def test_get_supercell_nacl_snf(convcell_nacl: PhonopyAtoms, helper_methods):
"""Test of get_supercell using SNF by NaCl."""
cell = convcell_nacl
smat = [[-1, 1, 1], [1, -1, 1], [1, 1, -1]]
scell = get_supercell(cell, smat, is_old_style=True)
scell_snf = get_supercell(cell, smat, is_old_style=False)
helper_methods.compare_cells(scell, scell_snf)
def test_get_supercell_Cr(convcell_cr: PhonopyAtoms, helper_methods):
"""Test of get_supercell using SNF by Cr with magnetic moments."""
convcell_cr.magnetic_moments = [1, -1]
smat = [[-1, 1, 1], [1, -1, 1], [1, 1, -1]]
scell = get_supercell(convcell_cr, smat, is_old_style=True)
np.testing.assert_allclose(
scell.magnetic_moments,
[1.0, 1.0, 1.0, 1.0, -1.0, -1.0, -1.0, -1.0],
atol=1e-8,
)
scell_snf = get_supercell(convcell_cr, smat, is_old_style=False)
helper_methods.compare_cells(scell, scell_snf)
convcell_cr.magnetic_moments = None
def get_commensurate_points(supercell_matrix): # wrt primitive cell
rec_primitive = Atoms(numbers=[1],
scaled_positions=[[0, 0, 0]],
cell=np.diag([1, 1, 1]),
pbc=True)
rec_supercell = get_supercell(rec_primitive, supercell_matrix.T)
return rec_supercell.get_scaled_positions()
def __init__(self,
dynamical_matrix,
dimension,
phonon_modes,
delta_q=None,
derivative_order=None,
nac_q_direction=None,
factor=VaspToTHz):
"""Class describe atomic modulations
Atomic modulations corresponding to phonon modes are created.
"""
self._dm = dynamical_matrix
self._primitive = dynamical_matrix.get_primitive()
self._phonon_modes = phonon_modes
self._dimension = dimension
self._delta_q = delta_q # 1st/2nd order perturbation direction
self._nac_q_direction = nac_q_direction
self._ddm = DerivativeOfDynamicalMatrix(dynamical_matrix)
self._derivative_order = derivative_order
self._factor = factor
self._u = []
self._eigvecs = []
self._eigvals = []
self._supercell = None
dim = self._get_dimension_3x3()
self._supercell = get_supercell(self._primitive, dim)
def _arrange_supercell_fc(self, cell, q2r_fc, is_full_fc=False):
dim = self.dimension
q2r_spos = self._get_q2r_positions(cell)
scell = get_supercell(cell, np.diag(dim))
pcell = get_primitive(scell, np.diag(1.0 / dim))
diff = cell.get_scaled_positions() - pcell.get_scaled_positions()
diff -= np.rint(diff)
assert (np.abs(diff) < 1e-8).all()
assert scell.get_number_of_atoms() == len(q2r_spos)
site_map = self._get_site_mapping(scell.get_scaled_positions(),
q2r_spos,
scell.get_cell())
natom = pcell.get_number_of_atoms()
ndim = np.prod(dim)
natom_s = natom * ndim
if is_full_fc:
fc = np.zeros((natom_s, natom_s, 3, 3), dtype='double', order='C')
p2s = pcell.get_primitive_to_supercell_map()
fc[p2s, :] = q2r_fc[:, site_map]
distribute_force_constants_by_translations(fc,
pcell,
scell)
else:
fc = np.zeros((natom, natom_s, 3, 3), dtype='double', order='C')
fc[:, :] = q2r_fc[:, site_map]
return fc, pcell, scell
def _extract_independent_borns(borns,
ucell,
primitive_matrix=None,
supercell_matrix=None,
is_symmetry=True,
symprec=1e-5):
if primitive_matrix is None:
pmat = np.eye(3)
else:
pmat = primitive_matrix
if supercell_matrix is None:
smat = np.eye(3, dtype='intc')
else:
smat = supercell_matrix
inv_smat = np.linalg.inv(smat)
scell = get_supercell(ucell, smat, symprec=symprec)
pcell = get_primitive(scell, np.dot(inv_smat, pmat), symprec=symprec)
p2s = np.array(pcell.get_primitive_to_supercell_map(), dtype='intc')
p_sym = Symmetry(pcell, is_symmetry=is_symmetry, symprec=symprec)
s_indep_atoms = p2s[p_sym.get_independent_atoms()]
u2u = scell.get_unitcell_to_unitcell_map()
u_indep_atoms = [u2u[x] for x in s_indep_atoms]
reduced_borns = borns[u_indep_atoms].copy()
return reduced_borns, s_indep_atoms
def get_born_OUTCAR(
poscar_filename="POSCAR",
outcar_filename="OUTCAR",
primitive_axis=np.eye(3),
supercell_matrix=np.eye(3, dtype="intc"),
is_symmetry=True,
