def parse_args_main_util(args):
parser = argparse.ArgumentParser(epilog=epilog,
description=description +
"""
This command provide some utilities related to the VASP calculations""")
subparsers = parser.add_subparsers()
dirs_parser = add_sub_parser(argparse, name="dirs")
unitcell_parser = add_sub_parser(argparse, name="unitcell")
si_parser = add_sub_parser(argparse, name="supercell_info")
no_calc_results = add_sub_parser(argparse, name="no_calc_results_check")
# -- composition energies from mp ------------------------------------------
parser_comp_es_from_mp = subparsers.add_parser(
name="composition_energies_from_mp",
description="Retrieve composition energies from Materials Project.",
formatter_class=argparse.ArgumentDefaultsHelpFormatter,
aliases=['cefm'])
parser_comp_es_from_mp.add_argument(
"-e",
"--elements",
type=str,
nargs="+",
help="Element names considered in chemical potential diagram. Used for "
"creating the diagram from mp data with atom energy alignment.")
parser_comp_es_from_mp.add_argument(
"-a",
"--atom_energy_yaml",
type=str,
help="Yaml file storing atom energies for energy alignment.")
parser_comp_es_from_mp.set_defaults(func=composition_energies_from_mp)
# -- add interstitials from local extrema ----------------------------------
parser_ai = subparsers.add_parser(
name="add_interstitials_from_local_extrema",
description="Add interstitials via volumetric_data_local_extrema.json "
"file.",
parents=[si_parser],
formatter_class=argparse.ArgumentDefaultsHelpFormatter,
aliases=['ai'])
parser_ai.add_argument(
"--local_extrema",
required=True,
type=loadfn,
help="volumetric_data_local_extrema.json file name.")
parser_ai.add_argument(
"-i",
"--indices",
required=True,
type=int,
nargs="+",
help="Indices starting from 1 to be added to SupercellInfo.")
parser_ai.set_defaults(func=add_interstitials_from_local_extrema)
# -- make defect vesta file ------------------------------------------------
parser_dvf = subparsers.add_parser(
name="defect_vesta_file",
description="Generate VESTA file for visualizing defect structure.",
parents=[dirs_parser],
formatter_class=argparse.ArgumentDefaultsHelpFormatter,
aliases=['dvf'])
parser_dvf.add_argument(
"--cutoff",
type=float,
default=defaults.show_structure_cutoff,
help="Cutoff radius in which atoms are shown in VESTA files.")
parser_dvf.add_argument(
"--min_displace_w_arrows",
type=float,
default=0.1,
help="Minimum displacement that shows arrows to visualize "
"displacements.")
parser_dvf.add_argument("--arrow_factor",
type=float,
default=3.0,
help="Factor to enhance the displacements.")
parser_dvf.add_argument("--title",
type=str,
help="Title to be shown in VESTA files.")
parser_dvf.set_defaults(func=make_defect_vesta_file)
# -- gkfo correction -------------------------------------------------------
parser_gkfo = subparsers.add_parser(
name="gkfo",
description="Generate GKFO correction files.",
parents=[unitcell_parser],
formatter_class=argparse.ArgumentDefaultsHelpFormatter,
aliases=['gkfo'])
parser_gkfo.add_argument(
"-iefnv",
"--initial_efnv_correction",
required=True,
type=loadfn,
help="Path to the initial efnv correction.json file.")
parser_gkfo.add_argument(
"-icr",
"--initial_calc_results",
required=True,
type=loadfn,
help="Path to the initial calc_results.json file.")
parser_gkfo.add_argument("-fcr",
"--final_calc_results",
required=True,
type=loadfn,
help="Path to the final calc_results.json file.")
parser_gkfo.add_argument(
"-cd",
"--charge_diff",
required=True,
type=int,
help="Charge difference of final state from initial state.")
parser_gkfo.set_defaults(func=make_gkfo_correction_from_vasp)
# ------------------------------------------------------------------------
return parser.parse_args(args)
def parse_args_main_vasp_util(args):
parser = argparse.ArgumentParser(epilog=epilog,
description=description + """
This command provides some utilities related to the VASP calculations""")
subparsers = parser.add_subparsers()
dir_parser = add_sub_parser(argparse, name="dir")
# -- calc charge state -----------------------------------------------------
parser_calc_charge_state = subparsers.add_parser(
name="calc_charge_state",
description="Calc defect charge states from INCAR, POSCAR and POTCAR"
"files.",
parents=[dir_parser],
formatter_class=argparse.ArgumentDefaultsHelpFormatter,
aliases=['ccs'])
parser_calc_charge_state.set_defaults(func=calc_charge_state)
# -- make defect entry -----------------------------------------------------
parser_make_defect_entry = subparsers.add_parser(
name="make_defect_entry",
description="Make defect entry from INCAR, POSCAR and POTCAR"
"files.",
parents=[dir_parser],
formatter_class=argparse.ArgumentDefaultsHelpFormatter,
aliases=['de'])
parser_make_defect_entry.add_argument(
"-n",
"--name",
type=str,
required=True,
help="Name used for plotting energy diagram.")
