, input POSCAR-type structure is symmetrized -and standardized conventional unit cell and primitive cell (“unitcell” and -“primitive_cell”, respectively) are written in velph.toml.

    -
    -
    -

    --no-find-primitive#

    -

    By this option, the input POSCAR-type structure is used as the primitive cell -even if it is not a primitive cell.

    -
    -
    -

    --kspacing and --kspacing-dense#

    -

    Sampling k-point meshes are calculated from these values in the similar way to -VASP KSPACING definition by overwriting the template.

    -
    -
    -

    --max-num-atoms#

    -

    Supercell shape is determined so that its number of atoms is equal or less than -this number respecting the crystallographic point group.

    -
    -
    -

    --phonopy-max-num-atoms and --phono3py-max-num-atoms#

    -

    Supercell shapes for phonopy and phono3py are determined in the same manner as ---max-num-atoms.

    -
    -
    -

    --cell-for-relax#

    -

    This chooses unit cell or primitive cell for structure optimization (relax). -The default is unitcell. Specify primitive to use primitive cell.

    -
    -
    -

    --cell-for-nac#

    -

    This chooses unit cell or primitive cell for NAC calculation (nac). The -default is primitive. Specify primitive to use primitive cell.

    -
    -
    -

    --primitive-cell-choice#

    -

    Primitive cell choice, “standardized” (default) or “reduced”.

    -
    -
    -

    --use-grg#

    -

    Use generalized regular grid.

    -
    -
    -

    --amplitude#

    -

    Distance of displacements in Angstrom.

    -
    -
    -

    --magmom#

    -

    String corresponding to INCAR MAGMOM tag value for unit cell, e.g., “24*1” or “0 -0 1”. This is similar to MAGMOM tag in phonopy, see -https://phonopy.github.io/phonopy/setting-tags.html#magmom. In velph, the -asterisk symbol (*) is supported.

    -
    -
    -
    -
    -

    velph init template#

    -

    velph init is the command to prepare velph.toml. Without specifying a -velph-toml-template, the default template is used. Custom template can be -specified as follows:

    -
    % velph init [OPTIONS] CELL_FILENAME PROJECT_FOLDER --template-toml velph-tmpl.toml
-
    -
    -

    The velph-tmpl.toml (arbitrary file name) is almost like the velph.toml -file. It means that the velph-tmpl.toml may be created modifying -velph.toml. The sections that exist only in the velph-tmpl.toml but not in -velph.toml is [init.options]. This can be used as alternatives of command -options of velph-init, e.g.,

    -
    [init.options]
-kspacing = 0.2
-kspacing_dense = 0.1
-max_num_atoms = 120
-
    -
    -

    These [init.options] keywords can be found along with the list of the command -options by

    -
    % velph init --help
-
    -
    -
    -
    -

    Settings in sections of velph.toml#

    -

    Note that the same can be applied to velph-tmpl.toml.

    -
    -

    Default INCAR settings#

    -

    The default INCAR settins are written in [vasp.incar]. These settings are -overwritten by [vasp.CALC_TYPE.incar] (CALC_TYPE can be phelel, relax, -nac, transport, phono3py, phono3py.phonon, etc).

    -
    -
    -

    Scheduler settings#

    -

    The parameters used for generating the job submission script are specified as -strings in [scheduler]. If [vasp.CALC_TYPE.scheduler] is -specified, [scheduler] settings are overwritten by the settings for -[vasp.CALC_TYPE]. The content in this section operates through Python string -formatting, using -replacement fields named after keyword arguments. Each parameter line in the -[scheduler] section is treated as a keyword argument, which is then inserted -into the string format.

    -

    In the [scheduler] section, the parameters scheduler_name and -scheduler_template have special roles:

    -
      -

    • scheduler_name: Specifies the template type, with options slurm, sge, or -custom. For slurm and sge, the template string (i.e., -scheduler_template) is -hard-coded. -If custom is selected, the string provided by scheduler_template is used, -into which the parameters are inserted.

      • -

    • scheduler_template: The string template where parameters defined in this -section are inserted.

      • -
    -

    An example is shown below.

    -
    [scheduler]
-scheduler_name = "sge"
-job_name = "PbTe"
-mpirun_command = "mpirun"
-vasp_binary = "/usr/local/cluster-1/bin/vasp_std"
-pe = "vienna 32"
-prepend_text = '''
-source /opt/intel/oneapi/setvars.sh --config="/home/togo/.oneapi-config"
-'''
-
-...
-[vasp.phelel.scheduler]
-pe = "paris 24"
-
-...
-[vasp.phonopy.scheduler]
-scheduler_template = '''#!/bin/bash
-#QSUB2 core 192
-#QSUB2 mpi 192
-#QSUB2 smp 1
-#QSUB2 wtime 48:00:00
-#PBS -N {job_name}
-cd $PBS_O_WORKDIR
-
-{prepend_text}
-{mpirun_command} {vasp_binary} | tee vasp_output
-{append_text}
-'''
-job_name = "PbTe"
-mpirun_command = "mpijob"
-vasp_binary = "/usr/local/cluster-2/bin/vasp_std"
-prepend_text = '''
-. /etc/profile.d/modules.sh
-module load inteloneapi22u3
-'''
-append_text = ""
-
    -
    -
    -
    -
    -

    Example (NiTiSn)#

    -

    POSCAR-unitcell, POTCAR, and velph-tmpl.toml are located in the current directory.

    -

    Initial POSCAR-unitcell,

    -
    Ti4Sn4Ni4
-1.0
-5.906882041566931   0.000000000000000   0.000000000000000
-0.000000000000000   5.906882041566931   0.000000000000000
-0.000000000000000   0.000000000000000   5.906882041566931
-Ti   Sn   Ni
-4   4   4
-Direct
-0.000000000000000   0.000000000000000   0.000000000000000
-0.000000000000000   0.500000000000000   0.500000000000000
-0.500000000000000   0.000000000000000   0.500000000000000
-0.500000000000000   0.500000000000000   0.000000000000000
-0.500000000000000   0.500000000000000   0.500000000000000
-0.500000000000000   0.000000000000000   0.000000000000000
-0.000000000000000   0.500000000000000   0.000000000000000
-0.000000000000000   0.000000000000000   0.500000000000000
-0.250000000000000   0.250000000000000   0.250000000000000
-0.250000000000000   0.750000000000000   0.750000000000000
-0.750000000000000   0.250000000000000   0.750000000000000
-0.750000000000000   0.750000000000000   0.250000000000000
-
    -
    -

    velph-tmpl.toml,

    -
    [init.options]
-kspacing = 0.1
-kspacing_dense = 0.2
-max_num_atoms = 100
-
-[vasp.incar]
-encut = 520
-ncore = 4
-
-[vasp.phelel.incar]
-kpar = 2
-[vasp.phelel.scheduler]
-pe = "mpi* 48"
-
-[vasp.transport.scheduler]
-pe = "mpi* 144"
-
-[scheduler]
-scheduler_name = "sge"
-job_name = "TiNiSn"
-mpirun_command = "mpirun"
-vasp_binary = "/usr/local/vasp/bin/vasp_std"
-pe = "vienna 32"
-prepend_text = '''
-source /opt/intel/oneapi/setvars.sh intel64 --config="/home/togo/.oneapi-config"
-'''
-append_text = ""
-
    -
    -

