def _search_primitive_symmetry(self):
self._primitive_symmetry = Symmetry(self._primitive, self._symprec,
self._is_symmetry)
if (len(self._symmetry.get_pointgroup_operations()) != len(
self._primitive_symmetry.get_pointgroup_operations())):
print("Warning: point group symmetries of supercell and primitive"
"cell are different.")
def check_symmetry(input_cell,
primitive_axis=np.eye(3, dtype=float),
symprec=1e-5,
phonopy_version=None):
cell = Primitive(input_cell, primitive_axis, symprec)
symmetry = Symmetry(cell, symprec)
print get_symmetry_yaml(cell, symmetry, phonopy_version),
if input_cell.get_magnetic_moments() == None:
primitive = find_primitive(cell, symprec)
if not primitive == None:
print "# Primitive cell was found. It is written into PPOSCAR."
write_vasp('PPOSCAR', primitive)
# Overwrite symmetry and cell
symmetry = Symmetry(primitive, symprec)
cell = primitive
bravais_lattice, bravais_pos, bravais_numbers = \
spg.refine_cell(cell, symprec)
bravais = Atoms(numbers=bravais_numbers,
scaled_positions=bravais_pos,
cell=bravais_lattice,
pbc=True)
print "# Bravais lattice is written into BPOSCAR."
write_vasp('BPOSCAR', bravais)
def write_supercells_with_displacements(supercell,
cells_with_displacements,
npts,
r0s,
rmts,
supercell_matrix,
filename="wien2k-"):
v = supercell_matrix
det = v[0,0] * v[1,1] * v[2,2] \
+ v[0,1] * v[1,2] * v[2,0] \
+ v[0,2] * v[1,0] * v[2,1] \
- v[0,0] * v[1,2] * v[2,1] \
- v[0,1] * v[1,0] * v[2,2] \
- v[0,2] * v[1,1] * v[2,0]
npts_super = []
r0s_super = []
rmts_super = []
for i, j, k in zip(npts, r0s, rmts):
for l in range(abs(det)):
npts_super.append(i)
r0s_super.append(j)
rmts_super.append(k)
w = open(filename.split('/')[-1] + "S", 'w')
w.write(get_wien2k_struct(supercell, npts_super, r0s_super, rmts_super))
w.close()
for i, cell in enumerate(cells_with_displacements):
symmetry = Symmetry(cell)
print "Number of non-equivalent atoms in %sS-%03d: %d" % (
filename, i + 1, len(symmetry.get_independent_atoms()))
w = open(filename.split('/')[-1] + "S-%03d" % (i + 1), 'w')
w.write(get_wien2k_struct(cell, npts_super, r0s_super, rmts_super))
w.close()
def get_born_OUTCAR(
poscar_filename="POSCAR",
outcar_filename="OUTCAR",
primitive_axis=np.eye(3),
supercell_matrix=np.eye(3, dtype="intc"),
is_symmetry=True,
symmetrize_tensors=False,
symprec=1e-5,
):
ucell = read_vasp(poscar_filename)
outcar = open(outcar_filename)
borns, epsilon = _read_born_and_epsilon(outcar)
num_atom = len(borns)
assert num_atom == ucell.get_number_of_atoms()
if symmetrize_tensors:
lattice = ucell.get_cell().T
positions = ucell.get_scaled_positions()
u_sym = Symmetry(ucell, is_symmetry=is_symmetry, symprec=symprec)
point_sym = [similarity_transformation(lattice, r) for r in u_sym.get_pointgroup_operations()]
epsilon = _symmetrize_tensor(epsilon, point_sym)
borns = _symmetrize_borns(borns, u_sym, lattice, positions, symprec)
inv_smat = np.linalg.inv(supercell_matrix)
scell = get_supercell(ucell, supercell_matrix, symprec=symprec)
pcell = get_primitive(scell, np.dot(inv_smat, primitive_axis), symprec=symprec)
p2s = np.array(pcell.get_primitive_to_supercell_map(), dtype="intc")
p_sym = Symmetry(pcell, is_symmetry=is_symmetry, symprec=symprec)
s_indep_atoms = p2s[p_sym.get_independent_atoms()]
u2u = scell.get_unitcell_to_unitcell_map()
u_indep_atoms = [u2u[x] for x in s_indep_atoms]
reduced_borns = borns[u_indep_atoms].copy()
return reduced_borns, epsilon
def gencastep(fn,modenum,basis,natom,typatsym,symprec,atpos):
from phonopy import Phonopy
import phonopy.structure.spglib as spg
from phonopy.structure.atoms import PhonopyAtoms as Atoms
from phonopy.structure.symmetry import Symmetry, find_primitive, get_pointgroup
fh=open(fn,'w')
unitcell = Atoms(symbols=typatsym, cell=basis, positions=atpos)
pbasis=np.eye(3)
for i in range(len(basis)):
pbasis[i]=basis[i]/np.linalg.norm(basis[i])
symmetry = Symmetry(unitcell, symprec)
rotations = symmetry.get_symmetry_operations()['rotations']
translations = symmetry.get_symmetry_operations()['translations']
print('Space group International symbol: %s' % symmetry.get_international_table())
fh.write('%BLOCK LATTICE_CART\n')
for bl in basis:
fh.write('%s\n' % ''.join(' %12.8f' % b for b in bl))
fh.write('%ENDBLOCK LATTICE_CART\n\n')
fh.write('%BLOCK POSITIONS_ABS\n')
for i in range(len(typatsym)):
fh.write(" %3s " % typatsym[i])
fh.write('%s\n' % ''.join(' %12.8f' % p for p in atpos[i].tolist()))
fh.write('%ENDBLOCK POSITIONS_ABS\n\n')
fh.write('SYMMETRY_TOL : %f ang\n' % symprec)
fh.write('SYMMETRY_GENERATE \n')
fh.write('#KPOINT_MP_GRID : 4 4 4\n#KPOINT_MP_OFFSET : 0.5 0.5 0.5\n')
def gencastep(fn, modenum, basis, natom, typatsym, symprec, atpos):
from phonopy import Phonopy
import phonopy.structure.spglib as spg
from phonopy.structure.atoms import PhonopyAtoms as Atoms
from phonopy.structure.symmetry import Symmetry, find_primitive, get_pointgroup
fh = open(fn, 'w')
unitcell = Atoms(symbols=typatsym, cell=basis, positions=atpos)
pbasis = np.eye(3)
for i in range(len(basis)):
pbasis[i] = basis[i] / np.linalg.norm(basis[i])
symmetry = Symmetry(unitcell, symprec)
rotations = symmetry.get_symmetry_operations()['rotations']
translations = symmetry.get_symmetry_operations()['translations']
print('Space group International symbol: %s' %
symmetry.get_international_table())
fh.write('%BLOCK LATTICE_CART\n')
for bl in basis:
fh.write('%s\n' % ''.join(' %12.8f' % b for b in bl))
fh.write('%ENDBLOCK LATTICE_CART\n\n')
fh.write('%BLOCK POSITIONS_ABS\n')
for i in range(len(typatsym)):
fh.write(" %3s " % typatsym[i])
fh.write('%s\n' % ''.join(' %12.8f' % p for p in atpos[i].tolist()))
fh.write('%ENDBLOCK POSITIONS_ABS\n\n')
fh.write('SYMMETRY_TOL : %f ang\n' % symprec)
fh.write('SYMMETRY_GENERATE \n')
fh.write('#KPOINT_MP_GRID : 4 4 4\n#KPOINT_MP_OFFSET : 0.5 0.5 0.5\n')
def __init__(self,
fc4,
supercell,
primitive,
mesh,
temperatures=None,
band_indices=None,
frequency_factor_to_THz=VaspToTHz,
is_nosym=False,
symprec=1e-3,
cutoff_frequency=1e-4,
log_level=False,
lapack_zheev_uplo='L'):
self._fc4 = fc4
self._supercell = supercell
self._primitive = primitive
self._masses = np.double(self._primitive.get_masses())
self._mesh = np.intc(mesh)
if temperatures is None:
self._temperatures = np.double([0])
else:
self._temperatures = np.double(temperatures)
num_band = primitive.get_number_of_atoms() * 3
if band_indices is None:
self._band_indices = np.arange(num_band, dtype='intc')
else:
self._band_indices = np.intc(band_indices)
self._frequency_factor_to_THz = frequency_factor_to_THz
self._is_nosym = is_nosym
self._symprec = symprec
self._cutoff_frequency = cutoff_frequency
self._log_level = log_level
self._lapack_zheev_uplo = lapack_zheev_uplo
symmetry = Symmetry(primitive, symprec=symprec)
self._point_group_operations = symmetry.get_pointgroup_operations()
self._grid_address = None
self._bz_map = None
self._set_grid_address()
self._grid_point = None
self._quartets_at_q = None
self._weights_at_q = None
self._phonon_done = None
self._frequencies = None
self._eigenvectors = None
self._dm = None
self._nac_q_direction = None
self._frequency_shifts = None
# Unit to THz of Delta
self._unit_conversion = (EV / Angstrom ** 4 / AMU ** 2
/ (2 * np.pi * THz) ** 2
* Hbar * EV / (2 * np.pi * THz) / 8
/ np.prod(self._mesh))
self._allocate_phonon()
def read_crystal(filename):
f_crystal = open(filename)
crystal_in = CrystalIn(f_crystal.readlines())
f_crystal.close()
tags = crystal_in.get_tags()
cell = Atoms(cell=tags['lattice_vectors'],
symbols=tags['atomic_species'],
scaled_positions=tags['coordinates'])
magmoms = tags['magnetic_moments']
if magmoms is not None:
# Print out symmetry information for magnetic cases
# Original code from structure/symmetry.py
symmetry = Symmetry(cell, symprec=1e-5)
print("CRYSTAL-interface: Magnetic structure, number of operations without spin: %d" %
len(symmetry.get_symmetry_operations()['rotations']))
print("CRYSTAL-interface: Spacegroup without spin: %s" % symmetry.get_international_table())
cell.set_magnetic_moments(magmoms)
symmetry = Symmetry(cell, symprec=1e-5)
print("CRYSTAL-interface: Magnetic structure, number of operations with spin: %d" %
len(symmetry.get_symmetry_operations()['rotations']))
print("")
return cell, tags['conv_numbers']
def write_supercells_with_displacements(supercell,
cells_with_displacements,
ids,
npts,
r0s,
rmts,
num_unitcells_in_supercell,
pre_filename="wien2k",
width=3):
npts_super = []
r0s_super = []
rmts_super = []
for i, j, k in zip(npts, r0s, rmts):
for l in range(num_unitcells_in_supercell):
npts_super.append(i)
r0s_super.append(j)
rmts_super.append(k)
_pre_filename = pre_filename.split('/')[-1] + "S"
write_wein2k(_pre_filename, supercell, npts_super, r0s_super, rmts_super)
for i, cell in zip(ids, cells_with_displacements):
symmetry = Symmetry(cell)
filename = "{pre_filename}-{0:0{width}}.in".format(
i, pre_filename=_pre_filename, width=width)
print("Number of non-equivalent atoms in %s: %d" %
(filename, len(symmetry.get_independent_atoms())))
write_wein2k(filename, cell, npts_super, r0s_super, rmts_super)
def write_born_file(initial_structure, phonopy_inputs, dielectric_tensor,
born_effective_charge_tensor, file_path):
"""
Creates the born file that phonopy needs for the non-analytical correction to be applied.
"""
phonon = get_initialized_phononopy_instance(initial_structure,
phonopy_inputs)
symm = Symmetry(cell=phonon.get_primitive(),
symprec=phonopy_inputs['symprec'])
independent_atom_indices_list = symm.get_independent_atoms()
born_file = File()
born_file += "14.400"
flat_dielectric_list = misc.flatten_multi_dimensional_list(
dielectric_tensor)
born_file += " ".join(str(component) for component in flat_dielectric_list)
print "Independent atom indices:", independent_atom_indices_list
for atomic_bec_index in independent_atom_indices_list:
atomic_bec = born_effective_charge_tensor[atomic_bec_index]
flat_atomic_bec = misc.flatten_multi_dimensional_list(atomic_bec)
born_file += " ".join(str(component) for component in flat_atomic_bec)
born_file.write_to_path(file_path)
def _extract_independent_borns(borns,
ucell,
primitive_matrix=None,
supercell_matrix=None,
is_symmetry=True,
symprec=1e-5):
if primitive_matrix is None:
pmat = np.eye(3)
else:
pmat = primitive_matrix
if supercell_matrix is None:
smat = np.eye(3, dtype='intc')
else:
smat = supercell_matrix
inv_smat = np.linalg.inv(smat)
scell = get_supercell(ucell, smat, symprec=symprec)
pcell = get_primitive(scell, np.dot(inv_smat, pmat), symprec=symprec)
p2s = np.array(pcell.get_primitive_to_supercell_map(), dtype='intc')
p_sym = Symmetry(pcell, is_symmetry=is_symmetry, symprec=symprec)
s_indep_atoms = p2s[p_sym.get_independent_atoms()]
u2u = scell.get_unitcell_to_unitcell_map()
u_indep_atoms = [u2u[x] for x in s_indep_atoms]
reduced_borns = borns[u_indep_atoms].copy()
return reduced_borns, s_indep_atoms
def write_supercells_with_displacements( supercell,
cells_with_displacements,
npts, r0s, rmts,
supercell_matrix,
filename="wien2k-" ):
v = supercell_matrix
det = v[0,0] * v[1,1] * v[2,2] \
+ v[0,1] * v[1,2] * v[2,0] \
+ v[0,2] * v[1,0] * v[2,1] \
- v[0,0] * v[1,2] * v[2,1] \
- v[0,1] * v[1,0] * v[2,2] \
- v[0,2] * v[1,1] * v[2,0]
npts_super = []
r0s_super = []
rmts_super = []
for i, j, k in zip(npts, r0s, rmts):
for l in range(abs(det)):
npts_super.append(i)
r0s_super.append(j)
rmts_super.append(k)
w = open(filename.split('/')[-1]+"S", 'w')
w.write( get_wien2k_struct(supercell, npts_super, r0s_super, rmts_super) )
w.close()
for i, cell in enumerate( cells_with_displacements ):
symmetry = Symmetry( cell )
print "Number of non-equivalent atoms in %sS-%03d: %d" % (
filename, i+1, len( symmetry.get_independent_atoms() ) )
w = open(filename.split('/')[-1]+"S-%03d" % (i+1), 'w')
w.write( get_wien2k_struct(cell, npts_super, r0s_super, rmts_super) )
w.close()
def check_symmetry(input_cell,
primitive_axis=None,
symprec=1e-5,
distance_to_A=1.0,
phonopy_version=None):
if primitive_axis is None:
cell = get_primitive(input_cell, np.eye(3), symprec=symprec)
else:
cell = get_primitive(input_cell, primitive_axis, symprec=symprec)
lattice = cell.get_cell() * distance_to_A
cell.set_cell(lattice)
symmetry = Symmetry(cell, symprec)
print(_get_symmetry_yaml(cell, symmetry, phonopy_version))
if input_cell.get_magnetic_moments() is None:
primitive = find_primitive(cell, symprec)
if primitive is not None:
print("# Primitive cell was found. It is written into PPOSCAR.")
write_vasp('PPOSCAR', primitive)
# Overwrite symmetry and cell
symmetry = Symmetry(primitive, symprec)
cell = primitive
(bravais_lattice, bravais_pos,
bravais_numbers) = spg.refine_cell(cell, symprec)
bravais = Atoms(numbers=bravais_numbers,
scaled_positions=bravais_pos,
cell=bravais_lattice,
pbc=True)
print("# Bravais lattice is written into BPOSCAR.")
