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:
print "Solving fc3[ %d, x, x ] with" % (first_atom_num + 1),
if len(displacements_first) > 1:
print "displacements:"
else:
print "a displacement:"
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 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:
print "Solving fc3[ %d, x, x ] with" % (first_atom_num + 1),
if len(displacements_first) > 1:
print "displacements:"
else:
print "a displacement:"
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 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"):
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)