    POTCAR choice,

    -
      PAW_PBE Ti_sv 26Sep2005
-  PAW_PBE Sn_d 06Sep2000
-  PAW_PBE Ni 02Aug2007
-
    -
    -
    % velph init POSCAR_Ti4Sn4Ni4 relax --template-toml velph-tmpl.toml
-Crystal structure file: "POSCAR_Ti4Sn4Ni4".
-Velph template file: "velph-tmpl.toml".
-Read crystal structure file "POSCAR_Ti4Sn4Ni4".
-Read velph template file "velph-tmpl.toml".
-Following options were found in "velph-tmpl.toml":
-  kspacing = "0.1"
-  kspacing_dense = "0.2"
-  max_num_atoms = "100"
-The command options were prefered to [init.options] in "velph-tmpl.toml".
-Found a primitive cell whose transformation matrix is
-  [ 0.000  0.500  0.500]
-  [ 0.500  0.000  0.500]
-  [ 0.500  0.500  0.000]
-Supercell is generated with respect to the cell below.
---------------------------------------------------------------------------------
-lattice:
-- [     5.906882041566931,     0.000000000000000,     0.000000000000000 ] # a
-- [     0.000000000000000,     5.906882041566931,     0.000000000000000 ] # b
-- [     0.000000000000000,     0.000000000000000,     5.906882041566931 ] # c
-points:
-- symbol: Ti # 1
-  coordinates: [  0.000000000000000,  0.000000000000000,  0.000000000000000 ]
-  mass: 47.867000
-- symbol: Ti # 2
-  coordinates: [  0.000000000000000,  0.500000000000000,  0.500000000000000 ]
-  mass: 47.867000
-- symbol: Ti # 3
-  coordinates: [  0.500000000000000,  0.000000000000000,  0.500000000000000 ]
-  mass: 47.867000
-- symbol: Ti # 4
-  coordinates: [  0.500000000000000,  0.500000000000000,  0.000000000000000 ]
-  mass: 47.867000
-- symbol: Sn # 5
-  coordinates: [  0.500000000000000,  0.500000000000000,  0.500000000000000 ]
-  mass: 118.710000
-- symbol: Sn # 6
-  coordinates: [  0.500000000000000,  0.000000000000000,  0.000000000000000 ]
-  mass: 118.710000
-- symbol: Sn # 7
-  coordinates: [  0.000000000000000,  0.500000000000000,  0.000000000000000 ]
-  mass: 118.710000
-- symbol: Sn # 8
-  coordinates: [  0.000000000000000,  0.000000000000000,  0.500000000000000 ]
-  mass: 118.710000
-- symbol: Ni # 9
-  coordinates: [  0.250000000000000,  0.250000000000000,  0.250000000000000 ]
-  mass: 58.693400
-- symbol: Ni # 10
-  coordinates: [  0.250000000000000,  0.750000000000000,  0.750000000000000 ]
-  mass: 58.693400
-- symbol: Ni # 11
-  coordinates: [  0.750000000000000,  0.250000000000000,  0.750000000000000 ]
-  mass: 58.693400
-- symbol: Ni # 12
-  coordinates: [  0.750000000000000,  0.750000000000000,  0.250000000000000 ]
-  mass: 58.693400
---------------------------------------------------------------------------------
-[vasp.incar] (basic INCAR settings)
-  ismear = 0
-  sigma = 0.01
-  ediff = 1e-08
-  encut = 520
-  prec = accurate
-  lreal = False
-  lwave = False
-  lcharg = False
-  ncore = 4
-[phelel]
-  supercell_dimension: [2 2 2]
-[vasp.*.kpoints.mesh] (*kspacing=0.1)
-  selfenergy: [18 18 18]*
-  el_bands: [18 18 18]*
-  phelel: [5 5 5]*
-  relax: [11 11 11]*
-  nac: [18 18 18]*
-[vasp.*.kpoints_dense.mesh] (*kspacing_dense=0.2)
-  selfenergy: [9 9 9]*
-  el_bands: [9 9 9]*
-Created new folder "relax".
-Initial settings were written to "relax/velph.toml".
-Found "POTCAR".
-  PAW_PBE Ti_sv 26Sep2005
-  PAW_PBE Sn_d 06Sep2000
-  PAW_PBE Ni 02Aug2007
-  Max ENMAX in "POTCAR" is 274.61.
-"POTCAR" was copied to "relax/POTCAR".
-
    -
    -

    A directory relax is created and velph.toml is stored in it.