write_vasp('BPOSCAR', bravais)
def get_born_OUTCAR(poscar_filename="POSCAR",
outcar_filename="OUTCAR",
primitive_axis=np.eye(3),
is_symmetry=True,
symmetrize_tensors=False):
cell = read_vasp(poscar_filename)
primitive = Primitive(cell, primitive_axis)
p2p = primitive.get_primitive_to_primitive_map()
symmetry = Symmetry(primitive, is_symmetry=is_symmetry)
independent_atoms = symmetry.get_independent_atoms()
prim_lat = primitive.get_cell().T
outcar = open(outcar_filename)
borns = []
while True:
line = outcar.readline()
if not line:
break
if "NIONS" in line:
num_atom = int(line.split()[11])
if "MACROSCOPIC STATIC DIELECTRIC TENSOR" in line:
epsilon = []
outcar.readline()
epsilon.append([float(x) for x in outcar.readline().split()])
epsilon.append([float(x) for x in outcar.readline().split()])
epsilon.append([float(x) for x in outcar.readline().split()])
if "BORN" in line:
outcar.readline()
line = outcar.readline()
if "ion" in line:
for i in range(num_atom):
born = []
born.append([float(x) for x in outcar.readline().split()][1:])
born.append([float(x) for x in outcar.readline().split()][1:])
born.append([float(x) for x in outcar.readline().split()][1:])
outcar.readline()
borns.append(born)
reduced_borns = []
for p_i, u_i in enumerate(p2p):
if p_i in independent_atoms:
if symmetrize_tensors:
site_sym = [similarity_transformation(prim_lat, rot)
for rot in symmetry.get_site_symmetry(p_i)]
reduced_borns.append(symmetrize_tensor(borns[u_i], site_sym))
else:
reduced_borns.append(borns[u_i])
if symmetrize_tensors:
point_sym = [similarity_transformation(prim_lat, rot)
for rot in symmetry.get_pointgroup_operations()]
epsilon = symmetrize_tensor(epsilon, point_sym)
else:
epsilon = np.array(epsilon)
return np.array(reduced_borns), epsilon
def write_supercells_with_displacements(supercell,
cells_with_displacements,
npts,
r0s,
rmts,
num_unitcells_in_supercell,
filename="wien2k-"):
npts_super = []
r0s_super = []
rmts_super = []
for i, j, k in zip(npts, r0s, rmts):
for l in range(num_unitcells_in_supercell):
npts_super.append(i)
r0s_super.append(j)
rmts_super.append(k)
w = open(filename.split('/')[-1] + "S", 'w')
w.write(_get_wien2k_struct(supercell, npts_super, r0s_super, rmts_super))
w.close()
for i, cell in enumerate(cells_with_displacements):
symmetry = Symmetry(cell)
supercell_filename = filename.split('/')[-1] + "S-%03d" % (i + 1)
print("Number of non-equivalent atoms in %s: %d" %
(supercell_filename, len(symmetry.get_independent_atoms())))
w = open(supercell_filename, 'w')
w.write(_get_wien2k_struct(cell, npts_super, r0s_super, rmts_super))
w.close()
def __init__(self,
fc4,
supercell,
primitive,
mesh,
temperatures=None,
band_indices=None,
frequency_factor_to_THz=VaspToTHz,
is_nosym=False,
symprec=1e-3,
cutoff_frequency=1e-4,
log_level=False,
lapack_zheev_uplo='L'):
self._fc4 = fc4
self._supercell = supercell
self._primitive = primitive
self._masses = np.double(self._primitive.get_masses())
self._mesh = np.intc(mesh)
if temperatures is None:
self._temperatures = np.double([0])
else:
self._temperatures = np.double(temperatures)
num_band = primitive.get_number_of_atoms() * 3
if band_indices is None:
self._band_indices = np.arange(num_band, dtype='intc')
else:
self._band_indices = np.intc(band_indices)
self._frequency_factor_to_THz = frequency_factor_to_THz
self._is_nosym = is_nosym
self._symprec = symprec
self._cutoff_frequency = cutoff_frequency
self._log_level = log_level
self._lapack_zheev_uplo = lapack_zheev_uplo
symmetry = Symmetry(primitive, symprec=symprec)
self._point_group_operations = symmetry.get_pointgroup_operations()
self._grid_address = None
self._bz_map = None
self._set_grid_address()
self._grid_point = None
self._quartets_at_q = None
self._weights_at_q = None
self._phonon_done = None
self._frequencies = None
self._eigenvectors = None
self._dm = None
self._nac_q_direction = None
self._frequency_shifts = None
# Unit to THz of Delta
self._unit_conversion = (EV / Angstrom**4 / AMU**2 /
(2 * np.pi * THz)**2 * Hbar * EV /
(2 * np.pi * THz) / 8 / np.prod(self._mesh))
self._allocate_phonon()
def _distribute_forces(supercell, disp, forces, filename, symprec):
natom = supercell.get_number_of_atoms()
lattice = supercell.get_cell()
symbols = supercell.get_chemical_symbols()
positions = supercell.get_positions()
positions[disp[0]] += disp[1]
cell = Atoms(cell=lattice, positions=positions, symbols=symbols, pbc=True)
symmetry = Symmetry(cell, symprec)
independent_atoms = symmetry.get_independent_atoms()
# Rotation matrices in Cartesian
rotations = []
for r in symmetry.get_symmetry_operations()["rotations"]:
rotations.append(similarity_transformation(lattice.T, r))
map_operations = symmetry.get_map_operations()
map_atoms = symmetry.get_map_atoms()
atoms_in_dot_scf = _get_independent_atoms_in_dot_scf(filename)
if len(forces) != len(atoms_in_dot_scf):
print("%s does not contain necessary information." % filename)
print('Plese check if there are "FGL" lines with')
print('"total forces" are required.')
return False
if len(atoms_in_dot_scf) == natom:
print("It is assumed that there is no symmetrically-equivalent " "atoms in ")
print("'%s' at wien2k calculation." % filename)
force_set = forces
elif len(forces) != len(independent_atoms):
print("Non-equivalent atoms of %s could not be recognized by phonopy." % filename)
return False
else:
# 1. Transform wien2k forces to those on independent atoms
indep_atoms_to_wien2k = []
forces_remap = []
for i, pos_wien2k in enumerate(atoms_in_dot_scf):
for j, pos in enumerate(cell.get_scaled_positions()):
diff = pos_wien2k - pos
diff -= np.rint(diff)
if (abs(diff) < symprec).all():
forces_remap.append(np.dot(rotations[map_operations[j]], forces[i]))
indep_atoms_to_wien2k.append(map_atoms[j])
break
if len(forces_remap) != len(forces):
print("Atomic position mapping between Wien2k and phonopy failed.")
print("If you think this is caused by a bug of phonopy")
print("please report it in the phonopy mainling list.")
return False
# 2. Distribute forces from independent to dependent atoms.
force_set = []
for i in range(natom):
j = indep_atoms_to_wien2k.index(map_atoms[i])
force_set.append(np.dot(rotations[map_operations[i]].T, forces_remap[j]))
return force_set
def __init__(self,
mesh,
primitive,
supercell,
fc2,
nac_params=None,
nac_q_direction=None,
sigma=None,
cutoff_frequency=None,
frequency_step=None,
num_frequency_points=None,
temperatures=None,
frequency_factor_to_THz=VaspToTHz,
frequency_scale_factor=1.0,
is_mesh_symmetry=True,
symprec=1e-5,
filename=None,
log_level=False,
lapack_zheev_uplo='L'):
self._grid_point = None
self._mesh = np.array(mesh, dtype='intc')
self._primitive = primitive
self._supercell = supercell
self._fc2 = fc2
self._nac_params = nac_params
self._nac_q_direction = None
self.set_nac_q_direction(nac_q_direction)
self._sigma = None
self.set_sigma(sigma)
if cutoff_frequency is None:
self._cutoff_frequency = 0
else:
self._cutoff_frequency = cutoff_frequency
self._frequency_step = frequency_step
self._num_frequency_points = num_frequency_points
self._temperatures = temperatures
self._frequency_factor_to_THz = frequency_factor_to_THz
self._frequency_scale_factor = frequency_scale_factor
self._is_mesh_symmetry = is_mesh_symmetry
self._symprec = symprec
self._filename = filename
self._log_level = log_level
self._lapack_zheev_uplo = lapack_zheev_uplo
self._num_band = self._primitive.get_number_of_atoms() * 3
self._reciprocal_lattice = np.linalg.inv(self._primitive.get_cell())
self._init_dynamical_matrix()
self._symmetry = Symmetry(primitive, symprec)
self._tetrahedron_method = None
self._phonon_done = None
self._frequencies = None
self._eigenvectors = None
self._joint_dos = None
self._frequency_points = None
def _search_primitive_symmetry_ideal(self):
self._primitive_symmetry = Symmetry(self._primitive_ideal,
self._symprec,
self._is_symmetry)
n0 = len(self._symmetry.get_pointgroup_operations())
n1 = len(self._primitive_symmetry.get_pointgroup_operations())
if n0 != n1:
raise Warning("Point group symmetries of supercell and primitive"
"cell are different.")
def get_number_of_triplets(primitive, mesh, grid_point, symprec=1e-5):
mesh = np.array(mesh, dtype='intc')
symmetry = Symmetry(primitive, symprec)
point_group = symmetry.get_pointgroup_operations()
primitive_lattice = np.linalg.inv(primitive.get_cell())
triplets_at_q, _, _, _, _, _ = get_triplets_at_q(grid_point, mesh,
point_group,
primitive_lattice)
return len(triplets_at_q)
def test_magmom(self):
symprec = 1e-5
cell = get_unitcell_from_phonopy_yaml(os.path.join(data_dir,"Cr.yaml"))
symmetry_nonspin = Symmetry(cell, symprec=symprec)
atom_map_nonspin = symmetry_nonspin.get_map_atoms()
len_sym_nonspin = len(
symmetry_nonspin.get_symmetry_operations()['rotations'])
spin = [1, -1]
cell_withspin = cell.copy()
cell_withspin.set_magnetic_moments(spin)
symmetry_withspin = Symmetry(cell_withspin, symprec=symprec)
atom_map_withspin = symmetry_withspin.get_map_atoms()
len_sym_withspin = len(
symmetry_withspin.get_symmetry_operations()['rotations'])
broken_spin = [1, -2]
cell_brokenspin = cell.copy()
cell_brokenspin = cell.copy()
cell_brokenspin.set_magnetic_moments(broken_spin)
symmetry_brokenspin = Symmetry(cell_brokenspin, symprec=symprec)
atom_map_brokenspin = symmetry_brokenspin.get_map_atoms()
len_sym_brokenspin = len(
symmetry_brokenspin.get_symmetry_operations()['rotations'])
self.assertTrue((atom_map_nonspin == atom_map_withspin).all())
self.assertFalse((atom_map_nonspin == atom_map_brokenspin).all())
self.assertTrue(len_sym_nonspin == len_sym_withspin)
self.assertFalse(len_sym_nonspin == len_sym_brokenspin)
def test_magmom(convcell_cr: PhonopyAtoms):
"""Test symmetry search with hmagnetic moments."""
symprec = 1e-5
symmetry_nonspin = Symmetry(convcell_cr, symprec=symprec)
atom_map_nonspin = symmetry_nonspin.get_map_atoms()
len_sym_nonspin = len(symmetry_nonspin.symmetry_operations["rotations"])
spin = [1, -1]
cell_withspin = convcell_cr.copy()
cell_withspin.magnetic_moments = spin
symmetry_withspin = Symmetry(cell_withspin, symprec=symprec)
atom_map_withspin = symmetry_withspin.get_map_atoms()
len_sym_withspin = len(symmetry_withspin.symmetry_operations["rotations"])
broken_spin = [1, -2]
cell_brokenspin = convcell_cr.copy()
cell_brokenspin = convcell_cr.copy()
cell_brokenspin.magnetic_moments = broken_spin
symmetry_brokenspin = Symmetry(cell_brokenspin, symprec=symprec)
atom_map_brokenspin = symmetry_brokenspin.get_map_atoms()
len_sym_brokenspin = len(
symmetry_brokenspin.symmetry_operations["rotations"])
assert (atom_map_nonspin == atom_map_withspin).all()
assert (atom_map_nonspin != atom_map_brokenspin).any()
assert len_sym_nonspin == len_sym_withspin
assert len_sym_nonspin != len_sym_brokenspin
def get_coarse_ir_grid_points(primitive,
mesh,
mesh_divisors,
coarse_mesh_shifts,
is_kappa_star=True,
symprec=1e-5):
mesh = np.array(mesh, dtype='intc')
symmetry = Symmetry(primitive, symprec)
point_group = symmetry.get_pointgroup_operations()
if mesh_divisors is None:
(ir_grid_points,
ir_grid_weights,
grid_address,
grid_mapping_table) = get_ir_grid_points(mesh, point_group)
else:
mesh_divs = np.array(mesh_divisors, dtype='intc')
coarse_mesh = mesh // mesh_divs
if coarse_mesh_shifts is None:
coarse_mesh_shifts = [False, False, False]
if not is_kappa_star:
coarse_grid_address = get_grid_address(coarse_mesh)
coarse_grid_points = np.arange(np.prod(coarse_mesh), dtype='intc')
coarse_grid_weights = np.ones(len(coarse_grid_points), dtype='intc')
else:
(coarse_ir_grid_points,
coarse_ir_grid_weights,
coarse_grid_address,
coarse_grid_mapping_table) = get_ir_grid_points(
coarse_mesh,
point_group,
mesh_shifts=coarse_mesh_shifts)
ir_grid_points = from_coarse_to_dense_grid_points(
mesh,
mesh_divs,
coarse_grid_points,
coarse_grid_address,
coarse_mesh_shifts=coarse_mesh_shifts)
grid_address = get_grid_address(mesh)
ir_grid_weights = ir_grid_weights
primitive_lattice = np.linalg.inv(primitive.get_cell())
bz_grid_address, bz_map = spg.relocate_BZ_grid_address(grid_address,
mesh,
primitive_lattice)
return (ir_grid_points,
ir_grid_weights,
bz_grid_address,
grid_mapping_table)
def get_coarse_ir_grid_points(primitive,
mesh,
mesh_divisors,
coarse_mesh_shifts,
is_kappa_star=True,
symprec=1e-5):
mesh = np.array(mesh, dtype='intc')
symmetry = Symmetry(primitive, symprec)
point_group = symmetry.get_pointgroup_operations()
if mesh_divisors is None:
(ir_grid_points,
ir_grid_weights,
grid_address,
grid_mapping_table) = get_ir_grid_points(mesh, point_group)
else:
mesh_divs = np.array(mesh_divisors, dtype='intc')
coarse_mesh = mesh // mesh_divs
if coarse_mesh_shifts is None:
coarse_mesh_shifts = [False, False, False]
if not is_kappa_star:
coarse_grid_address = get_grid_address(coarse_mesh)
coarse_grid_points = np.arange(np.prod(coarse_mesh), dtype='uintp')
else:
(coarse_ir_grid_points,
coarse_ir_grid_weights,
coarse_grid_address,
coarse_grid_mapping_table) = get_ir_grid_points(
coarse_mesh,
point_group,
mesh_shifts=coarse_mesh_shifts)
ir_grid_points = from_coarse_to_dense_grid_points(
mesh,
mesh_divs,
coarse_grid_points,
coarse_grid_address,
coarse_mesh_shifts=coarse_mesh_shifts)
grid_address = get_grid_address(mesh)
ir_grid_weights = ir_grid_weights
reciprocal_lattice = np.linalg.inv(primitive.get_cell())
bz_grid_address, bz_map = spg.relocate_BZ_grid_address(grid_address,
mesh,
reciprocal_lattice,
is_dense=True)
return (ir_grid_points,
ir_grid_weights,
bz_grid_address,
grid_mapping_table)
def _expand_borns(borns, primitive: PhonopyAtoms, prim_symmetry: Symmetry):
# Expand Born effective charges to all atoms in the primitive cell
rotations = prim_symmetry.symmetry_operations["rotations"]
map_operations = prim_symmetry.get_map_operations()
map_atoms = prim_symmetry.get_map_atoms()
for i in range(len(primitive)):
# R_cart = L R L^-1
rot_cartesian = similarity_transformation(primitive.cell.T,
rotations[map_operations[i]])
# R_cart^T B R_cart^-T (inverse rotation is required to transform)
borns[i] = similarity_transformation(rot_cartesian.T,
borns[map_atoms[i]])
def test_parse_wien2k_struct(self):
cell, npts, r0s, rmts = parse_wien2k_struct("BaGa2.struct")
lattice = cell.get_cell().T
displacements, supercell = parse_disp_yaml("disp_BaGa2.yaml",
return_cell=True)
symmetry = Symmetry(cell)
print(PhonopyAtoms(atoms=cell))
sym_op = symmetry.get_symmetry_operations()
print(symmetry.get_international_table())
for i, (r, t) in enumerate(
zip(sym_op['rotations'], sym_op['translations'])):
print("--- %d ---" % (i + 1))
print(r)
print(t)
def get_born_parameters(f, primitive, is_symmetry):
# Read unit conversion factor, damping factor, ...
factors = [float(x) for x in f.readline().split()]
if len(factors) < 1:
print "BORN file format of line 1 is incorrect"
return False
if len(factors) < 2:
factors = factors[0]
# Read dielectric constant
line = f.readline().split()
if not len(line) == 9:
print "BORN file format of line 2 is incorrect"
return False
dielectric = np.reshape([float(x) for x in line], (3, 3))
# Read Born effective charge
symmetry = Symmetry(primitive, is_symmetry=is_symmetry)
independent_atoms = symmetry.get_independent_atoms()
born = np.zeros((primitive.get_number_of_atoms(), 3, 3), dtype=float)
for i in independent_atoms:
line = f.readline().split()
if len(line) == 0:
print "Number of lines for Born effect charge is not enough."
