def _run_c_dynamical_matrix(self, q):
import phonopy._phonopy as phonoc
fc = self._force_constants
vectors = self._smallest_vectors
mass = self._pcell.get_masses()
multiplicity = self._multiplicity
size_prim = len(mass)
dm = np.zeros((size_prim * 3, size_prim * 3),
dtype=self._dtype_complex)
if fc.shape[0] == fc.shape[1]: # full FC
phonoc.dynamical_matrix(dm.view(dtype='double'), fc,
np.array(q, dtype='double'), vectors,
multiplicity, mass, self._s2p_map,
self._p2s_map)
else:
phonoc.dynamical_matrix(
dm.view(dtype='double'), fc, np.array(q, dtype='double'),
vectors, multiplicity, mass, self._s2pp_map,
np.arange(len(self._p2s_map), dtype='intc'))
# Data of dm array are stored in memory by the C order of
# (size_prim * 3, size_prim * 3, 2), where the last 2 means
# real and imaginary parts. This code assumes this memory
# order is that expected by numpy. Otherwise, numpy complex array
# should be created as follows:
# dm_double = dm.view(dtype='double').reshape(size_prim * 3,
# size_prim * 3, 2)
# dm = dm_double[:, :, 0] + 1j * dm_double[:, :, 1]
self._dynamical_matrix = dm
def _set_c_dynamical_matrix(self, q):
import phonopy._phonopy as phonoc
fc = self._force_constants
vectors = self._smallest_vectors
mass = self._pcell.get_masses()
multiplicity = self._multiplicity
size_prim = len(mass)
itemsize = self._force_constants.itemsize
dm = np.zeros((size_prim * 3, size_prim * 3),
dtype=("c%d" % (itemsize * 2)))
phonoc.dynamical_matrix(dm.view(dtype='double'), fc,
np.array(q, dtype='double'), vectors,
multiplicity, mass, self._s2p_map,
self._p2s_map)
self._dynamical_matrix = dm
def _set_c_dynamical_matrix(self, q):
import phonopy._phonopy as phonoc
fc = self._force_constants
vectors = self._smallest_vectors
mass = self._pcell.get_masses()
multiplicity = self._multiplicity
size_prim = len(mass)
size_super = fc.shape[0]
dynamical_matrix_real = np.zeros((size_prim * 3, size_prim * 3),
dtype='double')
dynamical_matrix_image = np.zeros_like(dynamical_matrix_real)
phonoc.dynamical_matrix(dynamical_matrix_real, dynamical_matrix_image,
fc, np.array(q, dtype='double'), vectors,
multiplicity, mass, self._s2p_map,
self._p2s_map)
dm = dynamical_matrix_real + dynamical_matrix_image * 1j
self._dynamical_matrix = (dm + dm.conj().transpose()) / 2
def _set_c_dynamical_matrix(self, q):
import phonopy._phonopy as phonoc
fc = self._force_constants
vectors = self._smallest_vectors
mass = self._pcell.get_masses()
multiplicity = self._multiplicity
size_prim = len(mass)
itemsize = self._force_constants.itemsize
dm = np.zeros((size_prim * 3, size_prim * 3),
dtype=("c%d" % (itemsize * 2)))
phonoc.dynamical_matrix(dm.view(dtype='double'),
fc,
np.array(q, dtype='double'),
vectors,
multiplicity,
mass,
self._s2p_map,
self._p2s_map)
self._dynamical_matrix = dm
def _set_c_dynamical_matrix(self, q):
import phonopy._phonopy as phonoc
fc = self._force_constants
vectors = self._smallest_vectors
mass = self._pcell.get_masses()
multiplicity = self._multiplicity
size_prim = len(mass)
itemsize = self._force_constants.itemsize
dm = np.zeros((size_prim * 3, size_prim * 3),
dtype=("c%d" % (itemsize * 2)))
if fc.shape[0] == fc.shape[1]: # full FC
phonoc.dynamical_matrix(dm.view(dtype='double'),
fc,
np.array(q, dtype='double'),
vectors,
multiplicity,
mass,
self._s2p_map,
self._p2s_map)
else:
phonoc.dynamical_matrix(
dm.view(dtype='double'),
fc,
np.array(q, dtype='double'),
vectors,
multiplicity,
mass,
self._s2pp_map,
np.arange(len(self._p2s_map), dtype='intc'))
# Data of dm array are stored in memory by the C order of
# (size_prim * 3, size_prim * 3, 2), where the last 2 means
# real and imaginary parts. This code assumes this memory
# order is that expected by numpy. Otherwise, numpy complex array
# should be created as follows:
# dm_double = dm.view(dtype='double').reshape(size_prim * 3,
# size_prim * 3, 2)
# dm = dm_double[:, :, 0] + 1j * dm_double[:, :, 1]
self._dynamical_matrix = dm
def set_c_dynamical_matrix(self, q):
import phonopy._phonopy as phonoc
fc = self.force_constants
vectors = self.smallest_vectors
mass = self.pcell.get_masses()
multiplicity = self.multiplicity
size_prim = len( mass )
size_super = fc.shape[0]
dynamical_matrix_real = np.zeros((size_prim * 3, size_prim * 3), dtype=float)
dynamical_matrix_image = np.zeros((size_prim * 3, size_prim * 3), dtype=float)
phonoc.dynamical_matrix( dynamical_matrix_real,
dynamical_matrix_image,
fc,
np.array(q),
vectors,
multiplicity,
mass,
np.array(self.s2p_map),
np.array(self.p2s_map) )
dm = dynamical_matrix_real + dynamical_matrix_image * 1j
self.dynamical_matrix = (dm + dm.conj().transpose()) / 2
def _set_c_dynamical_matrix(self, q):
import phonopy._phonopy as phonoc
fc = self._force_constants
vectors = self._smallest_vectors
mass = self._pcell.get_masses()
multiplicity = self._multiplicity
size_prim = len(mass)
size_super = fc.shape[0]
dynamical_matrix_real = np.zeros((size_prim * 3, size_prim * 3),
dtype='double')
dynamical_matrix_image = np.zeros_like(dynamical_matrix_real)
phonoc.dynamical_matrix(dynamical_matrix_real,
dynamical_matrix_image,
fc,
np.array(q, dtype='double'),
vectors,
multiplicity,
mass,
self._s2p_map,
self._p2s_map)
dm = dynamical_matrix_real + dynamical_matrix_image * 1j
self._dynamical_matrix = (dm + dm.conj().transpose()) / 2