    -

    relax/velph.toml,

    -
    [phelel]
-version = "0.6.0"
-supercell_dimension = [2, 2, 2]
-amplitude = 0.03
-diagonal = true
-plusminus = true
-fft_mesh = [32, 32, 32]
-
-# ...
-
-[vasp.relax]
-cell = "unitcell"
-[vasp.relax.incar]
-ediffg = -1e-06
-ibrion = 2
-isif = 3
-nsw = 10
-ismear = 0
-sigma = 0.01
-ediff = 1e-08
-encut = 520
-prec = "accurate"
-lreal = false
-lwave = false
-lcharg = false
-ncore = 4
-[vasp.relax.kpoints]
-mesh = [11, 11, 11]
-
-# ...
-
-[scheduler]
-scheduler_name = "sge"
-job_name = "TiNiSn"
-mpirun_command = "mpirun"
-vasp_binary = "/usr/local/vasp/bin/vasp_std"
-pe = "vienna 32"
-prepend_text = "source /opt/intel/oneapi/setvars.sh intel64 --config=\"/home/togo/.oneapi-config\"\n"
-append_text = ""
-
-[symmetry]
-spacegroup_type = "F-43m"
-tolerance = 1e-05
-primitive_matrix = [
-  [  0.000000000000000,  0.500000000000000,  0.500000000000000 ],
-  [  0.500000000000000,  0.000000000000000,  0.500000000000000 ],
-  [  0.500000000000000,  0.500000000000000,  0.000000000000000 ],
-]
-
-[unitcell]
-lattice = [
-  [     5.906882041566931,     0.000000000000000,     0.000000000000000 ], # a
-  [     0.000000000000000,     5.906882041566931,     0.000000000000000 ], # b
-  [     0.000000000000000,     0.000000000000000,     5.906882041566931 ], # c
-]
-[[unitcell.points]]  # 1
-symbol = "Ti"
-coordinates = [  0.000000000000000,  0.000000000000000,  0.000000000000000 ]
-[[unitcell.points]]  # 2
-symbol = "Ti"
-coordinates = [  0.000000000000000,  0.500000000000000,  0.500000000000000 ]
-[[unitcell.points]]  # 3
-symbol = "Ti"
-coordinates = [  0.500000000000000,  0.000000000000000,  0.500000000000000 ]
-[[unitcell.points]]  # 4
-symbol = "Ti"
-coordinates = [  0.500000000000000,  0.500000000000000,  0.000000000000000 ]
-[[unitcell.points]]  # 5
-symbol = "Sn"
-coordinates = [  0.500000000000000,  0.500000000000000,  0.500000000000000 ]
-[[unitcell.points]]  # 6
-symbol = "Sn"
-coordinates = [  0.500000000000000,  0.000000000000000,  0.000000000000000 ]
-[[unitcell.points]]  # 7
-symbol = "Sn"
-coordinates = [  0.000000000000000,  0.500000000000000,  0.000000000000000 ]
-[[unitcell.points]]  # 8
-symbol = "Sn"
-coordinates = [  0.000000000000000,  0.000000000000000,  0.500000000000000 ]
-[[unitcell.points]]  # 9
-symbol = "Ni"
-coordinates = [  0.250000000000000,  0.250000000000000,  0.250000000000000 ]
-[[unitcell.points]]  # 10
-symbol = "Ni"
-coordinates = [  0.250000000000000,  0.750000000000000,  0.750000000000000 ]
-[[unitcell.points]]  # 11
-symbol = "Ni"
-coordinates = [  0.750000000000000,  0.250000000000000,  0.750000000000000 ]
-[[unitcell.points]]  # 12
-symbol = "Ni"
-coordinates = [  0.750000000000000,  0.750000000000000,  0.250000000000000 ]
-[primitive_cell]
-lattice = [
-  [     0.000000000000000,     2.953441020783465,     2.953441020783465 ], # a
-  [     2.953441020783465,     0.000000000000000,     2.953441020783465 ], # b
-  [     2.953441020783465,     2.953441020783465,     0.000000000000000 ], # c
-]
-[[primitive_cell.points]]  # 1
-symbol = "Ti"
-coordinates = [  0.000000000000000,  0.000000000000000,  0.000000000000000 ]
-[[primitive_cell.points]]  # 2
-symbol = "Sn"
-coordinates = [  0.500000000000000,  0.500000000000000,  0.500000000000000 ]
-[[primitive_cell.points]]  # 3
-symbol = "Ni"
-coordinates = [  0.250000000000000,  0.250000000000000,  0.250000000000000 ]
-
    -
    -

    fft_mesh is calculated from encut value in the [vasp.selfenergy.incar] section.

    -

    Change directory to relax.

    -
    % velph relax generate
-% cd relax/iter1
-% qsub _job.sh
-
    -
    -

    Structure optimization is done until stress becomes less than 0.1kB (0.01GPa). -Go back to the top directory and start supercell calculation.

    -
    % velph init --template-toml velph-tmpl.toml `ls relax/relax/iter*/CONTCAR|tail -n 1` calc
-Crystal structure file: "relax/relax/iter2/CONTCAR".
-Velph template file: "velph-tmpl.toml".
-Read crystal structure file "relax/relax/iter2/CONTCAR".
-Read velph template file "velph-tmpl.toml".
-Following options were found in "velph-tmpl.toml":
-  kspacing = "0.1"
-  kspacing_dense = "0.2"
-  max_num_atoms = "100"
-The command options were prefered to [init.options] in "velph-tmpl.toml".
-Found a primitive cell whose transformation matrix is
-  [ 0.000  0.500  0.500]
-  [ 0.500  0.000  0.500]
-  [ 0.500  0.500  0.000]
-Supercell is generated with respect to the cell below.
---------------------------------------------------------------------------------
-lattice:
-- [     5.949975748250650,     0.000000000000000,     0.000000000000000 ] # a
-- [     0.000000000000000,     5.949975748250650,    -0.000000000000000 ] # b
-- [     0.000000000000000,     0.000000000000000,     5.949975748250650 ] # c
-points:
-- symbol: Ti # 1
-  coordinates: [  0.000000000000000,  0.000000000000000,  0.000000000000000 ]
-  mass: 47.867000
-- symbol: Ti # 2
-  coordinates: [  0.000000000000000,  0.500000000000000,  0.500000000000000 ]
-  mass: 47.867000
-- symbol: Ti # 3
-  coordinates: [  0.500000000000000,  0.000000000000000,  0.500000000000000 ]
-  mass: 47.867000
-- symbol: Ti # 4
-  coordinates: [  0.500000000000000,  0.500000000000000,  0.000000000000000 ]
-  mass: 47.867000
-- symbol: Sn # 5
-  coordinates: [  0.500000000000000,  0.500000000000000,  0.500000000000000 ]
-  mass: 118.710000
-- symbol: Sn # 6
-  coordinates: [  0.500000000000000,  0.000000000000000,  0.000000000000000 ]
-  mass: 118.710000
-- symbol: Sn # 7
-  coordinates: [  0.000000000000000,  0.500000000000000,  0.000000000000000 ]
-  mass: 118.710000
-- symbol: Sn # 8
-  coordinates: [  0.000000000000000,  0.000000000000000,  0.500000000000000 ]
-  mass: 118.710000
-- symbol: Ni # 9
-  coordinates: [  0.250000000000000,  0.250000000000000,  0.250000000000000 ]
-  mass: 58.693400
-- symbol: Ni # 10
-  coordinates: [  0.250000000000000,  0.750000000000000,  0.750000000000000 ]
-  mass: 58.693400
-- symbol: Ni # 11
-  coordinates: [  0.750000000000000,  0.250000000000000,  0.750000000000000 ]
-  mass: 58.693400
-- symbol: Ni # 12
-  coordinates: [  0.750000000000000,  0.750000000000000,  0.250000000000000 ]
-  mass: 58.693400
---------------------------------------------------------------------------------
-[vasp.incar] (basic INCAR settings)
-  ismear = 0
-  sigma = 0.01
-  ediff = 1e-08
-  encut = 520
-  prec = accurate
-  lreal = False
-  lwave = False
-  lcharg = False
-  ncore = 4
-[phelel]
-  supercell_dimension: [2 2 2]
-[vasp.*.kpoints.mesh] (*kspacing=0.1)
-  selfenergy: [18 18 18]*
-  el_bands: [18 18 18]*
-  phelel: [5 5 5]*
-  relax: [11 11 11]*
-  nac: [18 18 18]*
-[vasp.*.kpoints_dense.mesh] (*kspacing_dense=0.2)
-  selfenergy: [9 9 9]*
-  el_bands: [9 9 9]*
-Created new folder "calc".
-Initial settings were written to "calc/velph.toml".
-Found "POTCAR".
-  PAW_PBE Ti_sv 26Sep2005
-  PAW_PBE Sn_d 06Sep2000
-  PAW_PBE Ni 02Aug2007
-  Max ENMAX in "POTCAR" is 274.61.
-"POTCAR" was copied to "calc/POTCAR".
-
    -
    -

    Change directory to calc.

