def _set_stage1(self, cell):
prim_cell = get_primitive(cell, tolerance=self._symmetry_tolerance)
sym_dataset = get_symmetry_dataset(prim_cell)
self._space_group_type = sym_dataset['international_standard']
spg_number = sym_dataset['number']
if (spg_number >= 143 and
spg_number <= 194 and
not self._space_group_type[0] == 'R'): # Hexagonal lattice
self._supercell_dimensions = [[3, 3, 2], [2, 2, 2]]
else: # Other cases
self._supercell_dimensions = [[2, 2, 2]]
# Long cell axis is not multiplied.
for dimension in self._supercell_dimensions:
for i, length in enumerate(
get_lattice_parameters(prim_cell.get_lattice())):
if length * dimension[i] > 20:
dimension[i] = 1
self._tasks = []
for i, dimension in enumerate(self._supercell_dimensions):
task = self._get_phonon_task(prim_cell,
np.diag(dimension),
"phonon-%d" % (i + 1))
self._phre_tasks.append(task)
self._tasks.append(task)
def _get_points_with_margin(cell, margin=1e-5):
abc = get_lattice_parameters(cell.get_lattice())
points = cell.get_points()
points_new = []
symbols_new = []
for p, s in zip(points.T, cell.get_symbols()):
for i in (-1, 0, 1):
for j in (-1, 0, 1):
for k in (-1, 0, 1):
p_inspect = p + np.array([i, j, k])
if ((p_inspect > 0 - margin / abc).all() and
(p_inspect < 1 + margin / abc).all()):
points_new.append(p_inspect)
symbols_new.append(s)
return np.transpose(points_new), symbols_new
def _get_points_with_margin(cell, margin=1e-5):
abc = get_lattice_parameters(cell.get_lattice())
points = cell.get_points()
points_new = []
symbols_new = []
for p, s in zip(points.T, cell.get_symbols()):
for i in (-1, 0, 1):
for j in (-1, 0, 1):
for k in (-1, 0, 1):
p_inspect = p + np.array([i, j, k])
if ((p_inspect > 0 - margin / abc).all()
and (p_inspect < 1 + margin / abc).all()):
points_new.append(p_inspect)
symbols_new.append(s)
return np.transpose(points_new), symbols_new
def write_cif_P1(cell, filename=None):
a, b, c = get_lattice_parameters(cell.get_lattice())
alpha, beta, gamma = get_angles(cell.get_lattice())
cif = """data_cogue_crystal_converter
_symmetry_space_group_name_H-M 'P 1'
_symmetry_Int_Tables_number 1
_cell_length_a %.5f
_cell_length_b %.5f
_cell_length_c %.5f
_cell_angle_alpha %.5f
_cell_angle_beta %.5f
_cell_angle_gamma %.5f
_cell_volume %.5f
_cell_formula_units_Z 1
loop_
_space_group_symop_operation_xyz
x,y,z
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_occupancy\n""" % (a, b, c, alpha, beta, gamma, cell.get_volume())
symbols = []
for s, p in zip(cell.get_symbols(), cell.get_points().T):
symbols.append(s)
cif += "%-7s%2s %10.5f%10.5f%10.5f 1.00000\n" % (s + "%d" % symbols.count(s), s, p[0], p[1], p[2])
if filename:
w = open(filename, 'w')
w.write(cif)
w.close()
else:
print cif,
def _set_stage1(self, cell):
prim_cell = get_primitive(cell, tolerance=self._symmetry_tolerance)
sym_dataset = get_symmetry_dataset(prim_cell)
self._space_group_type = sym_dataset['international_standard']
spg_number = sym_dataset['number']
if (spg_number >= 143 and spg_number <= 194
and not self._space_group_type[0] == 'R'): # Hexagonal lattice
self._supercell_dimensions = [[3, 3, 2], [2, 2, 2]]
else: # Other cases
self._supercell_dimensions = [[2, 2, 2]]
# Long cell axis is not multiplied.
for dimension in self._supercell_dimensions:
for i, length in enumerate(
get_lattice_parameters(prim_cell.get_lattice())):
if length * dimension[i] > 20:
dimension[i] = 1
self._tasks = []
for i, dimension in enumerate(self._supercell_dimensions):
task = self._get_phonon_task(prim_cell, np.diag(dimension),
"phonon-%d" % (i + 1))
self._phre_tasks.append(task)
self._tasks.append(task)
