def read_doses(self):
"""
Return a |AttrDict| with the DOSes available in the file. Empty dict if
DOSes are not available.
"""
if "gruns_nomega" not in self.rootgrp.dimensions:
cprint("File `%s` does not contain ph-DOSes, returning empty dict" % self.path, "yellow")
return {}
# Read q-point sampling used to compute DOSes.
qptrlatt = self.read_value("gruns_qptrlatt")
shifts = self.read_value("gruns_shiftq")
qsampling = KSamplingInfo.from_kptrlatt(qptrlatt, shifts, kptopt=1)
frac_coords_ibz = self.read_value("gruns_qibz")
weights = self.read_value("gruns_wtq")
qpoints = IrredZone(self.structure.reciprocal_lattice, frac_coords_ibz,
weights=weights, names=None, ksampling=qsampling)
# DOSes are in 1/Hartree.
d = AttrDict(wmesh=self.read_value("gruns_omega_mesh") * abu.Ha_eV, qpoints=qpoints)
for dos_name in _ALL_DOS_NAMES:
dos_idos = self.read_value(dos_name)
dos_idos[0] *= abu.eV_Ha # Here we convert to eV. IDOS are not changed.
d[dos_name] = dos_idos
return d
def read_doses(self):
"""
Return a |AttrDict| with the DOSes available in the file. Empty dict if
DOSes are not available.
"""
if "gruns_nomega" not in self.rootgrp.dimensions:
cprint("File `%s` does not contain ph-DOSes, returning empty dict" % self.path, "yellow")
return {}
# Read q-point sampling used to compute DOSes.
qptrlatt = self.read_value("gruns_qptrlatt")
shifts = self.read_value("gruns_shiftq")
qsampling = KSamplingInfo.from_kptrlatt(qptrlatt, shifts, kptopt=1)
frac_coords_ibz = self.read_value("gruns_qibz")
weights = self.read_value("gruns_wtq")
qpoints = IrredZone(self.structure.reciprocal_lattice, frac_coords_ibz,
weights=weights, names=None, ksampling=qsampling)
# DOSes are in 1/Hartree.
d = AttrDict(wmesh=self.read_value("gruns_omega_mesh") * abu.Ha_eV, qpoints=qpoints)
for dos_name in _ALL_DOS_NAMES:
dos_idos = self.read_value(dos_name)
dos_idos[0] *= abu.eV_Ha # Here we convert to eV. IDOS are not changed.
d[dos_name] = dos_idos
return d
def test_ksampling(self):
"""Test KsamplingInfo API."""
# from_mpdivs constructor
mpdivs, shifts = [2, 3, 4], [0.5, 0.5, 0.5]
kptopt = 1
ksi = KSamplingInfo.from_mpdivs(mpdivs, shifts, kptopt)
self.assert_equal(ksi.mpdivs, mpdivs)
self.assert_equal(ksi.kptrlatt, np.diag(mpdivs))
self.assert_equal(ksi.shifts.flatten(), shifts)
assert ksi.kptopt == kptopt
assert ksi.is_homogeneous
print(ksi)
# from kptrlatt constructor
kptrlatt = np.diag(mpdivs)
ksi = KSamplingInfo.from_kptrlatt(kptrlatt, shifts, kptopt)
self.assert_equal(ksi.kptrlatt, np.diag(mpdivs))
self.assert_equal(ksi.mpdivs, np.diag(ksi.kptrlatt))
self.assert_equal(ksi.shifts.flatten(), shifts)
assert ksi.kptopt == kptopt
assert ksi.is_homogeneous
print(ksi)
# kptrlatt with non-zero off-diagonal elements.
shifts = [0.5, 0.5, 0.5]
kptrlatt = [1, 1, 1, 2, 2, 2, 3, 3, 3]
kptopt = 1
ksi = KSamplingInfo.from_kptrlatt(kptrlatt, shifts, kptopt)
assert ksi.mpdivs is None
print(ksi)
# from_kbounds constructor
kbounds = [0, 0, 0, 1, 1, 1]
ksi = KSamplingInfo.from_kbounds(kbounds)
assert (ksi.mpdivs, ksi.kptrlatt, ksi.kptrlatt_orig, ksi.shifts,
ksi.shifts_orig) == 5 * (None, )
assert ksi.kptopt == 1
assert not ksi.is_homogeneous
print(ksi)
with self.assertRaises(ValueError):
foo = KSamplingInfo(foo=1)
def test_ksampling(self):
"""Test KsamplingInfo API."""
