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Merge pull request #241 from phonopy/pypolymlp 

Add option for produce_fc3 using pypolymlp
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Atsushi Togo 2024-06-26 23:02:20 +09:00 committed by GitHub
parent ae612d49c7 1550b912f8
commit 8d7f41485b
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5 changed files with 237 additions and 38 deletions
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221
phono3py/api_phono3py.py
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@ -40,10 +40,12 @@ from collections.abc import Sequence
from typing import Literal, Optional, Union
import numpy as np
from phonopy import Phonopy
from phonopy.exception import ForceCalculatorRequiredError
from phonopy.harmonic.displacement import (
directions_to_displacement_dataset,
get_least_displacements,
get_random_displacements_dataset,
)
from phonopy.harmonic.dynamical_matrix import DynamicalMatrix
from phonopy.harmonic.force_constants import get_fc2 as get_phonopy_fc2
@ -54,6 +56,7 @@ from phonopy.harmonic.force_constants import (
symmetrize_force_constants,
)
from phonopy.interface.fc_calculator import get_fc2
from phonopy.interface.pypolymlp import PypolymlpParams
from phonopy.structure.atoms import PhonopyAtoms
from phonopy.structure.cells import (
Primitive,
@ -288,10 +291,13 @@ class Phono3py:
self._frequency_points = None
self._temperatures = None
# Other variables
# Force constants
self._fc2 = None
self._fc3 = None
# MLP container
self._mlp_phonopy = None
# Setup interaction
self._interaction = None
self._band_indices = None
@ -984,6 +990,30 @@ class Phono3py:
def phonon_supercell_energies(self, values):
self._set_phonon_forces_energies(values, target="supercell_energies")
@property
def mlp_dataset(self) -> Optional[dict]:
"""Return displacement-force dataset.
The supercell matrix is equal to that of usual displacement-force
dataset. Only type 2 format is supported. "displacements",
"forces", and "supercell_energies" should be contained.
"""
if self._mlp_phonopy is None:
return None
return self._mlp_phonopy.mlp_dataset
@mlp_dataset.setter
def mlp_dataset(self, mlp_dataset: dict):
if self._mlp_phonopy is None:
self._mlp_phonopy = Phonopy(
self._unitcell,
supercell_matrix=self._supercell_matrix,
symprec=self._symprec,
log_level=self._log_level,
)
self._mlp_phonopy.mlp_dataset = mlp_dataset
@property
def phph_interaction(self):
"""Return Interaction instance."""
@ -1166,6 +1196,10 @@ class Phono3py:
cutoff_pair_distance=None,
is_plusminus="auto",
is_diagonal=True,
number_of_snapshots: Optional[int] = None,
random_seed: Optional[int] = None,
is_random_distance: bool = False,
min_distance: Optional[float] = None,
):
"""Generate displacement dataset in supercell for fc3.
@ -1211,20 +1245,48 @@ class Phono3py:
vectors of the supercell. With True, direction not along the basis
vectors can be chosen when the number of the displacements
may be reduced.
number_of_snapshots : int or None, optional
Number of snapshots of supercells with random displacements. Random
displacements are generated displacing all atoms in random
directions with a fixed displacement distance specified by
'distance' parameter, i.e., all atoms in supercell are displaced
with the same displacement distance in direct space. Default is
None.
random_seed : int or None, optional
Random seed for random displacements generation. Default is None.
is_random_distance : bool, optional
Random direction displacements are generated also with random
amplitudes. The maximum value is defined by `distance` and minimum
value is given by `min_distance`. Default is False.
min_distance : float or None, optional
In random direction displacements generation with random distance
(`is_random_distance=True`), the minimum distance is given by this
value.
"""
direction_dataset = get_third_order_displacements(
self._supercell,
self._symmetry,
is_plusminus=is_plusminus,
is_diagonal=is_diagonal,
)
self._dataset = direction_to_displacement(
direction_dataset,
distance,
self._supercell,
cutoff_distance=cutoff_pair_distance,
)
if number_of_snapshots is not None and number_of_snapshots > 0:
self._dataset = self._generate_random_displacements(
number_of_snapshots,
len(self._supercell),
distance=distance,
is_plusminus=is_plusminus is True,
random_seed=random_seed,
is_random_distance=is_random_distance,
min_distance=min_distance,
)
else:
direction_dataset = get_third_order_displacements(
self._supercell,
self._symmetry,
is_plusminus=is_plusminus,
is_diagonal=is_diagonal,
)
self._dataset = direction_to_displacement(
direction_dataset,
distance,
self._supercell,
cutoff_distance=cutoff_pair_distance,
)
self._supercells_with_displacements = None
if self._phonon_supercell_matrix is not None and self._phonon_dataset is None:
@ -1233,7 +1295,14 @@ class Phono3py:
)
def generate_fc2_displacements(
self, distance=0.03, is_plusminus="auto", is_diagonal=False
self,
distance: float = 0.03,
is_plusminus: str = "auto",
is_diagonal: bool = False,
number_of_snapshots: Optional[int] = None,
random_seed: Optional[int] = None,
is_random_distance: bool = False,
min_distance: Optional[float] = None,
):
"""Generate displacement dataset in phonon supercell for fc2.
@ -1263,6 +1332,23 @@ class Phono3py:
vectors of the supercell. With True, direction not along the basis
vectors can be chosen when the number of the displacements
may be reduced. Default is False.
number_of_snapshots : int or None, optional
Number of snapshots of supercells with random displacements. Random
displacements are generated displacing all atoms in random
directions with a fixed displacement distance specified by
'distance' parameter, i.e., all atoms in supercell are displaced