return False
if not len(line) == 9:
print "BORN file format of line %d is incorrect" % (i + 3)
return False
born[i] = np.reshape([float(x) for x in line], (3, 3))
# Expand Born effective charges to all atoms in the primitive cell
rotations = symmetry.get_symmetry_operations()['rotations']
map_operations = symmetry.get_map_operations()
map_atoms = symmetry.get_map_atoms()
for i in range(primitive.get_number_of_atoms()):
# R_cart = L R L^-1
rot_cartesian = similarity_transformation(
primitive.get_cell().transpose(), rotations[map_operations[i]])
# R_cart^T B R_cart^-T (inverse rotation is required to transform)
born[i] = similarity_transformation(rot_cartesian.transpose(),
born[map_atoms[i]])
non_anal = {'born': born,
'factor': factors,
'dielectric': dielectric }
return non_anal
def get_number_of_triplets(primitive,
mesh,
grid_point,
symprec=1e-5):
mesh = np.array(mesh, dtype='intc')
symmetry = Symmetry(primitive, symprec)
point_group = symmetry.get_pointgroup_operations()
primitive_lattice = np.linalg.inv(primitive.get_cell())
triplets_at_q, _, _, _, _, _ = get_triplets_at_q(
grid_point,
mesh,
point_group,
primitive_lattice)
return len(triplets_at_q)
def parse_BORN( primitive, filename = "BORN" ):
file = open( filename, 'r' )
# Read unit conversion factor, damping factor, ...
factors = [ float( x ) for x in file.readline().split() ]
if len( factors ) < 1:
print "BORN file format of line 1 is incorrect"
return None
if len( factors ) < 2:
factors.append( Damping_Factor )
# Read dielectric constant
line = file.readline().split()
if 9 < len( line ) or len( line ) < 9:
print "BORN file format of line 2 is incorrect"
return None
dielectric = np.reshape( [ float( x ) for x in line ], ( 3, 3 ) )
# Read Born effective charge
symmetry = Symmetry( primitive )
independent_atoms = symmetry.get_independent_atoms()
born = np.zeros( ( primitive.get_number_of_atoms(), 3, 3 ), dtype=float )
for i in independent_atoms:
line = file.readline().split()
if 9 < len( line ) or len( line ) < 9:
print "BORN file format of line %d is incorrect" % ( i + 3 )
return None
born[ i ] = np.reshape( [ float( x ) for x in line ], ( 3, 3 ) )
# Expand Born effective charges to all atoms in the primitive cell
rotations = symmetry.get_symmetry_operations()['rotations']
map_operations = symmetry.get_map_operations()
map_atoms = symmetry.get_map_atoms()
for i in range( primitive.get_number_of_atoms() ):
# R_cart = L R L^-1
rot_cartesian = similarity_transformation(
primitive.get_cell().transpose(), rotations[ map_operations[i] ] )
# R_cart^T B R_cart^-T ( inverse rotation is required to transform )
born[i] = similarity_transformation( rot_cartesian.transpose(),
born[ map_atoms[ i ] ] )
non_anal = {'born': born,
'factor': factors,
'dielectric': dielectric }
return non_anal
def __init__(
self,
supercell: Supercell,
primitive: Primitive,
fc2,
mesh=None,
nac_params=None,
nac_q_direction=None,
sigmas=None,
cutoff_frequency=1e-4,
frequency_step=None,
num_frequency_points=None,
num_points_in_batch=None,
temperatures=None,
frequency_factor_to_THz=VaspToTHz,
frequency_scale_factor=None,
use_grg=False,
SNF_coordinates="reciprocal",
is_mesh_symmetry=True,
is_symmetry=True,
store_dense_gp_map=False,
symprec=1e-5,
output_filename=None,
log_level=0,
):
"""Init method."""
self._primitive = primitive
self._supercell = supercell
self._fc2 = fc2
self._temperatures = temperatures
self._nac_params = nac_params
self._nac_q_direction = nac_q_direction
if sigmas is None:
self._sigmas = [None]
else:
self._sigmas = sigmas
self._cutoff_frequency = cutoff_frequency
self._frequency_factor_to_THz = frequency_factor_to_THz
self._frequency_scale_factor = frequency_scale_factor
self._is_mesh_symmetry = is_mesh_symmetry
self._is_symmetry = is_symmetry
self._store_dense_gp_map = store_dense_gp_map
self._use_grg = use_grg
self._SNF_coordinates = SNF_coordinates
self._symprec = symprec
self._filename = output_filename
self._log_level = log_level
self._bz_grid = None
self._joint_dos = None
self._num_frequency_points_in_batch = num_points_in_batch
self._frequency_step = frequency_step
self._num_frequency_points = num_frequency_points
self._primitive_symmetry = Symmetry(self._primitive, self._symprec,
self._is_symmetry)
if mesh is not None:
self.mesh_numbers = mesh
self.initialize(mesh)
def parse_BORN_from_strings(strings,
primitive,
symprec=1e-5,
is_symmetry=True):
f = StringIO.StringIO(strings)
symmetry = Symmetry(primitive, symprec=symprec, is_symmetry=is_symmetry)
return get_born_parameters(f, primitive, symmetry)
def get_data(args, interface_mode=None):
args = parse_args()
cell, _ = read_crystal_structure(args.filenames[0],
interface_mode=interface_mode)
f = h5py.File(args.filenames[1])
primitive_matrix = np.reshape(
[fracval(x) for x in args.primitive_matrix.split()], (3, 3))
primitive = get_primitive(cell, primitive_matrix)
symmetry = Symmetry(primitive)
data = {}
data['cell'] = primitive
data['symmetry'] = symmetry
data['mesh'] = np.array(f['mesh'][:], dtype='intc') # (3)
data['weight'] = f['weight'][:] # (gp)
data['group_velocity'] = f['group_velocity'][:] # (gp, band, 3)
data['qpoint'] = f['qpoint'][:] # (gp, 3)
data['frequency'] = f['frequency'][:] # (gp, band)
if 'gamma_N' in f:
data['gamma_N'] = f['gamma_N'][:] # (temps, gp, band)
data['gamma_U'] = f['gamma_U'][:] # (temps, gp, band)
if 'gamma_isotope' in f:
data['gamma_isotope'] = f['gamma_isotope'][:] # (gp, band)
data['heat_capacity'] = f['heat_capacity'][:] # (temps, gp, band)
data['temperature'] = np.array(f['temperature'][:],
dtype='double') # (temps)
ir_grid_points, grid_address, _ = get_grid_symmetry(data)
data['ir_grid_points'] = ir_grid_points
data['grid_address'] = grid_address
return data
def _search_phonon_supercell_symmetry(self):
if self._phonon_supercell_matrix is None:
self._phonon_supercell_symmetry = self._symmetry
else:
self._phonon_supercell_symmetry = Symmetry(self._phonon_supercell,
self._symprec,
self._is_symmetry)
def get_equivalent_q_points_by_symmetry(q_point, structure):
from phonopy.structure.symmetry import Symmetry
bulk = PhonopyAtoms(symbols=structure.get_atomic_elements(),
scaled_positions=structure.get_scaled_positions(),
cell=structure.get_cell().T)
tot_points = []
for operation_matrix in Symmetry(bulk).get_reciprocal_operations():
operation_matrix_q = np.dot(
np.linalg.inv(structure.get_primitive_matrix()),
operation_matrix.T)
operation_matrix_q = np.dot(operation_matrix_q,
structure.get_primitive_matrix())
q_point_test = np.dot(q_point, operation_matrix_q)
if (q_point_test >= 0).all():
tot_points.append(q_point_test)
# print tot_points
# print(np.vstack({tuple(row) for row in tot_points}))
return np.vstack({tuple(row) for row in tot_points})
def get_BORN_txt(structure, parameters, nac_data, symprec=1.e-5):
from phonopy.structure.cells import get_primitive, get_supercell
from phonopy.structure.symmetry import Symmetry
from phonopy.interface import get_default_physical_units
from phonopy.structure.atoms import Atoms as PhonopyAtoms
born_charges = nac_data.get_array('born_charges')
epsilon = nac_data.get_array('epsilon')
print ('inside born parameters')
pmat = parameters['primitive']
smat = parameters['supercell']
ucell = PhonopyAtoms(symbols=[site.kind_name for site in structure.sites],
positions=[site.position for site in structure.sites],
cell=structure.cell)
num_atom = len(born_charges)
assert num_atom == ucell.get_number_of_atoms(), \
"num_atom %d != len(borns) %d" % (ucell.get_number_of_atoms(),
len(born_charges))
inv_smat = np.linalg.inv(smat)
scell = get_supercell(ucell, smat, symprec=symprec)
pcell = get_primitive(scell, np.dot(inv_smat, pmat), symprec=symprec)
p2s = np.array(pcell.get_primitive_to_supercell_map(), dtype='intc')
p_sym = Symmetry(pcell, is_symmetry=True, symprec=symprec)
s_indep_atoms = p2s[p_sym.get_independent_atoms()]
u2u = scell.get_unitcell_to_unitcell_map()
u_indep_atoms = [u2u[x] for x in s_indep_atoms]
reduced_borns = born_charges[u_indep_atoms].copy()
factor = get_default_physical_units('vasp')['nac_factor'] # born charges in VASP units
born_txt = ('{}\n'.format(factor))
for num in epsilon.flatten():
born_txt += ('{0:4.8f}'.format(num))
born_txt += ('\n')
for atom in reduced_borns:
for num in atom:
born_txt += ('{0:4.8f}'.format(num))
born_txt += ('\n')
born_txt += ('{}\n'.format(factor))
return born_txt
def _search_primitive_symmetry(self):
self._primitive_symmetry = Symmetry(self._primitive,
self._symprec,
self._is_symmetry)
if (len(self._symmetry.get_pointgroup_operations()) !=
len(self._primitive_symmetry.get_pointgroup_operations())):
print("Warning: point group symmetries of supercell and primitive"
"cell are different.")
def set_grid(self):
self._point_operations= get_pointgroup_operations(
Symmetry(self._cell).get_pointgroup_operations())
self._kpoint_operations = get_kpoint_group(self._mesh, self._point_operations)
(mapping, rot_mappings) =get_mappings(self._mesh,
Symmetry(self._cell).get_pointgroup_operations(),
qpoints=np.array([0,0,0],dtype="double"))
self._rot_mappings = self._kpoint_operations[rot_mappings]
self._mapping, self._grid=spg.get_ir_reciprocal_mesh(self._mesh, self._cell)
assert (self._mapping==mapping).all()
self._map_to_ir_index=np.zeros_like(mapping)
reverse_mapping=[]
for i,u in enumerate(np.unique(mapping)):
reverse_mapping.append(np.where(mapping==u)[0])
self._map_to_ir_index[np.where(mapping==u)] = i
self._reverse_mapping=reverse_mapping
def __init__(self,
mesh,
primitive,
supercell,
fc2,
nac_params=None,
nac_q_direction=None,
sigma=None,
cutoff_frequency=None,
frequency_step=None,
num_frequency_points=None,
temperatures=None,
frequency_factor_to_THz=VaspToTHz,
frequency_scale_factor=1.0,
is_nosym=False,
symprec=1e-5,
filename=None,
log_level=False,
lapack_zheev_uplo='L'):
self._grid_point = None
self._mesh = np.array(mesh, dtype='intc')
self._primitive = primitive
self._supercell = supercell
self._fc2 = fc2
self._nac_params = nac_params
self._nac_q_direction = None
self.set_nac_q_direction(nac_q_direction)
self._sigma = None
self.set_sigma(sigma)
if cutoff_frequency is None:
self._cutoff_frequency = 0
else:
self._cutoff_frequency = cutoff_frequency
self._frequency_step = frequency_step
self._num_frequency_points = num_frequency_points
self._temperatures = temperatures
self._frequency_factor_to_THz = frequency_factor_to_THz
self._frequency_scale_factor = frequency_scale_factor
self._is_nosym = is_nosym
self._symprec = symprec
self._filename = filename
self._log_level = log_level
self._lapack_zheev_uplo = lapack_zheev_uplo
self._num_band = self._primitive.get_number_of_atoms() * 3
self._reciprocal_lattice = np.linalg.inv(self._primitive.get_cell())
self._set_dynamical_matrix()
self._symmetry = Symmetry(primitive, symprec)
self._tetrahedron_method = None
self._phonon_done = None
self._frequencies = None
self._eigenvectors = None
self._joint_dos = None
self._frequency_points = None
def read_castep(filename):
f_castep = open(filename)
castep_in = CastepIn(f_castep.readlines())
f_castep.close()
tags = castep_in.get_tags()
# 1st stage is to create Atoms object ignoring Spin polarization. General case.
cell = Atoms(cell=tags['lattice_vectors'],
symbols=tags['atomic_species'],
scaled_positions=tags['coordinates'])
# Analyse spin states and add data to Atoms instance "cell" if ones exist
magmoms = tags['magnetic_moments']
if magmoms is not None:
# Print out symmetry information for magnetic cases
# Original code from structure/symmetry.py
symmetry = Symmetry(cell, symprec=1e-5)
print(
"CASTEP-interface: Magnetic structure, number of operations without spin: %d"
% len(symmetry.get_symmetry_operations()['rotations']))
print("CASTEP-interface: Spacegroup without spin: %s" %
symmetry.get_international_table())
cell.set_magnetic_moments(magmoms)
symmetry = Symmetry(cell, symprec=1e-5)
print(
"CASTEP-interface: Magnetic structure, number of operations with spin: %d"
% len(symmetry.get_symmetry_operations()['rotations']))
print("")
return cell
def read_crystal(filename):
f_crystal = open(filename)
crystal_in = CrystalIn(f_crystal.readlines())
f_crystal.close()
tags = crystal_in.get_tags()
cell = Atoms(cell=tags['lattice_vectors'],
symbols=tags['atomic_species'],
scaled_positions=tags['coordinates'])
magmoms = tags['magnetic_moments']
if magmoms is not None:
# Print out symmetry information for magnetic cases
# Original code from structure/symmetry.py
symmetry = Symmetry(cell, symprec=1e-5)
print(
"CRYSTAL-interface: Magnetic structure, number of operations without spin: %d"
% len(symmetry.get_symmetry_operations()['rotations']))
print("CRYSTAL-interface: Spacegroup without spin: %s" %
symmetry.get_international_table())
cell.set_magnetic_moments(magmoms)
symmetry = Symmetry(cell, symprec=1e-5)
print(
"CRYSTAL-interface: Magnetic structure, number of operations with spin: %d"
% len(symmetry.get_symmetry_operations()['rotations']))
print("")
return cell, tags['conv_numbers']
def __init__(
self,
mesh,
primitive,
mass_variances=None, # length of list is num_atom.
