def _run(self):
self._set_best_arguments_of_vectors_and_supercell()
max_num_op = 0
best_cells = []
points_on_sphere = []
for i, point in enumerate(self._get_all_points_on_sphere()):
modcell = self._get_cell_with_modulation(
self._get_modulation(point))
symmetry = get_symmetry_dataset(modcell,
tolerance=self._symmetry_tolerance)
if self._store_all:
self._all_cells.append(modcell)
refined_cell = get_crystallographic_cell(
modcell, tolerance=self._symmetry_tolerance)
num_op = len(symmetry['rotations'])
if num_op > max_num_op:
max_num_op = num_op
best_cells = [refined_cell]
points_on_sphere = [point.copy()]
if num_op == max_num_op:
is_found = True
for bc in best_cells:
if xtal_compare(bc,
refined_cell,
tolerance=self._symmetry_tolerance,
angle_tolerance=1.0):
is_found = False
break
if is_found:
best_cells.append(refined_cell)
points_on_sphere.append(point.copy())
self._points_on_sphere = points_on_sphere
def _set_phonon(self):
if self._supercell_matrix is None:
cell = sort_cell_by_symbols(
get_crystallographic_cell(self.get_cell()))
self._supercell_matrix = estimate_supercell_matrix(
cell,
max_num_atoms=self._max_num_atoms)
else:
cell = self.get_cell()
phonopy_cell = cell2atoms(cell)
self._phonon = Phonopy(phonopy_cell,
self._supercell_matrix,
primitive_matrix=self._primitive_matrix,
dynamical_matrix_decimals=14,
force_constants_decimals=14,
symprec=self._symmetry_tolerance)
self._phonon.generate_displacements(
distance=self._distance,
is_plusminus=self._displace_plusminus,
is_diagonal=self._displace_diagonal)
supercell = self._phonon.get_supercell()
displacements = self._phonon.get_displacements()
write_poscar(cell, filename="POSCAR-unitcell")
write_poscar_yaml(cell, filename="POSCAR-unitcell.yaml")
write_disp_yaml(displacements, supercell)
def get_primitive(cell, tolerance=1e-5):
# spglib returns R-centred lattice for Rhombohedrals
brv_cell = get_crystallographic_cell(cell, tolerance)
sym_dataset = get_symmetry_dataset(brv_cell)
spg_symbol = sym_dataset['international'][0]
if spg_symbol == 'F':
brv_cell = _fc2prim(brv_cell)
elif spg_symbol == 'I':
brv_cell = _bc2prim(brv_cell)
elif spg_symbol == 'A':
brv_cell = _abc2prim(brv_cell)
elif spg_symbol == 'B':
brv_cell = _bbc2prim(brv_cell)
elif spg_symbol == 'C':
brv_cell = _cbc2prim(brv_cell)
return brv_cell
def get_primitive(cell, tolerance=1e-5):
# spglib returns R-centred lattice for Rhombohedrals
std_cell = get_crystallographic_cell(cell, tolerance)
sym_dataset = get_symmetry_dataset(std_cell)
spg_symbol = sym_dataset['international'][0]
if spg_symbol == 'F':
std_cell = _fc2prim(std_cell)
elif spg_symbol == 'I':
std_cell = _bc2prim(std_cell)
elif spg_symbol == 'A':
std_cell = _abc2prim(std_cell)
elif spg_symbol == 'B':
std_cell = _bbc2prim(std_cell)
elif spg_symbol == 'C':
std_cell = _cbc2prim(std_cell)
return std_cell
def _run(self):
self._set_best_arguments_of_vectors_and_supercell()
max_num_op = 0
best_cells = []
points_on_sphere = []
for i, point in enumerate(self._get_all_points_on_sphere()):
modcell = self._get_cell_with_modulation(
self._get_modulation(point))
symmetry = get_symmetry_dataset(
modcell, tolerance=self._symmetry_tolerance)
if self._store_all:
self._all_cells.append(modcell)
refined_cell = get_crystallographic_cell(
modcell,
tolerance=self._symmetry_tolerance)
num_op = len(symmetry['rotations'])
if num_op > max_num_op:
max_num_op = num_op
best_cells = [refined_cell]
points_on_sphere = [point.copy()]
if num_op == max_num_op:
is_found = True
for bc in best_cells:
if xtal_compare(bc,
refined_cell,
tolerance=self._symmetry_tolerance,
angle_tolerance=1.0):
is_found = False
break
if is_found:
best_cells.append(refined_cell)
points_on_sphere.append(point.copy())
self._points_on_sphere = points_on_sphere
'icsd_ids': get_icsd_ids,
'e_above_hull': get_e_above_hull,
'pretty_formula': get_pretty_formula,
'created_at': get_created_at,
'is_hubbard': get_is_hubbard,
'nsites': get_nsites,
'elasticity': get_elasticity,
'final_structure': get_final_structure,
'initial_structure': get_initial_structure,
'icsd_id': get_icsd_id,
'spacegroup': get_spacegroup,
'magnetic_type': get_magnetic_type,
'exp_lattice': get_exp_lattice}
functions = {'band_gap': get_band_gap,
'e_above_hull': get_e_above_hull,
'is_hubbard': get_is_hubbard,
'final_structure': get_final_structure,
'initial_structure': get_initial_structure,
'magnetic_type': get_magnetic_type}
mid = sys.argv[2]
for line in open(sys.argv[1]):
words = line.partition(':')
key = words[0].strip()
if key in functions:
if key == 'final_structure':
retval = functions[key](words[2].strip(), show=False)
brv_cell = get_crystallographic_cell(retval, tolerance=1e-1)
write_poscar(brv_cell, filename="BPOSCAR-%s" % mid)