"""
Module of functions to read output-files from phonopy.
"""
# Standard library imports
from typing import Tuple, Union
# Internal library imports
import aim2dat.io.utils as io_utils
from aim2dat.ext_interfaces import _return_ext_interface_modules
def _create_load_parameters(
parameter_file_name, force_sets_file_name, force_constants_file_name, phonopy_kwargs
):
load_parameters = {
"phonopy_yaml": parameter_file_name,
}
if force_sets_file_name is not None:
load_parameters["force_sets_filename"] = force_sets_file_name
elif force_constants_file_name is not None:
load_parameters["force_constants_filename"] = force_constants_file_name
else:
raise ValueError("`force_sets_file_path` or `force_constants_file_path` needs to be set.")
if phonopy_kwargs is not None:
load_parameters.update(phonopy_kwargs)
return load_parameters
[docs]
@io_utils.read_band_structure(r".*\.ya?ml$")
def read_phonopy_band_structure(
file_path: str,
kpath: list,
npoints: int,
force_sets_file_path: str = None,
force_constants_file_path: str = None,
path_labels: list = None,
phonopy_kwargs: dict = None,
) -> Tuple[dict, list]:
"""
Read band structure using phonopy.
Parameters
------------
file_path : str
Phonopy yaml-file containing all settings and parameters.
kpath : list
Nested list of high-symmetry points.
npoints : int
Nr of points on the k-path.
force_sets_file_path : str or None
Force sets file. If set to ``None``, ``force_constants_file_path`` needs to be set.
force_constants_file_path : str or None
Force constants file. If set to ``None``, ``force_sets_file_path`` needs to be set.
path_labels : list or None
List of labels for the high-symmetry points specified in ``kpath``.
phonopy_kwargs : dict
Additional keywords for ``phonopy.load``.
Returns
-------
output_bands : dict
Dictionary containing the k-path and the eigenvalues.
reference_cell : list
Reference cell.
"""
load_parameters = _create_load_parameters(
file_path, force_sets_file_path, force_constants_file_path, phonopy_kwargs
)
ph_bands, reference_cell = _return_ext_interface_modules("phonopy")._extract_band_structure(
load_parameters, kpath, path_labels, npoints, False
)
output_bands = {
"kpoints": [],
"unit_y": "THz",
"bands": [],
"path_labels": [],
}
counter_points = 0
counter_seg = 0
path_start = 0
for cont_idx, cont_segment in enumerate(kpath):
path_end = path_start + len(cont_segment) - 1
for qpoints, band_seg in zip(
ph_bands["qpoints"][path_start:path_end], ph_bands["frequencies"][path_start:path_end]
):
output_bands["path_labels"].append((counter_points, path_labels[counter_seg]))
counter_seg += 1
counter_points += npoints - 1
output_bands["kpoints"] += [
[float(pt[0]), float(pt[1]), float(pt[2])] for pt in qpoints
]
output_bands["bands"] += [[float(ev) for ev in pt] for pt in band_seg]
output_bands["path_labels"].append((counter_points, path_labels[counter_seg]))
counter_points += 1
path_start = path_end
counter_seg += 1
return output_bands, reference_cell.tolist()
[docs]
@io_utils.read_total_dos(r".*\.ya?ml$")
def read_phonopy_total_dos(
file_path: str,
mesh: Union[int, list] = 100,
force_sets_file_path: str = None,
force_constants_file_path: str = None,
phonopy_kwargs: dict = None,
) -> dict:
"""
Read the total density of phonon states from phonopy.
Parameters
----------
file_path : str
Phonopy yaml-file containing all settings and parameters.
mesh : list
Number of points in each dimension.
force_sets_file_path : str or None
Force sets file. If set to ``None``, ``force_constants_file_path`` needs to be set.
force_constants_file_path : str or None
Force constants file. If set to ``None``, ``force_sets_file_path`` needs to be set.
phonopy_kwargs : dict
Additional keywords for ``phonopy.load``.
