mirror of https://github.com/phonopy/phono3py.git
Add Phono3py.fc3_nonzero_indices
This commit is contained in:
Atsushi Togo
parent
03a26d1b6d
commit
8d0db5c396
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@ -38,9 +38,10 @@ from __future__ import annotations
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import copy
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import warnings
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from collections.abc import Sequence
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from typing import Literal, Optional, Union
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from typing import Literal, Optional, Union, cast
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import numpy as np
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from numpy.typing import NDArray
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from phonopy.harmonic.displacement import (
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directions_to_displacement_dataset,
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get_least_displacements,
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@ -58,6 +59,7 @@ from phonopy.interface.mlp import PhonopyMLP
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from phonopy.interface.pypolymlp import (
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PypolymlpParams,
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)
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from phonopy.interface.symfc import SymfcFCSolver
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from phonopy.physical_units import get_physical_units
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from phonopy.structure.atoms import PhonopyAtoms
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from phonopy.structure.cells import (
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@ -298,7 +300,7 @@ class Phono3py:
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# Force constants
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self._fc2 = None
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self._fc3 = None
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self._fc3_nonzero_elems = None # available only symfc
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self._fc3_nonzero_indices = None # available only symfc
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# MLP
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self._mlp = None
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@ -333,7 +335,7 @@ class Phono3py:
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return self._calculator
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@property
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def fc3(self) -> Optional[np.ndarray]:
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def fc3(self) -> NDArray | None:
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"""Setter and getter of third order force constants (fc3).
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ndarray
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@ -350,7 +352,18 @@ class Phono3py:
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self._fc3 = fc3
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@property
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def fc2(self) -> Optional[np.ndarray]:
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def fc3_nonzero_indices(self) -> NDArray | None:
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"""Return non-zero indices of fc3.
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ndarray
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Non-zero indices of fc3. This is available only when
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SymfcFCSolver is used.
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"""
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return self._fc3_nonzero_indices
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@property
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def fc2(self) -> NDArray | None:
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"""Setter and getter of second order force constants (fc2).
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ndarray
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@ -367,7 +380,7 @@ class Phono3py:
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self._fc2 = fc2
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@property
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def force_constants(self) -> Optional[np.ndarray]:
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def force_constants(self) -> NDArray | None:
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"""Return fc2. This is same as the getter attribute `fc2`."""
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return self.fc2
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@ -538,7 +551,7 @@ class Phono3py:
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return self._phonon_supercell_symmetry
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@property
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def supercell_matrix(self) -> np.ndarray:
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def supercell_matrix(self) -> NDArray:
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"""Return transformation matrix to supercell cell from unit cell.
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ndarray
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@ -549,7 +562,7 @@ class Phono3py:
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return self._supercell_matrix
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@property
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def phonon_supercell_matrix(self) -> Optional[np.ndarray]:
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def phonon_supercell_matrix(self) -> NDArray | None:
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"""Return transformation matrix to phonon supercell from unit cell.
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ndarray
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@ -560,7 +573,7 @@ class Phono3py:
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return self._phonon_supercell_matrix
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@property
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def primitive_matrix(self) -> np.ndarray:
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def primitive_matrix(self) -> NDArray:
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"""Return transformation matrix to primitive cell from unit cell.
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ndarray
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@ -731,10 +744,10 @@ class Phono3py:
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self._mlp = mlp
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@property
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def band_indices(self) -> list[np.ndarray]:
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def band_indices(self) -> list[NDArray]:
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"""Setter and getter of band indices.
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list[np.ndarray]
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list[NDArray]
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List of band indices specified to select specific bands
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to computer ph-ph interaction related properties.
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@ -754,7 +767,7 @@ class Phono3py:
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self._band_indices_flatten = np.hstack(self._band_indices).astype("int64")
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@property
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def masses(self) -> np.ndarray:
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def masses(self) -> NDArray:
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"""Setter and getter of atomic masses of primitive cell."""