parser_make_defect_entry.add_argument(
"-p",
"--perfect",
type=Structure.from_file,
required=True,
help="Perfect supercell POSCAR file name.")
parser_make_defect_entry.set_defaults(func=make_defect_entry_main)
# -- make parchg dir -----------------------------------------------
parser_make_parchg_dir = subparsers.add_parser(
name="parchg_dir",
description="Make parchg directory containing a set of VASP files "
"required for generating PARCHG files.",
parents=[dir_parser],
formatter_class=argparse.ArgumentDefaultsHelpFormatter,
aliases=['pd'])
parser_make_parchg_dir.set_defaults(func=make_parchg_dir)
# -- make refine defect poscar ---------------------------------------------
parser_make_refine_defect_poscar = subparsers.add_parser(
name="refine_defect_poscar",
description="Refine defect structure POSCAR.",
formatter_class=argparse.ArgumentDefaultsHelpFormatter,
aliases=['rdp'])
parser_make_refine_defect_poscar.add_argument("-p",
"--poscar",
dest="structure",
type=Structure.from_file)
parser_make_refine_defect_poscar.add_argument("-d",
"--defect_entry",
type=loadfn)
parser_make_refine_defect_poscar.add_argument("-n",
"--poscar_name",
type=str)
parser_make_refine_defect_poscar.set_defaults(
func=make_refine_defect_poscar)
# -- calc grids ------------------------------------------------------------
parser_calc_grids = subparsers.add_parser(
name="calc_grids",
description="Calc Grids.",
formatter_class=argparse.ArgumentDefaultsHelpFormatter,
aliases=['cg'])
parser_calc_grids.add_argument("-c",
"--chgcar",
type=Chgcar.from_file,
required=True)
parser_calc_grids.set_defaults(func=calc_grids)
# -- calc defect charge info -----------------------------------------------
parser_calc_def_charge_info = subparsers.add_parser(
name="calc_defect_charge_info",
description="Calc defect charge info.",
formatter_class=argparse.ArgumentDefaultsHelpFormatter,
aliases=['cdc'])
parser_calc_def_charge_info.add_argument("-p",
"--parchgs",
type=str,
nargs="+",
required=True,
help="PARCHG files.")
parser_calc_def_charge_info.add_argument("-b",
"--bin_interval",
type=float,
default=0.2)
parser_calc_def_charge_info.add_argument("-g",
"--grids",
type=Grids.from_file,
required=True)
parser_calc_def_charge_info.set_defaults(func=make_defect_charge_info_main)
return parser.parse_args(args)
def parse_args_main_vasp(args):
parser = argparse.ArgumentParser(epilog=epilog,
description=description + """
The command is used for creating and analyzing VASP input and output
files.""")
subparsers = parser.add_subparsers()
dirs_parser = add_sub_parser(argparse, name="dirs")
perfect_band_edge_parser = add_sub_parser(argparse,
name="perfect_band_edge_state")
# -- unitcell ------------------------------------------------
parser_unitcell = subparsers.add_parser(
name="unitcell",
description="Parse unitcell info from vasp output files and create "
"unitcell.yaml.",
formatter_class=argparse.ArgumentDefaultsHelpFormatter,
aliases=['u'])
parser_unitcell.add_argument(
"-vb", "--vasprun_band", required=True, type=Vasprun,
help="vasprun.xml file of band structure calculation.")
parser_unitcell.add_argument(
"-ob", "--outcar_band", required=True, type=Outcar,
help="OUTCAR file of band structure calculation.")
parser_unitcell.add_argument(
"-odc", "--outcar_dielectric_clamped", required=True, type=Outcar,
help="OUTCAR file of ion-clamped dielectric constant calculation.")
parser_unitcell.add_argument(
"-odi", "--outcar_dielectric_ionic", required=True, type=Outcar,
help="OUTCAR file for calculating dielectric constant of ionic "
"contribution.")
parser_unitcell.add_argument(
"-n", "--name", type=str,
help="System name used for plotting defect formation energies.")
parser_unitcell.set_defaults(func=make_unitcell)
# -- make_poscars ------------------------------------------------
parser_make_poscars = subparsers.add_parser(
name="make_poscars",
description="Make directories and poscar files in these that are "
"retrieved via the Materials Project API.",
formatter_class=argparse.ArgumentDefaultsHelpFormatter,
aliases=['mp'])
parser_make_poscars.add_argument(
"-e", "--elements", required=True, nargs="+", type=str,
help="Element names involved. ")
parser_make_poscars.add_argument(
"--e_above_hull", default=defaults.e_above_hull, type=float,
help="Allowed energy above hull in eV/atom.")