symmetrize_tensors=False,
symprec=1e-5,
):
ucell = read_vasp(poscar_filename)
outcar = open(outcar_filename)
borns, epsilon = _read_born_and_epsilon(outcar)
num_atom = len(borns)
assert num_atom == ucell.get_number_of_atoms()
if symmetrize_tensors:
lattice = ucell.get_cell().T
positions = ucell.get_scaled_positions()
u_sym = Symmetry(ucell, is_symmetry=is_symmetry, symprec=symprec)
point_sym = [similarity_transformation(lattice, r) for r in u_sym.get_pointgroup_operations()]
epsilon = _symmetrize_tensor(epsilon, point_sym)
borns = _symmetrize_borns(borns, u_sym, lattice, positions, symprec)
inv_smat = np.linalg.inv(supercell_matrix)
scell = get_supercell(ucell, supercell_matrix, symprec=symprec)
pcell = get_primitive(scell, np.dot(inv_smat, primitive_axis), symprec=symprec)
p2s = np.array(pcell.get_primitive_to_supercell_map(), dtype="intc")
p_sym = Symmetry(pcell, is_symmetry=is_symmetry, symprec=symprec)
s_indep_atoms = p2s[p_sym.get_independent_atoms()]
u2u = scell.get_unitcell_to_unitcell_map()
u_indep_atoms = [u2u[x] for x in s_indep_atoms]
reduced_borns = borns[u_indep_atoms].copy()
return reduced_borns, epsilon
def _set_supercell(self):
supercell = get_supercell(self._unitcell, self._supercell_matrix,
self._symprec)
self.set_supercell(supercell)
self._primitive = Primitive(supercell,
np.linalg.inv(self._supercell_matrix),
self._symprec)
def _prepare_unfolding(self, qpoints, unfolding_supercell_matrix):
supercell = get_supercell(self._cell, np.diag([2, 2, 2]))
phonon = self._get_phonon(supercell)
mapping = range(supercell.get_number_of_atoms())
self._unfolding = Unfolding(phonon, unfolding_supercell_matrix,
supercell.get_scaled_positions(), mapping,
qpoints)
def dynmat(self, supercell, q=None, cutoff=0.1):
"""Returns the non-zero eigenvalues and their corresponding eigenvectors
for the specified supercell.
Args:
supercell (numpy.ndarray): supercell matrix to use in generating the
configs.
q (numpy.ndarray): q-vector that the resulting supercell should be
compatible with.
cutoff (float): minimum value an eigenvalue should have before it is
included in the set.
"""
#We need to determine the supercell matrix that is compatible with the
#given `q` and has `N` atoms.
scell = get_supercell(self.primitive, supercell)
eigvals, eigvecs = self.diagonalize(q)
result = {
"template": phonopy_to_ase(scell),
"eigvals": [],
"eigvecs": []
}
for i, l in enumerate(eigvals):
if np.abs(l) > 0.1:
meigvec = self._map_eigvec_supercell(scell, eigvecs[:, i])
result["eigvals"].append(l)
result["eigvecs"].append(meigvec)
return result
def __init__(
self,
dynamical_matrix: Union[DynamicalMatrix, DynamicalMatrixNAC],
dimension,
phonon_modes,
delta_q=None,
derivative_order=None,
nac_q_direction=None,
factor=VaspToTHz,
):
"""Init method."""
self._dm = dynamical_matrix
self._primitive = dynamical_matrix.primitive
self._phonon_modes = phonon_modes
self._dimension = np.array(dimension).ravel()
self._delta_q = delta_q # 1st/2nd order perturbation direction
self._nac_q_direction = nac_q_direction
self._ddm = DerivativeOfDynamicalMatrix(dynamical_matrix)
self._derivative_order = derivative_order
self._factor = factor
dim = self._get_dimension_3x3()
self._supercell = get_supercell(self._primitive, dim)
complex_dtype = "c%d" % (np.dtype("double").itemsize * 2)
self._u = np.zeros(
(len(self._phonon_modes), len(self._supercell), 3),
dtype=complex_dtype,
order="C",
)
self._eigvals = np.zeros(len(self._phonon_modes), dtype="double")
self._eigvecs = np.zeros(
(len(self._phonon_modes), len(self._primitive) * 3), dtype=complex_dtype
)
def __init__(self,
dynamical_matrix,
dimension,
phonon_modes,
delta_q=None,
derivative_order=None,
nac_q_direction=None,
factor=VaspToTHz):
"""Class describe atomic modulations
Atomic modulations corresponding to phonon modes are created.
