def make_parchg_dir(args):
os.chdir(args.dir)
if is_file("WAVECAR") is False:
raise FileNotFoundError("WAVECAR does not exist or is empty.")
try:
calc_results: CalcResults = loadfn("calc_results.json")
except FileNotFoundError:
logger.info("Need to create calc_results.json beforehand.")
raise
calc_results.show_convergence_warning()
# Increment index by 1 as VASP band index begins from 1.
incar = ViseIncar.from_file("INCAR")
band_edge_states = loadfn("band_edge_states.json")
iband = [i + 1 for i in band_edge_states.band_indices_from_vbm_to_cbm]
incar.update({"LPARD": True, "LSEPB": True, "KPAR": 1, "IBAND": iband})
parchg = Path("parchg")
parchg.mkdir()
os.chdir("parchg")
incar.write_file("INCAR")
FileLink(Path("../WAVECAR")).transfer(Path.cwd())
FileLink(Path("../POSCAR")).transfer(Path.cwd())
FileLink(Path("../POTCAR")).transfer(Path.cwd())
FileLink(Path("../KPOINTS")).transfer(Path.cwd())
os.chdir("..")
def test_make_parchg_dir(tmpdir, mocker):
print(tmpdir)
tmpdir.chdir()
Path("WAVECAR").touch()
Path("INCAR").write_text("ALGO = Normal")
Path("POSCAR").write_text("a")
Path("POTCAR").write_text("b")
Path("KPOINTS").write_text("c")
band_edge_states = mocker.Mock(spec=BandEdgeStates, autospec=True)
band_edge_states.band_indices_from_vbm_to_cbm = [1, 2]
calc_results = mocker.Mock(spec=CalcResults, autospec=True)
def side_effect(key):
if str(key) == "band_edge_states.json":
return band_edge_states
elif str(key) == "calc_results.json":
return calc_results
else:
raise ValueError
mock_loadfn = mocker.patch(f"{_filepath}.loadfn", side_effect=side_effect)
args = Namespace(dir=Path(tmpdir))
with pytest.raises(FileNotFoundError):
make_parchg_dir(args)
Path("WAVECAR").write_text("d")
make_parchg_dir(args)
assert Path("parchg/POSCAR").read_text() == "a"
assert Path("parchg/POTCAR").read_text() == "b"
assert Path("parchg/KPOINTS").read_text() == "c"
assert Path("parchg/WAVECAR").read_text() == "d"
actual = ViseIncar.from_file("parchg/INCAR")
expected = {
"ALGO": "Normal",
"LPARD": True,
"LSEPB": True,
"KPAR": 1,
"IBAND": "2 3"
}
assert actual == expected
def incar(self) -> ViseIncar:
incar = ViseIncar.from_dict(self._incar_settings)
return incar
def from_prev_calc(cls,
dirname: str,
task: Optional[Task] = None,
xc: Optional[Xc] = None,
json_filename: str = "vise.json",
parse_calc_results: bool = True,
parse_incar: bool = True,
sort_structure: bool = True,
standardize_structure: bool = False,
files_to_transfer: Optional[dict] = None,
user_incar_settings: Optional[dict] = None,
contcar_filename: str = "CONTCAR",
**kwargs) -> "ViseInputSet":
"""Constructor based on the previous calculations.
If the task and/or xc are not set, the previous ones are assumed.
Args:
dirname (str):
Directory name to be parsed.
xc (Xc):
Exchange-correlation (xc) defined in Xc.
task (Task):
Task defined in Task.
json_filename (str):
Json filename including ViseInputSet data.
parse_calc_results (bool):
Whether to parse the previous calculation results for band
edges, magnetization.
parse_incar (bool):
Whether to parse the previous INCAR files, which could include
other options that are not determined in vise.
sort_structure (bool):
Whether to sort the elements using get_sorted_structure method
of Structure class in pymatgen.
standardize_structure (bool):
Whether to convert the structure to a standardized primitive.
files_to_transfer (dict):
Keys are file names to be transferred in the directory.
Values mean the transfer modes, where there are three modes,
"c": copy file, "m": move file, "l": make symbolic link
e.g., {"CHGCAR": "c", "WAVECAR": "l", ..}
user_incar_settings (dict):
User INCAR settings.
e.g., {"NSW": 100, "LWAVE": True, "LASPH": "A", ..}
contcar_filename (str):
CONTCAR type filename. Used if the user change the name.
kwargs:
Other OPTION arguments.
Return:
ViseInputSet class object.
"""
kwargs = kwargs or {}
kwargs["sort_structure"] = sort_structure
kwargs["standardize_structure"] = standardize_structure
path = Path(dirname)
input_set = ViseInputSet.load_json(path / json_filename)
if parse_calc_results:
vasprun, outcar = get_vasprun_outcar(dirname)
structure = get_structure_from_prev_run(vasprun, outcar)
gap_properties = band_gap_properties(vasprun)
if gap_properties:
_, vbm, cbm = gap_properties
kwargs["vbm_cbm"] = [vbm["energy"], cbm["energy"]]
if "magmom" in structure.site_properties.keys():
abs_max_mag = abs(
max(structure.site_properties["magmom"], key=abs))
else:
abs_max_mag = 0
if vasprun.is_spin and abs_max_mag > 0.05:
kwargs["is_magnetization"] = True
else:
contcar = path / contcar_filename
poscar = path / "POSCAR"
if contcar.is_file and os.stat(contcar).st_size != 0:
logger.info(f"{contcar} is parsed for structure.")
structure = Structure.from_file(contcar)
elif poscar.is_file and os.stat(poscar).st_size != 0:
logger.warning(f"{poscar} is parsed for structure.")
structure = Structure.from_file(poscar)
else:
raise FileNotFoundError("CONTCAR or POSCAR does not exist.")
if parse_incar:
input_set.incar_settings = ViseIncar.from_file(path / "INCAR")
if files_to_transfer:
abs_files_to_transfer = {}
for filename, value in files_to_transfer.items():
f = path / filename
if not f.is_file():
logger.warning(f"{f} does not exist.")
elif os.stat(f).st_size == 0:
logger.warning(f"{f} is empty.")
elif value[0].lower() not in ["l", "c", "m"]:
logger.warning(
f"{value} option for {filename} is invalid.")
else:
abs_files_to_transfer[str(f)] = value[0].lower()
files_to_transfer = abs_files_to_transfer
return cls.make_input(structure=structure,
task=task or input_set.task,
xc=xc or input_set.xc,
prev_set=input_set,
abs_files_to_transfer=files_to_transfer,
user_incar_settings=user_incar_settings,
**kwargs)
def incar(self):
print(self.incar_settings)
incar = ViseIncar.from_dict(self.incar_settings)
return incar