def run(**kwargs):
"""
Run AMSET on an ab initio band structure
"""
from amset.constants import defaults
from amset.log import initialize_amset_logger
from amset.core.run import AmsetRunner
if kwargs["print_log"] is not False:
initialize_amset_logger()
settings_override: Dict[str, Dict[str, Any]] = defaultdict(dict)
for setting in defaults:
if setting in kwargs and kwargs[setting] is not None:
settings_override[setting] = kwargs[setting]
runner = AmsetRunner.from_directory(
directory=kwargs["directory"],
vasprun=kwargs["vasprun"],
settings_file=kwargs["settings"],
settings_override=settings_override,
)
runner.run()
def test_get_energies_interpolater(self):
initialize_amset_logger()
amset_data = self.interpolater.get_amset_data()
energies, velocities, projections, sym_info = self.interpolater.get_energies(
amset_data.kpoints,
None,
return_velocity=True,
atomic_units=True,
curvature=False,
return_projections=True,
symprec=0.1,
return_vel_outer_prod=True,
return_kpoint_mapping=True,
)
np.testing.assert_array_almost_equal(energies[Spin.up],
amset_data.energies[Spin.up])
np.testing.assert_array_almost_equal(
velocities[Spin.up], amset_data.velocities_product[Spin.up])
for l in projections[Spin.up]:
np.testing.assert_array_almost_equal(
projections[Spin.up][l], amset_data._projections[Spin.up][l])
np.testing.assert_array_equal(sym_info["ir_kpoints_idx"],
amset_data.ir_kpoints_idx)
np.testing.assert_array_equal(sym_info["ir_to_full_idx"],
amset_data.ir_to_full_kpoint_mapping)
def _run_wrapper(self,
directory: Union[str, Path] = ".",
prefix: Optional[str] = None):
if self.settings["print_log"]:
log_file = "{}_amset.log".format(prefix) if prefix else "amset.log"
initialize_amset_logger(directory=directory, filename=log_file)
tt = time.perf_counter()
_log_amset_intro()
_log_settings(self)
_log_structure_information(self._band_structure.structure,
self.settings["symprec"])
_log_band_structure_information(self._band_structure)
amset_data, interpolation_time = self._do_interpolation()
timing = {"interpolation": interpolation_time}
amset_data, dos_time = self._do_dos(amset_data)
timing["dos"] = dos_time
amset_data, scattering_time = self._do_scattering(amset_data)
timing["scattering"] = scattering_time
amset_data, transport_time = self._do_transport(amset_data)
timing["transport"] = scattering_time
filepath, writing_time = self._do_writing(amset_data, directory,
prefix)
timing["writing"] = writing_time
timing["total"] = time.perf_counter() - tt
return amset_data, timing
def __init__(self,
data,
interpolation_factor=1,
print_log=defaults["print_log"]):
super().__init__(data)
self.interpolation_factor = interpolation_factor
if print_log:
initialize_amset_logger(filename="amset_lineshape_plot.log")
def __init__(
self,
data,
interpolation_factor=5,
print_log=defaults["print_log"],
symprec=defaults["symprec"],
):
super().__init__(data)
self.interpolation_factor = interpolation_factor
if print_log:
initialize_amset_logger(filename="lineshape.log")
self.symprec = symprec
def _run_wrapper(self,
directory: Union[str, Path] = ".",
prefix: Optional[str] = None):
if self.settings["print_log"] or self.settings["write_log"]:
if self.settings["write_log"]:
log_file = "{}_amset.log".format(
prefix) if prefix else "amset.log"
else:
log_file = False
initialize_amset_logger(
directory=directory,
filename=log_file,
print_log=self.settings["print_log"],
)
self._check_wavefunction()
tt = time.perf_counter()
_log_amset_intro()
_log_settings(self)
_log_structure_information(self._band_structure.structure,
self.settings["symprec"])
_log_band_structure_information(self._band_structure)
amset_data, interpolation_time = self._do_interpolation()
timing = {"interpolation": interpolation_time}
amset_data, dos_time = self._do_dos(amset_data)
timing["dos"] = dos_time
amset_data, scattering_time = self._do_scattering(amset_data)
timing["scattering"] = scattering_time
if isinstance(self.settings["fd_tol"], numeric_types):
amset_data, timing = self._do_fd_tol(amset_data, directory, prefix,
timing)
else:
amset_data, timing = self._do_many_fd_tol(amset_data,
self.settings["fd_tol"],
directory, prefix,
timing)
timing["total"] = time.perf_counter() - tt
return amset_data, timing
def __init__(
self,
bandstructure: BandStructure,
nelect: int,
soc: bool = False,
interpolation_factor=defaults["interpolation_factor"],
print_log=defaults["print_log"],
symprec=defaults["symprec"],
energy_cutoff=None,
):
if print_log:
initialize_amset_logger(filename="amset_electronic_structure_plot.log")
self.symprec = symprec
self.interpolater = Interpolator(
bandstructure, nelect, interpolation_factor=interpolation_factor, soc=soc
)
self.structure = bandstructure.structure
self.energy_cutoff = energy_cutoff
def test_get_energies_symprec(self):
# vr = Vasprun(os.path.join(tin_dioxide_files, 'vasprun.xml.gz'),
# parse_projected_eigen=True)
vr = Vasprun(os.path.join(pbs_files, "vasprun.xml.gz"),
parse_projected_eigen=True)
bs = vr.get_band_structure()
num_electrons = vr.parameters["NELECT"]
interpolater = Interpolator(bs,
num_electrons,
interpolate_projections=True,
interpolation_factor=1)
ir_kpoints, weights, kpoints, ir_kpoints_idx, ir_to_full_idx = get_kpoints(
[13, 15, 29],
vr.final_structure,
boltztrap_ordering=True,
return_full_kpoints=True,
)
initialize_amset_logger()
(
energies,
velocities,
curvature,
projections,
sym_info,
) = interpolater.get_energies(
kpoints,
None,
return_velocity=True,
atomic_units=True,
return_curvature=True,
return_projections=True,
symprec=0.1,
return_vel_outer_prod=True,
return_kpoint_mapping=True,
)
(
energies_no_sym,
velocities_no_sym,
curvature_no_sym,
projections_no_sym,
) = interpolater.get_energies(
kpoints,
None,
return_velocity=True,
atomic_units=True,
return_curvature=True,
return_projections=True,
return_vel_outer_prod=True,
symprec=None,
)
np.testing.assert_array_equal(ir_to_full_idx,
sym_info["ir_to_full_idx"])
np.testing.assert_array_equal(ir_kpoints_idx,
sym_info["ir_kpoints_idx"])
# print(velocities[Spin.up][5, :, :, -3:])
# print(velocities_no_sym[Spin.up][5, :, :, -3:])
# print(sym_info["ir_to_full_idx"][-10:])
np.testing.assert_array_almost_equal(energies[Spin.up],
energies_no_sym[Spin.up],
decimal=12)
np.testing.assert_array_almost_equal(velocities[Spin.up],
velocities_no_sym[Spin.up],
decimal=12)
np.testing.assert_array_almost_equal(curvature[Spin.up],
curvature_no_sym[Spin.up],
decimal=12)
for l in projections[Spin.up]:
np.testing.assert_array_almost_equal(
projections[Spin.up][l], projections_no_sym[Spin.up][l])