with self.assertRaises(ValueError):
KSamplingInfo(foo=1)
# from_mpdivs constructor
mpdivs, shifts = [2, 3, 4], [0.5, 0.5, 0.5]
kptopt = 1
ksi = KSamplingInfo.from_mpdivs(mpdivs, shifts, kptopt)
repr(ksi)
str(ksi)
self.assert_equal(ksi.mpdivs, mpdivs)
self.assert_equal(ksi.kptrlatt, np.diag(mpdivs))
self.assert_equal(ksi.shifts.flatten(), shifts)
assert ksi.shifts.shape == (1, 3)
assert ksi.kptopt == kptopt
assert ksi.is_mesh
assert ksi.has_diagonal_kptrlatt
assert not ksi.is_path
# from kptrlatt constructor
kptrlatt = np.diag(mpdivs)
ksi = KSamplingInfo.from_kptrlatt(kptrlatt, shifts, kptopt)
repr(ksi)
str(ksi)
assert ksi.kptrlatt.shape == (3, 3)
self.assert_equal(ksi.kptrlatt, np.diag(mpdivs))
self.assert_equal(ksi.mpdivs, np.diag(ksi.kptrlatt))
self.assert_equal(ksi.shifts.flatten(), shifts)
assert ksi.kptopt == kptopt
assert ksi.is_mesh
assert ksi.has_diagonal_kptrlatt
assert not ksi.is_path
# kptrlatt with non-zero off-diagonal elements.
shifts = [0.5, 0.5, 0.5]
kptrlatt = [1, 1, 1, 2, 2, 2, 3, 3, 3]
kptopt = 1
ksi = KSamplingInfo.from_kptrlatt(kptrlatt, shifts, kptopt)
repr(ksi)
str(ksi)
assert ksi.mpdivs is None
assert not ksi.has_diagonal_kptrlatt
assert not ksi.is_path
# from_kbounds constructor
kbounds = [0, 0, 0, 1, 1, 1]
ksi = KSamplingInfo.from_kbounds(kbounds)
repr(ksi)
str(ksi)
assert (ksi.mpdivs, ksi.kptrlatt, ksi.kptrlatt_orig, ksi.shifts,
ksi.shifts_orig) == 5 * (None, )
assert ksi.kptopt == -1
assert ksi.kptrlatt is None
assert not ksi.is_mesh
assert not ksi.has_diagonal_kptrlatt
assert ksi.is_path
assert ksi is KSamplingInfo.as_ksampling(ksi)
ksi_from_dict = KSamplingInfo.as_ksampling(
{k: v
for k, v in ksi.items()})
assert ksi_from_dict.kptopt == ksi.kptopt
ksi_none = KSamplingInfo.as_ksampling(None)
repr(ksi_none)
str(ksi_none)
assert ksi_none.kptopt == 0
assert not ksi_none.is_mesh
assert not ksi_none.is_path
def test_ksampling(self):
"""Test KsamplingInfo API."""
with self.assertRaises(ValueError):
KSamplingInfo(foo=1)
# from_mpdivs constructor
mpdivs, shifts = [2, 3, 4], [0.5, 0.5, 0.5]
kptopt = 1
ksi = KSamplingInfo.from_mpdivs(mpdivs, shifts, kptopt)
repr(ksi); str(ksi)
self.assert_equal(ksi.mpdivs, mpdivs)
self.assert_equal(ksi.kptrlatt, np.diag(mpdivs))
self.assert_equal(ksi.shifts.flatten(), shifts)
assert ksi.shifts.shape == (1, 3)
assert ksi.kptopt == kptopt
assert ksi.is_mesh
assert ksi.has_diagonal_kptrlatt
assert not ksi.is_path
# from kptrlatt constructor
kptrlatt = np.diag(mpdivs)
ksi = KSamplingInfo.from_kptrlatt(kptrlatt, shifts, kptopt)
repr(ksi); str(ksi)
assert ksi.kptrlatt.shape == (3, 3)
self.assert_equal(ksi.kptrlatt, np.diag(mpdivs))
self.assert_equal(ksi.mpdivs, np.diag(ksi.kptrlatt))
self.assert_equal(ksi.shifts.flatten(), shifts)
assert ksi.kptopt == kptopt
assert ksi.is_mesh
assert ksi.has_diagonal_kptrlatt
assert not ksi.is_path
# kptrlatt with non-zero off-diagonal elements.
shifts = [0.5, 0.5, 0.5]
kptrlatt = [1, 1, 1, 2, 2, 2, 3, 3, 3]
kptopt = 1
ksi = KSamplingInfo.from_kptrlatt(kptrlatt, shifts, kptopt)
repr(ksi); str(ksi)
assert ksi.mpdivs is None
assert not ksi.has_diagonal_kptrlatt
assert not ksi.is_path
# from_kbounds constructor
kbounds = [0, 0, 0, 1, 1, 1]
ksi = KSamplingInfo.from_kbounds(kbounds)
repr(ksi); str(ksi)
assert (ksi.mpdivs, ksi.kptrlatt, ksi.kptrlatt_orig, ksi.shifts, ksi.shifts_orig) == 5 * (None,)
assert ksi.kptopt == -1
assert ksi.kptrlatt is None
assert not ksi.is_mesh
assert not ksi.has_diagonal_kptrlatt
assert ksi.is_path
assert ksi is KSamplingInfo.as_ksampling(ksi)
ksi_from_dict = KSamplingInfo.as_ksampling({k: v for k, v in ksi.items()})
assert ksi_from_dict.kptopt == ksi.kptopt
ksi_none = KSamplingInfo.as_ksampling(None)
repr(ksi_none); str(ksi_none)
assert ksi_none.kptopt == 0
assert not ksi_none.is_mesh
assert not ksi_none.is_path