def _set_gruneisen(self):
dV = self._volume_plus - self._volume_minus
# dV1 = self._volume - self._volume_minus
# dV2 = self._volume_plus - self._volume
if self._is_band_connection:
self._q_direction = self._qpoints[0] - self._qpoints[-1]
dD = []
# ddD = [] # For dg/dV
eigvals = []
for i, q in enumerate(self._qpoints):
if (self._is_band_connection and self._dynmat.is_nac()):
self._dynmat.set_dynamical_matrix(
q, q_direction=self._q_direction)
else:
self._dynmat.set_dynamical_matrix(q)
dm = self._dynmat.get_dynamical_matrix()
eigvals_at_q, eigvecs = np.linalg.eigh(dm)
eigvals_at_q = eigvals_at_q.real
dD_at_q = [
np.vdot(
eig,
np.dot(
self._get_dD(q, self._dynmat_minus, self._dynmat_plus),
eig)).real for eig in eigvecs.T
]
# dD_minus = self._get_dD(q, self._dynmat_minus, self._dynmat)
# dD_plus = self._get_dD(q, self._dynmat, self._dynmat_plus)
# ddD_at_q = [
# np.vdot(eig, np.dot(dD_plus / dV2 - dD_minus / dV1 , eig)).real
# for eig in eigvecs.T]
if self._is_band_connection:
if self._prev_eigvecs is not None:
self._band_order = estimate_band_connection(
self._prev_eigvecs, eigvecs, self._band_order)
eigvals.append([eigvals_at_q[b] for b in self._band_order])
dD.append([dD_at_q[b] for b in self._band_order])
# ddD.append([ddD_at_q[b] for b in self._band_order])
self._prev_eigvecs = eigvecs
else:
eigvals.append(eigvals_at_q)
dD.append(dD_at_q)
# ddD.append(ddD_at_q)
dD = np.array(dD, dtype='double', order='C')
# ddD = np.array(ddD, dtype='double', order='C')
eigvals = np.array(eigvals, dtype='double', order='C')
self._gruneisen = -dD / dV / eigvals * self._volume / 2
# self._gamma_prime = -ddD / (dV / 2) / eigvals * self._volume ** 2 / 2
self._eigenvalues = eigvals
def _set_gruneisen(self):
dV = self._volume_plus - self._volume_minus
# dV1 = self._volume - self._volume_minus
# dV2 = self._volume_plus - self._volume
if self._is_band_connection:
self._q_direction = self._qpoints[0] - self._qpoints[-1]
dD = []
# ddD = [] # For dg/dV
eigvals = []
for i, q in enumerate(self._qpoints):
if (self._is_band_connection and
self._dynmat.is_nac()):
self._dynmat.set_dynamical_matrix(
q, q_direction=self._q_direction)
else:
self._dynmat.set_dynamical_matrix(q)
dm = self._dynmat.get_dynamical_matrix()
eigvals_at_q, eigvecs = np.linalg.eigh(dm)
eigvals_at_q = eigvals_at_q.real
dD_at_q = [np.vdot(eig, np.dot(
self._get_dD(q, self._dynmat_minus, self._dynmat_plus), eig)
).real for eig in eigvecs.T]
# dD_minus = self._get_dD(q, self._dynmat_minus, self._dynmat)
# dD_plus = self._get_dD(q, self._dynmat, self._dynmat_plus)
# ddD_at_q = [
# np.vdot(eig, np.dot(dD_plus / dV2 - dD_minus / dV1 , eig)).real
# for eig in eigvecs.T]
if self._is_band_connection:
if self._prev_eigvecs is not None:
self._band_order = estimate_band_connection(
self._prev_eigvecs,
eigvecs,
self._band_order)
eigvals.append([eigvals_at_q[b] for b in self._band_order])
dD.append([dD_at_q[b] for b in self._band_order])
# ddD.append([ddD_at_q[b] for b in self._band_order])
self._prev_eigvecs = eigvecs
else:
eigvals.append(eigvals_at_q)
dD.append(dD_at_q)
# ddD.append(ddD_at_q)
dD = np.array(dD, dtype='double', order='C')
# ddD = np.array(ddD, dtype='double', order='C')
eigvals = np.array(eigvals, dtype='double', order='C')
self._gruneisen = -dD / dV / eigvals * self._volume / 2
# self._gamma_prime = -ddD / (dV / 2) / eigvals * self._volume ** 2 / 2
self._eigenvalues = eigvals
def _set_band_connection(self):
nqpoint, nband = self._frequencies.shape
is_non_degenerate = np.all(self._degenerates == np.arange(nband), axis=1)
connect_done = np.zeros(nqpoint, dtype='bool')
start = np.where(is_non_degenerate)[0][0]
while True:
connect_done[start] = True
neighbors = np.argsort(np.sum(np.abs(self._grid_address - self._grid_address[start]), axis=1))
undone = np.extract(connect_done[neighbors]==False, neighbors)
if not (len(undone) == 0 or (is_non_degenerate[undone] == False).all()):
new = np.extract(is_non_degenerate[undone], undone)[0]
new_neighbors = np.argsort(np.sum(np.abs(self._grid_address - self._grid_address[new]), axis=1))
new_neighbor_done = np.extract(connect_done[new_neighbors], new_neighbors)[0]
bo = estimate_band_connection(self._eigenvectors[new_neighbor_done],
self._eigenvectors[new],
np.arange(nband))
if bo is not None:
self._frequencies[new] = (self._frequencies[new])[bo]
self._eigenvectors[new] = (self._eigenvectors[new].T)[bo].T