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return self._primitive.masses
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@ -815,7 +828,7 @@ class Phono3py:
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return self._bz_grid.D_diag
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@mesh_numbers.setter
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def mesh_numbers(self, mesh_numbers: Union[int, float, Sequence, np.ndarray]):
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def mesh_numbers(self, mesh_numbers: Union[int, float, Sequence, NDArray]):
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self._set_mesh_numbers(mesh_numbers)
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@property
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@ -1319,8 +1332,6 @@ class Phono3py:
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number_of_snapshots == "auto" or number_of_snapshots > 0
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):
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if number_of_snapshots == "auto":
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from phonopy.interface.symfc import SymfcFCSolver
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if cutoff_pair_distance is None:
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options = None
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else:
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@ -1431,8 +1442,6 @@ class Phono3py:
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number_of_snapshots == "auto" or number_of_snapshots > 0
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):
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if number_of_snapshots == "auto":
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from phonopy.interface.symfc import SymfcFCSolver
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_number_of_snapshots = (
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SymfcFCSolver(
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self._supercell, symmetry=self._symmetry
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@ -1520,20 +1529,21 @@ class Phono3py:
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symmetrize_force_constants(fc2)
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self._fc3 = fc3
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self._fc3_nonzero_elems = None
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self._fc3_nonzero_indices = None
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if fc_calculator == "symfc":
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fc_cutoff = fc_solver.fc_solver.basis_set[3].fc_cutoff
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if fc_cutoff is not None:
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fc3_nonzero_elems = fc_cutoff.nonzero_atomic_indices_fc3()
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N = len(self._supercell)
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assert len(fc3_nonzero_elems) == N**3
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fc3_nonzero_elems = fc3_nonzero_elems.reshape((N, N, N))
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symfc_solver = cast(SymfcFCSolver, fc_solver.fc_solver)
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fc3_nonzero_elems = symfc_solver.get_nonzero_atomic_indices_fc3()
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if fc3_nonzero_elems is not None:
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if is_compact_fc:
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self._fc3_nonzero_elems = np.array(
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fc3_nonzero_elems[self._primitive.p2s_map, :, :], dtype="byte"
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self._fc3_nonzero_indices = np.array(
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fc3_nonzero_elems[self._primitive.p2s_map],
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dtype="byte",
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order="C",
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)
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else:
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self._fc3_nonzero_elems = np.array(fc3_nonzero_elems, dtype="byte")
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self._fc3_nonzero_indices = np.array(
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fc3_nonzero_elems, dtype="byte", order="C"
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)
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# fc2 as obtained above will not be set when "|" in fc-calculator setting.
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if fc_calculator is not None and "|" in fc_calculator:
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@ -2542,7 +2552,7 @@ class Phono3py:
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def _set_mesh_numbers(
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self,
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mesh: Union[int, float, Sequence, np.ndarray],
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mesh: Union[int, float, Sequence, NDArray],
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):
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# initialization related to mesh
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self._interaction = None
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@ -2588,7 +2598,7 @@ class Phono3py:
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def _get_forces_energies(
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self, target: Literal["forces", "supercell_energies"]
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) -> Optional[np.ndarray]:
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) -> NDArray | None:
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"""Return fc3 forces and supercell energies.
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Return None if tagert data is not found rather than raising exception.
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@ -2653,7 +2663,7 @@ class Phono3py:
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def _get_phonon_forces_energies(
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self, target: Literal["forces", "supercell_energies"]
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) -> Optional[np.ndarray]:
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) -> NDArray | None:
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"""Return fc2 forces and supercell energies.
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Return None if tagert data is not found rather than raising exception.
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@ -322,6 +322,49 @@ def si_pbesol_111_222_alm_cutoff(request) -> Phono3py:
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)
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@pytest.fixture(scope="session")
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def si_pbesol_111_222_symfc_cutoff() -> Phono3py:
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"""Return Phono3py instance of Si 1x1x1.