"""
self._dm = dynamical_matrix
self._primitive = dynamical_matrix.get_primitive()
self._phonon_modes = phonon_modes
self._dimension = dimension
self._delta_q = delta_q # 1st/2nd order perturbation direction
self._nac_q_direction = nac_q_direction
self._ddm = DerivativeOfDynamicalMatrix(dynamical_matrix)
self._derivative_order = derivative_order
self._factor = factor
self._u = []
self._eigvecs = []
self._eigvals = []
self._supercell = None
dim = self._get_dimension_3x3()
self._supercell = get_supercell(self._primitive, dim)
def _arrange_supercell_fc(self, cell, q2r_fc, is_full_fc=False):
dim = self.dimension
q2r_spos = self._get_q2r_positions(cell)
scell = get_supercell(cell, np.diag(dim))
pcell = get_primitive(scell, np.diag(1.0 / dim))
diff = cell.get_scaled_positions() - pcell.get_scaled_positions()
diff -= np.rint(diff)
assert (np.abs(diff) < 1e-8).all()
assert scell.get_number_of_atoms() == len(q2r_spos)
site_map = self._get_site_mapping(scell.get_scaled_positions(),
q2r_spos,
scell.get_cell())
natom = pcell.get_number_of_atoms()
ndim = np.prod(dim)
natom_s = natom * ndim
if is_full_fc:
fc = np.zeros((natom_s, natom_s, 3, 3), dtype='double', order='C')
p2s = pcell.get_primitive_to_supercell_map()
fc[p2s, :] = q2r_fc[:, site_map]
distribute_force_constants_by_translations(fc,
pcell,
scell)
else:
fc = np.zeros((natom, natom_s, 3, 3), dtype='double', order='C')
fc[:, :] = q2r_fc[:, site_map]
return fc, pcell, scell
def ph2fc(ph_orig, supercell_matrix):
"""Transform force constants in Phonopy instance to other shape
For example, ph_orig.supercell_matrix is np.diag([2, 2, 2]) and
supercell_matrix is np.diag([4, 4, 4]), force constants having the
later shape are returned. This is considered useful when ph_orig
has non-analytical correction (NAC). The effect of this correction
is included in the returned force constants. Phonons before and after
this operation at commensurate points of the later supercell_matrix
should agree.
"""
smat = shape_supercell_matrix(supercell_matrix)
scell = get_supercell(ph_orig.unitcell, smat)
pcell = get_primitive(
scell,
np.dot(np.linalg.inv(smat), ph_orig.primitive_matrix),
positions_to_reorder=ph_orig.primitive.scaled_positions)
d2f = DynmatToForceConstants(pcell, scell)
ph_orig.run_qpoints(d2f.commensurate_points, with_dynamical_matrices=True)
ph_dict = ph_orig.get_qpoints_dict()
d2f.dynamical_matrices = ph_dict['dynamical_matrices']
d2f.run()
return d2f.force_constants
def get_commensurate_points(supercell_matrix): # wrt primitive cell
"""Commensurate q-points are returned.
Parameters
----------
supercell_matrix : array_like
Supercell matrix with respect to primitive cell basis vectors.
shape=(3, 3), dtype=int
Returns
-------
commensurate_points : ndarray
Commensurate points corresponding to supercell matrix.
shape=(N, 3), dtype='double', order='C'
where N = det(supercell_matrix)
"""
smat = np.array(supercell_matrix, dtype=int)
rec_primitive = PhonopyAtoms(numbers=[1],
scaled_positions=[[0, 0, 0]],
cell=np.diag([1, 1, 1]),
pbc=True)
rec_supercell = get_supercell(rec_primitive, smat.T)
q_pos = rec_supercell.scaled_positions
return np.array(np.where(q_pos > 1 - 1e-15, q_pos - 1, q_pos),
dtype='double',
order='C')
def _extract_independent_borns(borns,
ucell,
primitive_matrix=None,
supercell_matrix=None,
is_symmetry=True,
symprec=1e-5):
if primitive_matrix is None:
pmat = np.eye(3)
else:
pmat = primitive_matrix
if supercell_matrix is None:
smat = np.eye(3, dtype='intc')
else:
smat = supercell_matrix
inv_smat = np.linalg.inv(smat)
scell = get_supercell(ucell, smat, symprec=symprec)
pcell = get_primitive(scell, np.dot(inv_smat, pmat), symprec=symprec)
p2s = np.array(pcell.get_primitive_to_supercell_map(), dtype='intc')
p_sym = Symmetry(pcell, is_symmetry=is_symmetry, symprec=symprec)
s_indep_atoms = p2s[p_sym.get_independent_atoms()]
u2u = scell.get_unitcell_to_unitcell_map()
u_indep_atoms = [u2u[x] for x in s_indep_atoms]
reduced_borns = borns[u_indep_atoms].copy()
return reduced_borns, s_indep_atoms
def _set_supercell(self):
supercell = get_supercell(self._unitcell,
self._supercell_matrix,
self._symprec)
self.set_supercell(supercell)
self._primitive = Primitive(supercell,
np.linalg.inv(self._supercell_matrix),
self._symprec)
def get_commensurate_points(primitive, supercell):
supercell_matrix = np.linalg.inv(primitive.get_primitive_matrix()).T
rec_primitive = Atoms(numbers=[1],
scaled_positions=[[0, 0, 0]],
cell=np.diag([1, 1, 1]),
pbc=True)
rec_supercell = get_supercell(rec_primitive, supercell_matrix)
return rec_supercell.get_scaled_positions()
def get_commensurate_points(primitive, supercell):
supercell_matrix = np.linalg.inv(primitive.get_primitive_matrix()).T
rec_primitive = Atoms(numbers=[1],
scaled_positions=[[0, 0, 0]],
cell=np.diag([1, 1, 1]),
pbc=True)
rec_supercell = get_supercell(rec_primitive, supercell_matrix)
return rec_supercell.get_scaled_positions()
def _prepare_unfolding(self, qpoints, unfolding_supercell_matrix):
supercell = get_supercell(self._cell, np.diag([2, 2, 2]))
phonon = self._get_phonon(supercell)
self._set_nac_params(phonon)
mapping = range(supercell.get_number_of_atoms())
self._unfolding = Unfolding(
phonon, unfolding_supercell_matrix, supercell.get_scaled_positions(), mapping, qpoints
)
def test_get_commensurate_points(self):
smat = np.diag([2, 2, 2])
pmat = np.dot(np.linalg.inv(smat),
[[0, 0.5, 0.5], [0.5, 0, 0.5], [0.5, 0.5, 0]])
supercell = get_supercell(self._cell, smat)
primitive = get_primitive(supercell, pmat)
comm_points = get_commensurate_points(primitive, supercell)
for i, p in enumerate(comm_points):
print("%d %s" % (i + 1, p))
def test_get_primitive_convcell_Cr(convcell_cr: PhonopyAtoms, helper_methods):
"""Test get_primitive by NaCl."""
