def test_only_symmetrize(self):
borns, epsilon = symmetrize_borns_and_epsilon(
self.borns,
self.epsilon,
self.cell)
np.testing.assert_allclose(borns, self.borns)
np.testing.assert_allclose(epsilon, self.epsilon)
def test_symmetrize_borns_and_epsilon_tio2(ph_tio2):
nac_params = ph_tio2.nac_params
borns, epsilon = symmetrize_borns_and_epsilon(nac_params['born'],
nac_params['dielectric'],
ph_tio2.primitive)
# np.testing.assert_allclose(borns, nac_params['born'], atol=1e-8)
np.testing.assert_allclose(epsilon, nac_params['dielectric'], atol=1e-8)
def test_symmetrize_borns_and_epsilon_tio2(ph_tio2):
"""Test symmetrization of Born charges and dielectric tensors by TiO2."""
nac_params = ph_tio2.nac_params
borns, epsilon = symmetrize_borns_and_epsilon(nac_params["born"],
nac_params["dielectric"],
ph_tio2.primitive)
# np.testing.assert_allclose(borns, nac_params['born'], atol=1e-8)
np.testing.assert_allclose(epsilon, nac_params["dielectric"], atol=1e-8)
def test_symmetrize_borns_and_epsilon_nacl(ph_nacl):
"""Test symmetrization of Born charges and dielectric tensors by NaCl."""
nac_params = ph_nacl.nac_params
borns, epsilon = symmetrize_borns_and_epsilon(nac_params["born"],
nac_params["dielectric"],
ph_nacl.primitive)
np.testing.assert_allclose(borns, nac_params["born"], atol=1e-8)
np.testing.assert_allclose(epsilon, nac_params["dielectric"], atol=1e-8)
def test_with_pmat_and_smat(self):
borns, epsilon = symmetrize_borns_and_epsilon(
self.borns,
self.epsilon,
self.cell,
primitive_matrix=self.pmat,
supercell_matrix=self.smat)
np.testing.assert_allclose(borns, self.borns[self.idx])
np.testing.assert_allclose(epsilon, self.epsilon)
def test_with_pmat_and_smat(ph_nacl):
pcell = ph_nacl.primitive
scell = ph_nacl.supercell
idx = [scell.u2u_map[i] for i in scell.s2u_map[pcell.p2s_map]]
uborns, uepsilon = _get_nac_params_in_unitcell(ph_nacl)
borns, epsilon = symmetrize_borns_and_epsilon(
uborns,
uepsilon,
ph_nacl.unitcell,
primitive_matrix=ph_nacl.primitive_matrix,
supercell_matrix=ph_nacl.supercell_matrix)
np.testing.assert_allclose(borns, uborns[idx], atol=1e-8)
np.testing.assert_allclose(epsilon, uepsilon, atol=1e-8)
def test_with_pcell(self):
idx2 = _get_mapping_between_cells(self.pcell, self.pcell)
np.testing.assert_array_equal(
idx2, np.arange(self.pcell.get_number_of_atoms()))
borns, epsilon = symmetrize_borns_and_epsilon(
self.borns,
self.epsilon,
self.cell,
primitive=self.pcell)
np.testing.assert_allclose(borns, self.borns[self.idx][idx2])
np.testing.assert_allclose(epsilon, self.epsilon)
def test_with_pcell(ph_nacl):
pcell = ph_nacl.primitive
scell = ph_nacl.supercell
idx = [scell.u2u_map[i] for i in scell.s2u_map[pcell.p2s_map]]
idx2 = _get_mapping_between_cells(pcell, pcell)
np.testing.assert_array_equal(idx2, np.arange(len(pcell)))
uborns, uepsilon = _get_nac_params_in_unitcell(ph_nacl)
borns, epsilon = symmetrize_borns_and_epsilon(uborns,
uepsilon,
ph_nacl.unitcell,
primitive=pcell)
np.testing.assert_allclose(borns, uborns[idx][idx2], atol=1e-8)
np.testing.assert_allclose(epsilon, uepsilon, atol=1e-8)
def test_with_pmat_and_smat(ph_nacl):
"""Test Born charges and dielectric tensor symmetrization with pmat and smat."""
