def wave(**kwargs):
"""Extract wavefunction coefficients from a WAVECAR"""
from pymatgen.io.vasp import BSVasprun
from amset.constants import defaults
from amset.electronic_structure.common import (
get_band_structure,
get_ibands,
get_zero_weighted_kpoint_indices,
)
from amset.tools.common import echo_ibands
from amset.wavefunction.io import write_coefficients
output = kwargs.pop("output")
planewave_cutoff = kwargs.pop("planewave_cutoff")
pawpyseed = kwargs.pop("pawpyseed")
energy_cutoff = kwargs.pop("energy_cutoff")
if not energy_cutoff:
energy_cutoff = defaults["energy_cutoff"]
if kwargs["directory"]:
vasprun_file = Path(kwargs["directory"]) / "vasprun.xml"
else:
vasprun_file = kwargs["vasprun"]
try:
vr = BSVasprun(vasprun_file)
except FileNotFoundError:
vr = BSVasprun(str(vasprun_file) + ".gz")
zwk_mode = kwargs.pop("zero_weighted_kpoints")
if not zwk_mode:
zwk_mode = defaults["zero_weighted_kpoints"]
bs = get_band_structure(vr, zero_weighted=zwk_mode)
if "bands" in kwargs and kwargs["bands"] is not None:
ibands = parse_ibands(kwargs["bands"])
else:
ibands = get_ibands(energy_cutoff, bs)
ikpoints = get_zero_weighted_kpoint_indices(vr, zwk_mode)
click.echo("******* Getting wavefunction coefficients *******\n")
echo_ibands(ibands, bs.is_spin_polarized)
click.echo("")
if pawpyseed:
coeffs, gpoints, kpoints = _wavefunction_pawpy(bs, ibands,
planewave_cutoff,
ikpoints, **kwargs)
else:
coeffs, gpoints = _wavefunction_vasp(ibands, planewave_cutoff,
ikpoints, **kwargs)
kpoints = np.array([k.frac_coords for k in bs.kpoints])
structure = vr.final_structure
click.echo("Writing coefficients to {}".format(output))
write_coefficients(coeffs, gpoints, kpoints, structure, filename=output)
def parse_calculation(folder,
zero_weighted_kpoints=defaults["zero_weighted_kpoints"]):
vr = Vasprun(get_gzipped_file("vasprun.xml", folder))
out = Outcar(get_gzipped_file("OUTCAR", folder))
bs = get_band_structure(vr, zero_weighted=zero_weighted_kpoints)
reference_level = get_reference_energy(bs, out)
return {"reference": reference_level, "bandstructure": bs}
def from_vasprun(cls,
vasprun,
zero_weighted_kpoints=defaults["zero_weighted_kpoints"],
**kwargs):
from pymatgen.io.vasp import Vasprun
if isinstance(vasprun, Path):
vasprun = vasprun.as_posix()
if isinstance(vasprun, str):
vasprun_gz = vasprun + ".gz"
if Path(vasprun).exists():
vasprun = Vasprun(vasprun)
elif Path(vasprun_gz).exists():
vasprun = Vasprun(vasprun_gz)
bandstructure = get_band_structure(vasprun,
zero_weighted=zero_weighted_kpoints)
nelect = vasprun.parameters["NELECT"]
soc = vasprun.parameters["LSORBIT"]
return cls(bandstructure, nelect, soc=soc, **kwargs)
def from_vasprun(vasprun: Union[str, Path, Vasprun],
settings: Dict[str, Any]) -> "Runner":
"""Initialise an AmsetRunner from a Vasprun.
The nelect and soc options will be determined from the Vasprun
automatically.
Args:
vasprun: Path to a vasprun or a Vasprun pymatgen object.
settings: AMSET settings.
Returns:
A Runner object that can be used to calculate transport properties.
"""
if not isinstance(vasprun, Vasprun):
vasprun = Vasprun(vasprun, parse_projected_eigen=True)
zwk_option = settings.get("zero_weighted_kpoints", "keep")
band_structure = get_band_structure(vasprun, zero_weighted=zwk_option)
nelect = vasprun.parameters["NELECT"]
settings["soc"] = vasprun.parameters["LSORBIT"]
return Runner(band_structure, nelect, settings)