def _calculate(self):
unique_first_atom_nums = np.unique(
[x['number'] for x in self._dataset['first_atoms']])
for first_atom_num in unique_first_atom_nums:
disp_pairs = []
sets_of_forces = []
for dataset_1st in self._dataset['first_atoms']:
if first_atom_num != dataset_1st['number']:
continue
d, f = self._collect_disp_pairs_and_forces(dataset_1st)
disp_pairs.append(d)
sets_of_forces.append(f)
self._fit(first_atom_num, disp_pairs, sets_of_forces)
rotations = self._symmetry.get_symmetry_operations()['rotations']
translations = self._symmetry.get_symmetry_operations()['translations']
print "ditributing fc3..."
distribute_fc3(self._fc3,
unique_first_atom_nums,
self._lattice,
self._positions,
rotations,
translations,
self._symprec,
self._verbose)
def _calculate(self):
unique_first_atom_nums = np.unique(
[x['number'] for x in self._dataset['first_atoms']])
for first_atom_num in unique_first_atom_nums:
disp_triplets = []
sets_of_forces = []
for dataset_1st in self._dataset['first_atoms']:
if first_atom_num != dataset_1st['number']:
continue
d1 = dataset_1st['displacement']
d3, f = self._collect_forces_and_disps(dataset_1st)
disp_triplets.append(d3)
sets_of_forces.append(f)
self._fit(first_atom_num, disp_triplets, sets_of_forces)
rotations = self._symmetry.get_symmetry_operations()['rotations']
translations = self._symmetry.get_symmetry_operations()['translations']
print "ditributing fc4..."
distribute_fc4(self._fc4, unique_first_atom_nums, self._lattice,
self._positions, rotations, translations, self._symprec,
self._verbose)
print "ditributing fc3..."
distribute_fc3(self._fc3, unique_first_atom_nums, self._lattice,
self._positions, rotations, translations, self._symprec,
self._verbose)
print "ditributing fc2..."
distribute_force_constants(self._fc2, range(self._num_atom),
unique_first_atom_nums, self._lattice,
self._positions, rotations, translations,
self._symprec)
def _calculate(self):
unique_first_atom_nums = np.unique(
[x['number'] for x in self._dataset['first_atoms']])
for first_atom_num in unique_first_atom_nums:
disp_triplets = []
sets_of_forces = []
for dataset_1st in self._dataset['first_atoms']:
if first_atom_num != dataset_1st['number']:
continue
d1 = dataset_1st['displacement']
d3, f = self._collect_forces_and_disps(dataset_1st)
disp_triplets.append(d3)
sets_of_forces.append(f)
self._fit(first_atom_num, disp_triplets, sets_of_forces)
rotations = self._symmetry.get_symmetry_operations()['rotations']
translations = self._symmetry.get_symmetry_operations()['translations']
print "ditributing fc4..."
distribute_fc4(self._fc4,
unique_first_atom_nums,
self._lattice,
self._positions,
rotations,
translations,
self._symprec,
self._verbose)
print "ditributing fc3..."
distribute_fc3(self._fc3,
unique_first_atom_nums,
self._lattice,
self._positions,
rotations,
translations,
self._symprec,
self._verbose)
print "ditributing fc2..."
distribute_force_constants(self._fc2,
range(self._num_atom),
unique_first_atom_nums,
self._lattice,
self._positions,
rotations,
translations,
self._symprec)
def _calculate(self):
unique_first_atom_nums = np.unique(
[x['number'] for x in self._dataset['first_atoms']])
for first_atom_num in unique_first_atom_nums:
disp_pairs = []
sets_of_forces = []
for dataset_1st in self._dataset['first_atoms']:
if first_atom_num != dataset_1st['number']:
continue
d, f = self._collect_disp_pairs_and_forces(dataset_1st)
disp_pairs.append(d)
sets_of_forces.append(f)
self._fit(first_atom_num, disp_pairs, sets_of_forces)
rotations = self._symmetry.get_symmetry_operations()['rotations']
translations = self._symmetry.get_symmetry_operations()['translations']
print "ditributing fc3..."