with the same displacement distance in direct space. Default is
None.
random_seed : int or None, optional
Random seed for random displacements generation. Default is None.
is_random_distance : bool, optional
Random direction displacements are generated also with random
amplitudes. The maximum value is defined by `distance` and minimum
value is given by `min_distance`. Default is False.
min_distance : float or None, optional
In random direction displacements generation with random distance
(`is_random_distance=True`), the minimum distance is given by this
value.
"""
if self._phonon_supercell_matrix is None:
@ -1273,54 +1359,85 @@ class Phono3py:
)
raise RuntimeError(msg)
phonon_displacement_directions = get_least_displacements(
self._phonon_supercell_symmetry,
is_plusminus=is_plusminus,
is_diagonal=is_diagonal,
)
self._phonon_dataset = directions_to_displacement_dataset(
phonon_displacement_directions, distance, self._phonon_supercell
)
if number_of_snapshots is not None and number_of_snapshots > 0:
self._phonon_dataset = self._generate_random_displacements(
number_of_snapshots,
len(self._phonon_supercell),
distance=distance,
is_plusminus=is_plusminus is True,
random_seed=random_seed,
is_random_distance=is_random_distance,
min_distance=min_distance,
)
else:
phonon_displacement_directions = get_least_displacements(
self._phonon_supercell_symmetry,
is_plusminus=is_plusminus,
is_diagonal=is_diagonal,
)
self._phonon_dataset = directions_to_displacement_dataset(
phonon_displacement_directions, distance, self._phonon_supercell
)
self._phonon_supercells_with_displacements = None
def produce_fc3(
self,
symmetrize_fc3r=False,
is_compact_fc=False,
fc_calculator=None,
fc_calculator_options=None,
symmetrize_fc3r: bool = False,
is_compact_fc: bool = False,
fc_calculator: Optional[str] = None,
fc_calculator_options: Optional[str] = None,
use_pypolymlp: bool = False,
mlp_params: Optional[Union[PypolymlpParams, dict]] = None,
):
"""Calculate fc3 from displacements and forces.
Parameters
----------
symmetrize_fc3r : bool
Only for type 1 displacement_dataset, translational and
permutation symmetries are applied after creating fc3. This
symmetrization is not very sophisticated and can break space
group symmetry, but often useful. If better symmetrization is
expected, it is recommended to use external force constants
calculator such as ALM. Default is False.
Only for type 1 displacement_dataset, translational and permutation
symmetries are applied after creating fc3. This symmetrization is
not very sophisticated and can break space group symmetry, but often
useful. If better symmetrization is expected, it is recommended to
use external force constants calculator such as ALM. Default is
False.
is_compact_fc : bool
fc3 shape is
False: (supercell, supercell, supecell, 3, 3, 3)
True: (primitive, supercell, supecell, 3, 3, 3)
False: (supercell, supercell, supecell, 3, 3, 3) True:
(primitive, supercell, supecell, 3, 3, 3)
where 'supercell' and 'primitive' indicate number of atoms in these
cells. Default is False.
fc_calculator : str or None
Force constants calculator given by str.
fc_calculator_options : dict
Options for external force constants calculator.
use_pypolymlp : bool
Use MLP of pypolymlp to calculate fc3. Default is False. mlp_dataset
has to be set before calling this method.
mlp_params : PypolymlpParams or dict, optional
Parameters for developing MLP. Default is None. When dict is given,
PypolymlpParams instance is created from the dict.
"""
disp_dataset = self._dataset
if use_pypolymlp:
if self._mlp_phonopy is None:
msg = "mlp_dataset has to be set before calling this method."
raise RuntimeError(msg)
if self._dataset is None or "displacements" not in self._dataset:
raise RuntimeError(
"Type 2 displacements are not set. Run generate_displacements."
)
self._mlp_phonopy.develop_mlp(params=mlp_params)
self._mlp_phonopy.displacements = self._dataset["displacements"]
self._mlp_phonopy.evaluate_mlp()
self._dataset["forces"] = self._mlp_phonopy.forces
self._dataset["supercell_energies"] = self._mlp_phonopy.supercell_energies
fc3_calculator, fc3_calculator_options = self._extract_fc2_fc3_calculators(
fc_calculator, fc_calculator_options, 3
)
if fc3_calculator is not None:
disps, forces = get_displacements_and_forces_fc3(disp_dataset)
disps, forces = get_displacements_and_forces_fc3(self._dataset)
fc2, fc3 = get_fc3(
self._supercell,
self._primitive,
@ -1333,7 +1450,7 @@ class Phono3py:
log_level=self._log_level,
)
else:
if "displacements" in disp_dataset:
if "displacements" in self._dataset:
msg = (
"fc_calculator has to be set to produce force "
"constans from this dataset."
@ -1342,7 +1459,7 @@ class Phono3py:
fc2, fc3 = get_phono3py_fc3(
self._supercell,
self._primitive,
disp_dataset,
self._dataset,
self._symmetry,
is_compact_fc=is_compact_fc,
verbose=self._log_level,
@ -2404,3 +2521,31 @@ class Phono3py:
self._phonon_dataset[target] = _values
else:
raise RuntimeError("Set of FC2 displacements is not available.")
def _generate_random_displacements(
self,
number_of_snapshots: int,
number_of_atoms: int,
distance: float = 0.03,
is_plusminus: bool = False,
random_seed: Optional[int] = None,
is_random_distance: bool = False,
min_distance: Optional[float] = None,
):
if random_seed is not None and random_seed >= 0 and random_seed < 2**32:
_random_seed = random_seed
dataset = {"random_seed": _random_seed}
else:
_random_seed = None
dataset = {}
d = get_random_displacements_dataset(
number_of_snapshots,
number_of_atoms,
distance,
random_seed=_random_seed,
is_plusminus=is_plusminus,
is_random_distance=is_random_distance,
min_distance=min_distance,
)
dataset["displacements"] = d
return dataset