# Since all the phonons here are non-degenerate, the step is missed
start = new
else:
break
for new in undone:
new_neighbors = np.argsort(np.sum(np.abs(self._grid_address - self._grid_address[new]), axis=1))
new_neighbor_done = np.extract(connect_done[new_neighbors], new_neighbors)[0]
deg = [np.where(self._degenerates[new] == j)[0] for j in np.unique(self._degenerates[new])]
bo = estimate_band_connection(self._eigenvectors[new_neighbor_done],
self._eigenvectors[new],
np.arange(nband),
degenerate_sets=deg)
if bo is not None:
self._frequencies[new] = (self._frequencies[new])[bo]
self._eigenvectors[new] = (self._eigenvectors[new].T)[bo].T
self._degenerates[new] = (self._degenerates[new])[bo].copy()
def _set_gruneisen(self):
dV = self._volume_plus - self._volume_minus
if self._is_band_connection:
self._q_direction = self._qpoints[0] - self._qpoints[-1]
band_order = range(self._dynmat.get_dimension())
prev_eigvecs = None
edDe = [] # <e|dD|e>
eigvals = []
eigvecs = []
for i, q in enumerate(self._qpoints):
if self._is_band_connection and self._dynmat.is_nac():
self._dynmat.set_dynamical_matrix(
q, q_direction=self._q_direction)
else:
self._dynmat.set_dynamical_matrix(q)
dm = self._dynmat.get_dynamical_matrix()
evals, evecs = np.linalg.eigh(dm)
evals_at_q = evals.real
dD = self._get_dD(q, self._dynmat_minus, self._dynmat_plus)
evecs_at_q, edDe_at_q = rotate_eigenvectors(evals_at_q, evecs, dD)
if self._is_band_connection:
if prev_eigvecs is not None:
band_order = estimate_band_connection(
prev_eigvecs,
evecs_at_q,
band_order)
eigvals.append(evals_at_q[band_order])
eigvecs.append(evecs_at_q[:, band_order])
edDe.append(edDe_at_q[band_order])
prev_eigvecs = evecs_at_q
else:
eigvals.append(evals_at_q)
eigvecs.append(evecs_at_q)
edDe.append(edDe_at_q)
edDe = np.array(edDe, dtype='double', order='C')
self._eigenvalues = np.array(eigvals, dtype='double', order='C')
itemsize = self._eigenvalues.itemsize
self._eigenvectors = np.array(eigvecs,
dtype=("c%d" % (itemsize * 2)), order='C')
self._gruneisen = -edDe / dV / self._eigenvalues * self._volume / 2
def _set_gruneisen(self):
if self._is_band_connection:
self._q_direction = self._qpoints[0] - self._qpoints[-1]
band_order = range(len(self._dynmat.primitive) * 3)
prev_eigvecs = None
edDe = [] # <e|dD|e>
eigvals = []
eigvecs = []
for i, q in enumerate(self._qpoints):
if self._is_band_connection and self._dynmat.is_nac():
self._dynmat.run(q, q_direction=self._q_direction)
else:
self._dynmat.run(q)
dm = self._dynmat.dynamical_matrix
evals, evecs = np.linalg.eigh(dm)
evals_at_q = evals.real
dD = self._get_dD(q, self._dynmat_minus, self._dynmat_plus)
evecs_at_q, edDe_at_q = rotate_eigenvectors(evals_at_q, evecs, dD)
if self._is_band_connection:
if prev_eigvecs is not None:
band_order = estimate_band_connection(
prev_eigvecs, evecs_at_q, band_order
)
eigvals.append(evals_at_q[band_order])
eigvecs.append(evecs_at_q[:, band_order])
edDe.append(edDe_at_q[band_order])
prev_eigvecs = evecs_at_q
else:
eigvals.append(evals_at_q)
eigvecs.append(evecs_at_q)
edDe.append(edDe_at_q)
edDe = np.array(edDe, dtype="double", order="C")
self._eigenvalues = np.array(eigvals, dtype="double", order="C")
itemsize = self._eigenvalues.itemsize
self._eigenvectors = np.array(
eigvecs, dtype=("c%d" % (itemsize * 2)), order="C"
)
self._gruneisen = -edDe / self._delta_strain / self._eigenvalues / 2
def _set_gruneisen(self):
if self._is_band_connection:
self._q_direction = self._qpoints[0] - self._qpoints[-1]
dD = []
eigvals = []
for i, q in enumerate(self._qpoints):
if (self._is_band_connection and
self._dynmat.is_nac()):
self._dynmat.set_dynamical_matrix(
q, q_direction=self._q_direction)
else:
self._dynmat.set_dynamical_matrix(q)
dm = self._dynmat.get_dynamical_matrix()
eigvals_at_q, eigvecs = np.linalg.eigh(dm)
eigvals_at_q = eigvals_at_q.real
dD_at_q = [np.vdot(eig, np.dot(self._get_dD(q), eig)).real
for eig in eigvecs.T]
if self._is_band_connection:
if self._prev_eigvecs is not None:
self._band_order = estimate_band_connection(
self._prev_eigvecs,
eigvecs,
self._band_order)
eigvals.append([eigvals_at_q[b] for b in self._band_order])
dD.append([dD_at_q[b] for b in self._band_order])
self._prev_eigvecs = eigvecs
else:
eigvals.append(eigvals_at_q)
dD.append(dD_at_q)
dD = np.array(dD)
eigvals = np.array(eigvals)
self._gruneisen = -dD / eigvals * self._volume / self._dV / 2
self._eigenvalues = eigvals