fc3 = distribute_fc3(self._fc3,
unique_first_atom_nums,
self._lattice,
self._positions,
rotations,
translations,
self._symprec,
self._verbose)
self._fc3 = fc3
def _get_constrained_fc3(supercell, displacements, reduced_site_sym,
translational_symmetry_type, is_permutation_symmetry,
symprec, verbose):
"""
Two displacements and force constants calculation (e.g. DFPT)
displacements = {'number': 3,
'displacement': [0.01, 0.00, 0.01]
'second_atoms': [{'number': 7,
'displacement': [],
'delta_fc2': }]}
Three displacements and force calculation
displacements = {'number': 3,
'displacement': [0.01, 0.00, 0.01]
'second_atoms': [{'number': 7,
'displacement': [],
'third_atoms': ... }]}
third_atoms is like:
'third_atoms': [{'number': 56,
'displacement': [],
'delta_forces': ... }]}
"""
num_atom = supercell.get_number_of_atoms()
atom1 = displacements['number']
disp1 = displacements['displacement']
delta_fc3 = np.zeros((num_atom, num_atom, num_atom, 3, 3, 3),
dtype='double')
if 'delta_forces' in displacements['second_atoms'][0]:
fc2_with_one_disp = get_constrained_fc2(
supercell, displacements['second_atoms'], atom1, reduced_site_sym,
translational_symmetry_type, is_permutation_symmetry, symprec)
atom_list = np.unique([x['number'] for x in displacements['second_atoms']])
for atom2 in atom_list:
bond_sym = get_bond_symmetry(reduced_site_sym,
supercell.get_scaled_positions(), atom1,
atom2, symprec)
disps2 = []
delta_fc2s = []
for disps_second in displacements['second_atoms']:
if atom2 != disps_second['number']:
continue
disps2.append(disps_second['displacement'])
if 'delta_fc2' in disps_second:
delta_fc2s.append(disps_second['delta_fc2'])
else:
direction = np.dot(disps_second['displacement'],
np.linalg.inv(supercell.get_cell()))
reduced_bond_sym = get_reduced_site_symmetry(
bond_sym, direction, symprec)
delta_fc2s.append(
get_delta_fc2(disps_second['third_atoms'], atom2,
fc2_with_one_disp, supercell,
reduced_bond_sym,
translational_symmetry_type,
is_permutation_symmetry, symprec))
if verbose > 1:
print("Second displacements for fc4[ %d, %d, x, x ]" %
(atom1 + 1, atom2 + 1))
for i, v in enumerate(disps2):
print " [%7.4f %7.4f %7.4f]" % tuple(v)
solve_fc3(delta_fc3,
atom2,
supercell,
bond_sym,
disps2,
delta_fc2s,
symprec=symprec,
verbose=False)
# Shift positions according to set atom1 is at origin
lattice = supercell.get_cell().T
positions = supercell.get_scaled_positions()
pos_center = positions[atom1].copy()
positions -= pos_center
if verbose:
print "Expanding delta fc3"
distribute_fc3(delta_fc3,
atom_list,
lattice,
positions,
np.array(reduced_site_sym, dtype='intc', order='C'),
np.zeros((len(reduced_site_sym), 3), dtype='double'),
symprec,
verbose=verbose)
if translational_symmetry_type > 0:
set_translational_invariance_fc3_per_index(delta_fc3)
if is_permutation_symmetry:
set_permutation_symmetry_fc3(delta_fc3)
return delta_fc3
def _get_constrained_fc3(supercell,
displacements,
reduced_site_sym,
is_translational_symmetry,
is_permutation_symmetry,
symprec,
verbose):
"""
Two displacements and force constants calculation (e.g. DFPT)
displacements = {'number': 3,
'displacement': [0.01, 0.00, 0.01]
'second_atoms': [{'number': 7,
'displacement': [],
'delta_fc2': }]}
Three displacements and force calculation
displacements = {'number': 3,
'displacement': [0.01, 0.00, 0.01]
'second_atoms': [{'number': 7,
'displacement': [],
'third_atoms': ... }]}
third_atoms is like:
'third_atoms': [{'number': 56,
'displacement': [],
'delta_forces': ... }]}
"""
num_atom = supercell.get_number_of_atoms()
atom1 = displacements['number']
disp1 = displacements['displacement']
fc3 = np.zeros((num_atom, num_atom, num_atom, 3, 3, 3), dtype='double')
atom_list_done = []
if 'delta_forces' in displacements['second_atoms'][0]:
fc2_with_one_disp = get_constrained_fc2(supercell,
displacements['second_atoms'],
atom1,
reduced_site_sym,
is_translational_symmetry,
is_permutation_symmetry,
symprec)
atom_list = np.unique([x['number'] for x in displacements['second_atoms']])
for atom2 in atom_list:
disps2 = []
delta_fc2s = []
for disps_second in displacements['second_atoms']:
if atom2 != disps_second['number']:
continue
atom_list_done.append(atom2)
bond_sym = get_bond_symmetry(
reduced_site_sym,
supercell.get_scaled_positions(),
atom1,
atom2,
symprec)
disps2.append(disps_second['displacement'])
if 'delta_fc2' in disps_second:
delta_fc2s.append(disps_second['delta_fc2'])
else:
direction = np.dot(disps_second['displacement'],
np.linalg.inv(supercell.get_cell()))
reduced_bond_sym = get_reduced_site_symmetry(
bond_sym, direction, symprec)
delta_fc2s.append(get_delta_fc2(
disps_second['third_atoms'],
atom2,
fc2_with_one_disp,
supercell,
reduced_bond_sym,
is_translational_symmetry,
is_permutation_symmetry,
symprec))
if verbose > 1:
print ("Second displacements for fc4[ %d, %d, x, x ]" %
(atom1 + 1, atom2 + 1))
for i, v in enumerate(disps2):
print " [%7.4f %7.4f %7.4f]" % tuple(v)
solve_fc3(fc3,
atom2,
supercell,
bond_sym,
disps2,
delta_fc2s,
symprec=symprec)
# Shift positions according to set atom1 is at origin
lattice = supercell.get_cell().T
positions = supercell.get_scaled_positions()
pos_center = positions[atom1].copy()
positions -= pos_center
if verbose:
print "(Copying delta fc3...)"
distribute_fc3(fc3,
atom_list_done,
lattice,
positions,
np.intc(reduced_site_sym).copy(),
np.zeros((len(reduced_site_sym), 3), dtype='double'),
symprec,
verbose)
if is_translational_symmetry:
set_translational_invariance_fc3_per_index(fc3)
if is_permutation_symmetry:
set_permutation_symmetry_fc3(fc3)
return fc3
