from typing import Any, Dict
import numpy as np
from ase import Atoms
from ase.calculators.singlepoint import SinglePointCalculator
try:
from phonopy import Phonopy
from phonopy.structure.atoms import PhonopyAtoms
except ModuleNotFoundError: # pragma: no cover
raise ModuleNotFoundError('phonopy (https://pypi.org/project/phonopy/) is '
'required in order to use the functionality '
'in the phonons module.'
) # pragma: no cover
[docs]
def get_force_constants(structure: Atoms,
calculator: SinglePointCalculator,
supercell_matrix: np.ndarray,
kwargs_phonopy: Dict[str, Any] = {},
kwargs_generate_displacements: Dict[str, Any] = {}) -> Phonopy:
"""
Calculates the force constants for a given structure using
`phonopy <https://phonopy.github.io/phonopy/>`_, which needs to be cited if this function
is used for generating data for publication.
The function returns a `Phonopy` object that can be used to calculate, e.g.,
the phonon dispersion, the phonon density of states as well as related quantities such
as the thermal displacements and the free energy.
Parameters
----------
structure
structure for which to compute the phonon dispersion; usually this is a primitive cell
calculator
ASE calculator to use for the calculation of forces
supercell_matrix
specification of supercell size handed over to phonopy;
should be a tuple of three values or a matrix
kwargs_phonopy
*Expert option*:
keyword arguments used when initializing the `Phonopy` object;
this includes, e.g., the tolerance used when determining the symmetry (`symprec`) and
`parameters for the non-analytical corrections
<https://phonopy.github.io/phonopy/phonopy-module.html#non-analytical-term-correction>`_
(`nac_params`)
kwargs_generate_displacements
*Expert option*:
keyword arguments to be handed over to the `generate_displacements` method;
this includes in particular the `distance` keyword, which specifies the
magnitude of the atomic displacement imposed when calculating the force constant matrix
"""
# prepare primitive unit cell for phonopy
structure_ph = PhonopyAtoms(symbols=structure.symbols,
cell=structure.cell,
scaled_positions=structure.get_scaled_positions(),
pbc=structure.pbc)
# make sure we are using the masses intended by the user
structure_ph.masses = structure.get_masses()
# prepare supercells
phonon = Phonopy(structure_ph, supercell_matrix, **kwargs_phonopy)
phonon.generate_displacements(**kwargs_generate_displacements)
# compute force constant matrix
forces = []
for structure_ph in phonon.supercells_with_displacements:
structure_ase = Atoms(symbols=structure_ph.symbols,
cell=structure_ph.cell,
scaled_positions=structure_ph.scaled_positions,
pbc=structure.pbc)
structure_ase.calc = calculator
forces.append(structure_ase.get_forces().copy())
phonon.forces = forces
phonon.produce_force_constants()
return phonon