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Supercell energies in type-2 dataset #223

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Apr 29, 2024
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Supercell energies in type-2 dataset #223

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16 changes: 11 additions & 5 deletions phono3py/api_phono3py.py
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Original file line number Diff line number Diff line change
Expand Up @@ -582,6 +582,7 @@ def dataset(self):
{'number': atom index of second displaced atom,
'displacement': displacement in Cartesian coordinates},
'forces': forces on atoms in supercell,
'supercell_energy': energy of supercell,
'pair_distance': distance between paired atoms,
'included': with cutoff pair distance in displacement
pair generation, this indicates if this
Expand All @@ -591,9 +592,11 @@ def dataset(self):
... ] }, ... ] }
Type 2. All atomic displacements in each supercell:
{'displacements': ndarray, dtype='double', order='C',
shape=(supercells, atoms in supercell, 3)
shape=(supercells, atoms in supercell, 3),
'forces': ndarray, dtype='double',, order='C',
shape=(supercells, atoms in supercell, 3)}
shape=(supercells, atoms in supercell, 3),
'supercell_energies': ndarray, dtype='double',
shape=(supercells,)}
In type 2, displacements and forces can be given by numpy array
with different shape but that can be reshaped to
(supercells, natom, 3).
Expand Down Expand Up @@ -622,12 +625,15 @@ def phonon_dataset(self):
'first_atoms': [
{'number': atom index of first displaced atom,
'displacement': displacement in Cartesian coordinates,
'forces': forces on atoms in supercell} ... ]}
'forces': forces on atoms in supercell,
'supercell_energy': energy of supercell}, ... ]}
Type 2. All atomic displacements in each supercell:
{'displacements': ndarray, dtype='double', order='C',
shape=(supercells, atoms in supercell, 3)
shape=(supercells, atoms in supercell, 3),
'forces': ndarray, dtype='double',, order='C',
shape=(supercells, atoms in supercell, 3)}
shape=(supercells, atoms in supercell, 3),
'supercell_energies': ndarray, dtype='double',
shape=(supercells,)}
In type 2, displacements and forces can be given by numpy array
with different shape but that can be reshaped to
(supercells, natom, 3).
Expand Down
83 changes: 60 additions & 23 deletions phono3py/cui/create_force_sets.py
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Original file line number Diff line number Diff line change
Expand Up @@ -40,6 +40,7 @@
import sys
from typing import Optional

import numpy as np
from phonopy.cui.create_force_sets import check_number_of_force_files
from phonopy.cui.load_helper import get_nac_params
from phonopy.cui.phonopy_script import file_exists, files_exist, print_error
Expand Down Expand Up @@ -227,8 +228,16 @@ def _get_force_sets_fc2(
interface_mode = settings.calculator
if log_level:
print(f'FC2 displacement dataset was read from "{disp_filename}".')
num_atoms = disp_dataset["natom"]
num_disps = len(disp_dataset["first_atoms"])

if "first_atoms" in disp_dataset: # type-1
num_atoms = disp_dataset["natom"]
num_disps = len(disp_dataset["first_atoms"])
elif "displacements" in disp_dataset: # type-2:
num_disps = len(disp_dataset["displacements"])
num_atoms = len(disp_dataset["displacements"][0])
else:
raise RuntimeError("FC2 displacement dataset is broken.")

force_filenames = settings.create_forces_fc2
for filename in force_filenames:
file_exists(filename, log_level)
Expand Down Expand Up @@ -276,12 +285,18 @@ def _get_force_sets_fc3(
print("")
print(f'FC3 Displacement dataset was read from "{disp_filename}".')

num_atoms = disp_dataset["natom"]
num_disps = len(disp_dataset["first_atoms"])
for d1 in disp_dataset["first_atoms"]:
for d2 in d1["second_atoms"]:
if "included" not in d2 or d2["included"]:
num_disps += 1
if "first_atoms" in disp_dataset: # type-1
num_atoms = disp_dataset["natom"]
num_disps = len(disp_dataset["first_atoms"])
for d1 in disp_dataset["first_atoms"]:
for d2 in d1["second_atoms"]:
if "included" not in d2 or d2["included"]:
num_disps += 1
elif "displacements" in disp_dataset: # type-2:
num_disps = len(disp_dataset["displacements"])
num_atoms = len(disp_dataset["displacements"][0])
else:
raise RuntimeError("FC3 displacement dataset is broken.")

