def write_settings(settings: Dict[str, Any], filename: str):
"""Write amset configuration settings to a formatted yaml file.
Args:
settings: The configuration settings.
filename: A filename.
"""
settings = cast_dict_list(settings)
dumpfn(settings, filename, indent=4, default_flow_style=False)
def to_dict(self, include_mesh=defaults["write_mesh"]):
data = {
"doping": self.doping * cm_to_bohr ** 3,
"temperatures": self.temperatures,
"fermi_levels": self.fermi_levels * hartree_to_ev,
"conductivity": self.conductivity,
"seebeck": self.seebeck,
"electronic_thermal_conductivity": self.electronic_thermal_conductivity,
"mobility": self.mobility,
}
if include_mesh:
rates = self.scattering_rates
energies = self.energies
vv = self.velocities_product
ir_rates = {s: r[..., self.ir_kpoints_idx] for s, r in rates.items()}
ir_energies = {
s: e[:, self.ir_kpoints_idx] * hartree_to_ev
for s, e in energies.items()
}
ir_vv = {s: v[..., self.ir_kpoints_idx] for s, v in vv.items()}
mesh_data = {
"energies": cast_dict_list(ir_energies),
"kpoints": self.kpoints,
"ir_kpoints": self.ir_kpoints,
"ir_to_full_kpoint_mapping": self.ir_to_full_kpoint_mapping,
"efermi": self.intrinsic_fermi_level * hartree_to_ev,
"vb_idx": cast_dict_list(self.vb_idx),
"dos": self.dos, # TODO: Convert dos to eV
"velocities_product": cast_dict_list(ir_vv), # TODO: convert units
"scattering_rates": cast_dict_list(ir_rates),
"scattering_labels": self.scattering_labels,
"is_metal": self.is_metal,
"fd_cutoffs": (
self.fd_cutoffs[0] * hartree_to_ev,
self.fd_cutoffs[1] * hartree_to_ev,
),
"structure": get_angstrom_structure(self.structure),
"soc": self._soc,
}
data.update(mesh_data)
return data
def to_dict(self, include_mesh=defaults["write_mesh"]):
data = {
"doping": self.doping,
"temperatures": self.temperatures,
"fermi_levels": self.fermi_levels,
"conductivity": self.conductivity,
"seebeck": self.seebeck,
"electronic_thermal_conductivity":
self.electronic_thermal_conductivity,
"mobility": self.mobility,
}
if include_mesh:
rates = self.scattering_rates
energies = self.energies
ir_rates = {
s: r[..., self.ir_kpoints_idx]
for s, r in rates.items()
}
ir_energies = {
s: e[:, self.ir_kpoints_idx]
for s, e in energies.items()
}
mesh_data = {
"energies": cast_dict_list(ir_energies),
"kpoints": self.kpoints,
"ir_kpoints": self.ir_kpoints,
"ir_to_full_kpoint_mapping": self.ir_to_full_kpoint_mapping,
"efermi": self.intrinsic_fermi_level,
"vb_idx": cast_dict_list(self.vb_idx),
"dos": self.dos,
"scattering_rates": cast_dict_list(ir_rates),
"scattering_labels": self.scattering_labels,
"is_metal": self.is_metal,
"fd_cutoffs": self.fd_cutoffs,
"structure": self.structure,
"soc": self._soc,
}
data.update(mesh_data)
return data
def to_file(
self,
directory: str = ".",
prefix: Optional[str] = None,
write_mesh_file: bool = defaults["write_mesh"],
file_format: str = defaults["file_format"],
suffix_mesh: bool = True,
):
if self.conductivity is None:
raise ValueError(
"Can't write AmsetData, transport properties not set")
if not prefix:
prefix = ""
else:
prefix += "_"
if suffix_mesh:
suffix = "_{}".format("x".join(map(str, self.kpoint_mesh)))
else:
suffix = ""
if file_format in ["json", "yaml"]:
data = self.to_dict()
data = cast_dict_list(data)
filename = joinpath(
directory, "{}transport{}.{}".format(prefix, suffix,
file_format))
dumpfn(data, filename, indent=4)
elif file_format in ["csv", "txt"]:
# don't write the data as JSON, instead write raw text files
data, headers = self.to_data()
filename = joinpath(
directory, "{}transport{}.{}".format(prefix, suffix,
file_format))
np.savetxt(filename, data, header=" ".join(headers))
else:
raise ValueError(
"Unrecognised output format: {}".format(file_format))
if write_mesh_file:
mesh_data = self.to_dict(include_mesh=True)["mesh"]
mesh_filename = joinpath(directory,
"{}mesh{}.h5".format(prefix, suffix))
write_mesh(mesh_data, filename=mesh_filename)
return filename, mesh_filename
else:
return filename
def test_cast_dict_list(value, expected):
assert cast_dict_list(value) == expected