    -
    % cd calc
-
    -
    -

    velph.toml,

    -
    [phelel]
-version = "0.6.0"
-supercell_dimension = [2, 2, 2]
-amplitude = 0.03
-diagonal = true
-plusminus = true
-fft_mesh = [32, 32, 32]
-
-[vasp.phelel.incar]
-lwap = true
-isym = 0
-kpar = 2
-ismear = 0
-sigma = 0.01
-ediff = 1e-08
-encut = 520
-prec = "accurate"
-lreal = false
-lwave = false
-lcharg = false
-ncore = 4
-[vasp.phelel.kpoints]
-mesh = [5, 5, 5]
-[vasp.phelel.scheduler]
-pe = "mpi* 48"
-
-# ...
-
-[vasp.nac]
-cell = "primitive"
-[vasp.nac.incar]
-lepsilon = true
-ismear = 0
-sigma = 0.01
-ediff = 1e-08
-encut = 520
-prec = "accurate"
-lreal = false
-lwave = false
-lcharg = false
-[vasp.nac.kpoints]
-mesh = [18, 18, 18]
-
-# ...
-
    -
    -

    NAC and supercell calculations,

    -
    % velph nac generate
-% cd nac; qsub _job.sh; cd ..
-% velph phelel init
-Found "nac" directory. Read NAC params.
-"phelel/phelel_disp.yaml" was generated by phelel.
-VASP input files will be generated by "velph phelel generate".
-% velph supercell generate
-VASP input files were generated in "supercell/disp-000".
-VASP input files were generated in "supercell/disp-001".
-VASP input files were generated in "supercell/disp-002".
-VASP input files were generated in "supercell/disp-003".
-VASP input files were generated in "supercell/disp-004".
-VASP input files were generated in "supercell/disp-005".
-VASP input files were generated in "supercell/disp-006".
-% for i in {000..006};do cd phelel/disp-$i; qsub _job.sh; cd ../..;done
-
    -
    -

    Using the VASP results of the supercell calculations, derivatives of properties -are computed using the phelel code. The results are stored in a newly created -file phelel/phelel_params.hdf5. This process creates only -phelel/phelel_params.hdf5 and is invoked by the following velph command:

    -
    % velph phelel differentiate
-Running finufft (eps=1.000e-06)...
-Running finufft (eps=1.000e-06)...
-Running finufft (eps=1.000e-06)...
-"phelel/phelel_params.hdf5" has been made.
-
    -
    -

    NAC parameters in phelel/phelel_params.hdf5 comes from -phelel/phelel_disp.yaml, i.e.,

    -
      -

    1. NAC parameters are stored in phelel/phelel_disp.yaml when -phelel/phelel_disp.yaml is created by velph phelel init.

      2. -

    2. NAC data in phelel/phelel_disp.yaml are transfered to -phelel/phelel_params.hdf5 by velph phelel differentiate.

      3. -
    -

    Therefore, nac calculation has to exist in the initial step velph phelel init. If the nac calculation is performed after the supercell calculation, -velph phelel init and velph phelel differentiate have to be re-executed to -store the NAC parameters in phelel/phelel_params.hdf5.

    -
    @@ -1038,11 +385,11 @@

    Example (NiTiSn)

    next

    -

    Change Log

    +

    velph init

     @@ -1065,33 +412,7 @@

    Example (NiTiSn)
  • What does the velph command do?
  • Listing velph subcommands
    • -
  • velph command operations -
    • -
  • velph init template
    • -
  • Settings in sections of velph.toml -
    • -
  • Example (NiTiSn)
    • +
  • velph hints
    • diff --git a/velph-example.html b/velph-example.html new file mode 100644 index 0000000..233aae1 --- /dev/null +++ b/velph-example.html @@ -0,0 +1,862 @@ + + + + + + + + + + + velph example — Phelel v.0.8.0 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    + + + + + + +
    + + + Ctrl+K +
    +     + +
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    +

    velph example

    + +
    +
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    +

    Contents

    +
    + +
    +
    +
    + + + + +
    + +
    +

    velph example#

    +
    +

    NiTiSn#

    +

    POSCAR-unitcell, POTCAR, and velph-tmpl.toml are located in the current directory.

    +

    Initial POSCAR-unitcell,

    +
    Ti4Sn4Ni4
+1.0
+5.906882041566931   0.000000000000000   0.000000000000000
+0.000000000000000   5.906882041566931   0.000000000000000
+0.000000000000000   0.000000000000000   5.906882041566931
+Ti   Sn   Ni
+4   4   4
+Direct
+0.000000000000000   0.000000000000000   0.000000000000000
+0.000000000000000   0.500000000000000   0.500000000000000
+0.500000000000000   0.000000000000000   0.500000000000000
+0.500000000000000   0.500000000000000   0.000000000000000
+0.500000000000000   0.500000000000000   0.500000000000000
+0.500000000000000   0.000000000000000   0.000000000000000
+0.000000000000000   0.500000000000000   0.000000000000000
+0.000000000000000   0.000000000000000   0.500000000000000
+0.250000000000000   0.250000000000000   0.250000000000000
+0.250000000000000   0.750000000000000   0.750000000000000
+0.750000000000000   0.250000000000000   0.750000000000000
+0.750000000000000   0.750000000000000   0.250000000000000
+
    +
    +

    velph-tmpl.toml,

    +
    [init.options]
+kspacing = 0.1
+kspacing_dense = 0.2
+max_num_atoms = 100
+
+[vasp.incar]
+encut = 520
+ncore = 4
+
+[vasp.phelel.incar]
+kpar = 2
+[vasp.phelel.scheduler]
+pe = "mpi* 48"
+
+[vasp.transport.scheduler]
+pe = "mpi* 144"
+
+[scheduler]
+scheduler_name = "sge"
+job_name = "TiNiSn"
+mpirun_command = "mpirun"
+vasp_binary = "/usr/local/vasp/bin/vasp_std"
+pe = "vienna 32"
+prepend_text = '''
+source /opt/intel/oneapi/setvars.sh intel64 --config="/home/togo/.oneapi-config"
+'''
+append_text = ""
+
    +
    +

