def test_is_diagonal(self):
"""Testing is_diagonal"""
from abipy.core.kpoints import is_diagonal
assert is_diagonal(np.eye(3, dtype=np.int))
assert is_diagonal(np.eye(3, dtype=np.float))
a = np.eye(3, dtype=np.float)
atol = 1e-12
a[1, 2] = atol
assert is_diagonal(a, atol=atol)
assert not is_diagonal(a, atol=atol / 2)
def test_is_diagonal(self):
"""Testing is_diagonal"""
from abipy.core.kpoints import is_diagonal
assert is_diagonal(np.eye(3, dtype=np.int))
assert is_diagonal(np.eye(3, dtype=np.float))
a = np.eye(3, dtype=np.float)
atol = 1e-12
a[1, 2] = atol
assert is_diagonal(a, atol=atol)
assert not is_diagonal(a, atol=atol / 2)
def to_string(self, verbose=0):
"""String representation."""
lines = []; app = lines.append
app(marquee("File Info", mark="="))
app(self.filestat(as_string=True))
app("")
app(self.structure.to_string(verbose=verbose, title="Structure"))
app("")
app(self.ebands.to_string(with_structure=False, title="Electronic Bands"))
app("Direct lattice of the primitive cell:")
to_s = lambda x: "%0.6f" % x
app("abc : " + " ".join([to_s(i).rjust(10) for i in self.pc_lattice.abc]))
app("angles: " + " ".join([to_s(i).rjust(10) for i in self.pc_lattice.angles]))
if is_diagonal(self.fold_matrix):
app("Diagonal folding: %s" % (str(np.diagonal(self.fold_matrix))))
else:
app("Folding matrix: %s" % str(self.fold_matrix))
if verbose:
app(self.uf_kpoints.to_string(verbose=verbose, title="Unfolded k-points"))
if verbose > 2:
app(self.hdr.to_string(verbose=verbose, title="Abinit Header"))
return "\n".join(lines)
def __init__(self, filepath):
super(Fold2BlochNcfile, self).__init__(filepath)
self.reader = ElectronsReader(filepath)
# Initialize the electron bands from file.
# Spectral weights are dimensioned with `nss`
# Fortran arrays.
# nctkarr_t("reduced_coordinates_of_unfolded_kpoints", "dp", "number_of_reduced_dimensions, nk_unfolded")
# nctkarr_t("unfolded_eigenvalues", "dp", "max_number_of_states, nk_unfolded, number_of_spins")
# nctkarr_t("spectral_weights", "dp", "max_number_of_states, nk_unfolded, nsppol_times_nspinor")
self._ebands = self.reader.read_ebands()
self.nss = max(self.nsppol, self.nspinor)
self.fold_matrix = self.reader.read_value("fold_matrix")
# Compute direct lattice of the primitive cell from fold_matrix.
if is_diagonal(self.fold_matrix):
folds = np.diagonal(self.fold_matrix)
self.pc_lattice = Lattice((self.structure.lattice.matrix.T * (1.0 / folds)).T.copy())
else:
raise NotImplementedError("non diagonal fold_matrix: %s" % str(self.fold_matrix))
# Read fold2bloch output data.
self.uf_kfrac_coords = self.reader.read_value("reduced_coordinates_of_unfolded_kpoints")
self.uf_kpoints = KpointList(self.pc_lattice.reciprocal_lattice, self.uf_kfrac_coords)
self.uf_nkpt = len(self.uf_kpoints)
def __init__(self, filepath):
super(Fold2BlochNcfile, self).__init__(filepath)
self.reader = ElectronsReader(filepath)
# Initialize the electron bands from file.
# Spectral weights are dimensioned with `nss`
# Fortran arrays.
# nctkarr_t("reduced_coordinates_of_unfolded_kpoints", "dp", "number_of_reduced_dimensions, nk_unfolded")
# nctkarr_t("unfolded_eigenvalues", "dp", "max_number_of_states, nk_unfolded, number_of_spins")
# nctkarr_t("spectral_weights", "dp", "max_number_of_states, nk_unfolded, nsppol_times_nspinor")
self._ebands = self.reader.read_ebands()
self.nss = max(self.nsppol, self.nspinor)
self.fold_matrix = self.reader.read_value("fold_matrix")
# Compute direct lattice of the primitive cell from fold_matrix.
if is_diagonal(self.fold_matrix):
folds = np.diagonal(self.fold_matrix)
self.pc_lattice = Lattice(
(self.structure.lattice.matrix.T * (1.0 / folds)).T.copy())
else:
raise NotImplementedError("non diagonal fold_matrix: %s" %
str(self.fold_matrix))
# Read fold2bloch output data.
self.uf_kfrac_coords = self.reader.read_value(
"reduced_coordinates_of_unfolded_kpoints")
self.uf_kpoints = KpointList(self.pc_lattice.reciprocal_lattice,
self.uf_kfrac_coords)
self.uf_nkpt = len(self.uf_kpoints)
def to_string(self, verbose=0):
"""String representation."""
lines = []
app = lines.append
app(marquee("File Info", mark="="))
app(self.filestat(as_string=True))
app("")
app(self.structure.to_string(verbose=verbose, title="Structure"))
app("")
app(
self.ebands.to_string(with_structure=False,
title="Electronic Bands"))
app("Direct lattice of the primitive cell:")
to_s = lambda x: "%0.6f" % x
app("abc : " +
" ".join([to_s(i).rjust(10) for i in self.pc_lattice.abc]))
app("angles: " +
" ".join([to_s(i).rjust(10) for i in self.pc_lattice.angles]))
if is_diagonal(self.fold_matrix):
app("Diagonal folding: %s" % (str(np.diagonal(self.fold_matrix))))
else:
app("Folding matrix: %s" % str(self.fold_matrix))
if verbose:
app(
self.uf_kpoints.to_string(verbose=verbose,
title="Unfolded k-points"))
if verbose > 2:
app(self.hdr.to_string(verbose=verbose, title="Abinit Header"))
return "\n".join(lines)
