def _solve_fc4(fc4,
first_atom_num,
supercell,
site_symmetry,
displacements_first,
delta_fc3s,
symprec):
lattice = supercell.get_cell().T
site_sym_cart = np.double([similarity_transformation(lattice, sym)
for sym in site_symmetry])
num_atom = supercell.get_number_of_atoms()
positions = supercell.get_scaled_positions()
pos_center = positions[first_atom_num].copy()
positions -= pos_center
rot_map_syms = get_positions_sent_by_rot_inv(positions,
site_symmetry,
symprec)
rot_disps = get_rotated_displacement(displacements_first, site_sym_cart)
inv_U = np.linalg.pinv(rot_disps)
for (i, j, k) in list(np.ndindex(num_atom, num_atom, num_atom)):
fc4[first_atom_num, i, j, k] = np.dot(
inv_U, _rotate_delta_fc3s(
i, j, k, delta_fc3s, rot_map_syms, site_sym_cart)
).reshape(3, 3, 3, 3)
def solve_fc3(fc3,
first_atom_num,
supercell,
site_symmetry,
displacements_first,
delta_fc2s,
symprec,
pinv="numpy"):
lattice = supercell.get_cell().T
site_sym_cart = [similarity_transformation(lattice, sym)
for sym in site_symmetry]
num_atom = supercell.get_number_of_atoms()
positions = supercell.get_scaled_positions()
pos_center = positions[first_atom_num].copy()
positions -= pos_center
rot_map_syms = get_positions_sent_by_rot_inv(positions,
site_symmetry,
symprec)
rot_disps = get_rotated_displacement(displacements_first, site_sym_cart)
if pinv == "numpy":
inv_U = np.linalg.pinv(rot_disps)
else:
try:
import anharmonic._phono3py as phono3c
inv_U = np.zeros((rot_disps.shape[1], rot_disps.shape[0]),
dtype='double')
phono3c.pinv(inv_U, rot_disps, 1e-13)
except ImportError:
inv_U = np.linalg.pinv(rot_disps)
for (i, j) in list(np.ndindex(num_atom, num_atom)):
fc3[first_atom_num, i, j] = np.dot(inv_U, _get_rotated_fc2s(
i, j, delta_fc2s, rot_map_syms, site_sym_cart)).reshape(3, 3, 3)
def solve_fc3(fc3,
first_atom_num,
supercell,
site_symmetry,
displacements_first,
delta_fc2s,
symprec,
pinv="numpy",
verbose=False):
if verbose:
text = "Solving fc3[ %d, x, x ] with " % (first_atom_num + 1)
if len(displacements_first) > 1:
text += "displacements:"
else:
text += "a displacement:"
print(text)
for i, v in enumerate(displacements_first):
print(" [%7.4f %7.4f %7.4f]" % tuple(v))
sys.stdout.flush()
if verbose > 2:
print(" Site symmetry:")
for i, v in enumerate(site_symmetry):
print(" [%2d %2d %2d] #%2d" % tuple(list(v[0]) + [i + 1]))
print(" [%2d %2d %2d]" % tuple(v[1]))
print(" [%2d %2d %2d]\n" % tuple(v[2]))
sys.stdout.flush()
lattice = supercell.get_cell().T
site_sym_cart = [
similarity_transformation(lattice, sym) for sym in site_symmetry
]
num_atom = supercell.get_number_of_atoms()
positions = supercell.get_scaled_positions()
pos_center = positions[first_atom_num].copy()
positions -= pos_center
rot_map_syms = get_positions_sent_by_rot_inv(positions, site_symmetry,
symprec)
rot_disps = get_rotated_displacement(displacements_first, site_sym_cart)
if pinv == "numpy":
inv_U = np.linalg.pinv(rot_disps)
else:
try:
import phonopy._lapackepy as lapackepy
inv_U = np.zeros((rot_disps.shape[1], rot_disps.shape[0]),
dtype='double')
lapackepy.pinv(inv_U, rot_disps, 1e-13)
except ImportError:
inv_U = np.linalg.pinv(rot_disps)
for (i, j) in list(np.ndindex(num_atom, num_atom)):
fc3[first_atom_num, i, j] = np.dot(
inv_U,
_get_rotated_fc2s(i, j, delta_fc2s, rot_map_syms,
site_sym_cart)).reshape(3, 3, 3)
def solve_fc3(fc3,
first_atom_num,
supercell,
site_symmetry,
displacements_first,
delta_fc2s,
symprec,
pinv="numpy",
verbose=False):
if verbose:
text = "Solving fc3[ %d, x, x ] with " % (first_atom_num + 1)
if len(displacements_first) > 1:
text += "displacements:"
else:
text += "a displacement:"
print(text)
for i, v in enumerate(displacements_first):
print(" [%7.4f %7.4f %7.4f]" % tuple(v))
sys.stdout.flush()
if verbose > 2:
print(" Site symmetry:")
for i, v in enumerate(site_symmetry):
print(" [%2d %2d %2d] #%2d" % tuple(list(v[0])+[i + 1]))
print(" [%2d %2d %2d]" % tuple(v[1]))
print(" [%2d %2d %2d]\n" % tuple(v[2]))
sys.stdout.flush()
lattice = supercell.get_cell().T
