def diag_kpts(self, kpts, vec=0, pmk=0, elec_field=0.):
"""
kpts: the coordinates of kpoints
vec: whether to calculate the eigen vectors
pmk: whether to calculate PMK for effective band structure
elec_field: the electric field perpendicular to graphane plane
fname: the file saveing results
"""
if pmk:
from tBG.fortran.spec_func import get_pk
val_out = []
vec_out = []
pmk_out = []
i = 1
if vec or pmk:
vec_calc = 1
else:
vec_calc = 0
for k in kpts:
print('%s/%s k' % (i, len(kpts)))
Hk = self.hamilt_cell_diff(k, elec_field)
vals, vecs, info = zheev(Hk, vec_calc)
if info:
raise ValueError('zheev failed')
if pmk:
Pk = get_pk(k,
np.array(self.layer_nsites) / 2, [1, 1], 2, 2,
vecs, self.coords, self.species())
pmk_out.append(Pk)
val_out.append(vals)
if vec:
vec_out.append(vecs)
i = i + 1
return np.array(val_out), np.array(vec_out), np.array(pmk_out)
def diag_hamiltonian(H):
vals = []
vecs = []
for i in [0, 1]:
val, vec, info = zheev(H[i], 1)
if info:
raise ValueError('lapack in scipy zheev failed!')
vals.append(val)
vecs.append(vec)
return vals, vecs
def diag_Hamiltonian(self, fname='EIGEN', vec=True):
"""
fname: the file saving the eigenvalues and eigenvectors
vec: True or False, whether eigenvectors are calculated
E: the electric field strength eV/Angstrom
"""
if vec:
vec_calc = 1
else:
vec_calc = 0
H = self.get_Hamiltonian()
vals, vecs, info = zheev(H, vec_calc)
if info:
raise ValueError('zheev failed')
if vec:
np.savez_compressed(fname, vals=vals, vecs=vecs)
else:
np.savez_compressed(fname, vals=vals)
def calculate_eigensystem_unfolded(self, only_eigenvals=False):
q_point = self.q_point
scell = self.supercell
atoms = self.atoms
cell = atoms.cell
n_unit_cell = atoms.positions.shape[0]
positions = atoms.positions
fc_s = self.second.dynmat.numpy()
fc_s = fc_s.reshape(
(n_unit_cell, 3, scell[0], scell[1], scell[2], n_unit_cell, 3))
sc_r_pos = self.second.supercell_positions
sc_r_pos_norm = 1 / 2 * np.linalg.norm(sc_r_pos, axis=1)**2
dyn_s = np.zeros((n_unit_cell, 3, n_unit_cell, 3), dtype=np.complex)
tt = self.second.supercell_replicas
for ind in range(tt.shape[0]):
t = tt[ind]
replica_position = np.tensordot(t, cell, (-1, 0))
for iat in np.arange(n_unit_cell):
for jat in np.arange(n_unit_cell):
distance = replica_position + (positions[iat, :] -
positions[jat, :])
projection = (np.dot(sc_r_pos, distance) -
sc_r_pos_norm[:])
if ((projection <= 1e-6).all()):
neq = (np.abs(projection) <= 1e-6).sum()
weight = 1.0 / (neq)
qr = 2. * np.pi * np.dot(q_point[:], t[:])
for ipol in np.arange(3):
for jpol in np.arange(3):
dyn_s[iat, ipol, jat,
jpol] += fc_s[jat, jpol, t[0], t[1],
t[2], iat, ipol] * np.exp(
-1j * qr) * weight
dyn = dyn_s[...].reshape((n_unit_cell * 3, n_unit_cell * 3))
omega2, eigenvect, info = zheev(dyn)
frequency = np.sign(omega2) * np.sqrt(np.abs(omega2))
frequency = frequency[:] / np.pi / 2
if only_eigenvals:
esystem = (frequency[:] * np.pi * 2)**2
else:
esystem = np.vstack(((frequency[:] * np.pi * 2)**2, eigenvect))
return esystem
def diag_kpts(self, kpts, vec=0):
"""
kpts: the coordinates of kpoints
vec: whether to calculate the eigen vectors
fname: the file saveing results
"""
val_out = []
vec_out = []
i = 1
if vec:
vec_calc = 1
else:
vec_calc = 0
for k in kpts:
print('%s/%s k' % (i, len(kpts)))
Hk = self.get_Hamiltonian_at_k(k)
vals, vecs, info = zheev(Hk, vec_calc)
if info:
raise ValueError('zheev failed')
val_out.append(vals)
if vec:
vec_out.append(vecs)
i = i + 1
return np.array(val_out), np.array(vec_out)
def diag_hamiltonian(H_mat):
vals, vecs, info = zheev(H_mat, 1)
if info:
raise ValueError('lapack in scipy zheev failed!')
return vals, vecs