    POTCAR choice,

    +
      PAW_PBE Ti_sv 26Sep2005
+  PAW_PBE Sn_d 06Sep2000
+  PAW_PBE Ni 02Aug2007
+
    +
    +
    % velph init POSCAR_Ti4Sn4Ni4 relax --template-toml velph-tmpl.toml
+Crystal structure file: "POSCAR_Ti4Sn4Ni4".
+Velph template file: "velph-tmpl.toml".
+Read crystal structure file "POSCAR_Ti4Sn4Ni4".
+Read velph template file "velph-tmpl.toml".
+Following options were found in "velph-tmpl.toml":
+  kspacing = "0.1"
+  kspacing_dense = "0.2"
+  max_num_atoms = "100"
+The command options were prefered to [init.options] in "velph-tmpl.toml".
+Found a primitive cell whose transformation matrix is
+  [ 0.000  0.500  0.500]
+  [ 0.500  0.000  0.500]
+  [ 0.500  0.500  0.000]
+Supercell is generated with respect to the cell below.
+--------------------------------------------------------------------------------
+lattice:
+- [     5.906882041566931,     0.000000000000000,     0.000000000000000 ] # a
+- [     0.000000000000000,     5.906882041566931,     0.000000000000000 ] # b
+- [     0.000000000000000,     0.000000000000000,     5.906882041566931 ] # c
+points:
+- symbol: Ti # 1
+  coordinates: [  0.000000000000000,  0.000000000000000,  0.000000000000000 ]
+  mass: 47.867000
+- symbol: Ti # 2
+  coordinates: [  0.000000000000000,  0.500000000000000,  0.500000000000000 ]
+  mass: 47.867000
+- symbol: Ti # 3
+  coordinates: [  0.500000000000000,  0.000000000000000,  0.500000000000000 ]
+  mass: 47.867000
+- symbol: Ti # 4
+  coordinates: [  0.500000000000000,  0.500000000000000,  0.000000000000000 ]
+  mass: 47.867000
+- symbol: Sn # 5
+  coordinates: [  0.500000000000000,  0.500000000000000,  0.500000000000000 ]
+  mass: 118.710000
+- symbol: Sn # 6
+  coordinates: [  0.500000000000000,  0.000000000000000,  0.000000000000000 ]
+  mass: 118.710000
+- symbol: Sn # 7
+  coordinates: [  0.000000000000000,  0.500000000000000,  0.000000000000000 ]
+  mass: 118.710000
+- symbol: Sn # 8
+  coordinates: [  0.000000000000000,  0.000000000000000,  0.500000000000000 ]
+  mass: 118.710000
+- symbol: Ni # 9
+  coordinates: [  0.250000000000000,  0.250000000000000,  0.250000000000000 ]
+  mass: 58.693400
+- symbol: Ni # 10
+  coordinates: [  0.250000000000000,  0.750000000000000,  0.750000000000000 ]
+  mass: 58.693400
+- symbol: Ni # 11
+  coordinates: [  0.750000000000000,  0.250000000000000,  0.750000000000000 ]
+  mass: 58.693400
+- symbol: Ni # 12
+  coordinates: [  0.750000000000000,  0.750000000000000,  0.250000000000000 ]
+  mass: 58.693400
+--------------------------------------------------------------------------------
+[vasp.incar] (basic INCAR settings)
+  ismear = 0
+  sigma = 0.01
+  ediff = 1e-08
+  encut = 520
+  prec = accurate
+  lreal = False
+  lwave = False
+  lcharg = False
+  ncore = 4
+[phelel]
+  supercell_dimension: [2 2 2]
+[vasp.*.kpoints.mesh] (*kspacing=0.1)
+  selfenergy: [18 18 18]*
+  el_bands: [18 18 18]*
+  phelel: [5 5 5]*
+  relax: [11 11 11]*
+  nac: [18 18 18]*
+[vasp.*.kpoints_dense.mesh] (*kspacing_dense=0.2)
+  selfenergy: [9 9 9]*
+  el_bands: [9 9 9]*
+Created new folder "relax".
+Initial settings were written to "relax/velph.toml".
+Found "POTCAR".
+  PAW_PBE Ti_sv 26Sep2005
+  PAW_PBE Sn_d 06Sep2000
+  PAW_PBE Ni 02Aug2007
+  Max ENMAX in "POTCAR" is 274.61.
+"POTCAR" was copied to "relax/POTCAR".
+
    +
    +

    A directory relax is created and velph.toml is stored in it.