convcell_cr.magnetic_moments = [1, -1]
smat = [[2, 0, 0], [0, 2, 0], [0, 0, 2]]
scell = get_supercell(convcell_cr, smat, is_old_style=True)
pmat = np.linalg.inv(smat)
pcell = get_primitive(scell, pmat)
helper_methods.compare_cells(convcell_cr, pcell)
convcell_cr.magnetic_moments = None
def test_get_commensurate_points(self):
smat = np.diag([2, 2, 2])
pmat = np.dot(np.linalg.inv(smat),
[[0, 0.5, 0.5], [0.5, 0, 0.5], [0.5, 0.5, 0]])
supercell = get_supercell(self._cell, smat)
primitive = get_primitive(supercell, pmat)
comm_points = get_commensurate_points(primitive, supercell)
for i, p in enumerate(comm_points):
print("%d %s" % (i + 1, p))
def _set_translations(self):
pcell = Atoms(numbers=[1],
scaled_positions=[[0, 0, 0]],
cell=np.diag([1, 1, 1]),
pbc=True)
smat = self._supercell_matrix
self._trans_s = get_supercell(pcell, smat).get_scaled_positions()
self._trans_p = np.dot(self._trans_s, self._supercell_matrix.T)
self._N = len(self._trans_s)
def _set_translations(self):
pcell = Atoms(numbers=[1],
scaled_positions=[[0, 0, 0]],
cell=np.diag([1, 1, 1]),
pbc=True)
smat = self._supercell_matrix
self._trans_s = get_supercell(pcell, smat).get_scaled_positions()
self._trans_p = np.dot(self._trans_s, self._supercell_matrix.T)
self._N = len(self._trans_s)
def get_commensurate_points(supercell_matrix): # wrt primitive cell
rec_primitive = Atoms(numbers=[1],
scaled_positions=[[0, 0, 0]],
cell=np.diag([1, 1, 1]),
pbc=True)
rec_supercell = get_supercell(rec_primitive, supercell_matrix.T)
q_pos = rec_supercell.get_scaled_positions()
return np.array(np.where(q_pos > 1 - 1e-15, q_pos - 1, q_pos),
dtype='double', order='C')
def get_commensurate_points(supercell_matrix): # wrt primitive cell
rec_primitive = PhonopyAtoms(numbers=[1],
scaled_positions=[[0, 0, 0]],
cell=np.diag([1, 1, 1]),
pbc=True)
rec_supercell = get_supercell(rec_primitive, supercell_matrix.T)
q_pos = rec_supercell.get_scaled_positions()
return np.array(np.where(q_pos > 1 - 1e-15, q_pos - 1, q_pos),
dtype='double', order='C')
def test_get_commensurate_points(self):
smat = np.diag([2, 2, 2])
pmat = np.dot(np.linalg.inv(smat),
[[0, 0.5, 0.5], [0.5, 0, 0.5], [0.5, 0.5, 0]])
supercell = get_supercell(self._cell, smat)
primitive = get_primitive(supercell, pmat)
supercell_matrix = np.linalg.inv(primitive.get_primitive_matrix())
supercell_matrix = np.rint(supercell_matrix).astype('intc')
comm_points = get_commensurate_points(supercell_matrix)
# self._write(comm_points)
self._compare(comm_points)
def _test_get_supercell_primcell_si(primcell_si: PhonopyAtoms,
helper_methods,
is_old_style=True):
smat = [[-1, 1, 1], [1, -1, 1], [1, 1, -1]]
fname = "Si-conv.yaml"
scell = get_supercell(primcell_si, smat, is_old_style=is_old_style)
cell_ref = read_cell_yaml(os.path.join(data_dir, fname))
if is_old_style is True:
helper_methods.compare_cells_with_order(scell, cell_ref)
else:
helper_methods.compare_cells(scell, cell_ref)
def _test_get_supercell_convcell_sio2(convcell_sio2: PhonopyAtoms,
helper_methods,
is_old_style=True):
smat = np.diag([1, 2, 3])
fname = "SiO2-123.yaml"
scell = get_supercell(convcell_sio2, smat, is_old_style=is_old_style)
cell_ref = read_cell_yaml(os.path.join(data_dir, fname))
if is_old_style is True:
helper_methods.compare_cells_with_order(scell, cell_ref)
else:
helper_methods.compare_cells(scell, cell_ref)
def test_get_commensurate_points(self):
smat = np.diag([2, 2, 2])
pmat = np.dot(np.linalg.inv(smat),
[[0, 0.5, 0.5], [0.5, 0, 0.5], [0.5, 0.5, 0]])
supercell = get_supercell(self._cell, smat)
primitive = get_primitive(supercell, pmat)
supercell_matrix = np.linalg.inv(primitive.get_primitive_matrix())
supercell_matrix = np.rint(supercell_matrix).astype('intc')
comm_points = get_commensurate_points(supercell_matrix)
# self._write(comm_points)
self._compare(comm_points)
def _build_phonon_supercell(self):
"""
phonon_supercell:
This supercell is used for harmonic phonons (frequencies,
eigenvectors, group velocities, ...)