band_indices=None,
sigma=None,
bz_grid=None,
frequency_factor_to_THz=VaspToTHz,
use_grg=False,
store_dense_gp_map=True,
symprec=1e-5,
cutoff_frequency=None,
lapack_zheev_uplo="L",
):
"""Init method."""
self._mesh = mesh
if mass_variances is None:
self._mass_variances = get_mass_variances(primitive)
else:
self._mass_variances = np.array(mass_variances, dtype="double")
self._primitive = primitive
self._sigma = sigma
self._bz_grid = bz_grid
self._symprec = symprec
if cutoff_frequency is None:
self._cutoff_frequency = 0
else:
self._cutoff_frequency = cutoff_frequency
self._frequency_factor_to_THz = frequency_factor_to_THz
self._lapack_zheev_uplo = lapack_zheev_uplo
self._nac_q_direction = None
self._grid_points = None
self._frequencies = None
self._eigenvectors = None
self._phonon_done = None
self._dm = None
self._gamma = None
self._tetrahedron_method = None
num_band = len(self._primitive) * 3
if band_indices is None:
self._band_indices = np.arange(num_band, dtype="int_")
else:
self._band_indices = np.array(band_indices, dtype="int_")
if self._bz_grid is None:
primitive_symmetry = Symmetry(self._primitive, self._symprec)
self._bz_grid = BZGrid(
self._mesh,
lattice=self._primitive.cell,
symmetry_dataset=primitive_symmetry.dataset,
use_grg=use_grg,
store_dense_gp_map=store_dense_gp_map,
)
def test_get_map_operations(self):
symprec = 1e-5
cell = get_unitcell_from_phonopy_yaml("../NaCl.yaml")
scell = get_supercell(cell, np.diag([2, 2, 2]), symprec=symprec)
symmetry = Symmetry(scell, symprec=symprec)
map_ops_cmp = [
0, 2, 51, 53, 8, 1, 65, 98, 3, 14, 34, 24, 76, 69, 54, 110, 576,
198, 229, 208, 201, 192, 210, 294, 5, 67, 36, 57, 18, 90, 23, 114,
0, 9, 1, 96, 6, 323, 98, 326, 3, 42, 17, 293, 16, 130, 99, 337,
192, 194, 202, 199, 205, 196, 200, 193, 12, 5, 30, 108, 37, 128,
291, 302
]
start = time.time()
symmetry._set_map_operations()
end = time.time()
# print(end - start)
map_ops = symmetry.get_map_operations()
self.assertTrue((map_ops_cmp == map_ops).all())
def _search_primitive_symmetry_ideal(self):
self._primitive_symmetry = Symmetry(self._primitive_ideal,
self._symprec,
self._is_symmetry)
n0 = len(self._symmetry.get_pointgroup_operations())
n1 = len(self._primitive_symmetry.get_pointgroup_operations())
if n0 != n1:
raise Warning("Point group symmetries of supercell and primitive"
"cell are different.")
def get_crystal_structure(cell, conv_numbers, write_symmetry=False):
lattice = cell.get_cell()
positions = cell.get_positions()
numbers = cell.get_atomic_numbers()
# Create and EXTERNAL file (fort.34)
# Dimensionality, centring, crystal type
lines = "3 1 1\n"
# Cartesian components of the lattice vectors
for lattvec in lattice:
lines += ("%12.8f" * 3 + "\n") % tuple(lattvec)
# Symmetry operators
if write_symmetry:
symmetry = Symmetry(cell, symprec=1e-5)
rotations = symmetry.get_symmetry_operations()['rotations']
translations = symmetry.get_symmetry_operations()['translations']
N_symmops = 0
symmlines = ""
for i in range(0, len(rotations)):
N_symmops += 1
for j in range(0, 3):
symmlines += (" %5.2f" * 3 + "\n") % tuple(rotations[i][j])
symmlines += (" %5.2f" * 3 + "\n") % tuple(translations[i])
lines += ("%d\n" % N_symmops)
lines += symmlines
else:
lines += "1\n"
lines += " 1.00 0.00 0.00\n"
lines += " 0.00 1.00 0.00\n"
lines += " 0.00 0.00 1.00\n"
lines += " 0.00 0.00 0.00\n"
# Number of atoms in the unit cell (asymmetric unit)
lines += ("%d\n") % len(positions)
# Conventional atomic number and cartesian coordinates of the atoms
for i, pos in zip(conv_numbers, positions):
lines += (" %d " + "%16.12f"*3 + "\n") % (i, pos[0], pos[1], pos[2])
return lines
def get_crystal_structure(cell, conv_numbers, write_symmetry=False):
lattice = cell.get_cell()
positions = cell.get_positions()
numbers = cell.get_atomic_numbers()
# Create and EXTERNAL file (fort.34)
# Dimensionality, centring, crystal type
lines = "3 1 1\n"
# Cartesian components of the lattice vectors
for lattvec in lattice:
lines += ("%12.8f" * 3 + "\n") % tuple(lattvec)
# Symmetry operators
if write_symmetry:
symmetry = Symmetry(cell, symprec=1e-5)
rotations = symmetry.get_symmetry_operations()['rotations']
translations = symmetry.get_symmetry_operations()['translations']
N_symmops = 0
symmlines = ""
for i in range(0, len(rotations)):
N_symmops += 1
for j in range(0, 3):
symmlines += (" %5.2f" * 3 + "\n") % tuple(rotations[i][j])
symmlines += (" %5.2f" * 3 + "\n") % tuple(translations[i])
lines += ("%d\n" % N_symmops)
lines += symmlines
else:
lines += "1\n"
lines += " 1.00 0.00 0.00\n"
lines += " 0.00 1.00 0.00\n"
lines += " 0.00 0.00 1.00\n"
lines += " 0.00 0.00 0.00\n"
# Number of atoms in the unit cell (asymmetric unit)
lines += ("%d\n") % len(positions)
# Conventional atomic number and cartesian coordinates of the atoms
for i, pos in zip(conv_numbers, positions):
lines += (" %d " + "%16.12f" * 3 + "\n") % (i, pos[0], pos[1], pos[2])
return lines
def get_born_parameters(phonon, born_charges, epsilon, symprec=1e-5):
from phonopy.structure.cells import get_primitive, get_supercell
from phonopy.structure.symmetry import Symmetry
from phonopy.interface import get_default_physical_units
print('inside born parameters')
pmat = phonon.get_primitive_matrix()
smat = phonon.get_supercell_matrix()
ucell = phonon.get_unitcell()
print pmat
print smat
print ucell
num_atom = len(born_charges)
assert num_atom == ucell.get_number_of_atoms(), \
"num_atom %d != len(borns) %d" % (ucell.get_number_of_atoms(),
len(born_charges))
inv_smat = np.linalg.inv(smat)
scell = get_supercell(ucell, smat, symprec=symprec)
pcell = get_primitive(scell, np.dot(inv_smat, pmat), symprec=symprec)
p2s = np.array(pcell.get_primitive_to_supercell_map(), dtype='intc')
p_sym = Symmetry(pcell, is_symmetry=True, symprec=symprec)
s_indep_atoms = p2s[p_sym.get_independent_atoms()]
u2u = scell.get_unitcell_to_unitcell_map()
u_indep_atoms = [u2u[x] for x in s_indep_atoms]
reduced_borns = born_charges[u_indep_atoms].copy()
factor = get_default_physical_units('vasp')[
'nac_factor'] # born charges in VASP units
born_dict = {
'born': reduced_borns,
'dielectric': epsilon,
'factor': factor
}
print('final born dict', born_dict)
return born_dict
def get_coarse_ir_grid_points(primitive,
mesh,
mesh_divisors,
coarse_mesh_shifts,
is_nosym=False,
symprec=1e-5):
if mesh_divisors is None:
mesh_divs = [1, 1, 1]
else:
mesh_divs = mesh_divisors
mesh = np.array(mesh, dtype='intc')
mesh_divs = np.array(mesh_divs, dtype='intc')
coarse_mesh = mesh // mesh_divs
if coarse_mesh_shifts is None:
coarse_mesh_shifts = [False, False, False]
if is_nosym:
coarse_grid_address = get_grid_address(coarse_mesh)
coarse_grid_points = np.arange(np.prod(coarse_mesh), dtype='intc')
coarse_grid_weights = np.ones(len(coarse_grid_points), dtype='intc')
else:
symmetry = Symmetry(primitive, symprec)
(coarse_grid_points,
coarse_grid_weights,
coarse_grid_address) = get_ir_grid_points(
coarse_mesh,
symmetry.get_pointgroup_operations(),
mesh_shifts=coarse_mesh_shifts)
grid_points = from_coarse_to_dense_grid_points(
mesh,
mesh_divs,
coarse_grid_points,
coarse_grid_address,
coarse_mesh_shifts=coarse_mesh_shifts)
grid_address = get_grid_address(mesh)
primitive_lattice = np.linalg.inv(primitive.get_cell())
bz_grid_address, _ = spg.relocate_BZ_grid_address(grid_address,
mesh,
primitive_lattice)
return grid_points, coarse_grid_weights, bz_grid_address
def set_grid_point(self,
grid_point,
grid_points2=None,
weights2 = None):
"The grid_point is numbered using the bz scheme"
self._grid_point = grid_point
if self._grid_address is None:
primitive_lattice = np.linalg.inv(self._primitive.get_cell())
self._grid_address, self._bz_map, self._bz_to_pp_map = get_bz_grid_address(
self._mesh, primitive_lattice, with_boundary=True, is_bz_map_to_pp=True)
if grid_points2 is not None:
self._grid_points2 = grid_points2
self._weights2 = weights2
elif not self._is_nosym:
symmetry = Symmetry(self._primitive, symprec=self._symprec)
qpoint = self._grid_address[grid_point] / np.double(self._mesh)
mapping, grid_points = spg.get_stabilized_reciprocal_mesh(self._mesh,
symmetry.get_pointgroup_operations(),
is_shift=np.zeros(3, dtype='intc'),
is_time_reversal=True,
qpoints=[qpoint])
grid_points2 = np.unique(mapping)
# weight = np.zeros_like(grid_points2)
# bz_grid_points2 = np.zeros_like(grid_points2)
# for g, grid in enumerate(grid_points2):
# weight[g] = len(np.where(grid == mapping)[0])
# bz_grid_points2[g] = np.where(grid == self._bz_to_pp_map)[0][0]
# self._grid_points2 = bz_grid_points2
weight_temp = np.bincount(mapping)
weight = weight_temp[np.nonzero(weight_temp)]
self._grid_points2 = grid_points2
self._weights2 = weight
else:
self._grid_points2 = np.arange(np.prod(self._mesh))
self._weights2 = np.ones_like(self._grid_points2, dtype="intc")
def test_get_map_operations(self):
symprec = 1e-5
cell = get_unitcell_from_phonopy_yaml(
os.path.join(data_dir,"../NaCl.yaml"))
scell = get_supercell(cell, np.diag([2, 2, 2]), symprec=symprec)
symmetry = Symmetry(scell, symprec=symprec)
start = time.time()
symmetry._set_map_operations()
end = time.time()
# print(end - start)
map_ops = symmetry.get_map_operations()
map_atoms = symmetry.get_map_atoms()
positions = scell.get_scaled_positions()
rotations = symmetry.get_symmetry_operations()['rotations']
translations = symmetry.get_symmetry_operations()['translations']
for i, (op_i, atom_i) in enumerate(zip(map_ops, map_atoms)):
r_pos = np.dot(rotations[op_i], positions[i]) + translations[op_i]
diff = positions[atom_i] - r_pos
diff -= np.rint(diff)
self.assertTrue((diff < symprec).all())
class Phonopy:
def __init__(self,
unitcell,
supercell_matrix,
primitive_matrix=None,
nac_params=None,
distance=0.01,
factor=VaspToTHz,
is_auto_displacements=True,
dynamical_matrix_decimals=None,
force_constants_decimals=None,
symprec=1e-5,
is_symmetry=True,
log_level=0):
self._symprec = symprec
self._factor = factor
self._is_symmetry = is_symmetry
self._log_level = log_level
# Create supercell and primitive cell
self._unitcell = unitcell
self._supercell_matrix = supercell_matrix
self._primitive_matrix = primitive_matrix
self._supercell = None
self._primitive = None
self._build_supercell()
self._build_primitive_cell()
# Set supercell and primitive symmetry
self._symmetry = None
self._primitive_symmetry = None
self._search_symmetry()
self._search_primitive_symmetry()
# set_displacements (used only in preprocess)
self._displacement_dataset = None
self._displacements = None
self._displacement_directions = None
self._supercells_with_displacements = None
if is_auto_displacements:
self.generate_displacements(distance=distance)
# set_force_constants or set_forces
self._force_constants = None
self._force_constants_decimals = force_constants_decimals
# set_dynamical_matrix
self._dynamical_matrix = None
self._nac_params = nac_params
self._dynamical_matrix_decimals = dynamical_matrix_decimals
# set_band_structure
self._band_structure = None
# set_mesh
self._mesh = None
# set_tetrahedron_method
self._tetrahedron_method = None
# set_thermal_properties
self._thermal_properties = None
# set_thermal_displacements
self._thermal_displacements = None
# set_thermal_displacement_matrices
self._thermal_displacement_matrices = None
# set_partial_DOS
self._pdos = None
# set_total_DOS
self._total_dos = None
# set_modulation
self._modulation = None
# set_character_table
self._irreps = None
# set_group_velocity
self._group_velocity = None
def set_post_process(self,
primitive_matrix=None,
sets_of_forces=None,
displacement_dataset=None,
force_constants=None,
is_nac=None):
print
print ("********************************** Warning"
"**********************************")
print "set_post_process will be obsolete."
print (" produce_force_constants is used instead of set_post_process"
" for producing")
print (" force constants from forces.")
if primitive_matrix is not None:
print (" primitive_matrix has to be given at Phonopy::__init__"
" object creation.")
print ("******************************************"
"**********************************")
print
if primitive_matrix is not None:
self._primitive_matrix = primitive_matrix
self._build_primitive_cell()
self._search_primitive_symmetry()
if sets_of_forces is not None:
self.set_forces(sets_of_forces)
elif displacement_dataset is not None:
self._displacement_dataset = displacement_dataset
elif force_constants is not None:
self.set_force_constants(force_constants)
if self._displacement_dataset is not None:
self.produce_force_constants()
def set_masses(self, masses):
p_masses = np.array(masses)
self._primitive.set_masses(p_masses)
p2p_map = self._primitive.get_primitive_to_primitive_map()
s_masses = p_masses[[p2p_map[x] for x in
self._primitive.get_supercell_to_primitive_map()]]
self._supercell.set_masses(s_masses)
u2s_map = self._supercell.get_unitcell_to_supercell_map()
u_masses = s_masses[u2s_map]
self._unitcell.set_masses(u_masses)
def get_primitive(self):
return self._primitive
primitive = property(get_primitive)
def get_unitcell(self):
return self._unitcell
unitcell = property(get_unitcell)
def get_supercell(self):
return self._supercell
supercell = property(get_supercell)
def set_supercell(self, supercell):
self._supercell = supercell
def get_symmetry(self):
"""return symmetry of supercell"""
return self._symmetry
symmetry = property(get_symmetry)
def get_primitive_symmetry(self):
"""return symmetry of primitive cell"""
return self._primitive_symmetry
def get_unit_conversion_factor(self):
return self._factor
unit_conversion_factor = property(get_unit_conversion_factor)
def produce_force_constants(self,
forces=None,
calculate_full_force_constants=True,
computation_algorithm="svd"):
if forces is not None:
self.set_forces(forces)
if calculate_full_force_constants:
self._run_force_constants_from_forces(
decimals=self._force_constants_decimals,
computation_algorithm=computation_algorithm)
else:
p2s_map = self._primitive.get_primitive_to_supercell_map()
self._run_force_constants_from_forces(
distributed_atom_list=p2s_map,
decimals=self._force_constants_decimals,
computation_algorithm=computation_algorithm)
def set_nac_params(self, nac_params=None, method=None):
if method is not None:
print "set_nac_params:"
print " Keyword argument of \"method\" is not more supported."
self._nac_params = nac_params
def generate_displacements(self,
distance=0.01,
is_plusminus='auto',
is_diagonal=True,
is_trigonal=False):
"""Generate displacements automatically
displacemsts: List of displacements in Cartesian coordinates.
