def _get_symmetry_yaml(cell, symmetry, phonopy_version=None):
rotations = symmetry.get_symmetry_operations()['rotations']
translations = symmetry.get_symmetry_operations()['translations']
atom_sets = symmetry.get_map_atoms()
independent_atoms = symmetry.get_independent_atoms()
wyckoffs = symmetry.get_Wyckoff_letters()
yaml = []
if phonopy_version is not None:
yaml.append("phonopy_version: '%s'" % phonopy_version)
if cell.get_magnetic_moments() is None:
spg_symbol, spg_number = symmetry.get_international_table().split()
spg_number = int(spg_number.replace('(', '').replace(')', ''))
yaml.append("space_group_type: '%s'" % spg_symbol)
yaml.append("space_group_number: %d" % spg_number)
yaml.append("point_group_type: '%s'" % symmetry.get_pointgroup())
yaml.append("space_group_operations:")
for i, (r, t) in enumerate(zip(rotations, translations)):
yaml.append("- rotation: # %d" % (i + 1))
for vec in r:
yaml.append(" - [%2d, %2d ,%2d]" % tuple(vec))
line = " translation: ["
for j, x in enumerate(t):
if abs(x - np.rint(x)) < 1e-5:
line += " 0.00000"
else:
line += "%8.5f" % x
if j < 2:
line += ", "
else:
line += " ]"
yaml.append(line)
yaml.append("atom_mapping:")
for i, atom_num in enumerate(atom_sets):
yaml.append(" %d: %d" % (i + 1, atom_num + 1))
yaml.append("site_symmetries:")
for i in independent_atoms:
sitesym = symmetry.get_site_symmetry(i)
yaml.append("- atom: %d" % (i + 1))
if cell.get_magnetic_moments() is None:
yaml.append(" Wyckoff: '%s'" % wyckoffs[i])
site_pointgroup = get_pointgroup(sitesym)
yaml.append(" site_point_group: '%s'" % site_pointgroup[0])
yaml.append(" orientation:")
for v in site_pointgroup[1]:
yaml.append(" - [%2d, %2d, %2d]" % tuple(v))
yaml.append(" rotations:")
for j, r in enumerate(sitesym):
yaml.append(" - # %d" % (j + 1))
for vec in r:
yaml.append(" - [%2d, %2d, %2d]" % tuple(vec))
return "\n".join(yaml)
def _get_symmetry_yaml(cell, symmetry, phonopy_version=None):
rotations = symmetry.get_symmetry_operations()['rotations']
translations = symmetry.get_symmetry_operations()['translations']
atom_sets = symmetry.get_map_atoms()
independent_atoms = symmetry.get_independent_atoms()
wyckoffs = symmetry.get_Wyckoff_letters()
lines = []
if phonopy_version is not None:
lines.append("phonopy_version: '%s'" % phonopy_version)
if cell.get_magnetic_moments() is None:
spg_symbol, spg_number = symmetry.get_international_table().split()
spg_number = int(spg_number.replace('(', '').replace(')', ''))
lines.append("space_group_type: '%s'" % spg_symbol)
lines.append("space_group_number: %d" % spg_number)
lines.append("point_group_type: '%s'" % symmetry.get_pointgroup())
lines.append("space_group_operations:")
for i, (r, t) in enumerate(zip(rotations, translations)):
lines.append("- rotation: # %d" % (i + 1))
for vec in r:
lines.append(" - [%2d, %2d ,%2d]" % tuple(vec))
line = " translation: ["
for j, x in enumerate(t):
if abs(x - np.rint(x)) < 1e-5:
line += " 0.00000"
else:
line += "%8.5f" % x
if j < 2:
line += ", "
else:
line += " ]"
lines.append(line)
lines.append("atom_mapping:")
for i, atom_num in enumerate(atom_sets):
lines.append(" %d: %d" % (i + 1, atom_num + 1))
lines.append("site_symmetries:")
for i in independent_atoms:
sitesym = symmetry.get_site_symmetry(i)
lines.append("- atom: %d" % (i + 1))
if cell.get_magnetic_moments() is None:
lines.append(" Wyckoff: '%s'" % wyckoffs[i])
site_pointgroup = get_pointgroup(sitesym)
lines.append(" site_point_group: '%s'" % site_pointgroup[0])
lines.append(" orientation:")
for v in site_pointgroup[1]:
lines.append(" - [%2d, %2d, %2d]" % tuple(v))
lines.append(" rotations:")
for j, r in enumerate(sitesym):
lines.append(" - # %d" % (j + 1))
for vec in r:
lines.append(" - [%2d, %2d, %2d]" % tuple(vec))
return "\n".join(lines)
def get_symmetry_yaml(cell, symmetry, phonopy_version=None):
rotations = symmetry.get_symmetry_operations()['rotations']
translations = symmetry.get_symmetry_operations()['translations']
atom_sets = symmetry.get_map_atoms()
independent_atoms = symmetry.get_independent_atoms()
wyckoffs = symmetry.get_Wyckoff_letters()
yaml = ""
if phonopy_version is not None:
yaml += "phonopy_version: %s\n" % phonopy_version
if cell.get_magnetic_moments() is None:
yaml += "space_group_type: " + symmetry.get_international_table(
) + "\n"
yaml += "point_group_type: " + symmetry.get_pointgroup() + "\n"
yaml += "space_group_operations:\n"
for i, (r, t) in enumerate(zip(rotations, translations)):
yaml += "- rotation: # %d\n" % (i + 1)
for vec in r:
yaml += " - [%2d, %2d ,%2d]\n" % tuple(vec)
yaml += " translation: ["
for j, x in enumerate(t):
if abs(x - np.rint(x)) < 1e-5:
yaml += " 0.00000"
else:
yaml += "%8.5f" % x
if j < 2:
yaml += ", "