Returns
-------
dict
Dictionary containing the total density of states.
"""
load_parameters = _create_load_parameters(
file_path, force_sets_file_path, force_constants_file_path, phonopy_kwargs
)
phonopy_tdos = _return_ext_interface_modules("phonopy")._extract_total_dos(
load_parameters, mesh
)
return {
"energy": phonopy_tdos["frequency_points"].tolist(),
"tdos": phonopy_tdos["total_dos"].tolist(),
"unit_x": "states/THz/cell",
}
[docs]
@io_utils.read_proj_dos(r".*\.ya?ml$")
def read_phonopy_proj_dos(
file_path: str,
mesh: Union[int, list] = 100,
force_sets_file_path: str = None,
force_constants_file_path: str = None,
phonopy_kwargs: dict = None,
) -> dict:
"""
Read the atom projected density of phonon states from phonopy.
Parameters
----------
file_path : str
Phonopy yaml-file containing all settings and parameters.
mesh : list
Number of points in each dimension.
force_sets_file_path : str or None
Force sets file. If set to ``None``, ``force_constants_file_path`` needs to be set.
force_constants_file_path : str or None
Force constants file. If set to ``None``, ``force_sets_file_path`` needs to be set.
phonopy_kwargs : dict
Additional keywords for ``phonopy.load``.
Returns
-------
dict
Dictionary containing the projected density of states for each kind.
"""
load_parameters = _create_load_parameters(
file_path, force_sets_file_path, force_constants_file_path, phonopy_kwargs
)
phonopy_pdos, symbols = _return_ext_interface_modules("phonopy")._extract_projected_dos(
load_parameters, mesh
)
# TODO: check equivalent sites?
pdos = {
"energy": phonopy_pdos["frequency_points"].tolist(),
"unit_x": "states/THz/cell",
"pdos": [
{"kind": symbol, "total": pdos.tolist()}
for symbol, pdos in zip(symbols, phonopy_pdos["projected_dos"])
],
}
return pdos
[docs]
def read_phonopy_thermal_properties(
file_path: str,
mesh: Union[int, list] = 100,
t_min: int = 0,
t_max: int = 1000,
t_step: int = 10,
force_sets_file_path: str = None,
force_constants_file_path: str = None,
phonopy_kwargs: dict = None,
):
"""
Read the thermal properties from phonopy.
Parameters
------------
file_path : str
Phonopy yaml-file containing all settings and parameters.
mesh : list
Number of points in each dimension.
t_min : int
Minimum temperature
t_max : int
Maximum temperature
force_sets_file_path : str or None
Force sets file. If set to ``None``, ``force_constants_file_path`` needs to be set.
force_constants_file_path : str or None
Force constants file. If set to ``None``, ``force_sets_file_path`` needs to be set.
phonopy_kwargs : dict
Additional keywords for ``phonopy.load``.
Returns
-------
dict
Dictionary containing the thermal properties.
"""
load_parameters = _create_load_parameters(
file_path, force_sets_file_path, force_constants_file_path, phonopy_kwargs
)
thermal_properties = _return_ext_interface_modules("phonopy")._extract_thermal_properties(
load_parameters, mesh, t_min, t_max, t_step
)
return {
"temperatures": thermal_properties["temperatures"].tolist(),
"free_energy": thermal_properties["free_energy"].tolist(),
"entropy": thermal_properties["entropy"].tolist(),
"heat_capacity": thermal_properties["heat_capacity"].tolist(),
}
[docs]
def read_phonopy_qha_properties(
calculation_folder_paths: list = None,
thermal_properties_file_paths: list = None,
ev_file_path: str = None,
stdout_file_path: str = None,
mesh: Union[int, list] = 100,
t_min: int = 0,
t_max: int = 1000,
t_step: int = 10,
phonopy_kwargs: dict = None,
):
"""
Read the outputs from a quasi-harmonic approximation calculation.