[[0, 0.01, 0.00, 0.00], ...]
where each set of elements is defined by:
First value: Atom index in supercell starting with 0
Second to fourth: Displacement in Cartesian coordinates
displacement_directions:
List of directions with respect to axes. This gives only the
symmetrically non equivalent directions. The format is like:
[[0, 1, 0, 0],
[7, 1, 0, 1], ...]
where each list is defined by:
First value: Atom index in supercell starting with 0
Second to fourth: If the direction is displaced or not ( 1, 0, or -1 )
with respect to the axes.
"""
displacement_directions = get_least_displacements(
self._symmetry,
is_plusminus=is_plusminus,
is_diagonal=is_diagonal,
is_trigonal=is_trigonal,
log_level=self._log_level)
displacement_dataset = direction_to_displacement(
displacement_directions,
distance,
self._supercell)
self.set_displacement_dataset(displacement_dataset)
def set_displacements(self, displacements):
print
print ("********************************** Warning"
"**********************************")
print "set_displacements is obsolete. Do nothing."
print ("******************************************"
"**********************************")
print
def get_displacements(self):
return self._displacements
displacements = property(get_displacements)
def get_displacement_directions(self):
return self._displacement_directions
displacement_directions = property(get_displacement_directions)
def get_displacement_dataset(self):
return self._displacement_dataset
def get_supercells_with_displacements(self):
if self._displacement_dataset is None:
return None
else:
self._build_supercells_with_displacements()
return self._supercells_with_displacements
def get_dynamical_matrix(self):
return self._dynamical_matrix
dynamical_matrix = property(get_dynamical_matrix)
def set_forces(self, sets_of_forces):
"""
sets_of_forces:
[[[f_1x, f_1y, f_1z], [f_2x, f_2y, f_2z], ...], # first supercell
[[f_1x, f_1y, f_1z], [f_2x, f_2y, f_2z], ...], # second supercell
... ]
"""
for disp, forces in zip(
self._displacement_dataset['first_atoms'], sets_of_forces):
disp['forces'] = forces
def set_force_constants_zero_with_radius(self, cutoff_radius):
cutoff_force_constants(self._force_constants,
self._supercell,
cutoff_radius,
symprec=self._symprec)
def set_force_constants(self, force_constants):
self._force_constants = force_constants
def set_force_sets(self, force_sets):
print
print ("********************************** Warning"
"**********************************")
print "set_force_sets will be obsolete."
print (" The method name is changed to set_displacement_dataset.")
print ("******************************************"
"**********************************")
print
self.set_displacement_dataset(force_sets)
def set_displacement_dataset(self, displacement_dataset):
"""
displacement_dataset:
{'natom': number_of_atoms_in_supercell,
'first_atoms': [
{'number': atom index of displaced atom,
'displacement': displacement in Cartesian coordinates,
'direction': displacement direction with respect to axes
'forces': forces on atoms in supercell},
{...}, ...]}
"""
self._displacement_dataset = displacement_dataset
self._displacements = []
self._displacement_directions = []
for disp in self._displacement_dataset['first_atoms']:
x = disp['displacement']
self._displacements.append([disp['number'], x[0], x[1], x[2]])
if 'direction' in disp:
y = disp['direction']
self._displacement_directions.append(
[disp['number'], y[0], y[1], y[2]])
if not self._displacement_directions:
self._displacement_directions = None
def symmetrize_force_constants(self, iteration=3):
symmetrize_force_constants(self._force_constants, iteration)
def symmetrize_force_constants_by_space_group(self):
rotations = self._symmetry.get_symmetry_operations()['rotations']
translations = self._symmetry.get_symmetry_operations()['translations']
set_tensor_symmetry(self._force_constants,
self._supercell.get_cell().T,
self._supercell.get_scaled_positions(),
rotations,
translations,
self._symprec)
def get_force_constants(self):
return self._force_constants
force_constants = property(get_force_constants)
def get_rotational_condition_of_fc(self):
return rotational_invariance(self._force_constants,
self._supercell,
self._primitive,
self._symprec)
def set_dynamical_matrix(self):
self._set_dynamical_matrix()
def get_dynamical_matrix_at_q(self, q):
self._set_dynamical_matrix()
self._dynamical_matrix.set_dynamical_matrix(q)
return self._dynamical_matrix.get_dynamical_matrix()
def get_frequencies(self, q):
"""
Calculate phonon frequencies at q
q: q-vector in reduced coordinates of primitive cell
"""
self._set_dynamical_matrix()
self._dynamical_matrix.set_dynamical_matrix(q)
dm = self._dynamical_matrix.get_dynamical_matrix()
frequencies = []
for eig in np.linalg.eigvalsh(dm).real:
if eig < 0:
frequencies.append(-np.sqrt(-eig))
else:
frequencies.append(np.sqrt(eig))
return np.array(frequencies) * self._factor
def get_frequencies_with_eigenvectors(self, q):
"""
Calculate phonon frequencies and eigenvectors at q
q: q-vector in reduced coordinates of primitive cell
"""
self._set_dynamical_matrix()
self._dynamical_matrix.set_dynamical_matrix(q)
dm = self._dynamical_matrix.get_dynamical_matrix()
frequencies = []
eigvals, eigenvectors = np.linalg.eigh(dm)
frequencies = []
for eig in eigvals:
if eig < 0:
frequencies.append(-np.sqrt(-eig))
else:
frequencies.append(np.sqrt(eig))
return np.array(frequencies) * self._factor, eigenvectors
def set_band_structure(self,
bands,
is_eigenvectors=False,
is_band_connection=False):
self._set_dynamical_matrix()
self._band_structure = BandStructure(
bands,
self._dynamical_matrix,
is_eigenvectors=is_eigenvectors,
is_band_connection=is_band_connection,
group_velocity=self._group_velocity,
factor=self._factor)
def get_band_structure(self):
band = self._band_structure
return (band.get_qpoints(),
band.get_distances(),
band.get_frequencies(),
band.get_eigenvectors())
def plot_band_structure(self, symbols=None):
return self._band_structure.plot_band(symbols)
def write_yaml_band_structure(self):
self._band_structure.write_yaml()
def set_mesh(self,
mesh,
shift=None,
is_time_reversal=True,
is_mesh_symmetry=True,
is_eigenvectors=False,
is_gamma_center=False):
self._set_dynamical_matrix()
self._mesh = Mesh(
self._dynamical_matrix,
mesh,
shift=shift,
is_time_reversal=is_time_reversal,
is_mesh_symmetry=is_mesh_symmetry,
is_eigenvectors=is_eigenvectors,
is_gamma_center=is_gamma_center,
group_velocity=self._group_velocity,
rotations=self._primitive_symmetry.get_pointgroup_operations(),
factor=self._factor)
def get_mesh(self):
return (self._mesh.get_qpoints(),
self._mesh.get_weights(),
self._mesh.get_frequencies(),
self._mesh.get_eigenvectors())
def write_yaml_mesh(self):
self._mesh.write_yaml()
def set_thermal_properties(self,
t_step=10,
t_max=1000,
t_min=0,
is_projection=False,
band_indices=None,
cutoff_frequency=None):
if self._mesh is None:
print "set_mesh has to be done before set_thermal_properties"
return False
else:
tp = ThermalProperties(self._mesh.get_frequencies(),
weights=self._mesh.get_weights(),
eigenvectors=self._mesh.get_eigenvectors(),
is_projection=is_projection,
band_indices=band_indices,
cutoff_frequency=cutoff_frequency)
tp.set_thermal_properties(t_step=t_step,
t_max=t_max,
t_min=t_min)
self._thermal_properties = tp
def get_thermal_properties(self):
temps, fe, entropy, cv = \
self._thermal_properties.get_thermal_properties()
return temps, fe, entropy, cv
def plot_thermal_properties(self):
return self._thermal_properties.plot_thermal_properties()
def write_yaml_thermal_properties(self, filename='thermal_properties.yaml'):
self._thermal_properties.write_yaml(filename=filename)
def set_partial_DOS(self,
sigma=None,
freq_min=None,
freq_max=None,
freq_pitch=None,
tetrahedron_method=False,
direction=None):
if self._mesh is None:
print "set_mesh has to be done before set_thermal_properties"
sys.exit(1)
if self._mesh.get_eigenvectors() is None:
print "Eigenvectors have to be calculated."
sys.exit(1)
if direction is not None:
direction_cart = np.dot(direction, self._primitive.get_cell())
else:
direction_cart = None
pdos = PartialDos(self._mesh,
sigma=sigma,
tetrahedron_method=tetrahedron_method,
direction=direction_cart)
pdos.set_draw_area(freq_min, freq_max, freq_pitch)
pdos.run()
self._pdos = pdos
def get_partial_DOS(self):
"""
Retern frequencies and partial_dos.
The first element is freqs and the second is partial_dos.
frequencies: [freq1, freq2, ...]
partial_dos:
[[atom1-freq1, atom1-freq2, ...],
[atom2-freq1, atom2-freq2, ...],
...]
"""
return self._pdos.get_partial_dos()
def plot_partial_DOS(self, pdos_indices=None, legend=None):
return self._pdos.plot_pdos(indices=pdos_indices,
legend=legend)
def write_partial_DOS(self):
self._pdos.write()
def set_total_DOS(self,
sigma=None,
freq_min=None,
freq_max=None,
freq_pitch=None,
tetrahedron_method=False):
if self._mesh is None:
print "set_mesh has to be done before set_thermal_properties"
sys.exit(1)
total_dos = TotalDos(self._mesh,
sigma=sigma,
tetrahedron_method=tetrahedron_method)
total_dos.set_draw_area(freq_min, freq_max, freq_pitch)
total_dos.run()
self._total_dos = total_dos
def get_total_DOS(self):
"""
Retern frequencies and total dos.
The first element is freqs and the second is total dos.
frequencies: [freq1, freq2, ...]
total_dos: [dos1, dos2, ...]
"""
return self._total_dos.get_dos()
def set_Debye_frequency(self, freq_max_fit=None):
self._total_dos.set_Debye_frequency(
self._primitive.get_number_of_atoms(),
freq_max_fit=freq_max_fit)
def get_Debye_frequency(self):
return self._total_dos.get_Debye_frequency()
def plot_total_DOS(self):
return self._total_dos.plot_dos()
def write_total_DOS(self):
self._total_dos.write()
def set_thermal_displacements(self,
t_step=10,
t_max=1000,
t_min=0,
direction=None,
cutoff_frequency=None):
"""
cutoff_frequency:
phonon modes that have frequencies below cutoff_frequency
are ignored.
direction:
Projection direction in reduced coordinates
"""
if self._mesh is None:
print "set_mesh has to be done before set_thermal_properties"
sys.exit(1)
eigvecs = self._mesh.get_eigenvectors()
frequencies = self._mesh.get_frequencies()
mesh_nums = self._mesh.get_mesh_numbers()
if self._mesh.get_eigenvectors() is None:
print "Eigenvectors have to be calculated."
sys.exit(1)
if np.prod(mesh_nums) != len(eigvecs):
print "Sampling mesh must not be symmetrized."
sys.exit(1)
td = ThermalDisplacements(frequencies,
eigvecs,
self._primitive.get_masses(),
cutoff_frequency=cutoff_frequency)
td.set_temperature_range(t_min, t_max, t_step)
if direction is not None:
td.project_eigenvectors(direction, self._primitive.get_cell())
td.run()
self._thermal_displacements = td
def get_thermal_displacements(self):
if self._thermal_displacements is not None:
return self._thermal_displacements.get_thermal_displacements()
def plot_thermal_displacements(self, is_legend=False):
return self._thermal_displacements.plot(is_legend)
def write_yaml_thermal_displacements(self):
self._thermal_displacements.write_yaml()
def set_thermal_displacement_matrices(self,
t_step=10,
t_max=1000,
t_min=0,
cutoff_frequency=None):
"""
cutoff_frequency:
phonon modes that have frequencies below cutoff_frequency
are ignored.
direction:
Projection direction in reduced coordinates
"""
if self._mesh is None:
print "set_mesh has to be done before set_thermal_properties"
sys.exit(1)
eigvecs = self._mesh.get_eigenvectors()
frequencies = self._mesh.get_frequencies()
mesh_nums = self._mesh.get_mesh_numbers()
if self._mesh.get_eigenvectors() is None:
print "Eigenvectors have to be calculated."
sys.exit(1)
if np.prod(mesh_nums) != len(eigvecs):
print "Sampling mesh must not be symmetrized."
sys.exit(1)
tdm = ThermalDisplacementMatrices(frequencies,
eigvecs,
self._primitive.get_masses(),
cutoff_frequency=cutoff_frequency)
tdm.set_temperature_range(t_min, t_max, t_step)
tdm.run()
self._thermal_displacement_matrices = tdm
def get_thermal_displacement_matrices(self):
if self._thermal_displacement_matrices is not None:
return self._thermal_displacement_matrices.get_thermal_displacement_matrices()
def write_yaml_thermal_displacement_matrices(self):
self._thermal_displacement_matrices.write_yaml()
def set_thermal_distances(self,
atom_pairs,
t_step=10,
t_max=1000,
t_min=0,
cutoff_frequency=None):
"""
atom_pairs: List of list
Mean square distances are calculated for the atom_pairs
e.g. [[1, 2], [1, 4]]
cutoff_frequency:
phonon modes that have frequencies below cutoff_frequency
are ignored.