    +

    relax/velph.toml,

    +
    [phelel]
+version = "0.6.0"
+supercell_dimension = [2, 2, 2]
+amplitude = 0.03
+diagonal = true
+plusminus = true
+fft_mesh = [32, 32, 32]
+
+# ...
+
+[vasp.relax]
+cell = "unitcell"
+[vasp.relax.incar]
+ediffg = -1e-06
+ibrion = 2
+isif = 3
+nsw = 10
+ismear = 0
+sigma = 0.01
+ediff = 1e-08
+encut = 520
+prec = "accurate"
+lreal = false
+lwave = false
+lcharg = false
+ncore = 4
+[vasp.relax.kpoints]
+mesh = [11, 11, 11]
+
+# ...
+
+[scheduler]
+scheduler_name = "sge"
+job_name = "TiNiSn"
+mpirun_command = "mpirun"
+vasp_binary = "/usr/local/vasp/bin/vasp_std"
+pe = "vienna 32"
+prepend_text = "source /opt/intel/oneapi/setvars.sh intel64 --config=\"/home/togo/.oneapi-config\"\n"
+append_text = ""
+
+[symmetry]
+spacegroup_type = "F-43m"
+tolerance = 1e-05
+primitive_matrix = [
+  [  0.000000000000000,  0.500000000000000,  0.500000000000000 ],
+  [  0.500000000000000,  0.000000000000000,  0.500000000000000 ],
+  [  0.500000000000000,  0.500000000000000,  0.000000000000000 ],
+]
+
+[unitcell]
+lattice = [
+  [     5.906882041566931,     0.000000000000000,     0.000000000000000 ], # a
+  [     0.000000000000000,     5.906882041566931,     0.000000000000000 ], # b
+  [     0.000000000000000,     0.000000000000000,     5.906882041566931 ], # c
+]
+[[unitcell.points]]  # 1
+symbol = "Ti"
+coordinates = [  0.000000000000000,  0.000000000000000,  0.000000000000000 ]
+[[unitcell.points]]  # 2
+symbol = "Ti"
+coordinates = [  0.000000000000000,  0.500000000000000,  0.500000000000000 ]
+[[unitcell.points]]  # 3
+symbol = "Ti"
+coordinates = [  0.500000000000000,  0.000000000000000,  0.500000000000000 ]
+[[unitcell.points]]  # 4
+symbol = "Ti"
+coordinates = [  0.500000000000000,  0.500000000000000,  0.000000000000000 ]
+[[unitcell.points]]  # 5
+symbol = "Sn"
+coordinates = [  0.500000000000000,  0.500000000000000,  0.500000000000000 ]
+[[unitcell.points]]  # 6
+symbol = "Sn"
+coordinates = [  0.500000000000000,  0.000000000000000,  0.000000000000000 ]
+[[unitcell.points]]  # 7
+symbol = "Sn"
+coordinates = [  0.000000000000000,  0.500000000000000,  0.000000000000000 ]
+[[unitcell.points]]  # 8
+symbol = "Sn"
+coordinates = [  0.000000000000000,  0.000000000000000,  0.500000000000000 ]
+[[unitcell.points]]  # 9
+symbol = "Ni"
+coordinates = [  0.250000000000000,  0.250000000000000,  0.250000000000000 ]
+[[unitcell.points]]  # 10
+symbol = "Ni"
+coordinates = [  0.250000000000000,  0.750000000000000,  0.750000000000000 ]
+[[unitcell.points]]  # 11
+symbol = "Ni"
+coordinates = [  0.750000000000000,  0.250000000000000,  0.750000000000000 ]
+[[unitcell.points]]  # 12
+symbol = "Ni"
+coordinates = [  0.750000000000000,  0.750000000000000,  0.250000000000000 ]
+[primitive_cell]
+lattice = [
+  [     0.000000000000000,     2.953441020783465,     2.953441020783465 ], # a
+  [     2.953441020783465,     0.000000000000000,     2.953441020783465 ], # b
+  [     2.953441020783465,     2.953441020783465,     0.000000000000000 ], # c
+]
+[[primitive_cell.points]]  # 1
+symbol = "Ti"
+coordinates = [  0.000000000000000,  0.000000000000000,  0.000000000000000 ]
+[[primitive_cell.points]]  # 2
+symbol = "Sn"
+coordinates = [  0.500000000000000,  0.500000000000000,  0.500000000000000 ]
+[[primitive_cell.points]]  # 3
+symbol = "Ni"
+coordinates = [  0.250000000000000,  0.250000000000000,  0.250000000000000 ]
+
    +
    +

    fft_mesh is calculated from encut value in the [vasp.selfenergy.incar] section.

    +

    Change directory to relax.

    +
    % velph relax generate
+% cd relax/iter1
+% qsub _job.sh
+
    +
    +

    Structure optimization is done until stress becomes less than 0.1kB (0.01GPa). +Go back to the top directory and start supercell calculation.

    +
    % velph init --template-toml velph-tmpl.toml `ls relax/relax/iter*/CONTCAR|tail -n 1` calc
+Crystal structure file: "relax/relax/iter2/CONTCAR".
+Velph template file: "velph-tmpl.toml".
+Read crystal structure file "relax/relax/iter2/CONTCAR".
+Read velph template file "velph-tmpl.toml".
+Following options were found in "velph-tmpl.toml":
+  kspacing = "0.1"
+  kspacing_dense = "0.2"
+  max_num_atoms = "100"
+The command options were prefered to [init.options] in "velph-tmpl.toml".
+Found a primitive cell whose transformation matrix is
+  [ 0.000  0.500  0.500]
+  [ 0.500  0.000  0.500]
+  [ 0.500  0.500  0.000]
+Supercell is generated with respect to the cell below.
+--------------------------------------------------------------------------------
+lattice:
+- [     5.949975748250650,     0.000000000000000,     0.000000000000000 ] # a
+- [     0.000000000000000,     5.949975748250650,    -0.000000000000000 ] # b
+- [     0.000000000000000,     0.000000000000000,     5.949975748250650 ] # c
+points:
+- symbol: Ti # 1
+  coordinates: [  0.000000000000000,  0.000000000000000,  0.000000000000000 ]
+  mass: 47.867000
+- symbol: Ti # 2
+  coordinates: [  0.000000000000000,  0.500000000000000,  0.500000000000000 ]
+  mass: 47.867000
+- symbol: Ti # 3
+  coordinates: [  0.500000000000000,  0.000000000000000,  0.500000000000000 ]
+  mass: 47.867000
+- symbol: Ti # 4
+  coordinates: [  0.500000000000000,  0.500000000000000,  0.000000000000000 ]
+  mass: 47.867000
+- symbol: Sn # 5
+  coordinates: [  0.500000000000000,  0.500000000000000,  0.500000000000000 ]
+  mass: 118.710000
+- symbol: Sn # 6
+  coordinates: [  0.500000000000000,  0.000000000000000,  0.000000000000000 ]
+  mass: 118.710000
+- symbol: Sn # 7
+  coordinates: [  0.000000000000000,  0.500000000000000,  0.000000000000000 ]
+  mass: 118.710000
+- symbol: Sn # 8
+  coordinates: [  0.000000000000000,  0.000000000000000,  0.500000000000000 ]
+  mass: 118.710000
+- symbol: Ni # 9
+  coordinates: [  0.250000000000000,  0.250000000000000,  0.250000000000000 ]
+  mass: 58.693400
+- symbol: Ni # 10
+  coordinates: [  0.250000000000000,  0.750000000000000,  0.750000000000000 ]
+  mass: 58.693400
+- symbol: Ni # 11
+  coordinates: [  0.750000000000000,  0.250000000000000,  0.750000000000000 ]
+  mass: 58.693400
+- symbol: Ni # 12
+  coordinates: [  0.750000000000000,  0.750000000000000,  0.250000000000000 ]
+  mass: 58.693400
+--------------------------------------------------------------------------------
+[vasp.incar] (basic INCAR settings)
+  ismear = 0
+  sigma = 0.01
+  ediff = 1e-08
+  encut = 520
+  prec = accurate
+  lreal = False
+  lwave = False
+  lcharg = False
+  ncore = 4
+[phelel]
+  supercell_dimension: [2 2 2]
+[vasp.*.kpoints.mesh] (*kspacing=0.1)
+  selfenergy: [18 18 18]*
+  el_bands: [18 18 18]*
+  phelel: [5 5 5]*
+  relax: [11 11 11]*
+  nac: [18 18 18]*
+[vasp.*.kpoints_dense.mesh] (*kspacing_dense=0.2)
+  selfenergy: [9 9 9]*
+  el_bands: [9 9 9]*
+Created new folder "calc".
+Initial settings were written to "calc/velph.toml".
+Found "POTCAR".
+  PAW_PBE Ti_sv 26Sep2005
+  PAW_PBE Sn_d 06Sep2000
+  PAW_PBE Ni 02Aug2007
+  Max ENMAX in "POTCAR" is 274.61.
+"POTCAR" was copied to "calc/POTCAR".
+
    +
    +

    Change directory to calc.

