def distribute_force_constants(
force_constants,
atom_list_done,
lattice, # column vectors
rotations, # scaled (fractional)
permutations,
atom_list=None,
):
"""Fill force constants elements by symmetry."""
map_atoms, map_syms = _get_sym_mappings_from_permutations(
permutations, atom_list_done)
rots_cartesian = np.array(
[similarity_transformation(lattice, r) for r in rotations],
dtype="double",
order="C",
)
if atom_list is None:
targets = np.arange(force_constants.shape[1], dtype="intc")
else:
targets = np.array(atom_list, dtype="intc")
import phonopy._phonopy as phonoc
phonoc.distribute_fc2(
force_constants,
targets,
rots_cartesian,
permutations,
np.array(map_atoms, dtype="intc"),
np.array(map_syms, dtype="intc"),
)
def _distribute_fc2_part(force_constants, positions, atom_disp, map_atom_disp,
lattice, r, t, symprec):
# L R L^-1
rot_cartesian = np.array(similarity_transformation(lattice, r),
dtype='double',
order='C')
try:
import phonopy._phonopy as phonoc
phonoc.distribute_fc2(force_constants, positions, atom_disp,
map_atom_disp, rot_cartesian,
np.array(r, dtype='intc', order='C'),
np.array(t, dtype='double'), symprec)
except ImportError:
for i, pos_i in enumerate(positions):
rot_pos = np.dot(pos_i, r.T) + t
rot_atom = -1
for j, pos_j in enumerate(positions):
diff = pos_j - rot_pos
if (abs(diff - np.rint(diff)) < symprec).all():
rot_atom = j
break
if rot_atom < 0:
print 'Input forces are not enough to calculate force constants,'
print 'or something wrong (e.g. crystal structure does not match).'
raise ValueError
# R^-1 P R (inverse transformation)
force_constants[atom_disp, i] += similarity_transformation(
rot_cartesian.T, force_constants[map_atom_disp, rot_atom])
def _distribute_fc2_part(force_constants,
positions,
atom_disp,
map_atom_disp,
lattice, # column vectors
r,
t,
symprec):
# L R L^-1
rot_cartesian = np.array(
similarity_transformation(lattice, r), dtype='double', order='C')
try:
import phonopy._phonopy as phonoc
phonoc.distribute_fc2(force_constants,
lattice,
positions,
atom_disp,
map_atom_disp,
rot_cartesian,
np.array(r, dtype='intc', order='C'),
np.array(t, dtype='double'),
symprec)
except ImportError:
for i, pos_i in enumerate(positions):
rot_pos = np.dot(pos_i, r.T) + t
rot_atom = -1
for j, pos_j in enumerate(positions):
diff = pos_j - rot_pos
diff -= np.rint(diff)
diff = np.dot(diff, lattice.T)
if np.linalg.norm(diff) < symprec:
rot_atom = j
break
if rot_atom < 0:
print("Input forces are not enough to calculate force constants,")
print("or something wrong (e.g. crystal structure does not match).")
raise ValueError
# R^-1 P R (inverse transformation)
force_constants[atom_disp, i] += similarity_transformation(
rot_cartesian.T,
force_constants[map_atom_disp, rot_atom])
def _distribute_fc2_part(force_constants,
positions,
atom_disp,
map_atom_disp,
rot_cartesian,
r,
t,
symprec):
try:
raise ImportError
import phonopy._phonopy as phonoc
phonoc.distribute_fc2(force_constants,
positions,
atom_disp,
map_atom_disp,
rot_cartesian,
r,
t,
symprec)
except ImportError:
for i, pos_i in enumerate(positions):
rot_pos = np.dot(pos_i, r.T) + t
rot_atom = -1
for j, pos_j in enumerate(positions):
diff = pos_j - rot_pos
if (abs(diff - np.rint(diff)) < symprec).all():
rot_atom = j
break
if rot_atom < 0:
print 'Input forces are not enough to calculate force constants,'
print 'or something wrong (e.g. crystal structure does not match).'
raise ValueError
# R^-1 P R (inverse transformation)
# f1 = np.dot(np.kron(rot_cartesian.T, rot_cartesian.T), force_constants[map_atom_disp, rot_atom].flatten()).reshape(3,3)
# f2= similarity_transformation(rot_cartesian.T,force_constants[map_atom_disp,rot_atom])
# diff=np.abs(f1-f2)
# assert diff.max()<1e-7
force_constants[atom_disp, i] += similarity_transformation(
rot_cartesian.T,
force_constants[map_atom_disp,
rot_atom])