Parameters
----------
calculation_folder_paths : list or None
Folders containing the calculations of different volumes. If ``None``
``thermal_properties_file_paths`` needs to be set instead.
thermal_properties_file_paths : list or None
List of thermal properties yaml files generated by phonopy.
thermal_properties_file_paths : str or None
File containing volumes and energies.
ev_file_path : str or None
Path to the e-V file.
stdout_file_path : str or None
File name of the standard output file.
mesh : list or int
Number of points in each dimension.
t_min : int
Minimum temperature
t_max : int
Maximum temperature
phonopy_kwargs : dict
Additional keywords for ``phonopy.load``.
Returns
-------
dict
Dictionary containing the qha properties.
"""
qha_kwargs = {}
if ev_file_path is None and (calculation_folder_paths is None and stdout_file_path is None):
raise ValueError(
"Either `ev_file_path` or `calculation_folder_paths` and `stdout_file_path` need to "
"be set."
)
if thermal_properties_file_paths is None and calculation_folder_paths is None:
raise ValueError(
"Either `thermal_properties_file_paths` or `calculation_folder_paths` needs to be set."
)
if thermal_properties_file_paths is not None:
if not isinstance(thermal_properties_file_paths, (list, tuple)):
raise TypeError("`thermal_properties_file_paths` needs to be of type list or tuple.")
(
qha_kwargs["temperatures"],
qha_kwargs["cv"],
qha_kwargs["entropy"],
qha_kwargs["free_energy"],
num_modes,
num_integrated_modes,
) = _return_ext_interface_modules("phonopy")._read_thermal_properties_yaml_files(
thermal_properties_file_paths
)
if ev_file_path is not None:
qha_kwargs["volumes"], qha_kwargs["electronic_energies"] = _return_ext_interface_modules(
"phonopy"
)._read_v_e_file(ev_file_path)
if calculation_folder_paths is not None:
if thermal_properties_file_paths is None:
qha_kwargs["cv"] = [[] for idx0 in range(int(t_min), int(t_max + t_step), int(t_step))]
qha_kwargs["entropy"] = [
[] for idx0 in range(int(t_min), int(t_max + t_step), int(t_step))
]
qha_kwargs["free_energy"] = [
[] for idx0 in range(int(t_min), int(t_max + t_step), int(t_step))
]
for calc_folder in calculation_folder_paths:
t_p = read_phonopy_thermal_properties(
calc_folder + "/phonopy_disp.yaml",
force_sets_file_path=calc_folder + "/FORCE_SETS",
mesh=mesh,
t_min=t_min,
t_max=t_max,
t_step=t_step,
phonopy_kwargs=phonopy_kwargs,
)
qha_kwargs["temperatures"] = t_p["temperatures"]
for idx0 in range(len(t_p["temperatures"])):
qha_kwargs["cv"][idx0].append(t_p["heat_capacity"][idx0])
qha_kwargs["entropy"][idx0].append(t_p["entropy"][idx0])
qha_kwargs["free_energy"][idx0].append(t_p["free_energy"][idx0])
if ev_file_path is None:
raise ValueError(
"Parsing volumes and energies from output files is not yet supported."