    +
    % cd calc
+
    +
    +

    velph.toml,

    +
    [phelel]
+version = "0.6.0"
+supercell_dimension = [2, 2, 2]
+amplitude = 0.03
+diagonal = true
+plusminus = true
+fft_mesh = [32, 32, 32]
+
+[vasp.phelel.incar]
+lwap = true
+isym = 0
+kpar = 2
+ismear = 0
+sigma = 0.01
+ediff = 1e-08
+encut = 520
+prec = "accurate"
+lreal = false
+lwave = false
+lcharg = false
+ncore = 4
+[vasp.phelel.kpoints]
+mesh = [5, 5, 5]
+[vasp.phelel.scheduler]
+pe = "mpi* 48"
+
+# ...
+
+[vasp.nac]
+cell = "primitive"
+[vasp.nac.incar]
+lepsilon = true
+ismear = 0
+sigma = 0.01
+ediff = 1e-08
+encut = 520
+prec = "accurate"
+lreal = false
+lwave = false
+lcharg = false
+[vasp.nac.kpoints]
+mesh = [18, 18, 18]
+
+# ...
+
    +
    +

    NAC and supercell calculations,

    +
    % velph nac generate
+% cd nac; qsub _job.sh; cd ..
+% velph phelel init
+Found "nac" directory. Read NAC params.
+"phelel/phelel_disp.yaml" was generated by phelel.
+VASP input files will be generated by "velph phelel generate".
+% velph supercell generate
+VASP input files were generated in "supercell/disp-000".
+VASP input files were generated in "supercell/disp-001".
+VASP input files were generated in "supercell/disp-002".
+VASP input files were generated in "supercell/disp-003".
+VASP input files were generated in "supercell/disp-004".
+VASP input files were generated in "supercell/disp-005".
+VASP input files were generated in "supercell/disp-006".
+% for i in {000..006};do cd phelel/disp-$i; qsub _job.sh; cd ../..;done
+
    +
    +

    Using the VASP results of the supercell calculations, derivatives of properties +are computed using the phelel code. The results are stored in a newly created +file phelel/phelel_params.hdf5. This process creates only +phelel/phelel_params.hdf5 and is invoked by the following velph command:

    +
    % velph phelel differentiate
+Running finufft (eps=1.000e-06)...
+Running finufft (eps=1.000e-06)...
+Running finufft (eps=1.000e-06)...
+"phelel/phelel_params.hdf5" has been made.
+
    +
    +

    NAC parameters in phelel/phelel_params.hdf5 comes from +phelel/phelel_disp.yaml, i.e.,

    +
      +

    1. NAC parameters are stored in phelel/phelel_disp.yaml when +phelel/phelel_disp.yaml is created by velph phelel init.

      2. +

    2. NAC data in phelel/phelel_disp.yaml are transfered to +phelel/phelel_params.hdf5 by velph phelel differentiate.

      3. +
    +

    Therefore, nac calculation has to exist in the initial step velph phelel init. If the nac calculation is performed after the supercell calculation, +velph phelel init and velph phelel differentiate have to be re-executed to +store the NAC parameters in phelel/phelel_params.hdf5.

    +
    +
    + + +
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    + + + + +
    + + +
    +
    + Contents +
    +
    + +
    + + +
    +
    + +
    + +
    + +

    +By Atsushi Togo +

    + +
    + +
    + + +

    + + © Copyright 2024, Atsushi Togo. +
    + +

    + +
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    + +
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    + + \ No newline at end of file diff --git a/velph-init.html b/velph-init.html new file mode 100644 index 0000000..69bf172 --- /dev/null +++ b/velph-init.html @@ -0,0 +1,629 @@ + + + + + + + + + + + velph init — Phelel v.0.8.0 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    + + + + + + +
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    +

    velph init

    + +
    + +
    +
    + + + + +
    + +
    +

    velph init#

    +

    velph init with command options will generate modified velph.toml from the +template.

    +
    % velph init [OPTIONS] CELL_FILENAME PROJECT_FOLDER
+
    +
    +

    velph init --help shows short documents of the options. Two arguments have to +be specified, POSCAR-format crystal structure and directory name that is created +where velph.toml is stored. The available options are explained below. Some +options can be specified in [init.options] section of the velph-toml template +file (see velph init template).

    +
    +

    velph init options#

    +
    +

    --template-toml#

    +

    Using this option, velph.toml like file is read as the template instead of the +template hard coded in velph code.

    +
    +
    +

    --tolerance#

    +

    This is used for the symmetry check tolerance in Angstrom. Symmetry is searched +always even without --symmetrize.

    +
    +
    +

    --symmetrize#

    +

    By default (no-symmetrize), the input POSCAR-type structure is simply used as +the unit cell. With --symmetrize, input POSCAR-type structure is symmetrized +and standardized conventional unit cell and primitive cell (“unitcell” and +“primitive_cell”, respectively) are written in velph.toml.

    +
    +
    +

    --no-find-primitive#

    +

    By this option, the input POSCAR-type structure is used as the primitive cell +even if it is not a primitive cell.

    +
    +
    +

    --kspacing and --kspacing-dense#

    +

    Sampling k-point meshes are calculated from these values in the similar way to +VASP KSPACING definition by overwriting the template.

    +
    +
    +

    --max-num-atoms#

    +

    Supercell shape is determined so that its number of atoms is equal or less than +this number respecting the crystallographic point group.

    +
    +
    +

    --phonopy-max-num-atoms and --phono3py-max-num-atoms#

    +

    Supercell shapes for phonopy and phono3py are determined in the same manner as +--max-num-atoms.

    +
    +
    +

    --cell-for-relax#

    +

    This chooses unit cell or primitive cell for structure optimization (relax). +The default is unitcell. Specify primitive to use primitive cell.

    +
    +
    +

    --cell-for-nac#

    +

    This chooses unit cell or primitive cell for NAC calculation (nac). The +default is primitive. Specify primitive to use primitive cell.

    +
    +
    +

    --primitive-cell-choice#

    +

    Primitive cell choice, “standardized” (default) or “reduced”.

    +
    +
    +

    --use-grg#

    +

    Use generalized regular grid.