phonon_supercell_matrix:
Different supercell size can be specified.
"""
if self._phonon_supercell_matrix is None:
self._phonon_supercell = self._supercell
else:
self._phonon_supercell = get_supercell(self._unitcell, self._phonon_supercell_matrix, self._symprec)
def _build_phonon_supercell(self):
"""
phonon_supercell:
This supercell is used for harmonic phonons (frequencies,
eigenvectors, group velocities, ...)
phonon_supercell_matrix:
Different supercell size can be specified.
"""
if self._phonon_supercell_matrix is None:
self._phonon_supercell = self._supercell
else:
self._phonon_supercell = get_supercell(
self._unitcell, self._phonon_supercell_matrix, self._symprec)
def setUp(self):
pmat = [[0, 0.5, 0.5], [0.5, 0, 0.5], [0.5, 0.5, 0]]
smat2 = np.eye(3, dtype='intc') * 2
pmat2 = np.dot(np.linalg.inv(smat2), pmat)
smat3 = np.eye(3, dtype='intc') * 3
pmat3 = np.dot(np.linalg.inv(smat3), pmat)
cell = read_cell_yaml(os.path.join(data_dir, "..", "NaCl.yaml"))
scell2 = get_supercell(cell, smat2)
scell3 = get_supercell(cell, smat3)
n = len(scell3) // 2
# swap first and last half of atomic order
indices = [i + n for i in range(n)] + list(range(n))
scell3_swap = PhonopyAtoms(
cell=scell3.cell,
scaled_positions=scell3.scaled_positions[indices],
numbers=scell3.numbers[indices])
self._tcell2 = TrimmedCell(pmat2, scell2)
self._tcell3 = TrimmedCell(
pmat3,
scell3_swap,
positions_to_reorder=self._tcell2.scaled_positions)
def test_TrimmedCell(convcell_nacl, helper_methods):
pmat = [[0, 0.5, 0.5],
[0.5, 0, 0.5],
[0.5, 0.5, 0]]
smat2 = np.eye(3, dtype='intc') * 2
pmat2 = np.dot(np.linalg.inv(smat2), pmat)
smat3 = np.eye(3, dtype='intc') * 3
pmat3 = np.dot(np.linalg.inv(smat3), pmat)
cell = convcell_nacl
scell2 = get_supercell(cell, smat2)
scell3 = get_supercell(cell, smat3)
n = len(scell3) // 2
# swap first and last half of atomic order
indices = [i + n for i in range(n)] + list(range(n))
scell3_swap = PhonopyAtoms(
cell=scell3.cell,
scaled_positions=scell3.scaled_positions[indices],
numbers=scell3.numbers[indices])
tcell2 = TrimmedCell(pmat2, scell2)
tcell3 = TrimmedCell(pmat3, scell3_swap,
positions_to_reorder=tcell2.scaled_positions)
helper_methods.compare_cells_with_order(tcell2, tcell3)
def get_BORN_txt(structure, parameters, nac_data, symprec=1.e-5):
from phonopy.structure.cells import get_primitive, get_supercell
from phonopy.structure.symmetry import Symmetry
from phonopy.interface import get_default_physical_units
from phonopy.structure.atoms import Atoms as PhonopyAtoms
born_charges = nac_data.get_array('born_charges')
epsilon = nac_data.get_array('epsilon')
print ('inside born parameters')
pmat = parameters['primitive']
smat = parameters['supercell']
ucell = PhonopyAtoms(symbols=[site.kind_name for site in structure.sites],
positions=[site.position for site in structure.sites],
cell=structure.cell)
num_atom = len(born_charges)
assert num_atom == ucell.get_number_of_atoms(), \
"num_atom %d != len(borns) %d" % (ucell.get_number_of_atoms(),
len(born_charges))
inv_smat = np.linalg.inv(smat)
