def get_constrained_fc2(supercell,
dataset_second_atoms,
atom1,
forces1,
reduced_site_sym,
symprec):
"""
dataset_second_atoms: [{'number': 7,
'displacement': [],
'forces': []}, ...]
"""
lattice = supercell.get_cell().T
positions = supercell.get_scaled_positions()
num_atom = supercell.get_number_of_atoms()
fc2 = np.zeros((num_atom, num_atom, 3, 3), dtype='double')
atom_list = np.unique([x['number'] for x in dataset_second_atoms])
for atom2 in atom_list:
disps2 = []
sets_of_forces = []
for disps_second in dataset_second_atoms:
if atom2 != disps_second['number']:
continue
bond_sym = get_bond_symmetry(
reduced_site_sym,
lattice,
positions,
atom1,
atom2,
symprec)
disps2.append(disps_second['displacement'])
sets_of_forces.append(disps_second['forces'] - forces1)
solve_force_constants(fc2,
atom2,
disps2,
sets_of_forces,
supercell,
bond_sym,
symprec)
# Shift positions according to set atom1 is at origin
pos_center = positions[atom1].copy()
positions -= pos_center
rotations = np.array(reduced_site_sym, dtype='intc', order='C')
translations = np.zeros((len(reduced_site_sym), 3),
dtype='double', order='C')
permutations = compute_all_sg_permutations(positions,
rotations,
translations,
lattice,
symprec)
distribute_force_constants(fc2,
atom_list,
lattice,
rotations,
permutations)
return fc2
def get_constrained_fc2(
supercell,
dataset_second_atoms,
atom1,
reduced_site_sym,
translational_symmetry_type,
is_permutation_symmetry,
symprec,
):
"""
dataset_second_atoms: [{'number': 7,
'displacement': [],
'delta_forces': []}, ...]
"""
num_atom = supercell.get_number_of_atoms()
fc2 = np.zeros((num_atom, num_atom, 3, 3), dtype="double")
atom_list = np.unique([x["number"] for x in dataset_second_atoms])
for atom2 in atom_list:
disps2 = []
sets_of_forces = []
for disps_second in dataset_second_atoms:
if atom2 != disps_second["number"]:
continue
bond_sym = get_bond_symmetry(reduced_site_sym, supercell.get_scaled_positions(), atom1, atom2, symprec)
disps2.append(disps_second["displacement"])
sets_of_forces.append(disps_second["delta_forces"])
solve_force_constants(fc2, atom2, disps2, sets_of_forces, supercell, bond_sym, 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
distribute_force_constants(
fc2,
range(num_atom),
atom_list,
lattice,
positions,
np.array(reduced_site_sym, dtype="intc", order="C"),
np.zeros((len(reduced_site_sym), 3), dtype="double"),
symprec,
)
if translational_symmetry_type:
set_translational_invariance(fc2, translational_symmetry_type=translational_symmetry_type)
if is_permutation_symmetry:
set_permutation_symmetry(fc2)
return fc2
def get_constrained_fc2(supercell, dataset_second_atoms, atom1,
reduced_site_sym, translational_symmetry_type,
is_permutation_symmetry, symprec):
"""
dataset_second_atoms: [{'number': 7,
'displacement': [],
'delta_forces': []}, ...]
"""
num_atom = supercell.get_number_of_atoms()
fc2 = np.zeros((num_atom, num_atom, 3, 3), dtype='double')
atom_list = np.unique([x['number'] for x in dataset_second_atoms])
atom_list_done = []
for atom2 in atom_list:
disps2 = []
sets_of_forces = []
for disps_second in dataset_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'])
sets_of_forces.append(disps_second['delta_forces'])
solve_force_constants(fc2, atom2, disps2, sets_of_forces, supercell,
bond_sym, 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
distribute_force_constants(
fc2, range(num_atom), atom_list_done, lattice, positions,
np.array(reduced_site_sym, dtype='intc', order='C'),
np.zeros((len(reduced_site_sym), 3), dtype='double'), symprec)
if translational_symmetry_type:
set_translational_invariance(
fc2, translational_symmetry_type=translational_symmetry_type)
if is_permutation_symmetry:
set_permutation_symmetry(fc2)
return fc2
def _get_constrained_fc2(supercell, dataset_second_atoms, atom1, forces1,
reduced_site_sym, symprec):
"""Return fc2 under reduced (broken) site symmetry by first displacement.
dataset_second_atoms: [{'number': 7,
'displacement': [],
'forces': []}, ...]
"""
lattice = supercell.cell.T
positions = supercell.scaled_positions
num_atom = len(supercell)
fc2 = np.zeros((num_atom, num_atom, 3, 3), dtype="double")
atom_list = np.unique([x["number"] for x in dataset_second_atoms])
for atom2 in atom_list:
disps2 = []
sets_of_forces = []
for disps_second in dataset_second_atoms:
if atom2 != disps_second["number"]:
continue
bond_sym = get_bond_symmetry(reduced_site_sym, lattice, positions,
atom1, atom2, symprec)
disps2.append(disps_second["displacement"])
sets_of_forces.append(disps_second["forces"] - forces1)
solve_force_constants(fc2, atom2, disps2, sets_of_forces, supercell,
bond_sym, symprec)
# Shift positions according to set atom1 is at origin
pos_center = positions[atom1].copy()
positions -= pos_center
rotations = np.array(reduced_site_sym, dtype="intc", order="C")
translations = np.zeros((len(reduced_site_sym), 3),
dtype="double",
order="C")
permutations = compute_all_sg_permutations(positions, rotations,
translations, lattice, symprec)
distribute_force_constants(fc2, atom_list, lattice, rotations,
permutations)
return fc2