if settings.create_forces_fc3_file:
file_exists(settings.create_forces_fc3_file, log_level)
Expand Down Expand Up @@ -336,23 +351,45 @@ def _get_force_sets_fc3(
def _set_forces_and_nac_params(
ph3py_yaml: Phono3pyYaml, settings, calc_dataset_fc3: dict, calc_dataset_fc2: dict
):
count = len(ph3py_yaml.dataset["first_atoms"])
for i, d1 in enumerate(ph3py_yaml.dataset["first_atoms"]):
d1["forces"] = calc_dataset_fc3["forces"][i]
if "energies" in calc_dataset_fc3:
d1["energy"] = float(calc_dataset_fc3["energies"][i])
for d2 in d1["second_atoms"]:
if "included" not in d2 or d2["included"]:
d2["forces"] = calc_dataset_fc3["forces"][count]
if "energies" in calc_dataset_fc3:
d2["energy"] = float(calc_dataset_fc3["energies"][count])
count += 1
if "first_atoms" in ph3py_yaml.dataset:
count = len(ph3py_yaml.dataset["first_atoms"])
for i, d1 in enumerate(ph3py_yaml.dataset["first_atoms"]):
d1["forces"] = calc_dataset_fc3["forces"][i]
if "supercell_energies" in calc_dataset_fc3:
d1["supercell_energy"] = float(
calc_dataset_fc3["supercell_energies"][i]
)
for d2 in d1["second_atoms"]:
if "included" not in d2 or d2["included"]:
d2["forces"] = calc_dataset_fc3["forces"][count]
if "supercell_energies" in calc_dataset_fc3:
d2["supercell_energy"] = float(
calc_dataset_fc3["supercell_energies"][count]
)
count += 1
else:
ph3py_yaml.dataset["forces"] = np.array(
calc_dataset_fc3["forces"], dtype="double", order="C"
)
ph3py_yaml.dataset["supercell_energies"] = np.array(
calc_dataset_fc3["supercell_energies"], dtype="double"
)

if settings.create_forces_fc2:
for i, d in enumerate(ph3py_yaml.phonon_dataset["first_atoms"]):
d["forces"] = calc_dataset_fc2["forces"][i]
if "energies" in calc_dataset_fc2:
d["energy"] = float(calc_dataset_fc2["energies"][i])
if "first_atoms" in ph3py_yaml.phonon_dataset:
for i, d in enumerate(ph3py_yaml.phonon_dataset["first_atoms"]):
d["forces"] = calc_dataset_fc2["forces"][i]
if "supercell_energies" in calc_dataset_fc2:
d["supercell_energy"] = float(
calc_dataset_fc2["supercell_energies"][i]
)
else:
ph3py_yaml.phonon_dataset["forces"] = np.array(
calc_dataset_fc2["forces"], dtype="double", order="C"
)
ph3py_yaml.phonon_dataset["supercell_energies"] = np.array(
calc_dataset_fc2["supercell_energies"], dtype="double"
)

nac_params = get_nac_params(primitive=ph3py_yaml.primitive)
if nac_params:
Expand Down
60 changes: 30 additions & 30 deletions phono3py/interface/phono3py_yaml.py
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Original file line number Diff line number Diff line change
Expand Up @@ -133,14 +133,11 @@ def _parse_dataset(self):

This method override PhonopyYaml._parse_dataset.

key="phonon_displacements" at v2.2 or later.
key="displacements" at older version than v2.2.

"""
self._data.phonon_dataset = self._get_dataset(
self._data.phonon_supercell, key="phonon_displacements"
self._data.phonon_supercell, key_prefix="phonon_"
)
if self._data.phonon_dataset is None: # key="displacements"
if self._data.phonon_dataset is None:
self._data.phonon_dataset = self._get_dataset(self._data.phonon_supercell)

def _parse_fc3_dataset(self):
Expand Down Expand Up @@ -192,8 +189,8 @@ def _parse_fc3_dataset_type1(self, natom):
data1["id"] = d1_id
if "forces" in d1:
data1["forces"] = np.array(d1["forces"], dtype="double", order="C")
if "energy" in d1:
data1["energy"] = d1["energy"]
if "supercell_energy" in d1:
data1["supercell_energy"] = d1["supercell_energy"]
d2_list = d1.get("paired_with")
if d2_list is None: # backward compatibility
d2_list = d1.get("second_atoms")
Expand Down Expand Up @@ -228,8 +225,8 @@ def _parse_fc3_dataset_type1_with_forces(self, data1, d2, disp2_id):
second_atom_dict["id"] = d2_id
if "pair_distance" in d2:
second_atom_dict["pair_distance"] = d2["pair_distance"]
if "energy" in d2:
second_atom_dict["energy"] = d2["energy"]
if "supercell_energy" in d2:
second_atom_dict["supercell_energy"] = d2["supercell_energy"]
disp2_id += 1
data1["second_atoms"].append(second_atom_dict)
return disp2_id
Expand Down Expand Up @@ -298,15 +295,6 @@ def _cell_info_yaml_lines(self):
lines += self._phonon_supercell_yaml_lines()
return lines