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* with symmetry
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* full fc
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* use symfc if available on test side
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* cutoff=3
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"""
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pytest.importorskip("symfc")
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yaml_filename = cwd / "phono3py_params_Si-111-222.yaml"
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return phono3py.load(
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yaml_filename,
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fc_calculator="symfc",
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fc_calculator_options="cutoff = 3",
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log_level=1,
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)
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@pytest.fixture(scope="session")
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def si_pbesol_111_222_symfc_cutoff_compact_fc() -> Phono3py:
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"""Return Phono3py instance of Si 1x1x1.
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* with symmetry
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* compact fc
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* use symfc if available on test side
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* cutoff=3
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"""
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pytest.importorskip("symfc")
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yaml_filename = cwd / "phono3py_params_Si-111-222.yaml"
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return phono3py.load(
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yaml_filename,
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fc_calculator="symfc",
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fc_calculator_options="cutoff = 3",
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is_compact_fc=True,
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log_level=1,
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)
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@pytest.fixture(scope="session")
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def si_pbesol_111_222_alm_cutoff_fc2(request) -> Phono3py:
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"""Return Phono3py instance of Si 1x1x1.
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@ -218,10 +218,40 @@ def test_phonon_smat_fd_symfc(si_pbesol_111_222_fd_symfc: Phono3py):
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def test_phonon_smat_alm_cutoff(si_pbesol_111_222_alm_cutoff: Phono3py):
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"""Test phonon smat and alm with Si PBEsol 1x1x1-2x2x2 cutoff."""
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ph = si_pbesol_111_222_alm_cutoff
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assert ph.fc3 is not None
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assert ph.fc2 is not None
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np.testing.assert_allclose(ph.fc3[0, 1, 7], 0, atol=1e-6, rtol=0)
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np.testing.assert_allclose(ph.fc2[0, 33], 0, atol=1e-6, rtol=0)
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def test_phonon_smat_symfc_cutoff(si_pbesol_111_222_symfc_cutoff: Phono3py):
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"""Test phonon smat and symfc with Si PBEsol 1x1x1-2x2x2 cutoff."""
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ph = si_pbesol_111_222_symfc_cutoff
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assert ph.fc3 is not None
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assert ph.fc2 is not None
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assert ph.fc3_nonzero_indices is not None
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np.testing.assert_allclose(ph.fc3[0, 1, 7], 0, atol=1e-6, rtol=0)
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np.testing.assert_allclose(ph.fc2[0, 33], 0, atol=1e-6, rtol=0)
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assert ph.fc3.shape == (8, 8, 8, 3, 3, 3)
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assert ph.fc3_nonzero_indices.shape == (8, 8, 8)
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assert ph.fc3_nonzero_indices.sum() == 104
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def test_phonon_smat_symfc_cutoff_compact_fc(
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si_pbesol_111_222_symfc_cutoff_compact_fc: Phono3py,
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):
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"""Test phonon smat and symfc with Si PBEsol 1x1x1-2x2x2 cutoff."""
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ph = si_pbesol_111_222_symfc_cutoff_compact_fc
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assert ph.fc3 is not None
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assert ph.fc2 is not None
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assert ph.fc3_nonzero_indices is not None
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np.testing.assert_allclose(ph.fc3[0, 1, 7], 0, atol=1e-6, rtol=0)
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np.testing.assert_allclose(ph.fc2[0, 33], 0, atol=1e-6, rtol=0)
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assert ph.fc3.shape == (2, 8, 8, 3, 3, 3)
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assert ph.fc3_nonzero_indices.shape == (2, 8, 8)
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assert ph.fc3_nonzero_indices.sum() == 26
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def test_phonon_smat_alm_cutoff_fc2(si_pbesol_111_222_alm_cutoff_fc2: Phono3py):
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"""Test phonon smat and alm with Si PBEsol 1x1x1-2x2x2 cutoff fc2."""
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ph = si_pbesol_111_222_alm_cutoff_fc2
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