scell = get_supercell(ucell, smat, symprec=symprec)
pcell = get_primitive(scell, np.dot(inv_smat, pmat), symprec=symprec)
p2s = np.array(pcell.get_primitive_to_supercell_map(), dtype='intc')
p_sym = Symmetry(pcell, is_symmetry=True, symprec=symprec)
s_indep_atoms = p2s[p_sym.get_independent_atoms()]
u2u = scell.get_unitcell_to_unitcell_map()
u_indep_atoms = [u2u[x] for x in s_indep_atoms]
reduced_borns = born_charges[u_indep_atoms].copy()
factor = get_default_physical_units('vasp')['nac_factor'] # born charges in VASP units
born_txt = ('{}\n'.format(factor))
for num in epsilon.flatten():
born_txt += ('{0:4.8f}'.format(num))
born_txt += ('\n')
for atom in reduced_borns:
for num in atom:
born_txt += ('{0:4.8f}'.format(num))
born_txt += ('\n')
born_txt += ('{}\n'.format(factor))
return born_txt
def _get_delta(self, eigvec, q):
dim = self._get_dimension_3x3()
supercell = get_supercell(self._primitive, dim)
m = supercell.get_masses()
s2u_map = supercell.get_supercell_to_unitcell_map()
u2u_map = supercell.get_unitcell_to_unitcell_map()
s2uu_map = [u2u_map[x] for x in s2u_map]
spos = supercell.get_scaled_positions()
coefs = np.exp(2j * np.pi * np.dot(np.dot(spos, dim.T), q)) / np.sqrt(m)
u = []
for i, coef in enumerate(coefs):
eig_index = s2uu_map[i] * 3
u.append(eigvec[eig_index:eig_index + 3] * coef)
self._supercell = supercell
return np.array(u)
def _get_delta(self, eigvec, q):
dim = self._get_dimension_3x3()
supercell = get_supercell(self._primitive, dim)
m = supercell.get_masses()
s2u_map = supercell.get_supercell_to_unitcell_map()
u2u_map = supercell.get_unitcell_to_unitcell_map()
s2uu_map = [u2u_map[x] for x in s2u_map]
spos = supercell.get_scaled_positions()
coefs = np.exp(
2j * np.pi * np.dot(np.dot(spos, dim.T), q)) / np.sqrt(m)
u = []
for i, coef in enumerate(coefs):
eig_index = s2uu_map[i] * 3
u.append(eigvec[eig_index:eig_index + 3] * coef)
self._supercell = supercell
return np.array(u)
def test_get_supercell(self):
for i, (cell, smat, fname) in enumerate(zip(self._cells,
self._smats,
self._fnames)):
scell = get_supercell(cell, smat)
scell_yaml = read_cell_yaml(os.path.join(data_dir, fname))
np.testing.assert_allclose(scell.get_cell(), scell_yaml.get_cell(),
atol=1e-5)
pos = scell.get_scaled_positions()
pos -= np.rint(pos)
pos_yaml = scell_yaml.get_scaled_positions()
pos_yaml -= np.rint(pos_yaml)
np.testing.assert_allclose(pos, pos_yaml, atol=1e-5)
np.testing.assert_array_equal(scell.get_atomic_numbers(),
scell_yaml.get_atomic_numbers())
np.testing.assert_allclose(scell.get_masses(),
scell_yaml.get_masses(),
atol=1e-5)
def _get_supercell_and_primitive(ucell,
primitive_matrix=None,
supercell_matrix=None,
symprec=1e-5):
if primitive_matrix is None:
pmat = np.eye(3)
else:
pmat = primitive_matrix
if supercell_matrix is None:
smat = np.eye(3, dtype='intc')
else:
smat = supercell_matrix
inv_smat = np.linalg.inv(smat)
scell = get_supercell(ucell, smat, symprec=symprec)
pcell = get_primitive(scell, np.dot(inv_smat, pmat), symprec=symprec)
return scell, pcell
def _set_translations(self):
"""Set primitive translations in supercell.
