def __init__(self,
force_constants=None,
atoms=None,
atoms_ideal=None,
supercell_matrix=None,
is_symmetrized=True):
"""
Args:
atoms: The "Atoms" object corresponding to the force constants.
"""
self.set_force_constants(force_constants)
if supercell_matrix is None:
supercell_matrix = np.eye(3)
print("supercell_matrix:")
print(supercell_matrix)
if atoms is not None:
self.set_atoms(Supercell(atoms, supercell_matrix))
if atoms_ideal is not None:
self.set_atoms_ideal(Supercell(atoms_ideal, supercell_matrix))
if is_symmetrized:
self.symmetrize_force_constants()
self._fc_distribution_analyzer = None
self.check_consistency()
def _generate_enlarged_cell(self):
"""
If The tag "replacements" is not given, we just copy the original
structure as the enlarged cell.
"""
if self._map_s2s is not None:
self._enlarged_cell_average = Supercell(
self._primitive_average,
self._enlargement_matrix,
symprec=self._symprec)
self._enlarged_cell = self._disorder_enlarged_cell()
else:
enlargement_matrix = np.eye(3, dtype=int)
self._enlarged_cell_average = self._atoms_average
self._enlarged_cell = Supercell(
self._atoms_disordered,
enlargement_matrix,
symprec=self._symprec)
return self
def __init__(self,
force_constants=None,
atoms=None,
atoms_ideal=None,
supercell_matrix=None,
is_symmetrized=True):
"""
Parameters
----------
force_constants: (natoms, natoms, 3, 3) array
atoms: The "Atoms" object
This is used to extract chemical symbols.
atoms_ideal: The "Atoms" object
This is used to judge the expected crystallographic symmetry.
supercell_matrix: (3, 3) array
"""
if supercell_matrix is None:
supercell_matrix = np.eye(3)
print("supercell_matrix:")
print(supercell_matrix)
self.set_force_constants(force_constants)
if atoms is not None:
self.set_atoms(Supercell(atoms, supercell_matrix))
if atoms_ideal is not None:
self.set_atoms_ideal(Supercell(atoms_ideal, supercell_matrix))
if is_symmetrized:
self.symmetrize_force_constants()
self._fc_distribution_analyzer = None
self.check_consistency()
def _configure(self, dict_input):
"""
supercell_disordered: The structure corresponding to the force
constants.
"""
self._atoms_disordered = read_vasp(dict_input["structure_disordered"])
self._atoms_average = read_vasp(dict_input["structure_average"])
self._symprec = dict_input["symprec"]
self._map_s2s = dict_input["map_s2s"]
self._random_seed = dict_input["random_seed"]
self._num_configurations = dict_input['num_configurations']
primitive_matrix = parse_3x3_matrix(dict_input["primitive_matrix"])
self._supercell_matrix = dict_input["supercell_matrix"]
self._enlargement_matrix = dict_input["enlargement_matrix"]
self._fc_filename = dict_input["force_constants"]
self._force_constants = parse_FORCE_CONSTANTS(self._fc_filename)
self._supercell_disordered = Supercell(
self._atoms_disordered,
self._supercell_matrix,
symprec=self._symprec)
self._supercell_average = Supercell(
self._atoms_average,
self._supercell_matrix,
symprec=self._symprec)
# TODO(ikeda): The following part should be separated from this method.
inv_supercell_matrix = np.linalg.inv(self._supercell_matrix)
trans_mat = np.dot(inv_supercell_matrix, primitive_matrix)
self._primitive_average = Primitive(
self._supercell_average, trans_mat, symprec=self._symprec)
def get_lattice_points_from_supercell(lattice: np.array,
dim: np.array) -> np.array:
"""
Get lattice points from supercell.
Args:
lattice: Lattice matrix.
dim: Dimension with its shape is (3,) or (3,3).
Returns:
np.array: Lattice points.
"""
unitcell = PhonopyAtoms(
symbols=['H'],
cell=lattice,
scaled_positions=np.array([[0., 0., 0]]),
)
super_lattice = Supercell(unitcell=unitcell,
supercell_matrix=reshape_dimension(dim))
lattice_points = super_lattice.scaled_positions
return lattice_points
def get_supercell(cell, supercell_matrix):
ph_cell = get_phonopy_structure(cell)
sup_mat = shape_supercell_matrix(supercell_matrix)
sup = Supercell(ph_cell, supercell_matrix=sup_mat)
sup_cell = get_cell_from_phonopy_structure(sup)
return sup_cell