)
qha_properties = _return_ext_interface_modules("phonopy")._extract_qha_properties(**qha_kwargs)
qha_properties["temperatures"] = [
float(val)
for val in qha_kwargs["temperatures"][: len(qha_properties["thermal_expansion"])]
]
qha_properties["bulk_modulus"] = float(qha_properties["bulk_modulus"])
qha_properties["thermal_expansion"] = [
float(val) for val in qha_properties["thermal_expansion"]
]
qha_properties["helmholtz_volume"] = qha_properties["helmholtz_volume"].tolist()
qha_properties["gibbs_temperature"] = qha_properties["gibbs_temperature"].tolist()
qha_properties["bulk_modulus_temperature"] = qha_properties[
"bulk_modulus_temperature"
].tolist()
qha_properties["volume_temperature"] = qha_properties["volume_temperature"].tolist()
qha_properties["heat_capacity_P_numerical"] = [
float(val) for val in qha_properties["heat_capacity_P_numerical"]
]
qha_properties["heat_capacity_P_polyfit"] = [
float(val) for val in qha_properties["heat_capacity_P_polyfit"]
]
qha_properties["gruneisen_temperature"] = [
float(val) for val in qha_properties["gruneisen_temperature"]
]
qha_properties["bulk_modulus_parameters"] = [
float(val) for val in qha_properties["bulk_modulus_parameters"]
]
qha_properties["volumes"] = qha_kwargs["volumes"].tolist()
return qha_properties
def read_band_structure(
parameter_file_name,
path,
npoints,
force_sets_file_name=None,
force_constants_file_name=None,
path_labels=None,
phonopy_kwargs=None,
):
"""
Read band structure using phonopy.
Notes
-----
This function is deprecated and will be removed, please use
`aim2dat.io.read_phonopy_band_structure` instead.
Parameters
------------
parameter_file_name : str
Phonopy yaml-file containing all settings and parameters.
path : list
Nested list of high-symmetry points.
force_sets_file_name : str or None
Force sets file. If set to ``None`` force_constants_filename needs to be set.
force_constants_file_name : str or None
Force constants file. If set to ``None`` force_sets_file_name needs to be set.
path_labels : list or None
List of labels for the high-symmetry points specified in ``path``.
phonopy_kwargs : dict
Additional keywords for ``phonopy.load``.
Returns
-------
output_bands : dict
Dictionary containing the k-path and the eigenvalues.
reference_cell : list
Reference cell.
"""
from warnings import warn
warn(
"This function will be removed, please use `aim2dat.io.read_phonopy_band_structure` "
"instead.",
DeprecationWarning,
2,
)
return read_phonopy_band_structure(
file_path=parameter_file_name,
kpath=path,
npoints=npoints,
force_sets_file_path=force_sets_file_name,
force_constants_file_path=force_constants_file_name,
path_labels=path_labels,
phonopy_kwargs=phonopy_kwargs,
)
def read_total_density_of_states(
parameter_file_name,
mesh=100,
force_sets_file_name=None,
force_constants_file_name=None,
phonopy_kwargs=None,
):
"""
Read the total density of phonon states from phonopy.
Notes
-----
This function is deprecated and will be removed, please use
`aim2dat.io.read_phonopy_total_dos` instead.
Parameters
----------
parameter_file_name : str
Phonopy yaml-file containing all settings and parameters.
mesh : list
Number of points in each dimension.
force_sets_file_name : str or None
Force sets file. If set to ``None`` force_constants_filename needs to be set.
force_constants_file_name : str or None
For constants file. If set to ``None`` force_sets_file_name needs to be set.
phonopy_kwargs : dict
Additional keywords for ``phonopy.load``.
Returns
-------
dict
Dictionary containing the total density of states.
"""
from warnings import warn
warn(
"This function will be removed, please use `aim2dat.io.read_phonopy_total_dos` "
"instead.",
DeprecationWarning,
2,
)
return read_phonopy_total_dos(
file_path=parameter_file_name,
mesh=mesh,
force_sets_file_path=force_sets_file_name,
force_constants_file_path=force_constants_file_name,
phonopy_kwargs=phonopy_kwargs,
)
def read_atom_proj_density_of_states(
parameter_file_name,
mesh=100,
force_sets_file_name=None,
force_constants_file_name=None,
phonopy_kwargs=None,
):
"""
Read the atom projected density of phonon states from phonopy.
Notes
-----
This function is deprecated and will be removed, please use
`aim2dat.io.read_phonopy_proj_dos` instead.