"""
td = ThermalDistances(self._mesh.get_frequencies(),
self._mesh.get_eigenvectors(),
self._supercell,
self._primitive,
self._mesh.get_qpoints(),
cutoff_frequency=cutoff_frequency)
td.set_temperature_range(t_min, t_max, t_step)
td.run(atom_pairs)
self._thermal_distances = td
def write_yaml_thermal_distances(self):
self._thermal_distances.write_yaml()
def set_qpoints_phonon(self,
q_points,
nac_q_direction=None,
is_eigenvectors=False,
write_dynamical_matrices=False,
factor=VaspToTHz):
self._set_dynamical_matrix()
self._qpoints_phonon = QpointsPhonon(
q_points,
self._dynamical_matrix,
nac_q_direction=nac_q_direction,
is_eigenvectors=is_eigenvectors,
group_velocity=self._group_velocity,
write_dynamical_matrices=write_dynamical_matrices,
factor=self._factor)
def get_qpoints_phonon(self):
return (self._qpoints_phonon.get_frequencies(),
self._qpoints_phonon.get_eigenvectors())
def write_yaml_qpoints_phonon(self):
self._qpoints_phonon.write_yaml()
def write_animation(self,
q_point=None,
anime_type='v_sim',
band_index=None,
amplitude=None,
num_div=None,
shift=None,
filename=None):
self._set_dynamical_matrix()
if q_point is None:
animation = Animation([0, 0, 0],
self._dynamical_matrix,
shift=shift)
else:
animation = Animation(q_point,
self._dynamical_matrix,
shift=shift)
if anime_type == 'v_sim':
if amplitude:
amplitude_ = amplitude
else:
amplitude_ = 1.0
if filename:
animation.write_v_sim(amplitude=amplitude_,
factor=self._factor,
filename=filename)
else:
animation.write_v_sim(amplitude=amplitude_,
factor=self._factor)
if (anime_type == 'arc' or
anime_type == 'xyz' or
anime_type == 'jmol' or
anime_type == 'poscar'):
if band_index is None or amplitude is None or num_div is None:
print "Parameters are not correctly set for animation."
sys.exit(1)
if anime_type == 'arc' or anime_type is None:
if filename:
animation.write_arc(band_index,
amplitude,
num_div,
filename=filename)
else:
animation.write_arc(band_index,
amplitude,
num_div)
if anime_type == 'xyz':
if filename:
animation.write_xyz(band_index,
amplitude,
num_div,
self._factor,
filename=filename)
else:
animation.write_xyz(band_index,
amplitude,
num_div,
self._factor)
if anime_type == 'jmol':
if filename:
animation.write_xyz_jmol(amplitude=amplitude,
factor=self._factor,
filename=filename)
else:
animation.write_xyz_jmol(amplitude=amplitude,
factor=self._factor)
if anime_type == 'poscar':
if filename:
animation.write_POSCAR(band_index,
amplitude,
num_div,
filename=filename)
else:
animation.write_POSCAR(band_index,
amplitude,
num_div)
def set_modulations(self,
dimension,
phonon_modes,
delta_q=None,
derivative_order=None,
nac_q_direction=None):
self._set_dynamical_matrix()
self._modulation = Modulation(self._dynamical_matrix,
dimension,
phonon_modes,
delta_q=delta_q,
derivative_order=derivative_order,
nac_q_direction=nac_q_direction,
factor=self._factor)
self._modulation.run()
def get_modulations(self):
"""Returns cells with modulations as Atoms objects"""
return self._modulation.get_modulations()
def get_delta_modulations(self):
"""Return modulations relative to equilibrium supercell
(modulations, supercell)
modulations: Atomic modulations of supercell in Cartesian coordinates
supercell: Supercell as an Atoms object.
"""
return self._modulation.get_delta_modulations()
def write_modulations(self):
"""Create MPOSCAR's"""
self._modulation.write()
def write_yaml_modulations(self):
self._modulation.write_yaml()
def set_irreps(self,
q,
is_little_cogroup=False,
nac_q_direction=None,
degeneracy_tolerance=1e-4):
self._set_dynamical_matrix()
self._irreps = IrReps(
self._dynamical_matrix,
q,
is_little_cogroup=is_little_cogroup,
nac_q_direction=nac_q_direction,
factor=self._factor,
symprec=self._symprec,
degeneracy_tolerance=degeneracy_tolerance,
log_level=self._log_level)
return self._irreps.run()
def get_irreps(self):
return self._irreps
def show_irreps(self, show_irreps=False):
self._irreps.show(show_irreps=show_irreps)
def write_yaml_irreps(self, show_irreps=False):
self._irreps.write_yaml(show_irreps=show_irreps)
def set_group_velocity(self, q_length=None):
self._set_dynamical_matrix()
self._group_velocity = GroupVelocity(
self._dynamical_matrix,
q_length=q_length,
symmetry=self._primitive_symmetry,
frequency_factor_to_THz=self._factor)
def get_group_velocity(self):
return self._group_velocity.get_group_velocity()
def get_group_velocity_at_q(self, q_point):
if self._group_velocity is None:
self.set_group_velocity()
self._group_velocity.set_q_points([q_point])
return self._group_velocity.get_group_velocity()[0]
def _run_force_constants_from_forces(self,
distributed_atom_list=None,
decimals=None,
computation_algorithm="svd"):
if self._displacement_dataset is not None:
self._force_constants = get_fc2(
self._supercell,
self._symmetry,
self._displacement_dataset,
atom_list=distributed_atom_list,
decimals=decimals,
computation_algorithm=computation_algorithm)
def _set_dynamical_matrix(self):
if self._nac_params is None:
self._dynamical_matrix = DynamicalMatrix(
self._supercell,
self._primitive,
self._force_constants,
decimals=self._dynamical_matrix_decimals,
symprec=self._symprec)
else:
self._dynamical_matrix = DynamicalMatrixNAC(
self._supercell,
self._primitive,
self._force_constants,
nac_params=self._nac_params,
decimals=self._dynamical_matrix_decimals,
symprec=self._symprec)
def _search_symmetry(self):
self._symmetry = Symmetry(self._supercell,
self._symprec,
self._is_symmetry)
def _search_primitive_symmetry(self):
self._primitive_symmetry = Symmetry(self._primitive,
self._symprec,
self._is_symmetry)
if (len(self._symmetry.get_pointgroup_operations()) !=
len(self._primitive_symmetry.get_pointgroup_operations())):
print ("Warning: point group symmetries of supercell and primitive"
"cell are different.")
def _build_supercell(self):
self._supercell = get_supercell(self._unitcell,
self._supercell_matrix,
self._symprec)
def _build_supercells_with_displacements(self):
supercells = []
for disp in self._displacement_dataset['first_atoms']:
positions = self._supercell.get_positions()
positions[disp['number']] += disp['displacement']
supercells.append(Atoms(
numbers=self._supercell.get_atomic_numbers(),
masses=self._supercell.get_masses(),
magmoms=self._supercell.get_magnetic_moments(),
positions=positions,
cell=self._supercell.get_cell(),
pbc=True))
self._supercells_with_displacements = supercells
def _build_primitive_cell(self):
"""
primitive_matrix:
Relative axes of primitive cell to the input unit cell.
Relative axes to the supercell is calculated by:
supercell_matrix^-1 * primitive_matrix
Therefore primitive cell lattice is finally calculated by:
(supercell_lattice * (supercell_matrix)^-1 * primitive_matrix)^T
"""
inv_supercell_matrix = np.linalg.inv(self._supercell_matrix)
if self._primitive_matrix is None:
trans_mat = inv_supercell_matrix
else:
trans_mat = np.dot(inv_supercell_matrix, self._primitive_matrix)
self._primitive = get_primitive(
self._supercell, trans_mat, self._symprec)
num_satom = self._supercell.get_number_of_atoms()
num_patom = self._primitive.get_number_of_atoms()
if abs(num_satom * np.linalg.det(trans_mat) - num_patom) < 0.1:
return True
else:
return False
class Phono3py:
def __init__(self,
unitcell,
supercell_matrix,
primitive_matrix=None,
phonon_supercell_matrix=None,
masses=None,
mesh=None,
band_indices=None,
sigmas=None,
cutoff_frequency=1e-4,
frequency_factor_to_THz=VaspToTHz,
is_symmetry=True,
is_nosym=False,
symmetrize_fc3_q=False,
symprec=1e-5,
log_level=0,
lapack_zheev_uplo='L'):
if sigmas is None:
sigmas = []
self._symprec = symprec
self._sigmas = sigmas
self._frequency_factor_to_THz = frequency_factor_to_THz
self._is_symmetry = is_symmetry
self._is_nosym = is_nosym
self._lapack_zheev_uplo = lapack_zheev_uplo
self._symmetrize_fc3_q = symmetrize_fc3_q
self._cutoff_frequency = cutoff_frequency
self._log_level = log_level
# Create supercell and primitive cell
self._unitcell = unitcell
self._supercell_matrix = supercell_matrix
self._primitive_matrix = primitive_matrix
self._phonon_supercell_matrix = phonon_supercell_matrix # optional
self._supercell = None
self._primitive = None
self._phonon_supercell = None
self._phonon_primitive = None
self._build_supercell()
self._build_primitive_cell()
self._build_phonon_supercell()
self._build_phonon_primitive_cell()
if masses is not None:
self._set_masses(masses)
# Set supercell, primitive, and phonon supercell symmetries
self._symmetry = None
self._primitive_symmetry = None
self._phonon_supercell_symmetry = None
self._search_symmetry()
self._search_primitive_symmetry()
self._search_phonon_supercell_symmetry()
# Displacements and supercells
self._supercells_with_displacements = None
self._displacement_dataset = None
self._phonon_displacement_dataset = None
self._phonon_supercells_with_displacements = None
# Thermal conductivity
self._thermal_conductivity = None # conductivity_RTA object
# Imaginary part of self energy at frequency points
self._imag_self_energy = None
self._scattering_event_class = None
# Linewidth (Imaginary part of self energy x 2) at temperatures
self._linewidth = None
self._grid_points = None
self._frequency_points = None
self._temperatures = None
# Other variables
self._fc2 = None
self._fc3 = None
# Setup interaction
self._interaction = None
self._mesh = None
self._band_indices = None
self._band_indices_flatten = None
if mesh is not None:
self._mesh = np.array(mesh, dtype='intc')
self.set_band_indices(band_indices)
def set_band_indices(self, band_indices):
if band_indices is None:
num_band = self._primitive.get_number_of_atoms() * 3
self._band_indices = [np.arange(num_band, dtype='intc')]
else:
self._band_indices = band_indices
self._band_indices_flatten = np.hstack(self._band_indices).astype('intc')
def set_phph_interaction(self,
nac_params=None,
nac_q_direction=None,
constant_averaged_interaction=None,
frequency_scale_factor=None,
unit_conversion=None):
self._interaction = Interaction(
self._supercell,
self._primitive,
self._mesh,
self._primitive_symmetry,
fc3=self._fc3,
band_indices=self._band_indices_flatten,
constant_averaged_interaction=constant_averaged_interaction,
frequency_factor_to_THz=self._frequency_factor_to_THz,
unit_conversion=unit_conversion,
cutoff_frequency=self._cutoff_frequency,
is_nosym=self._is_nosym,
symmetrize_fc3_q=self._symmetrize_fc3_q,
lapack_zheev_uplo=self._lapack_zheev_uplo)
self._interaction.set_dynamical_matrix(
self._fc2,
self._phonon_supercell,
self._phonon_primitive,
nac_params=nac_params,
frequency_scale_factor=frequency_scale_factor)
self._interaction.set_nac_q_direction(nac_q_direction=nac_q_direction)
def generate_displacements(self,
distance=0.03,
cutoff_pair_distance=None,
is_plusminus='auto',
is_diagonal=True):
direction_dataset = get_third_order_displacements(
self._supercell,
self._symmetry,
is_plusminus=is_plusminus,
is_diagonal=is_diagonal)
self._displacement_dataset = direction_to_displacement(
direction_dataset,
distance,
self._supercell,
cutoff_distance=cutoff_pair_distance)
if self._phonon_supercell_matrix is not None:
phonon_displacement_directions = get_least_displacements(
self._phonon_supercell_symmetry,
is_plusminus=is_plusminus,
is_diagonal=False)
self._phonon_displacement_dataset = direction_to_displacement_fc2(
phonon_displacement_directions,
distance,
self._phonon_supercell)
def produce_fc2(self,
forces_fc2,
displacement_dataset=None,
is_permutation_symmetry=False,
translational_symmetry_type=0):
if displacement_dataset is None:
disp_dataset = self._displacement_dataset
else:
disp_dataset = displacement_dataset
for forces, disp1 in zip(forces_fc2, disp_dataset['first_atoms']):
disp1['forces'] = forces
self._fc2 = get_fc2(self._phonon_supercell,
self._phonon_supercell_symmetry,
disp_dataset)
if is_permutation_symmetry:
set_permutation_symmetry(self._fc2)
if translational_symmetry_type:
set_translational_invariance(
self._fc2,
translational_symmetry_type=translational_symmetry_type)
def produce_fc3(self,
forces_fc3,
displacement_dataset=None,
cutoff_distance=None, # set fc3 zero
translational_symmetry_type=0,
is_permutation_symmetry=False,
is_permutation_symmetry_fc2=False):
if displacement_dataset is None:
disp_dataset = self._displacement_dataset
else:
disp_dataset = displacement_dataset
for forces, disp1 in zip(forces_fc3, disp_dataset['first_atoms']):
disp1['forces'] = forces
fc2 = get_fc2(self._supercell, self._symmetry, disp_dataset)
if is_permutation_symmetry_fc2:
set_permutation_symmetry(fc2)
if translational_symmetry_type:
set_translational_invariance(
fc2,
translational_symmetry_type=translational_symmetry_type)
count = len(disp_dataset['first_atoms'])
for disp1 in disp_dataset['first_atoms']:
for disp2 in disp1['second_atoms']:
disp2['delta_forces'] = forces_fc3[count] - disp1['forces']
count += 1
self._fc3 = get_fc3(
self._supercell,
disp_dataset,
fc2,
self._symmetry,
translational_symmetry_type=translational_symmetry_type,
is_permutation_symmetry=is_permutation_symmetry,
verbose=self._log_level)
# Set fc3 elements zero beyond cutoff_distance
if cutoff_distance:
if self._log_level:
print("Cutting-off fc3 by zero (cut-off distance: %f)" %
cutoff_distance)
self.cutoff_fc3_by_zero(cutoff_distance)
# Set fc2
if self._fc2 is None:
self._fc2 = fc2
def cutoff_fc3_by_zero(self, cutoff_distance):
cutoff_fc3_by_zero(self._fc3,
self._supercell,
cutoff_distance,
self._symprec)
def set_permutation_symmetry(self):
if self._fc2 is not None:
set_permutation_symmetry(self._fc2)
if self._fc3 is not None:
set_permutation_symmetry_fc3(self._fc3)
def set_translational_invariance(self,
translational_symmetry_type=1):
if self._fc2 is not None:
set_translational_invariance(
self._fc2,
translational_symmetry_type=translational_symmetry_type)
if self._fc3 is not None:
set_translational_invariance_fc3(
self._fc3,
translational_symmetry_type=translational_symmetry_type)
def get_interaction_strength(self):
return self._interaction
def get_fc2(self):
return self._fc2
def set_fc2(self, fc2):
self._fc2 = fc2
def get_fc3(self):
return self._fc3
def set_fc3(self, fc3):
self._fc3 = fc3
def get_primitive(self):
return self._primitive
def get_unitcell(self):
return self._unitcell
def get_supercell(self):
return self._supercell
def get_phonon_supercell(self):
return self._phonon_supercell
def get_phonon_primitive(self):