parser_make_poscars.set_defaults(func=make_competing_phase_dirs)
# -- make_composition_energies ---------------------------------------------
parser_make_composition_energies = subparsers.add_parser(
name="make_composition_energies",
description="Make composition energies from the directories in which "
"competing phases are calculated. ",
formatter_class=argparse.ArgumentDefaultsHelpFormatter,
parents=[dirs_parser],
aliases=['mce'])
parser_make_composition_energies.add_argument(
"-y", "--yaml_file", type=str,
help="composition_energies.yaml to be overwritten.")
parser_make_composition_energies.set_defaults(
func=make_composition_energies)
# -- make_local_extrema ----------------------------------------------------
parser_make_local_extrema = subparsers.add_parser(
name="local_extrema",
description="Make local volumetric_data_local_extrema.json file.",
formatter_class=argparse.ArgumentDefaultsHelpFormatter,
aliases=['le'])
parser_make_local_extrema.add_argument(
"-v", "--volumetric_data", type=Chgcar.from_file, required=True,
nargs="+",
help="File names such as CHGCAR or LOCPOT. When multiple files are "
"provided, the summed data (e.g., AECCAR0 + AECCAR2) will be "
"parsed.")
parser_make_local_extrema.add_argument(
"--find_max", dest="find_max", action="store_true",
help="Set when local maxima are searched instead of local minima.")
parser_make_local_extrema.add_argument(
"-i", "--info", type=str,
help="Information related to the parsed volumetric data written"
"as the name in volumetric_data_local_extrema.json.")
parser_make_local_extrema.add_argument(
"--threshold_frac", default=None, type=float,
help="""Optional fraction of extrema shown, which returns
`threshold_frac * tot_num_extrema` extrema fractional coordinates
based on highest/lowest intensity.
For example, there are 3 extrema with 0.1, 0.2, 0.3, and if
threshold_frac is set to 0.5, then those with 0.2 and 0.3 are shown
as the threshold is now 0.3 * 0.5 = 0.15.
It takes from 0 to 1, and default is 1.""")
parser_make_local_extrema.add_argument(
"--threshold_abs", default=None, type=float,
help="""Optional filter. When searching for local
minima, intensity <= threshold_abs returns; when searching for
local maxima, intensity >= threshold_abs returns.
Caveat: threshold_abs and threshold_frac should be set exclusively.""")
parser_make_local_extrema.add_argument(
"--min_dist", type=float, metavar="Angstrom", default=0.5,
help="""Used to remove the predicted sites that are too close to
*existing atoms* in the structure. The minimum distance that a vertex
needs to be from existing atoms. Set 0 when switch off this flag.""")
parser_make_local_extrema.add_argument(
"--tol", type=float, metavar="Angstrom", default=0.5,
help="""Group interstitials that are too close together using a tol.
Set 0 when switch off this flag.""")
parser_make_local_extrema.add_argument(
"--radius", type=float, default=0.4,
help="Radius of sphere around each site to evaluate the average "
"quantity.")
parser_make_local_extrema.set_defaults(func=make_local_extrema)
# -- defect_entries ------------------------------------------------
parser_defect_entries = subparsers.add_parser(
name="defect_entries",
description="Make POSCAR files and defect entries in defect "
"directories",
formatter_class=argparse.ArgumentDefaultsHelpFormatter,
aliases=['de'])
parser_defect_entries.set_defaults(func=make_defect_entries)
# -- calc_results ------------------------------------------------
parser_calc_results = subparsers.add_parser(
name="calc_results",
description="Generate calc_results.json files. "
"Run after VASP calculations.",
parents=[dirs_parser],
formatter_class=argparse.ArgumentDefaultsHelpFormatter,
aliases=['cr'])
parser_calc_results.set_defaults(func=make_calc_results)
# -- perfect band edge state ----------------------------------------------
parser_perf_band_edge_state = subparsers.add_parser(
name="perfect_band_edge_state",
description="Generate band_edge_orbital_infos.json and "
"eigenvalues.pdf.",
formatter_class=argparse.ArgumentDefaultsHelpFormatter,
aliases=['pbes'])
parser_perf_band_edge_state.add_argument(
"-d", "--dir", type=Path,
help="Directory path to the perfect supercell calculation.")
parser_perf_band_edge_state.set_defaults(func=make_perfect_band_edge_state)
# -- band edge orbital infos ----------------------------------------------
parser_band_edge_orb_infos = subparsers.add_parser(
name="band_edge_orbital_infos",
description="Generate band_edge_orbital_infos.json and "
"eigenvalues.pdf.",
parents=[dirs_parser, perfect_band_edge_parser],
formatter_class=argparse.ArgumentDefaultsHelpFormatter,
aliases=['beoi'])
parser_band_edge_orb_infos.add_argument(
"-y", "--y_range", nargs=2, type=float,
help="Energy range in y-axis for eigenvalue.pdf")
parser_band_edge_orb_infos.set_defaults(
func=make_band_edge_orb_infos_and_eigval_plot)
# ------------------------------------------------------------------------
return parser.parse_args(args)