def test_parse_ibands(value, expected):
if not isinstance(expected, dict):
with expected:
parse_ibands(value)
else:
parsed = parse_ibands(value)
parsed = {s: i.tolist() for s, i in parsed.items()}
assert parsed == expected
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 read(bulk_folder, deformation_folders, **kwargs):
"""
Read deformation calculations and extract deformation potentials.
"""
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
from pymatgen.util.string import unicodeify_spacegroup
from amset.constants import defaults
from amset.deformation.common import get_formatted_tensors
from amset.deformation.io import parse_calculation, write_deformation_potentials
from amset.deformation.potentials import (
calculate_deformation_potentials,
extract_bands,
get_strain_mapping,
get_symmetrized_strain_mapping,
strain_coverage_ok,
)
from amset.electronic_structure.common import get_ibands
from amset.electronic_structure.kpoints import get_kpoints_from_bandstructure
from amset.electronic_structure.symmetry import expand_bandstructure
energy_cutoff = kwargs.pop("energy_cutoff")
if not energy_cutoff:
energy_cutoff = defaults["energy_cutoff"]
zwk_mode = kwargs.pop("zero_weighted_kpoints")
if not zwk_mode:
zwk_mode = defaults["zero_weighted_kpoints"]
symprec = _parse_symprec(kwargs["symprec"])
symprec_deformation = kwargs["symprec_deformation"]
click.echo("Reading bulk (undeformed) calculation")
bulk_calculation = parse_calculation(bulk_folder, zero_weighted_kpoints=zwk_mode)
bulk_structure = bulk_calculation["bandstructure"].structure
deformation_calculations = []
for deformation_folder in deformation_folders:
click.echo("Reading deformation calculation in {}".format(deformation_folder))
deformation_calculation = parse_calculation(
deformation_folder, zero_weighted_kpoints=zwk_mode
)
if check_calculation(bulk_calculation, deformation_calculation):
deformation_calculations.append(deformation_calculation)
sga = SpacegroupAnalyzer(bulk_structure, symprec=symprec)
spg_symbol = unicodeify_spacegroup(sga.get_space_group_symbol())
spg_number = sga.get_space_group_number()
click.echo("\nSpacegroup: {} ({})".format(spg_symbol, spg_number))
lattice_match = reciprocal_lattice_match(
bulk_calculation["bandstructure"], symprec=symprec
)
if not lattice_match:
click.echo(
"\nWARNING: Reciprocal lattice and k-lattice belong to different\n"
" class of lattices. Often results are still useful but\n"
" it is recommended to regenerate deformations without\n"
" symmetry using: amset deform create --symprec N"
)
strain_mapping = get_strain_mapping(bulk_structure, deformation_calculations)
click.echo("\nFound {} strains:".format(len(strain_mapping)))
fmt_strain = get_formatted_tensors(strain_mapping.keys())
click.echo(" - " + "\n - ".join(fmt_strain))
strain_mapping = get_symmetrized_strain_mapping(
bulk_structure,
strain_mapping,
symprec=symprec,
symprec_deformation=symprec_deformation,
)
click.echo("\nAfter symmetrization found {} strains:".format(len(strain_mapping)))
fmt_strain = get_formatted_tensors(strain_mapping.keys())
click.echo(" - " + "\n - ".join(fmt_strain))
if not strain_coverage_ok(list(strain_mapping.keys())):
click.echo("\nERROR: Strains do not cover full tensor, check calculations")
sys.exit()
click.echo("\nCalculating deformation potentials")
bulk_calculation["bandstructure"] = expand_bandstructure(
bulk_calculation["bandstructure"], symprec=symprec
)
deformation_potentials = calculate_deformation_potentials(
bulk_calculation, strain_mapping
)
print_deformation_summary(bulk_calculation["bandstructure"], deformation_potentials)
if "bands" in kwargs and kwargs["bands"] is not None:
ibands = parse_ibands(kwargs["bands"])
else:
ibands = get_ibands(energy_cutoff, bulk_calculation["bandstructure"])
echo_ibands(ibands, bulk_calculation["bandstructure"].is_spin_polarized)
deformation_potentials = extract_bands(deformation_potentials, ibands)
kpoints = get_kpoints_from_bandstructure(bulk_calculation["bandstructure"])
filename = write_deformation_potentials(
deformation_potentials, kpoints, bulk_structure, filename=kwargs["output"]
)
click.echo("\nDeformation potentials written to {}".format(filename))