return self._phonon_primitive
def get_symmetry(self):
"""return symmetry of supercell"""
return self._symmetry
def get_primitive_symmetry(self):
return self._primitive_symmetry
def get_phonon_supercell_symmetry(self):
return self._phonon_supercell_symmetry
def set_displacement_dataset(self, dataset):
self._displacement_dataset = dataset
def get_displacement_dataset(self):
return self._displacement_dataset
def get_phonon_displacement_dataset(self):
return self._phonon_displacement_dataset
def get_supercells_with_displacements(self):
if self._supercells_with_displacements is None:
self._build_supercells_with_displacements()
return self._supercells_with_displacements
def get_phonon_supercells_with_displacements(self):
if self._phonon_supercells_with_displacements is None:
if self._phonon_displacement_dataset is not None:
self._phonon_supercells_with_displacements = \
self._build_phonon_supercells_with_displacements(
self._phonon_supercell,
self._phonon_displacement_dataset)
return self._phonon_supercells_with_displacements
def run_imag_self_energy(self,
grid_points,
frequency_step=None,
num_frequency_points=None,
temperatures=None,
scattering_event_class=None,
run_with_g=True,
write_details=False):
if temperatures is None:
temperatures = [0.0, 300.0]
self._grid_points = grid_points
self._temperatures = temperatures
self._scattering_event_class = scattering_event_class
self._imag_self_energy, self._frequency_points = get_imag_self_energy(
self._interaction,
grid_points,
self._sigmas,
frequency_step=frequency_step,
num_frequency_points=num_frequency_points,
temperatures=temperatures,
scattering_event_class=scattering_event_class,
run_with_g=run_with_g,
write_details=write_details,
log_level=self._log_level)
def write_imag_self_energy(self, filename=None):
write_imag_self_energy(
self._imag_self_energy,
self._mesh,
self._grid_points,
self._band_indices,
self._frequency_points,
self._temperatures,
self._sigmas,
scattering_event_class=self._scattering_event_class,
filename=filename)
def run_linewidth(self,
grid_points,
temperatures=np.arange(0, 1001, 10, dtype='double'),
run_with_g=True,
write_details=False):
self._grid_points = grid_points
self._temperatures = temperatures
self._linewidth = get_linewidth(self._interaction,
grid_points,
self._sigmas,
temperatures=temperatures,
run_with_g=run_with_g,
write_details=write_details,
log_level=self._log_level)
def write_linewidth(self, filename=None):
write_linewidth(self._linewidth,
self._band_indices,
self._mesh,
self._grid_points,
self._sigmas,
self._temperatures,
filename=filename)
def run_thermal_conductivity(
self,
is_LBTE=True,
temperatures=np.arange(0, 1001, 10, dtype='double'),
sigmas=None,
is_isotope=False,
mass_variances=None,
grid_points=None,
boundary_mfp=None, # in micrometre
use_averaged_pp_interaction=False,
gamma_unit_conversion=None,
mesh_divisors=None,
coarse_mesh_shifts=None,
is_reducible_collision_matrix=False,
no_kappa_stars=False,
gv_delta_q=None, # for group velocity
run_with_g=True, # integration weights for smearing method, too
pinv_cutoff=1.0e-8, # for pseudo-inversion of collision matrix
write_gamma=False,
read_gamma=False,
write_collision=False,
read_collision=False,
write_amplitude=False,
read_amplitude=False,
input_filename=None,
output_filename=None):
if sigmas is None:
sigmas = []
if is_LBTE:
self._thermal_conductivity = get_thermal_conductivity_LBTE(
self._interaction,
self._primitive_symmetry,
temperatures=temperatures,
sigmas=self._sigmas,
is_isotope=is_isotope,
mass_variances=mass_variances,
grid_points=grid_points,
boundary_mfp=boundary_mfp,
is_reducible_collision_matrix=is_reducible_collision_matrix,
no_kappa_stars=no_kappa_stars,
gv_delta_q=gv_delta_q,
pinv_cutoff=pinv_cutoff,
write_collision=write_collision,
read_collision=read_collision,
input_filename=input_filename,
output_filename=output_filename,
log_level=self._log_level)
else:
self._thermal_conductivity = get_thermal_conductivity_RTA(
self._interaction,
self._primitive_symmetry,
temperatures=temperatures,
sigmas=self._sigmas,
is_isotope=is_isotope,
mass_variances=mass_variances,
grid_points=grid_points,
boundary_mfp=boundary_mfp,
use_averaged_pp_interaction=use_averaged_pp_interaction,
gamma_unit_conversion=gamma_unit_conversion,
mesh_divisors=mesh_divisors,
coarse_mesh_shifts=coarse_mesh_shifts,
no_kappa_stars=no_kappa_stars,
gv_delta_q=gv_delta_q,
run_with_g=run_with_g,
write_gamma=write_gamma,
read_gamma=read_gamma,
input_filename=input_filename,
output_filename=output_filename,
log_level=self._log_level)
def get_thermal_conductivity(self):
return self._thermal_conductivity
def get_frequency_shift(self,
grid_points,
epsilons=None,
temperatures=np.arange(0, 1001, 10, dtype='double'),
output_filename=None):
if epsilons is None:
epsilons = [0.1]
self._grid_points = grid_points
get_frequency_shift(self._interaction,
self._grid_points,
self._band_indices,
epsilons,
temperatures,
output_filename=output_filename,
log_level=self._log_level)
def _search_symmetry(self):
self._symmetry = Symmetry(self._supercell,
self._symprec,
self._is_symmetry)
def _search_primitive_symmetry(self):
self._primitive_symmetry = Symmetry(self._primitive,
self._symprec,
self._is_symmetry)
if (len(self._symmetry.get_pointgroup_operations()) !=
len(self._primitive_symmetry.get_pointgroup_operations())):
print("Warning: point group symmetries of supercell and primitive"
"cell are different.")
def _search_phonon_supercell_symmetry(self):
if self._phonon_supercell_matrix is None:
self._phonon_supercell_symmetry = self._symmetry
else:
self._phonon_supercell_symmetry = Symmetry(self._phonon_supercell,
self._symprec,
self._is_symmetry)
def _build_supercell(self):
self._supercell = get_supercell(self._unitcell,
self._supercell_matrix,
self._symprec)
def _build_primitive_cell(self):
"""
primitive_matrix:
Relative axes of primitive cell to the input unit cell.
Relative axes to the supercell is calculated by:
supercell_matrix^-1 * primitive_matrix
Therefore primitive cell lattice is finally calculated by:
(supercell_lattice * (supercell_matrix)^-1 * primitive_matrix)^T
"""
self._primitive = self._get_primitive_cell(
self._supercell, self._supercell_matrix, self._primitive_matrix)
def _build_phonon_supercell(self):
"""
phonon_supercell:
This supercell is used for harmonic phonons (frequencies,
eigenvectors, group velocities, ...)
phonon_supercell_matrix:
Different supercell size can be specified.
"""
if self._phonon_supercell_matrix is None:
self._phonon_supercell = self._supercell
else:
self._phonon_supercell = get_supercell(
self._unitcell, self._phonon_supercell_matrix, self._symprec)
def _build_phonon_primitive_cell(self):
if self._phonon_supercell_matrix is None:
self._phonon_primitive = self._primitive
else:
self._phonon_primitive = self._get_primitive_cell(
self._phonon_supercell,
self._phonon_supercell_matrix,
self._primitive_matrix)
if self._primitive is not None:
if (self._primitive.get_atomic_numbers() !=
self._phonon_primitive.get_atomic_numbers()).any():
print("********************* Warning *********************")
print(" Primitive cells for fc2 and fc3 can be different.")
print("********************* Warning *********************")
def _build_phonon_supercells_with_displacements(self,
supercell,
displacement_dataset):
supercells = []
magmoms = supercell.get_magnetic_moments()
masses = supercell.get_masses()
numbers = supercell.get_atomic_numbers()
lattice = supercell.get_cell()
for disp1 in displacement_dataset['first_atoms']:
disp_cart1 = disp1['displacement']
positions = supercell.get_positions()
positions[disp1['number']] += disp_cart1
supercells.append(
Atoms(numbers=numbers,
masses=masses,
magmoms=magmoms,
positions=positions,
cell=lattice,
pbc=True))
return supercells
def _build_supercells_with_displacements(self):
supercells = []
magmoms = self._supercell.get_magnetic_moments()
masses = self._supercell.get_masses()
numbers = self._supercell.get_atomic_numbers()
lattice = self._supercell.get_cell()
supercells = self._build_phonon_supercells_with_displacements(
self._supercell,
self._displacement_dataset)
for disp1 in self._displacement_dataset['first_atoms']:
disp_cart1 = disp1['displacement']
for disp2 in disp1['second_atoms']:
if 'included' in disp2:
included = disp2['included']
else:
included = True
if included:
positions = self._supercell.get_positions()
positions[disp1['number']] += disp_cart1
positions[disp2['number']] += disp2['displacement']
supercells.append(Atoms(numbers=numbers,
masses=masses,
magmoms=magmoms,
positions=positions,
cell=lattice,
pbc=True))
else:
supercells.append(None)
self._supercells_with_displacements = supercells
def _get_primitive_cell(self, supercell, supercell_matrix, primitive_matrix):
inv_supercell_matrix = np.linalg.inv(supercell_matrix)
if primitive_matrix is None:
t_mat = inv_supercell_matrix
else:
t_mat = np.dot(inv_supercell_matrix, primitive_matrix)
return get_primitive(supercell, t_mat, self._symprec)
def _set_masses(self, masses):
p_masses = np.array(masses)
self._primitive.set_masses(p_masses)
p2p_map = self._primitive.get_primitive_to_primitive_map()
s_masses = p_masses[[p2p_map[x] for x in
self._primitive.get_supercell_to_primitive_map()]]
self._supercell.set_masses(s_masses)
u2s_map = self._supercell.get_unitcell_to_supercell_map()
u_masses = s_masses[u2s_map]
self._unitcell.set_masses(u_masses)
self._phonon_primitive.set_masses(p_masses)
p2p_map = self._phonon_primitive.get_primitive_to_primitive_map()
s_masses = p_masses[
[p2p_map[x] for x in
self._phonon_primitive.get_supercell_to_primitive_map()]]
self._phonon_supercell.set_masses(s_masses)
self._set_x_tags('xred')
def _set_x_tags(self, tagname):
xtag = []
natom = self._tags['natom']
for val in self._values:
xtag += self._get_numerical_values(val)
if len(xtag) >= natom * 3:
break
self._tags[tagname] = np.reshape(xtag[:natom * 3], (-1, 3))
def _set_znucl(self):
znucl = []
ntypat = self._tags['ntypat']
for val in self._values:
znucl += self._get_numerical_values(val, num_type='int')
if len(znucl) >= ntypat:
break
self._tags['znucl'] = znucl[:ntypat]
if __name__ == '__main__':
import sys
from phonopy.structure.symmetry import Symmetry
abinit = AbinitIn(open(sys.argv[1]).readlines())
cell = read_abinit(sys.argv[1])
symmetry = Symmetry(cell)
print("# %s" % symmetry.get_international_table())
print(get_abinit_structure(cell))
self._tags['plat'] = plat
def _set_alat(self, header):
hlist = header.split()
for j in hlist:
if j.startswith('alat'):
alat = float(j.split('=')[1])
break
self._tags['alat'] = alat
def _check_ord(self, header):
if not 'xpos' in header.split():
print('EXIT(1): LMTO Interface requires site', end=' ')
print('files to be in fractional co-ordinates')
sys.exit(1)
def get_variables(self, header, sites):
self._check_ord(header)
self._set_atoms(sites)
self._set_plat(header)
self._set_alat(header)
return self._tags
if __name__ == '__main__':
import sys
from phonopy.structure.symmetry import Symmetry
cell = read_lmto(sys.argv[1])
symmetry = Symmetry(cell)
print('# %s' % symmetry.get_international_table())
print(get_lmto_structure(cell))
def _search_symmetry(self):
self._symmetry = Symmetry(self._supercell,
self._symprec,
self._is_symmetry)
class JointDos:
def __init__(self,
mesh,
primitive,
supercell,
fc2,
nac_params=None,
nac_q_direction=None,
sigma=None,
cutoff_frequency=None,
frequency_step=None,
num_frequency_points=None,
temperatures=None,
frequency_factor_to_THz=VaspToTHz,
frequency_scale_factor=1.0,
is_nosym=False,
symprec=1e-5,
filename=None,
log_level=False,
lapack_zheev_uplo='L'):
self._grid_point = None
self._mesh = np.array(mesh, dtype='intc')
self._primitive = primitive
self._supercell = supercell
self._fc2 = fc2
self._nac_params = nac_params
self._nac_q_direction = None
self.set_nac_q_direction(nac_q_direction)
self._sigma = None
self.set_sigma(sigma)
if cutoff_frequency is None:
self._cutoff_frequency = 0
else:
self._cutoff_frequency = cutoff_frequency
self._frequency_step = frequency_step
self._num_frequency_points = num_frequency_points
self._temperatures = temperatures
self._frequency_factor_to_THz = frequency_factor_to_THz
self._frequency_scale_factor = frequency_scale_factor
self._is_nosym = is_nosym
self._symprec = symprec
self._filename = filename
self._log_level = log_level
self._lapack_zheev_uplo = lapack_zheev_uplo
self._num_band = self._primitive.get_number_of_atoms() * 3
self._reciprocal_lattice = np.linalg.inv(self._primitive.get_cell())
self._set_dynamical_matrix()
self._symmetry = Symmetry(primitive, symprec)
self._tetrahedron_method = None
self._phonon_done = None
self._frequencies = None
self._eigenvectors = None
self._joint_dos = None
self._frequency_points = None
def run(self):
try:
import anharmonic._phono3py as phono3c
self._run_c()
except ImportError:
print "Joint density of states in python is not implemented."
return None, None
def get_joint_dos(self):
return self._joint_dos
def get_frequency_points(self):
return self._frequency_points
def get_phonons(self):
return self._frequencies, self._eigenvectors, self._phonon_done
def get_primitive(self):
return self._primitive
def get_mesh_numbers(self):
return self._mesh
def set_nac_q_direction(self, nac_q_direction=None):
if nac_q_direction is not None:
self._nac_q_direction = np.array(nac_q_direction, dtype='double')
def set_sigma(self, sigma):
if sigma is None:
self._sigma = None
else:
self._sigma = float(sigma)
def set_grid_point(self, grid_point):
self._grid_point = grid_point
self._set_triplets()
num_grid = np.prod(len(self._grid_address))
num_band = self._num_band
if self._phonon_done is None:
self._phonon_done = np.zeros(num_grid, dtype='byte')
self._frequencies = np.zeros((num_grid, num_band), dtype='double')
self._eigenvectors = np.zeros((num_grid, num_band, num_band),
dtype='complex128')
self._joint_dos = None
self._frequency_points = None
self.set_phonon(np.array([grid_point], dtype='intc'))
def get_triplets_at_q(self):
return self._triplets_at_q, self._weights_at_q
def get_grid_address(self):
return self._grid_address
def get_bz_map(self):
return self._bz_map
def _run_c(self, lang='C'):
if self._sigma is None:
if lang == 'C':
self._run_c_with_g()
else:
if self._temperatures is not None:
print "JDOS with phonon occupation numbers doesn't work",
print "in this option."