site_sym_cart = [similarity_transformation(lattice, sym)
for sym in site_symmetry]
num_atom = supercell.get_number_of_atoms()
positions = supercell.get_scaled_positions()
pos_center = positions[first_atom_num].copy()
positions -= pos_center
rot_map_syms = get_positions_sent_by_rot_inv(positions,
site_symmetry,
symprec)
rot_disps = get_rotated_displacement(displacements_first, site_sym_cart)
if pinv == "numpy":
inv_U = np.linalg.pinv(rot_disps)
else:
try:
import phonopy._lapackepy as lapackepy
inv_U = np.zeros((rot_disps.shape[1], rot_disps.shape[0]),
dtype='double')
lapackepy.pinv(inv_U, rot_disps, 1e-13)
except ImportError:
inv_U = np.linalg.pinv(rot_disps)
for (i, j) in list(np.ndindex(num_atom, num_atom)):
fc3[first_atom_num, i, j] = np.dot(inv_U, _get_rotated_fc2s(
i, j, delta_fc2s, rot_map_syms, site_sym_cart)).reshape(3, 3, 3)
def solve_fc3(fc3,
first_atom_num,
supercell,
site_symmetry,
displacements_first,
delta_fc2s,
symprec,
pinv="numpy"):
lattice = supercell.get_cell().T
site_sym_cart = [
similarity_transformation(lattice, sym) for sym in site_symmetry
]
num_atom = supercell.get_number_of_atoms()
positions = supercell.get_scaled_positions()
pos_center = positions[first_atom_num].copy()
positions -= pos_center
rot_map_syms = get_positions_sent_by_rot_inv(positions, site_symmetry,
symprec)
rot_disps = get_rotated_displacement(displacements_first, site_sym_cart)
if pinv == "numpy":
inv_U = np.linalg.pinv(rot_disps)
else:
try:
import anharmonic._phono3py as phono3c
inv_U = np.zeros((rot_disps.shape[1], rot_disps.shape[0]),
dtype='double')
phono3c.pinv(inv_U, rot_disps, 1e-13)
except ImportError:
inv_U = np.linalg.pinv(rot_disps)
for (i, j) in list(np.ndindex(num_atom, num_atom)):
fc3[first_atom_num, i, j] = np.dot(
inv_U,
_get_rotated_fc2s(i, j, delta_fc2s, rot_map_syms,
site_sym_cart)).reshape(3, 3, 3)
def solve_fc3(first_atom_num,
supercell,
site_symmetry,
displacements_first,
delta_fc2s,
symprec,
pinv_solver="numpy",
verbose=False):
logger.debug("solve_fc3")
if pinv_solver == "numpy":
solver = "numpy.linalg.pinv"
else:
try:
import phono3py._lapackepy as lapackepy
solver = "lapacke-dgesvd"
except ImportError:
print("Phono3py C-routine is not compiled correctly.")
solver = "numpy.linalg.pinv"
if verbose:
text = ("Computing fc3[ %d, x, x ] using %s with " %
(first_atom_num + 1, solver))
if len(displacements_first) > 1:
text += "displacements:"
else:
text += "a displacement:"
print(text)
for i, v in enumerate(displacements_first):
print(" [%7.4f %7.4f %7.4f]" % tuple(v))
sys.stdout.flush()
if verbose > 2:
print(" Site symmetry:")
for i, v in enumerate(site_symmetry):
print(" [%2d %2d %2d] #%2d" % tuple(list(v[0]) + [i + 1]))
print(" [%2d %2d %2d]" % tuple(v[1]))
print(" [%2d %2d %2d]\n" % tuple(v[2]))
sys.stdout.flush()
lattice = supercell.get_cell().T
site_sym_cart = np.array(
[similarity_transformation(lattice, sym) for sym in site_symmetry],
dtype='double',
order='C')
num_atom = supercell.get_number_of_atoms()
positions = supercell.get_scaled_positions()
pos_center = positions[first_atom_num].copy()
positions -= pos_center
logger.debug("get_positions_sent_by_rot_inv")
rot_map_syms = get_positions_sent_by_rot_inv(lattice, positions,
site_symmetry, symprec)
rot_disps = get_rotated_displacement(displacements_first, site_sym_cart)
logger.debug("pinv")
if "numpy" in solver:
inv_U = np.array(np.linalg.pinv(rot_disps), dtype='double', order='C')
else:
inv_U = np.zeros((rot_disps.shape[1], rot_disps.shape[0]),
dtype='double',
order='C')
lapackepy.pinv(inv_U, rot_disps, 1e-13)
fc3 = np.zeros((num_atom, num_atom, 3, 3, 3), dtype='double', order='C')
logger.debug("rotate_delta_fc2s")
try:
import phono3py._phono3py as phono3c
phono3c.rotate_delta_fc2s(fc3, delta_fc2s, inv_U, site_sym_cart,
rot_map_syms)
except ImportError:
for i, j in np.ndindex(num_atom, num_atom):
fc3[i, j] = np.dot(
inv_U,
_get_rotated_fc2s(i, j, delta_fc2s, rot_map_syms,
site_sym_cart)).reshape(3, 3, 3)
return fc3