_trans_s
Translations with respect to supercell basis vectors
_trans_p
Translations with respect to primitive cell basis vectors
_N
Number of the translations = det(supercel_matrix)
"""
pcell = PhonopyAtoms(numbers=[1],
scaled_positions=[[0, 0, 0]],
cell=np.diag([1, 1, 1]))
smat = self._supercell_matrix
self._trans_s = get_supercell(pcell, smat).scaled_positions
self._trans_p = np.dot(self._trans_s, self._supercell_matrix.T)
self._N = len(self._trans_s)
def _get_supercell_and_primitive(ucell,
primitive_matrix=None,
supercell_matrix=None,
symprec=1e-5):
if primitive_matrix is None:
pmat = np.eye(3)
else:
pmat = primitive_matrix
if supercell_matrix is None:
smat = np.eye(3, dtype="intc")
else:
smat = supercell_matrix
inv_smat = np.linalg.inv(smat)
scell = get_supercell(ucell, smat, symprec=symprec)
pcell = get_primitive(scell, np.dot(inv_smat, pmat), symprec=symprec)
return scell, pcell
def get_born_OUTCAR(poscar_filename="POSCAR",
outcar_filename="OUTCAR",
primitive_matrix=None,
supercell_matrix=None,
is_symmetry=True,
symmetrize_tensors=False,
symprec=1e-5):
if primitive_matrix is None:
pmat = np.eye(3)
else:
pmat = primitive_matrix
if supercell_matrix is None:
smat = np.eye(3, dtype='intc')
else:
smat = supercell_matrix
ucell = read_vasp(poscar_filename)
outcar = open(outcar_filename)
borns, epsilon = _read_born_and_epsilon(outcar)
num_atom = len(borns)
assert num_atom == ucell.get_number_of_atoms()
if symmetrize_tensors:
lattice = ucell.get_cell().T
positions = ucell.get_scaled_positions()
u_sym = Symmetry(ucell, is_symmetry=is_symmetry, symprec=symprec)
point_sym = [
similarity_transformation(lattice, r)
for r in u_sym.get_pointgroup_operations()
]
epsilon = _symmetrize_tensor(epsilon, point_sym)
borns = _symmetrize_borns(borns, u_sym, lattice, positions, symprec)
inv_smat = np.linalg.inv(smat)
scell = get_supercell(ucell, smat, symprec=symprec)
pcell = get_primitive(scell, np.dot(inv_smat, pmat), symprec=symprec)
p2s = np.array(pcell.get_primitive_to_supercell_map(), dtype='intc')
p_sym = Symmetry(pcell, is_symmetry=is_symmetry, symprec=symprec)
s_indep_atoms = p2s[p_sym.get_independent_atoms()]
u2u = scell.get_unitcell_to_unitcell_map()
u_indep_atoms = [u2u[x] for x in s_indep_atoms]
reduced_borns = borns[u_indep_atoms].copy()
return reduced_borns, epsilon, s_indep_atoms
def _set_translations(self):
"""Set primitive translations in supercell
_trans_s
Translations with respect to supercell basis vectors
_trans_p
Translations with respect to primitive cell basis vectors
_N
Number of the translations = det(supercel_matrix)
"""
pcell = PhonopyAtoms(numbers=[1],
scaled_positions=[[0, 0, 0]],
cell=np.diag([1, 1, 1]))
smat = self._supercell_matrix
self._trans_s = get_supercell(pcell, smat).get_scaled_positions()
self._trans_p = np.dot(self._trans_s, self._supercell_matrix.T)
self._N = len(self._trans_s)
def test_get_map_operations(self):
symprec = 1e-5
cell = read_cell_yaml(os.path.join(data_dir, "..", "NaCl.yaml"))
scell = get_supercell(cell, np.diag([2, 2, 2]), symprec=symprec)
symmetry = Symmetry(scell, symprec=symprec)
# start = time.time()
symmetry._set_map_operations()
# end = time.time()
# print(end - start)
map_ops = symmetry.get_map_operations()
map_atoms = symmetry.get_map_atoms()
positions = scell.get_scaled_positions()
rotations = symmetry.get_symmetry_operations()['rotations']
translations = symmetry.get_symmetry_operations()['translations']
for i, (op_i, atom_i) in enumerate(zip(map_ops, map_atoms)):
r_pos = np.dot(rotations[op_i], positions[i]) + translations[op_i]
diff = positions[atom_i] - r_pos
diff -= np.rint(diff)
self.assertTrue((diff < symprec).all())
def test_get_map_operations(self):
symprec = 1e-5
cell = get_unitcell_from_phonopy_yaml(
os.path.join(data_dir,"../NaCl.yaml"))
scell = get_supercell(cell, np.diag([2, 2, 2]), symprec=symprec)
symmetry = Symmetry(scell, symprec=symprec)
start = time.time()
symmetry._set_map_operations()
end = time.time()
# print(end - start)
map_ops = symmetry.get_map_operations()
map_atoms = symmetry.get_map_atoms()
positions = scell.get_scaled_positions()
rotations = symmetry.get_symmetry_operations()['rotations']
translations = symmetry.get_symmetry_operations()['translations']
for i, (op_i, atom_i) in enumerate(zip(map_ops, map_atoms)):
r_pos = np.dot(rotations[op_i], positions[i]) + translations[op_i]
diff = positions[atom_i] - r_pos
diff -= np.rint(diff)
self.assertTrue((diff < symprec).all())
def get_commensurate_points(supercell_matrix): # wrt primitive cell
"""Commensurate q-points are returned.