self._run_py_tetrahedron_method()
else:
self._run_c_with_g()
# self._run_smearing_method() is an older and direct implementation.
# This requies less memory space. self._run_c_with_g can be used
# for smearing method and can share same code with tetrahedron
# method. Therefore maintainance cost of code can be reduced by
# without using self._run_smearing_method().
def _run_c_with_g(self):
self.set_phonon(self._triplets_at_q.ravel())
if self._sigma is None:
f_max = np.max(self._frequencies) * 2
else:
f_max = np.max(self._frequencies) * 2 + self._sigma * 4
f_max *= 1.005
f_min = 0
self._set_frequency_points(f_min, f_max)
num_freq_points = len(self._frequency_points)
num_mesh = np.prod(self._mesh)
if self._temperatures is None:
jdos = np.zeros((num_freq_points, 2), dtype='double')
else:
num_temps = len(self._temperatures)
jdos = np.zeros((num_temps, num_freq_points, 2), dtype='double')
occ_phonons = []
for t in self._temperatures:
freqs = self._frequencies[self._triplets_at_q[:, 1:]]
occ_phonons.append(np.where(freqs > self._cutoff_frequency,
occupation(freqs, t), 0))
for i, freq_point in enumerate(self._frequency_points):
g = get_triplets_integration_weights(
self,
np.array([freq_point], dtype='double'),
self._sigma,
is_collision_matrix=True,
neighboring_phonons=(i == 0))
if self._temperatures is None:
jdos[i, 0] = np.sum(
np.tensordot(g[0, :, 0], self._weights_at_q, axes=(0, 0)))
gx = g[2] - g[0]
jdos[i, 1] = np.sum(
np.tensordot(gx[:, 0], self._weights_at_q, axes=(0, 0)))
else:
for j, n in enumerate(occ_phonons):
for k, l in list(np.ndindex(g.shape[3:])):
jdos[j, i, 0] += np.dot(
(n[:, 0, k] + n[:, 1, l] + 1) *
g[0, :, 0, k, l], self._weights_at_q)
jdos[j, i, 1] += np.dot((n[:, 0, k] - n[:, 1, l]) *
g[1, :, 0, k, l],
self._weights_at_q)
self._joint_dos = jdos / num_mesh
def _run_py_tetrahedron_method(self):
thm = TetrahedronMethod(self._reciprocal_lattice, mesh=self._mesh)
self._vertices = get_tetrahedra_vertices(
thm.get_tetrahedra(),
self._mesh,
self._triplets_at_q,
self._grid_address,
self._bz_map)
self.set_phonon(self._vertices.ravel())
f_max = np.max(self._frequencies) * 2
f_max *= 1.005
f_min = 0
self._set_frequency_points(f_min, f_max)
num_freq_points = len(self._frequency_points)
jdos = np.zeros((num_freq_points, 2), dtype='double')
for vertices, w in zip(self._vertices, self._weights_at_q):
for i, j in list(np.ndindex(self._num_band, self._num_band)):
f1 = self._frequencies[vertices[0], i]
f2 = self._frequencies[vertices[1], j]
thm.set_tetrahedra_omegas(f1 + f2)
thm.run(self._frequency_points)
iw = thm.get_integration_weight()
jdos[:, 0] += iw * w
thm.set_tetrahedra_omegas(f1 - f2)
thm.run(self._frequency_points)
iw = thm.get_integration_weight()
jdos[:, 1] += iw * w
thm.set_tetrahedra_omegas(-f1 + f2)
thm.run(self._frequency_points)
iw = thm.get_integration_weight()
jdos[:, 1] += iw * w
self._joint_dos = jdos / np.prod(self._mesh)
def _run_smearing_method(self):
import anharmonic._phono3py as phono3c
self.set_phonon(self._triplets_at_q.ravel())
f_max = np.max(self._frequencies) * 2 + self._sigma * 4
f_min = np.min(self._frequencies) * 2 - self._sigma * 4
self._set_frequency_points(f_min, f_max)
jdos = np.zeros((len(self._frequency_points), 2), dtype='double')
phono3c.joint_dos(jdos,
self._frequency_points,
self._triplets_at_q,
self._weights_at_q,
self._frequencies,
self._sigma)
jdos /= np.prod(self._mesh)
self._joint_dos = jdos
def _set_dynamical_matrix(self):
self._dm = get_dynamical_matrix(
self._fc2,
self._supercell,
self._primitive,
nac_params=self._nac_params,
frequency_scale_factor=self._frequency_scale_factor,
symprec=self._symprec)
def _set_triplets(self):
if self._is_nosym:
if self._log_level:
print "Triplets at q without considering symmetry"
sys.stdout.flush()
(self._triplets_at_q,
self._weights_at_q,
self._grid_address,
self._bz_map,
map_triplets,
map_q) = get_nosym_triplets_at_q(
self._grid_point,
self._mesh,
self._reciprocal_lattice,
with_bz_map=True)
else:
(self._triplets_at_q,
self._weights_at_q,
self._grid_address,
self._bz_map,
map_triplets,
map_q) = get_triplets_at_q(
self._grid_point,
self._mesh,
self._symmetry.get_pointgroup_operations(),
self._reciprocal_lattice)
def set_phonon(self, grid_points):
set_phonon_c(self._dm,
self._frequencies,
self._eigenvectors,
self._phonon_done,
grid_points,
self._grid_address,
self._mesh,
self._frequency_factor_to_THz,
self._nac_q_direction,
self._lapack_zheev_uplo)
def _set_frequency_points(self, f_min, f_max):
if self._num_frequency_points is None:
if self._frequency_step is not None:
self._frequency_points = np.arange(
f_min, f_max, self._frequency_step, dtype='double')
else:
self._frequency_points = np.array(np.linspace(
f_min, f_max, 201), dtype='double')
else:
self._frequency_points = np.array(np.linspace(
f_min, f_max, self._num_frequency_points), dtype='double')
class PhonopyUnfolding(Phonopy):
"""
unitcell: before symmetrization
"""
def __init__(self,
unitcell,
unitcell_ideal,
supercell_matrix,
primitive_matrix_ideal,
nac_params=None,
distance=0.01,
factor=VaspToTHz,
is_auto_displacements=True,
dynamical_matrix_decimals=None,
force_constants_decimals=None,
star="none",
mode="eigenvector",
symprec=1e-5,
is_symmetry=True,
use_lapack_solver=False,
log_level=0):
self._symprec = symprec
self._distance = distance
self._factor = factor
self._is_auto_displacements = is_auto_displacements
self._is_symmetry = is_symmetry
self._use_lapack_solver = use_lapack_solver
self._log_level = log_level
# Create supercell and primitive cell
self._unitcell = unitcell
self._unitcell_ideal = unitcell_ideal
self._supercell_matrix = supercell_matrix
self._primitive_matrix = None
self._primitive_matrix_ideal = primitive_matrix_ideal
self._supercell = None
self._primitive = None
self._build_supercell()
self._build_primitive_cell()
self._build_supercell_ideal()
self._build_primitive_cell_ideal()
# Set supercell and primitive symmetry
self._symmetry = None
self._primitive_symmetry = None
self._search_symmetry()
self._search_primitive_symmetry()
self._search_symmetry_ideal()
self._search_primitive_symmetry_ideal()
# set_force_constants or set_forces
self._force_constants = None
self._force_constants_decimals = force_constants_decimals
# set_dynamical_matrix
self._dynamical_matrix = None
self._nac_params = nac_params
self._dynamical_matrix_decimals = dynamical_matrix_decimals
# set_band_structure
self._band_structure = None
# set_mesh
self._mesh = None
# set_tetrahedron_method
self._tetrahedron_method = None
# set_thermal_properties
self._thermal_properties = None
# set_thermal_displacements
self._thermal_displacements = None
# set_thermal_displacement_matrices
self._thermal_displacement_matrices = None
# set_partial_DOS
self._pdos = None
# set_total_DOS
self._total_dos = None
# set_modulation
self._modulation = None
# set_character_table
self._irreps = None
# set_group_velocity
self._group_velocity = None
self._star = star
self._mode = mode
# Single point
def run_single_point(self, qpoint, distance):
SinglePoint(
qpoint,
distance,
dynamical_matrix=self._dynamical_matrix,
unitcell_ideal=self._unitcell_ideal,
primitive_matrix_ideal=self._primitive_matrix_ideal,
factor=self._factor,
star=self._star,
mode=self._mode,
verbose=True)
# Band structure
def set_band_structure(self,
bands,
is_eigenvectors=False,
is_band_connection=False):
if self._dynamical_matrix is None:
print("Warning: Dynamical matrix has not yet built.")
self._band_structure = None
return False
self._band_structure = BandStructure(
bands,
self._dynamical_matrix,
self._unitcell_ideal,
self._primitive_matrix_ideal,
is_eigenvectors=is_eigenvectors,
is_band_connection=is_band_connection,
group_velocity=self._group_velocity,
factor=self._factor,
star=self._star,
mode=self._mode,
verbose=True)
return True
# Sampling mesh
def set_mesh(self,
mesh,
shift=None,
is_time_reversal=True,
is_mesh_symmetry=True,
is_eigenvectors=False,
is_gamma_center=False):
if self._dynamical_matrix is None:
print("Warning: Dynamical matrix has not yet built.")
self._mesh = None
return False
# TODO(ikeda): Check how "rotations" works.
self._mesh = MeshUnfolding(
self._dynamical_matrix,
self._unitcell_ideal,
self._primitive_matrix_ideal,
mesh,
shift=shift,
is_time_reversal=is_time_reversal,
is_mesh_symmetry=is_mesh_symmetry,
is_eigenvectors=is_eigenvectors,
is_gamma_center=is_gamma_center,
star=self._star,
group_velocity=self._group_velocity,
rotations=self._primitive_symmetry.get_pointgroup_operations(),
factor=self._factor,
use_lapack_solver=self._use_lapack_solver,
mode=self._mode)
return True
# DOS
def set_total_DOS(self,
sigma=None,
freq_min=None,
freq_max=None,
freq_pitch=None,
tetrahedron_method=False):
if self._mesh is None:
print("Warning: \'set_mesh\' has to finish correctly "
"before DOS calculation.")
self._total_dos = None
return False
total_dos = TotalDosUnfolding(
self._mesh,
sigma=sigma,
tetrahedron_method=tetrahedron_method)
total_dos.set_draw_area(freq_min, freq_max, freq_pitch)
total_dos.run()
self._total_dos = total_dos
return True
def _set_dynamical_matrix(self):
self._dynamical_matrix = None
if self._supercell is None or self._primitive is None:
print("Bug: Supercell or primitive is not created.")
return False
elif self._force_constants is None:
print("Warning: Force constants are not prepared.")
return False
elif self._primitive.get_masses() is None:
print("Warning: Atomic masses are not correctly set.")
return False
else:
if self._nac_params is None:
self._dynamical_matrix = DynamicalMatrix(
self._supercell,
self._primitive,
self._force_constants,
decimals=self._dynamical_matrix_decimals,
symprec=self._symprec)
else:
raise ValueError(
'Currently NAC is not available for unfolding.')
return True
def _search_symmetry_ideal(self):
self._symmetry = Symmetry(self._supercell_ideal,
self._symprec,
self._is_symmetry)
def _search_primitive_symmetry_ideal(self):
self._primitive_symmetry = Symmetry(self._primitive_ideal,
self._symprec,
self._is_symmetry)
n0 = len(self._symmetry.get_pointgroup_operations())
n1 = len(self._primitive_symmetry.get_pointgroup_operations())
if n0 != n1:
raise Warning("Point group symmetries of supercell and primitive"
"cell are different.")
def _build_supercell_ideal(self):
self._supercell_ideal = get_supercell(
self._unitcell_ideal,
self._supercell_matrix,
self._symprec)
def _build_primitive_cell_ideal(self):
"""
primitive_matrix:
Relative axes of primitive cell to the input unit cell.
Relative axes to the supercell is calculated by:
supercell_matrix^-1 * primitive_matrix
Therefore primitive cell lattice is finally calculated by:
(supercell_lattice * (supercell_matrix)^-1 * primitive_matrix)^T
"""
inv_supercell_matrix = np.linalg.inv(self._supercell_matrix)
if self._primitive_matrix_ideal is None:
trans_mat = inv_supercell_matrix
else:
trans_mat = np.dot(inv_supercell_matrix, self._primitive_matrix_ideal)
self._primitive_ideal = get_primitive(
self._supercell_ideal, trans_mat, self._symprec)
num_satom = self._supercell_ideal.get_number_of_atoms()
num_patom = self._primitive_ideal.get_number_of_atoms()
if abs(num_satom * np.linalg.det(trans_mat) - num_patom) < 0.1:
return True
else:
return False
def average_masses(self):
masses = self._unitcell.get_masses()
masses_average = calculate_average_masses(
masses, Symmetry(self._unitcell_ideal))
self._unitcell.set_masses(masses_average)
self._build_supercell()
self._build_primitive_cell()
self._search_symmetry()
self._search_primitive_symmetry()
def average_force_constants(self):
fc_symmetrizer_spg = FCSymmetrizerSPG(
force_constants=self._force_constants,
atoms=self._unitcell,
atoms_ideal=self._unitcell_ideal,
supercell_matrix=self._supercell_matrix,
)
fc_symmetrizer_spg.average_force_constants_spg()
fc_symmetrizer_spg.write_force_constants_symmetrized()
fc_average = fc_symmetrizer_spg.get_force_constants_symmetrized()
self.set_force_constants(fc_average) # Dynamical matrices are also prepared inside.
magmom = []
for numxmag in text.split():
if '*' in numxmag:
num, mag = numxmag.split('*')
magmom += [float(mag)] * int(num)
else:
magmom.append(float(numxmag))
return magmom
def parse_incar(filename):
for line in open(filename):
for conf in line.split(';'):
if 'MAGMOM' in conf:
return get_magmom(conf.split('=')[1])
cell = read_vasp("POSCAR")
symmetry = Symmetry(cell, symprec=1e-3)
map_nonspin = symmetry.get_map_atoms()
print "Number of operations w/o spin", len(symmetry.get_symmetry_operations()['rotations'])
magmoms = parse_incar("INCAR")
cell.set_magnetic_moments(magmoms)
symmetry = Symmetry(cell, symprec=1e-3)
print "Number of operations w spin", len(symmetry.get_symmetry_operations()['rotations'])
map_withspin = symmetry.get_map_atoms()
if ((map_nonspin - map_withspin) == 0).all():
print True
else:
print False
print map_nonspin
print map_withspin
elif tag == "atomiccoordinatesandatomicspecies":
lines = block.split('\n')[:-1]
self._tags["atomiccoordinates"] = [ [float(x) for x in atom.split()[:3]] for atom in lines ]
self._tags["atomicspecies"] = [ int(atom.split()[3]) for atom in lines]
#check if the block are present
self.check_present("atomicspecies")
self.check_present("atomiccoordinates")
self.check_present("latticevectors")
self.check_present("chemicalspecieslabel")
#translate the atomicspecies to atomic numbers
self._tags["atomicnumbers"] = [self._tags["atomicnumbers"][atype] for atype in self._tags["atomicspecies"]]
def check_present(self,tag):
if not self._tags[tag]:
print "%s not present"%tag
exit()
def __str__():
return self._tags
if __name__ == '__main__':
import sys
from phonopy.structure.symmetry import Symmetry
cell,atypes = read_siesta(sys.argv[1])
symmetry = Symmetry(cell)
print "#", symmetry.get_international_table()
print get_siesta_structure(cell,atypes)
shortest_indices = [i for i, d in enumerate(distances - min_dist)
if abs(d) < self._tolerance]
self._shortest_qpoints.append(
np.dot(search_space[shortest_indices] + q, self._tmat.T))
def get_shortest_qpoints(self):
return self._shortest_qpoints
if __name__ == '__main__':
from phonopy.interface.vasp import read_vasp
from phonopy.structure.symmetry import Symmetry, get_lattice_vector_equivalence
from phonopy.structure.spglib import get_ir_reciprocal_mesh, relocate_BZ_grid_address
import sys
cell = read_vasp(sys.argv[1])
symmetry = Symmetry(cell)
mesh = [4, 4, 4]
is_shift = np.array([0, 0, 0], dtype='intc')
mapping_table, grid_address = get_ir_reciprocal_mesh(
mesh,
cell,
is_shift=is_shift)
ir_grid_points = np.unique(mapping_table)
primitive_vectors = np.linalg.inv(cell.get_cell())
bz_grid_address, bz_map = relocate_BZ_grid_address(
grid_address,
mesh,
np.linalg.inv(cell.get_cell()),
is_shift=is_shift)
bz_points = np.extract(bz_map > -1, bz_map)
