def _distribute_forces(supercell, disp, forces, filename, symprec):
natom = supercell.get_number_of_atoms()
lattice = supercell.get_cell()
symbols = supercell.get_chemical_symbols()
positions = supercell.get_positions()
positions[disp[0]] += disp[1]
cell = Atoms(cell=lattice, positions=positions, symbols=symbols, pbc=True)
symmetry = Symmetry(cell, symprec)
independent_atoms = symmetry.get_independent_atoms()
# Rotation matrices in Cartesian
rotations = []
for r in symmetry.get_symmetry_operations()["rotations"]:
rotations.append(similarity_transformation(lattice.T, r))
map_operations = symmetry.get_map_operations()
map_atoms = symmetry.get_map_atoms()
atoms_in_dot_scf = _get_independent_atoms_in_dot_scf(filename)
if len(forces) != len(atoms_in_dot_scf):
print("%s does not contain necessary information." % filename)
print('Plese check if there are "FGL" lines with')
print('"total forces" are required.')
return False
if len(atoms_in_dot_scf) == natom:
print("It is assumed that there is no symmetrically-equivalent " "atoms in ")
print("'%s' at wien2k calculation." % filename)
force_set = forces
elif len(forces) != len(independent_atoms):
print("Non-equivalent atoms of %s could not be recognized by phonopy." % filename)
return False
else:
# 1. Transform wien2k forces to those on independent atoms
indep_atoms_to_wien2k = []
forces_remap = []
for i, pos_wien2k in enumerate(atoms_in_dot_scf):
for j, pos in enumerate(cell.get_scaled_positions()):
diff = pos_wien2k - pos
diff -= np.rint(diff)
if (abs(diff) < symprec).all():
forces_remap.append(np.dot(rotations[map_operations[j]], forces[i]))
indep_atoms_to_wien2k.append(map_atoms[j])
break
if len(forces_remap) != len(forces):
print("Atomic position mapping between Wien2k and phonopy failed.")
print("If you think this is caused by a bug of phonopy")
print("please report it in the phonopy mainling list.")
return False
# 2. Distribute forces from independent to dependent atoms.
force_set = []
for i in range(natom):
j = indep_atoms_to_wien2k.index(map_atoms[i])
force_set.append(np.dot(rotations[map_operations[i]].T, forces_remap[j]))
return force_set
def get_cell_from_phonopy_structure(ph_structure: PhonopyAtoms,
use_atomic_number: bool = False) -> tuple:
"""
Get cell from phonopy structure
Args:
ph_structure: PhonopyAtoms object
use_atomic_number: if True, use atomic number intead of atomic symbol
Returns:
tuple: (lattice, scaled_positions, symbols).
"""
lattice = ph_structure.get_cell()
scaled_positions = ph_structure.get_scaled_positions()
if use_atomic_number:
elements = list(ph_structure.get_atomic_numbers())
else:
elements = ph_structure.get_chemical_symbols()
return (lattice, scaled_positions, elements)
def _distribute_forces(supercell, disp, forces, filename, symprec):
natom = supercell.get_number_of_atoms()
lattice = supercell.get_cell()
symbols = supercell.get_chemical_symbols()
positions = supercell.get_positions()
positions[disp[0]] += disp[1]
cell = Atoms(cell=lattice, positions=positions, symbols=symbols, pbc=True)
symmetry = Symmetry(cell, symprec)
independent_atoms = symmetry.get_independent_atoms()
# Rotation matrices in Cartesian
rotations = []
for r in symmetry.get_symmetry_operations()['rotations']:
rotations.append(similarity_transformation(lattice.T, r))
map_operations = symmetry.get_map_operations()
map_atoms = symmetry.get_map_atoms()
atoms_in_dot_scf = _get_independent_atoms_in_dot_scf(filename)
if len(forces) != len(atoms_in_dot_scf):
print("%s does not contain necessary information." % filename)
print("Plese check if there are \"FGL\" lines with")
print("\"total forces\" are required.")
return False
if len(atoms_in_dot_scf) == natom:
print("It is assumed that there is no symmetrically-equivalent "
"atoms in ")
print("\'%s\' at wien2k calculation." % filename)
force_set = forces
elif len(forces) != len(independent_atoms):
print(
"Non-equivalent atoms of %s could not be recognized by phonopy." %
filename)
return False
else:
# 1. Transform wien2k forces to those on independent atoms
indep_atoms_to_wien2k = []
forces_remap = []
for i, pos_wien2k in enumerate(atoms_in_dot_scf):
for j, pos in enumerate(cell.get_scaled_positions()):
diff = pos_wien2k - pos
diff -= np.rint(diff)
if (abs(diff) < symprec).all():
forces_remap.append(
np.dot(rotations[map_operations[j]], forces[i]))
indep_atoms_to_wien2k.append(map_atoms[j])
break
if len(forces_remap) != len(forces):
print("Atomic position mapping between Wien2k and phonopy failed.")
print("If you think this is caused by a bug of phonopy")
print("please report it in the phonopy mainling list.")
return False
# 2. Distribute forces from independent to dependent atoms.
force_set = []
for i in range(natom):
j = indep_atoms_to_wien2k.index(map_atoms[i])
force_set.append(
np.dot(rotations[map_operations[i]].T, forces_remap[j]))
return force_set
def assert_same_phonopy_atoms(actual: PhonopyAtoms, expected: PhonopyAtoms):
assert (actual.get_cell() == expected.get_cell()).all()
assert (actual.get_scaled_positions() == expected.get_scaled_positions()
).all()
assert actual.symbols == expected.symbols