Parameters
----------
supercell_matrix : array_like
Supercell matrix with respect to primitive cell basis vectors.
shape=(3, 3)
dtype=intc
"""
smat = np.array(supercell_matrix, dtype=int)
rec_primitive = PhonopyAtoms(numbers=[1],
scaled_positions=[[0, 0, 0]],
cell=np.diag([1, 1, 1]),
pbc=True)
rec_supercell = get_supercell(rec_primitive, smat.T)
q_pos = rec_supercell.get_scaled_positions()
return np.array(np.where(q_pos > 1 - 1e-15, q_pos - 1, q_pos),
dtype='double', order='C')
def _arrange_supercell_fc(self, cell, q2r_fc):
dim = self.dimension
q2r_spos = self._get_q2r_positions(cell)
scell = get_supercell(cell, np.diag(dim))
assert scell.get_number_of_atoms() == len(q2r_spos)
site_map = self._get_site_mapping(scell.get_scaled_positions(),
q2r_spos,
scell.get_cell())
natom = cell.get_number_of_atoms()
ndim = np.prod(dim)
natom_s = natom * ndim
# full force constants
# fc = np.zeros((natom_s, natom_s, 3, 3), dtype='double', order='C')
# s_indices = [np.where(site_map==(i * ndim))[0][0] for i in range(natom)]
# for i, si in enumerate(s_indices):
# fc[si, :] = q2r_fc[i, site_map]
# self._distribute_fc2(fc, s_indices, scell)
# compact force constants
fc = np.zeros((natom, natom_s, 3, 3), dtype='double', order='C')
fc[:, :] = q2r_fc[:, site_map]
return fc
def get_born_OUTCAR(poscar_filename="POSCAR",
outcar_filename="OUTCAR",
primitive_axis=np.eye(3),
supercell_matrix=np.eye(3, dtype='intc'),
is_symmetry=True,
symmetrize_tensors=False):
ucell = read_vasp(poscar_filename)
scell = get_supercell(ucell, supercell_matrix)
inv_smat = np.linalg.inv(supercell_matrix)
pcell = get_primitive(scell, np.dot(inv_smat, primitive_axis))
u_sym = Symmetry(ucell, is_symmetry=is_symmetry)
p_sym = Symmetry(pcell, is_symmetry=is_symmetry)
lattice = ucell.get_cell().T
outcar = open(outcar_filename)
borns = []
while True:
line = outcar.readline()
if not line:
break
if "NIONS" in line:
num_atom = int(line.split()[11])
if "MACROSCOPIC STATIC DIELECTRIC TENSOR" in line:
epsilon = []
outcar.readline()
epsilon.append([float(x) for x in outcar.readline().split()])
epsilon.append([float(x) for x in outcar.readline().split()])
epsilon.append([float(x) for x in outcar.readline().split()])
if "BORN" in line:
outcar.readline()
line = outcar.readline()
if "ion" in line:
for i in range(num_atom):
born = []
born.append([float(x)
for x in outcar.readline().split()][1:])
born.append([float(x)
for x in outcar.readline().split()][1:])
born.append([float(x)
for x in outcar.readline().split()][1:])
outcar.readline()
borns.append(born)
borns = np.array(borns, dtype='double')
epsilon = np.array(epsilon, dtype='double')
if symmetrize_tensors:
borns_orig = borns.copy()
point_sym = [similarity_transformation(lattice, r)
for r in u_sym.get_pointgroup_operations()]
epsilon = symmetrize_tensor(epsilon, point_sym)
for i in range(num_atom):
z = borns[i]
site_sym = [similarity_transformation(lattice, r)
for r in u_sym.get_site_symmetry(i)]
borns[i] = symmetrize_tensor(z, site_sym)
rotations = u_sym.get_symmetry_operations()['rotations']
map_atoms = u_sym.get_map_atoms()
borns_copy = np.zeros_like(borns)
for i, m_i in enumerate(map_atoms):
count = 0
for j, r_j in enumerate(u_sym.get_map_operations()):
if map_atoms[j] == m_i:
count += 1
r_cart = similarity_transformation(lattice, rotations[r_j])
borns_copy[i] += similarity_transformation(r_cart, borns[j])
borns_copy[i] /= count
borns = borns_copy
sum_born = borns.sum(axis=0) / len(borns)
borns -= sum_born
if (np.abs(borns_orig - borns) > 0.1).any():
sys.stderr.write(
"Born effective charge symmetrization might go wrong.\n")
p2s = np.array(pcell.get_primitive_to_supercell_map(), dtype='intc')
s_indep_atoms = p2s[p_sym.get_independent_atoms()]
u2u = scell.get_unitcell_to_unitcell_map()
u_indep_atoms = [u2u[x] for x in s_indep_atoms]
reduced_borns = borns[u_indep_atoms].copy()
return reduced_borns, epsilon
def _build_supercell(self):
self._supercell = get_supercell(self._unitcell,
self._supercell_matrix,
self._symprec)
def __supercell(self):
self.supercell = get_supercell( self.unitcell,
self.supercell_matrix,
self.symprec )
def get_commensurate_points(supercell_matrix): # wrt primitive cell
rec_primitive = Atoms(numbers=[1], scaled_positions=[[0, 0, 0]], cell=np.diag([1, 1, 1]), pbc=True)
rec_supercell = get_supercell(rec_primitive, supercell_matrix.T)
return rec_supercell.get_scaled_positions()