pcell = ph_nacl.primitive
scell = ph_nacl.supercell
idx = [scell.u2u_map[i] for i in scell.s2u_map[pcell.p2s_map]]
uborns, uepsilon = _get_nac_params_in_unitcell(ph_nacl)
borns, epsilon = symmetrize_borns_and_epsilon(
uborns,
uepsilon,
ph_nacl.unitcell,
primitive_matrix=ph_nacl.primitive_matrix,
supercell_matrix=ph_nacl.supercell_matrix,
)
np.testing.assert_allclose(borns, uborns[idx], atol=1e-8)
np.testing.assert_allclose(epsilon, uepsilon, atol=1e-8)
def get_nac_params(born_charges, epsilon, nac_structure, **params):
"""Obtain Born effective charges and dielectric constants in primitive cell
When Born effective charges and dielectric constants are calculated within
phonopy workchain, those values are calculated in the primitive cell.
However using immigrant, the cell may not be primitive cell and can be
unit cell. In this case, conversion of data is necessary. This conversion
needs information of the structure where those values were calcualted and
the target primitive cell structure.
Two kargs parameters
primitive : StructureData
symmetry_tolerance : Float
"""
from phonopy.structure.symmetry import symmetrize_borns_and_epsilon
borns = born_charges.get_array('born_charges')
eps = epsilon.get_array('epsilon')
nac_cell = phonopy_atoms_from_structure(nac_structure)
kargs = {}
if 'symmetry_tolerance' in params:
kargs['symprec'] = params['symmetry_tolerance'].value
if 'primitive' in params:
pcell = phonopy_atoms_from_structure(params['primitive'])
kargs['primitive'] = pcell
borns_, epsilon_ = symmetrize_borns_and_epsilon(borns, eps, nac_cell,
**kargs)
nac_params = DataFactory('array')()
nac_params.set_array('born_charges', borns_)
nac_params.set_array('epsilon', epsilon_)
nac_params.label = 'born_charges & epsilon'
return nac_params
def _get_indep_borns(ucell,
borns,
epsilon,
primitive_matrix=None,
supercell_matrix=None,
is_symmetry=True,
symmetrize_tensors=False,
symprec=1e-5):
"""Parse Born effective charges and dielectric constants
Args:
ucell (Atoms): Unit cell structure
borns (np.array): Born effective charges of ucell
epsilon (np.array): Dielectric constant tensor
Returns:
(np.array) Born effective charges of symmetrically independent atoms
in primitive cell
(np.array) Dielectric constant
(np.array) Atomic index mapping table from supercell to primitive cell
of independent atoms
Raises:
AssertionError: Inconsistency of number of atoms or Born effective
charges.
Warning:
Broken symmetry of Born effective charges
"""
assert len(borns) == ucell.get_number_of_atoms(), \
"num_atom %d != len(borns) %d" % (ucell.get_number_of_atoms(),
len(borns))
if symmetrize_tensors:
borns_, epsilon_ = symmetrize_borns_and_epsilon(
borns, epsilon, ucell, symprec=symprec, is_symmetry=is_symmetry)
if (abs(borns - borns_) > 0.1).any():
lines = [
"Born effective charge symmetry is largely broken. "
"Largest different among elements: "
"%s" % np.amax(abs(borns - borns_))
]
import warnings
warnings.warn("\n".join(lines))
borns = borns_
epsilon = epsilon_
borns, s_indep_atoms = _extract_independent_borns(
borns,
ucell,
primitive_matrix=primitive_matrix,
supercell_matrix=supercell_matrix,
is_symmetry=is_symmetry,
symprec=symprec)
return borns, epsilon, s_indep_atoms