Parameters
----------
parameter_file_name : str
Phonopy yaml-file containing all settings and parameters.
mesh : list
Number of points in each dimension.
force_sets_file_name : str or None
Force sets file. If set to ``None`` force_constants_filename needs to be set.
force_constants_file_name : str or None
For ceonstants file. If set to ``None`` force_sets_file_name needs to be set.
phonopy_kwargs : dict
Additional keywords for ``phonopy.load``.
Returns
-------
dict
Dictionary containing the projected density of states for each kind.
"""
from warnings import warn
warn(
"This function will be removed, please use `aim2dat.io.read_phonopy_proj_dos` " "instead.",
DeprecationWarning,
2,
)
return read_phonopy_proj_dos(
file_path=parameter_file_name,
mesh=mesh,
force_sets_file_path=force_sets_file_name,
force_constants_file_path=force_constants_file_name,
)
def read_thermal_properties(
parameter_file_name,
mesh=100,
t_min=0,
t_max=1000,
t_step=10,
force_sets_file_name=None,
force_constants_file_name=None,
phonopy_kwargs={},
):
"""
Read the thermal properties from phonopy.
Notes
-----
This function is deprecated and will be removed, please use
`aim2dat.io.read_phonopy_thermal_properties` instead.
Parameters
------------
parameter_file_name : str
Phonopy yaml-file containing all settings and parameters.
mesh : list
Number of points in each dimension.
t_min : int
Minimum temperature
t_max : int
Maximum temperature
force_sets_file_name : str or None
Force sets file. If set to ``None`` force_constants_filename needs to be set.
force_constants_file_name : str or None
For ceonstants file. If set to ``None`` force_sets_file_name needs to be set.
phonopy_kwargs : dict
Additional keywords for ``phonopy.load``.
Returns
-------
dict
Dictionary containing the thermal properties.
"""
from warnings import warn
warn(
"This function will be removed, please use `aim2dat.io.read_phonopy_thermal_properties` "
"instead.",
DeprecationWarning,
2,
)
return read_phonopy_thermal_properties(
file_path=parameter_file_name,
mesh=mesh,
t_min=t_min,
t_max=t_max,
t_step=t_step,
force_sets_file_path=force_sets_file_name,
force_constants_file_path=force_constants_file_name,
phonopy_kwargs=phonopy_kwargs,
)
def read_qha_properties(
calculation_folders=None,
thermal_properties_file_names=None,
ev_file_name=None,
std_output_file_name=None,
mesh=100,
t_min=0,
t_max=1000,
t_step=10,
phonopy_kwargs=None,
):
"""
Read the outputs from a quasi-harmonic approximation calculation.
Notes
-----
This function is deprecated and will be removed, please use
`aim2dat.io.read_phonopy_qha_properties` instead.
Parameters
----------
calculation_folders : list or None
Folders containing the calculations of different volumes. If ``None``
``thermal_properties_file_names`` needs to be set instead.
thermal_properties_file_names : list or None
List of thermal properties yaml files generated by phonopy.
ev_file_name : str or None
File containing volumes and energies.
std_output_file_name : str or None
File name of the standard output files.
mesh : list or int
Number of points in each dimension.
t_min : int
Minimum temperature
t_max : int
Maximum temperature
phonopy_kwargs : dict
Additional keywords for ``phonopy.load``.
Returns
-------
dict
Dictionary containing the qha properties.
"""
from warnings import warn
warn(
"This function will be removed, please use `aim2dat.io.read_phonopy_qha_properties` "
"instead.",
DeprecationWarning,
2,
)
return read_phonopy_qha_properties(
calculation_folder_paths=calculation_folders,
thermal_properties_file_paths=thermal_properties_file_names,
ev_file_path=ev_file_name,
stdout_file_path=std_output_file_name,
mesh=mesh,
t_min=t_min,
t_max=t_max,
t_step=t_step,
phonopy_kwargs=phonopy_kwargs,
)