7
phono3py/cui/phono3py_argparse.py
View File

@ -618,6 +618,13 @@ def get_parser(fc_symmetry=False, is_nac=False, load_phono3py_yaml=False):
default=None,
help="Conversion factor for ph-ph interaction",
)
parser.add_argument(
"--pypolymlp",
dest="use_pypolymlp",
action="store_true",
default=None,
help="Use pypolymlp and symfc for generating force constants",
)
parser.add_argument(
"--qpoints",
nargs="+",

36
test/api/test_api_phono3py.py
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@ -5,6 +5,8 @@ from __future__ import annotations
from pathlib import Path
import numpy as np
import pytest
from phonopy.interface.pypolymlp import PypolymlpParams
from phono3py import Phono3py
@ -166,3 +168,37 @@ def test_type2_forces_energies_setter_Si(si_111_222_rd: Phono3py):
ph3.phonon_forces = ph3_in.phonon_forces + 1
np.testing.assert_allclose(ph3_in.forces + 1, ph3.forces)
np.testing.assert_allclose(ph3_in.phonon_forces + 1, ph3.phonon_forces)
def test_use_pypolymlp_mgs(mgo_222rd_444rd: Phono3py):
"""Test use_pypolymlp in produce_fc3."""
pytest.importorskip("pypolymlp")
ph3_in = mgo_222rd_444rd
ph3 = Phono3py(
ph3_in.unitcell,
supercell_matrix=ph3_in.supercell_matrix,
phonon_supercell_matrix=ph3_in.phonon_supercell_matrix,
primitive_matrix=ph3_in.primitive_matrix,
log_level=2,
)
ph3.mlp_dataset = {
"displacements": ph3_in.displacements[:10],
"forces": ph3_in.forces[:10],
"supercell_energies": ph3_in.supercell_energies[:10],
}
ph3.phonon_dataset = ph3_in.phonon_dataset
ph3.nac_params = ph3_in.nac_params
ph3.displacements = ph3_in.displacements[:100]
atom_energies = {"Mg": -0.00896717, "O": -0.95743902}
params = PypolymlpParams(gtinv_maxl=(4, 4), atom_energies=atom_energies)
ph3.produce_fc3(use_pypolymlp=True, mlp_params=params, fc_calculator="symfc")
ph3.produce_fc2(fc_calculator="symfc")
ph3.mesh_numbers = 30
ph3.init_phph_interaction()
ph3.run_thermal_conductivity(temperatures=[300])
assert (
pytest.approx(63.6001137, abs=1e-3) == ph3.thermal_conductivity.kappa[0, 0, 0]
)

11
test/conftest.py
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@ -497,6 +497,17 @@ def si_111_222_rd() -> Phono3py:
return phono3py.load(yaml_filename, produce_fc=False, log_level=1)
@pytest.fixture(scope="session")
def mgo_222rd_444rd() -> Phono3py:
"""Return Phono3py class instance of MgO-2x2x2-4x4x4 RD-RD.
4 and 400 supercells for fc2 and fc3, respectively.
"""
yaml_filename = cwd / "phono3py_params_MgO-222rd-444fd.yaml.xz"
return phono3py.load(yaml_filename, produce_fc=False, log_level=1)
@pytest.fixture(scope="session")
def ph_nacl() -> Phonopy:
"""Return Phonopy class instance of NaCl 2x2x2."""

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test/phono3py_params_MgO-222rd-444fd.yaml.xz Normal file
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