else:
yaml += "]\n"
yaml += "atom_mapping:\n"
for i, atom_num in enumerate(atom_sets):
yaml += " %d: %d\n" % (i + 1, atom_num + 1)
yaml += "site_symmetries:\n"
for i in independent_atoms:
sitesym = symmetry.get_site_symmetry(i)
yaml += "- atom: %d\n" % (i + 1)
if cell.get_magnetic_moments() is None:
yaml += " Wyckoff: %s\n" % (wyckoffs[i])
site_pointgroup = get_pointgroup(sitesym)
yaml += " site_point_group: %s\n" % (site_pointgroup[0])
yaml += " orientation:\n"
for v in site_pointgroup[1]:
yaml += " - [%2d, %2d, %2d]\n" % tuple(v)
yaml += " rotations:\n"
for j, r in enumerate(sitesym):
yaml += " - # %d\n" % (j + 1)
for vec in r:
yaml += " - [%2d, %2d, %2d]\n" % tuple(vec)
return yaml
def get_symmetry_yaml(cell, symmetry, phonopy_version=None):
rotations = symmetry.get_symmetry_operations()['rotations']
translations = symmetry.get_symmetry_operations()['translations']
atom_sets = symmetry.get_map_atoms()
independent_atoms = symmetry.get_independent_atoms()
wyckoffs = symmetry.get_Wyckoff_letters()
yaml = ""
if phonopy_version is not None:
yaml += "phonopy_version: %s\n" % phonopy_version
if cell.get_magnetic_moments() is None:
yaml += "space_group_type: " + symmetry.get_international_table() + "\n"
yaml += "point_group_type: " + symmetry.get_pointgroup() + "\n"
yaml += "space_group_operations:\n"
for i, (r, t) in enumerate(zip(rotations, translations)):
yaml += "- rotation: # %d\n" % (i+1)
for vec in r:
yaml += " - [%2d, %2d ,%2d]\n" % tuple(vec)
yaml += " translation: ["
for j, x in enumerate(t):
if abs(x - np.rint(x)) < 1e-5:
yaml += " 0.00000"
else:
yaml += "%8.5f" % x
if j < 2:
yaml += ", "
else:
yaml += "]\n"
yaml += "atom_mapping:\n"
for i, atom_num in enumerate(atom_sets):
yaml += " %d: %d\n" % (i+1, atom_num+1)
yaml += "site_symmetries:\n"
for i in independent_atoms:
sitesym = symmetry.get_site_symmetry(i)
yaml += "- atom: %d\n" % (i+1)
if cell.get_magnetic_moments() is None:
yaml += " Wyckoff: %s\n" % (wyckoffs[i])
site_pointgroup = get_pointgroup(sitesym)
yaml += " site_point_group: %s\n" % (site_pointgroup[0])
yaml += " orientation:\n"
for v in site_pointgroup[1]:
yaml += " - [%2d, %2d, %2d]\n" % tuple(v)
yaml += " rotations:\n"
for j, r in enumerate(sitesym):
yaml += " - # %d\n" % (j+1)
for vec in r:
yaml += " - [%2d, %2d, %2d]\n" % tuple(vec)
return yaml
def _get_conventional_rotations(self):
spacegroup_symbol = self._symmetry_dataset['international'][0]
spacegroup_number = self._symmetry_dataset['number']
rotations = self._rotations_at_q.copy()
pointgroup = get_pointgroup(rotations)
pointgroup_symbol = pointgroup[0]
transformation_matrix = pointgroup[1]
conventional_rotations = self._transform_rotations(
transformation_matrix, rotations)
return (pointgroup_symbol, transformation_matrix,
conventional_rotations)
def _create_conventional_rotations(self):
rotations = self._rotations
pointgroup = get_pointgroup(rotations)
pointgroup_symbol = pointgroup[0]
transformation_matrix = pointgroup[1]
conventional_rotations = self._transform_rotations(
transformation_matrix, rotations)
self._conventional_rotations = conventional_rotations
self._transformation_matrix = transformation_matrix
self._pointgroup_symbol = pointgroup_symbol
def _create_conventional_rotations(self):
rotations = self._rotations
pointgroup = get_pointgroup(rotations)
pointgroup_symbol = pointgroup[0]
transformation_matrix = pointgroup[1]
conventional_rotations = self._transform_rotations(
transformation_matrix, rotations)
self._conventional_rotations = conventional_rotations
self._transformation_matrix = transformation_matrix
self._pointgroup_symbol = pointgroup_symbol
def _get_conventional_rotations(self):
spacegroup_symbol = self._symmetry_dataset['international'][0]
spacegroup_number = self._symmetry_dataset['number']
rotations = self._rotations_at_q.copy()
pointgroup = get_pointgroup(rotations)
pointgroup_symbol = pointgroup[0]
transformation_matrix = pointgroup[1]
conventional_rotations = self._transform_rotations(
transformation_matrix, rotations)
return (pointgroup_symbol,
transformation_matrix,
conventional_rotations)
def _get_conventional_rotations(self):
spacegroup_symbol = self._symmetry_dataset['international'][0]
rotations = self._rotations_at_q.copy()
pointgroup = get_pointgroup(rotations)
pointgroup_symbol = pointgroup[0]
transformation_matrix = pointgroup[1]
# Set transfomration matrix pR --> hR
if spacegroup_symbol == 'R':
transformation_matrix = np.dot(transformation_matrix, r2h)
# Rotation matrices for the conventional lattice vectors
conventional_rotations = self._transform_rotations(
transformation_matrix, rotations)
return (pointgroup_symbol,
transformation_matrix,
conventional_rotations)