def _phonon_supercell_matrix_yaml_lines(self):
lines = []
if self._data.phonon_supercell_matrix is not None:
lines.append("phonon_supercell_matrix:")
for v in self._data.supercell_matrix:
lines.append("- [ %3d, %3d, %3d ]" % tuple(v))
lines.append("")
return lines

def _phonon_supercell_yaml_lines(self):
lines = []
if self._data.phonon_supercell is not None:
Expand All @@ -330,7 +318,7 @@ def _nac_yaml_lines(self):
else:
return self._nac_yaml_lines_given_symbols(self._data.primitive.symbols)

def _displacements_yaml_lines(self, with_forces=False, key="displacements"):
def _displacements_yaml_lines(self, with_forces: bool = False) -> list:
"""Get YAML lines for phonon_dataset and dataset.

This method override PhonopyYaml._displacements_yaml_lines.
Expand All @@ -341,24 +329,28 @@ def _displacements_yaml_lines(self, with_forces=False, key="displacements"):
lines = []
if self._data.phonon_supercell_matrix is not None:
lines += self._displacements_yaml_lines_2types(
self._data.phonon_dataset, with_forces=with_forces, key=f"phonon_{key}"
self._data.phonon_dataset,
with_forces=with_forces,
key_prefix="phonon_",
)
lines += self._displacements_yaml_lines_2types(
self._data.dataset, with_forces=with_forces, key=key
self._data.dataset, with_forces=with_forces
)
return lines

def _displacements_yaml_lines_type1(
self, dataset, with_forces=False, key="displacements"
):
self, dataset: dict, with_forces: bool = False, key_prefix: str = ""
) -> list:
"""Get YAML lines for type1 phonon_dataset and dataset.

This method override PhonopyYaml._displacements_yaml_lines_type1.
PhonopyYaml._displacements_yaml_lines_2types calls
Phono3pyYaml._displacements_yaml_lines_type1.

"""
return displacements_yaml_lines_type1(dataset, with_forces=with_forces, key=key)
return displacements_yaml_lines_type1(
dataset, with_forces=with_forces, key_prefix=key_prefix
)


class Phono3pyYaml(PhonopyYaml):
Expand Down Expand Up @@ -445,7 +437,9 @@ def set_phonon_info(self, phono3py: "Phono3py"):
self._data.phonon_supercell = phono3py.phonon_supercell


def displacements_yaml_lines_type1(dataset, with_forces=False, key="displacements"):
def displacements_yaml_lines_type1(
dataset: dict, with_forces: bool = False, key_prefix: str = ""
) -> list:
"""Get YAML lines for type1 phonon_dataset and dataset.

This is a function but not class method because used by other function.
Expand All @@ -456,7 +450,7 @@ def displacements_yaml_lines_type1(dataset, with_forces=False, key="displacement
if "second_atoms" in dataset["first_atoms"][0]:
lines = ["displacement_pairs:"]
else:
lines = [f"{key}:"]
lines = [f"{key_prefix}displacements:"]
for disp1_id, d1 in enumerate(dataset["first_atoms"]):
lines.append("- atom: %4d" % (d1["number"] + 1))
lines.append(" displacement:")
Expand All @@ -468,8 +462,12 @@ def displacements_yaml_lines_type1(dataset, with_forces=False, key="displacement
lines.append(" forces:")
for v in d1["forces"]:
lines.append(" - [ %19.16f, %19.16f, %19.16f ]" % tuple(v))
if "energy" in d1:
lines.append(" energy: {energy:.8f}".format(energy=d1["energy"]))
if "supercell_energy" in d1:
lines.append(
" supercell_energy: {energy:.8f}".format(
energy=d1["supercell_energy"]
)
)
if "second_atoms" in d1:
ret_lines, id_offset = _second_displacements_yaml_lines(
d1["second_atoms"], id_offset, with_forces=with_forces
Expand Down Expand Up @@ -548,9 +546,11 @@ def _second_displacements_yaml_lines(dataset2, id_offset, with_forces=False):
lines.append(" forces:")
for v in dataset2[j]["forces"]:
lines.append(" - [ %19.16f, %19.16f, %19.16f ]" % tuple(v))
if "energy" in dataset2[j]:
if "supercell_energy" in dataset2[j]:
lines.append(
" energy: {energy:.8f}".format(energy=dataset2[j]["energy"])
" supercell_energy: {energy:.8f}".format(
energy=dataset2[j]["supercell_energy"]
)
)
else:
lines.append(" - atom: %4d" % (i + 1))
Expand Down
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