    +
    +
    +

    --amplitude#

    +

    Distance of displacements in Angstrom.

    +
    +
    +

    --magmom#

    +

    String corresponding to INCAR MAGMOM tag value for unit cell, e.g., “24*1” or “0 +0 1”. This is similar to MAGMOM tag in phonopy, see +https://phonopy.github.io/phonopy/setting-tags.html#magmom. In velph, the +asterisk symbol (*) is supported.

    +
    +
    +
    +

    velph init template#

    +

    velph init is the command to prepare velph.toml. Without specifying a +velph-toml-template, the default template is used. Custom template can be +specified as follows:

    +
    % velph init [OPTIONS] CELL_FILENAME PROJECT_FOLDER --template-toml velph-tmpl.toml
+
    +
    +

    The velph-tmpl.toml (arbitrary file name) is almost like the velph.toml +file. It means that the velph-tmpl.toml may be created modifying +velph.toml. The sections that exist only in the velph-tmpl.toml but not in +velph.toml is [init.options]. This can be used as alternatives of command +options of velph-init, e.g.,

    +
    [init.options]
+kspacing = 0.2
+kspacing_dense = 0.1
+max_num_atoms = 120
+
    +
    +

    These [init.options] keywords can be found along with the list of the command +options by

    +
    % velph init --help
+
    +
    +
    +
    +

    Settings in sections of velph.toml#

    +

    Note that the same can be applied to velph-tmpl.toml.

    +
    +

    Default INCAR settings#

    +

    The default INCAR settins are written in [vasp.incar]. These settings are +overwritten by [vasp.CALC_TYPE.incar] (CALC_TYPE can be phelel, relax, +nac, transport, phono3py, phono3py.phonon, etc).

    +
    +
    +

    Scheduler settings#

    +

    The parameters used for generating the job submission script are specified as +strings in [scheduler]. If [vasp.CALC_TYPE.scheduler] is +specified, [scheduler] settings are overwritten by the settings for +[vasp.CALC_TYPE]. The content in this section operates through Python string +formatting, using +replacement fields named after keyword arguments. Each parameter line in the +[scheduler] section is treated as a keyword argument, which is then inserted +into the string format.

    +

    In the [scheduler] section, the parameters scheduler_name and +scheduler_template have special roles:

    +
      +

    • scheduler_name: Specifies the template type, with options slurm, sge, or +custom. For slurm and sge, the template string (i.e., +scheduler_template) is +hard-coded. +If custom is selected, the string provided by scheduler_template is used, +into which the parameters are inserted.

      • +

    • scheduler_template: The string template where parameters defined in this +section are inserted.

      • +
    +

    An example is shown below.

    +
    [scheduler]
+scheduler_name = "sge"
+job_name = "PbTe"
+mpirun_command = "mpirun"
+vasp_binary = "/usr/local/cluster-1/bin/vasp_std"
+pe = "vienna 32"
+prepend_text = '''
+source /opt/intel/oneapi/setvars.sh --config="/home/togo/.oneapi-config"
+'''
+
+...
+[vasp.phelel.scheduler]
+pe = "paris 24"
+
+...
+[vasp.phonopy.scheduler]
+scheduler_template = '''#!/bin/bash
+#QSUB2 core 192
+#QSUB2 mpi 192
+#QSUB2 smp 1
+#QSUB2 wtime 48:00:00
+#PBS -N {job_name}
+cd $PBS_O_WORKDIR
+
+{prepend_text}
+{mpirun_command} {vasp_binary} | tee vasp_output
+{append_text}
+'''
+job_name = "PbTe"
+mpirun_command = "mpijob"
+vasp_binary = "/usr/local/cluster-2/bin/vasp_std"
+prepend_text = '''
+. /etc/profile.d/modules.sh
+module load inteloneapi22u3
+'''
+append_text = ""
+
    +
    +
    +
    +
    + + +
    + + + + + + + + +
    + + + + + + + +
    +
    + +
    + +
    + +

    +By Atsushi Togo +

    + +
    + +
    + + +

    + + © Copyright 2024, Atsushi Togo. +
    + +

    + +
    + +
    + +
    + +
    + +
    + +
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    + + +
    +
    +
    + + + + + +
    +
    + + \ No newline at end of file diff --git a/velph-subcommands.html b/velph-subcommands.html new file mode 100644 index 0000000..d73d795 --- /dev/null +++ b/velph-subcommands.html @@ -0,0 +1,564 @@ + + + + + + + + + + + velph subcommands — Phelel v.0.8.0 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    + + + + + + +
    + + + Ctrl+K +
    +     + +
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    +

    velph subcommands

    + +
    + +
    +
    + + + + +
    + +
    +

    velph subcommands#

    +
    +

    velph phelel#

    +

    This command calculates the derivatives of local potentials and PAW strengths +with respect to displacement, performing similar operations as steps 1 and 3 +carried out by the phelel command in the workflow.

    +
    +

    velph phelel init#

    +
    +
    +

    velph phelel generate#

    +
    +
    +

    velph phelel differentiate#

    +
    +
    +

    velph phelel phonopy#

    +
    +
    +
    +

    velph transport#

    +
    +

    velph transport generate#

    +
    +
    +

    velph transport plot#

    +
    +
    +
    +

    velph relax#

    +
    +

    velph relax generate#

    +
    +
    +
    +

    velph nac#

    +
    +

    velph nac generate#

    +
    +
    +
    +

    velph el_bands#

    +
    +

    velph el_bands generate#

    +
    +
    +

    velph el_bands plot#

    +
    +
    +
    +

    velph ph_bands#

    +
    +

    velph ph_bands generate#

    +
    +
    +

    velph ph_bands plot#

    +
    +
    +
    +

    velph phono3py#

    +
    +

    velph phono3py init#

    +
    +
    +

    velph phono3py generate#

    +
    +
    +
    +

    velph phonopy#

    +
    +

    velph phonopy init#

    +
    +
    +

    velph phonopy generate#

    +
    +
    +
    + + +
    + + + + + + + + +
    + + + + + + + +
    +
    + +
    + +
    + +

    +By Atsushi Togo +

    + +
    + +
    + + +

    + + © Copyright 2024, Atsushi Togo. +
    + +

    + +
    + +
    + +
    + +
    + +
    + +
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    + + +
    +
    +
    + + + + + +
    +
    + + \ No newline at end of file diff --git a/workflow.html b/workflow.html index 65a73bd..ccd8e82 100644 --- a/workflow.html +++ b/workflow.html @@ -142,6 +142,9 @@
  • Workflow of el-ph calculation
  • phelel command
  • velph command
    • +
  • velph init
    • +
  • velph subcommands
    • +
  • velph example
  • Change Log