def run(self, atom_pairs):
s2p = self._primitive.get_supercell_to_primitive_map()
p2p = self._primitive.get_primitive_to_primitive_map()
dists = np.zeros((len(self._temperatures), len(atom_pairs)),
dtype=float)
for i, (atom1, atom2) in enumerate(atom_pairs):
patom1 = p2p[s2p[atom1]]
patom2 = p2p[s2p[atom2]]
delta_r = get_equivalent_smallest_vectors(
atom2, atom1, self._supercell, self._primitive.get_cell(),
self._symprec)[0]
self._project_eigenvectors(delta_r, self._primitive.get_cell())
for freqs, vecs, q in zip(self._frequencies, self._p_eigenvectors,
self._qpoints):
c_cross = 1.0 / np.sqrt(
self._masses[patom1] * self._masses[patom2])
c1 = 1.0 / self._masses[patom1]
c2 = 1.0 / self._masses[patom2]
for f, v in zip(freqs, vecs.T):
cross_term = self._get_cross(v, delta_r, q, patom1, patom2)
v2 = abs(v)**2
if f > self._cutoff_frequency:
for j, t in enumerate(self._temperatures):
dists[j, i] += self.get_Q2(f, t) * (
v2[patom1] * c1 + cross_term * c_cross +
v2[patom2] * c2)
self._atom_pairs = atom_pairs
self._distances = dists / len(self._frequencies)
def cutoff_fc3_by_zero(fc3, supercell, cutoff_distance, symprec=1e-5):
num_atom = supercell.get_number_of_atoms()
lattice = supercell.get_cell().T
min_distances = np.zeros((num_atom, num_atom), dtype='double')
for i in range(num_atom): # run in supercell
for j in range(num_atom): # run in primitive
min_distances[i, j] = np.linalg.norm(
np.dot(
lattice,
get_equivalent_smallest_vectors(i, j, supercell, lattice.T,
symprec)[0]))
for i, j, k in np.ndindex(num_atom, num_atom, num_atom):
for pair in ((i, j), (j, k), (k, i)):
if min_distances[pair] > cutoff_distance:
fc3[i, j, k] = 0
break
def get_third_order_displacements(cell,
symmetry,
is_plusminus='auto',
is_diagonal=False):
# Atoms 1, 2, and 3 are defined as follows:
#
# Atom 1: The first displaced atom. Third order force constant
# between Atoms 1, 2, and 3 is calculated.
# Atom 2: The second displaced atom. Second order force constant
# between Atoms 2 and 3 is calculated.
# Atom 3: Force is mesuared on this atom.
positions = cell.get_scaled_positions()
lattice = cell.get_cell().T
# Least displacements for third order force constants in yaml file
#
# Data structure
# [{'number': atom1,
# 'displacement': [0.00000, 0.007071, 0.007071],
# 'second_atoms': [ {'number': atom2,
# 'displacements': [[0.007071, 0.000000, 0.007071],
# [-0.007071, 0.000000, -0.007071]
# ,...]},
# {'number': ... } ] },
# {'number': atom1, ... } ]
# Least displacements of first atoms (Atom 1) are searched by
# using respective site symmetries of the original crystal.
disps_first = get_least_displacements(symmetry,
is_plusminus=is_plusminus,
is_diagonal=False)
symprec = symmetry.get_symmetry_tolerance()
dds = []
for disp in disps_first:
atom1 = disp[0]
disp1 = disp[1:4]
site_sym = symmetry.get_site_symmetry(atom1)
dds_atom1 = {'number': atom1,
'direction': disp1,
'second_atoms': []}
# Reduced site symmetry at the first atom with respect to
# the displacement of the first atoms.
reduced_site_sym = get_reduced_site_symmetry(site_sym, disp1, symprec)
# Searching orbits (second atoms) with respect to
# the first atom and its reduced site symmetry.
second_atoms = get_least_orbits(atom1,
cell,
reduced_site_sym,
symprec)
for atom2 in second_atoms:
dds_atom2 = get_next_displacements(atom1,
atom2,
reduced_site_sym,
lattice,
positions,
symprec,
is_diagonal)
min_distance = np.linalg.norm(
np.dot(lattice, get_equivalent_smallest_vectors(
atom1,
atom2,
cell,
lattice.T,
symprec)[0]))
dds_atom2['distance'] = min_distance
dds_atom1['second_atoms'].append(dds_atom2)
dds.append(dds_atom1)
return dds