def run(self):
"""
For disordered systems with relaxed atomic positions,
it might be better to use initial atomic positions to use the
symmetry of the structure (POSCAR_initial).
"""
poscar = Poscar('POSCAR')
number_of_atoms = poscar.get_atoms().get_number_of_atoms()
dummy_symbols = self.create_dummy_symbols(number_of_atoms)
poscar.get_atoms().set_chemical_symbols(dummy_symbols)
poscar.write_poscar('POSCAR_ideal')
class FCReducer(object):
def __init__(self,
poscar_filename="POSCAR",
fc_filename="FORCE_CONSTANTS"):
self._poscar = Poscar(poscar_filename)
self._force_constants = parse_FORCE_CONSTANTS(fc_filename)
self._fc_reduced = None
def find_indices_from_positions(self, positions):
"""Find atomic indices for removed FCs"""
poscar = self._poscar
indices_all = []
for position_combination in positions:
indices_combination = []
for p in position_combination:
index = poscar.get_index_from_position(p)
indices_combination.append(index)
indices_all.append(indices_combination)
indices_all = np.array(indices_all)
return indices_all
def write(self, filename):
write_FORCE_CONSTANTS(self._fc_reduced, filename=filename)
def do_postprocess(self):
poscar = self._poscar
fc_analyzer = FCAnalyzerBase(
atoms=poscar.get_atoms(),
force_constants=self._fc_reduced,
is_symmetrized=False,
)
fc_analyzer.force_translational_invariance()
self._fc_reduced = fc_analyzer.get_force_constants()
def keep_FCs_for_positions(self, positions):
"""
Parameters
----------
positions: n x 2 x 3 array
positions = np.array([
[[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]],
])
"""
poscar = self._poscar
force_constants_orig = self._force_constants
force_constants = np.zeros_like(force_constants_orig)
positions = np.array(positions)
indices_all = self.find_indices_from_positions(positions)
print('indices_all:', indices_all)
mappings = poscar.get_mappings_for_symops()
for mapping in mappings:
for indices_combination in indices_all:
indices_removed = mapping[indices_combination]
i0 = indices_removed[0]
i1 = indices_removed[1]
force_constants[i0, i1] = force_constants_orig[i0, i1]
force_constants[i1, i0] = force_constants_orig[i1, i0]
self._fc_reduced = force_constants
self.do_postprocess()
def remove_FCs_for_positions(self, positions):
"""
Parameters
----------
positions: n x 2 x 3 array
positions = np.array([
[[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]],
])
"""
poscar = self._poscar
force_constants = np.copy(self._force_constants)
positions = np.array(positions)
indices_all = self.find_indices_from_positions(positions)
print('indices_all:', indices_all)
mappings = poscar.get_mappings_for_symops()
for mapping in mappings:
for indices_combination in indices_all:
indices_removed = mapping[indices_combination]
i0 = indices_removed[0]
i1 = indices_removed[1]
force_constants[i0, i1] = 0.0
force_constants[i1, i0] = 0.0
self._fc_reduced = force_constants
self.do_postprocess()
def average_FCs_for_positions(self, positions):
"""
Parameters
----------
positions: n x 2 x 3 array
positions = np.array([
[[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]],
])
"""
poscar = self._poscar
force_constants = np.copy(self._force_constants)
force_constants_spg = self._create_fc_symmetrized_spg()
positions = np.array(positions)
indices_all = self.find_indices_from_positions(positions)
print('indices_all:', indices_all)
mappings = poscar.get_mappings_for_symops()
for mapping in mappings:
for indices_combination in indices_all:
indices_removed = mapping[indices_combination]
i0 = indices_removed[0]
i1 = indices_removed[1]
force_constants[i0, i1] = force_constants_spg[i0, i1]
force_constants[i1, i0] = force_constants_spg[i1, i0]
self._fc_reduced = force_constants
self.do_postprocess()
def _create_fc_symmetrized_spg(self):
from .fc_symmetrizer_spg import FCSymmetrizerSPG
force_constants = self._force_constants
atoms_ideal = self._poscar.get_atoms()
fc_symmetrizer_spg = FCSymmetrizerSPG(force_constants=force_constants,
atoms=atoms_ideal,
atoms_ideal=atoms_ideal,
is_symmetrized=False)
fc_symmetrizer_spg.average_force_constants_spg()
fc_spg = fc_symmetrizer_spg.get_force_constants_symmetrized()
return fc_spg