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(ScrReader, self).__init__(filepath)
# Read and store important quantities.
self.structure = self.read_structure()
qred_coords = self.read_value("qpoints_dielectric_function")
self.qpoints = KpointList(self.structure.reciprocal_lattice,
qred_coords)
self.wpts = self.read_value("frequencies_dielectric_function",
cmode="c")
def test_kpointlist(self):
"""Test KpointList."""
lattice = self.lattice
frac_coords = [0, 0, 0, 1/2, 1/2, 1/2, 1/3, 1/3, 1/3]
weights = [0.1, 0.2, 0.7]
klist = KpointList(lattice, frac_coords, weights=weights)
repr(klist); str(klist)
self.serialize_with_pickle(klist, protocols=[-1])
self.assertMSONable(klist, test_if_subclass=False)
self.assert_equal(klist.frac_coords.flatten(), frac_coords)
self.assert_equal(klist.get_cart_coords(), np.reshape([k.cart_coords for k in klist], (-1, 3)))
assert klist.sum_weights() == 1
assert len(klist) == 3
for i, kpoint in enumerate(klist):
assert kpoint in klist
assert klist.count(kpoint) == 1
assert klist.find(kpoint) == i
# Changing the weight of the Kpoint object should change the weights of klist.
for kpoint in klist: kpoint.set_weight(1.0)
assert np.all(klist.weights == 1.0)
# Test find_closest
iclose, kclose, dist = klist.find_closest([0, 0, 0])
assert iclose == 0 and dist == 0.
iclose, kclose, dist = klist.find_closest(Kpoint([0.001, 0.002, 0.003], klist.reciprocal_lattice))
assert iclose == 0
self.assert_almost_equal(dist, 0.001984943324127921)
# Compute mapping k_index --> (k + q)_index, g0
k2kqg = klist.get_k2kqg_map((0, 0, 0))
assert all(ikq == ik for ik, (ikq, g0) in k2kqg.items())
k2kqg = klist.get_k2kqg_map((1/2, 1/2, 1/2))
assert len(k2kqg) == 2
assert k2kqg[0][0] == 1 and np.all(k2kqg[0][1] == 0)
assert k2kqg[1][0] == 0 and np.all(k2kqg[1][1] == 1)
frac_coords = [0, 0, 0, 1/2, 1/3, 1/3]
other_klist = KpointList(lattice, frac_coords)
# Test __add__
add_klist = klist + other_klist
for k in itertools.chain(klist, other_klist):
assert k in add_klist
assert add_klist.count([0,0,0]) == 2
# Remove duplicated k-points.
add_klist = add_klist.remove_duplicated()
assert add_klist.count([0,0,0]) == 1
assert len(add_klist) == 4
assert add_klist == add_klist.remove_duplicated()
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(ScrReader, self).__init__(filepath)
# Read and store important quantities.
self.structure = self.read_structure()
qfrac_coords = self.read_value("qpoints_dielectric_function")
self.kpoints = KpointList(self.structure.reciprocal_lattice,
qfrac_coords)
self.wpoints = self.read_value("frequencies_dielectric_function",
cmode="c")
self.ng = self.read_dimvalue(
"number_of_coefficients_dielectric_function")
# Find number of real/imaginary frequencies.
self.nw = len(self.wpoints)
self.nrew = self.nw
self.nimw = 0
for i, w in enumerate(self.wpoints):
if np.iscomplex(w):
self.nrew = i
break
self.nimw = self.nw - self.nrew
if self.nimw and not np.all(np.iscomplex(
self.wpoints[self.nrew + 1:])):
raise ValueError(
"wpoints should contained real points packed in the first positions\n"
"followed by imaginary points but got: %s" % str(self.wpoints))
# Define self.netcdf_name from the data available on file.
nfound = 0
netcdf_names = [
"polarizability", "dielectric_function",
"inverse_dielectric_function"
]
for tryname in netcdf_names:
if tryname in self.rootgrp.variables:
self.netcdf_name = tryname
nfound += 1
if nfound == 0:
raise RuntimeError("Cannot find `%s` in netcdf file" %
str(netcdf_names))
if nfound > 1:
raise RuntimeError(
"Find multiple netcdf arrays (%s) in netcdf file!" %
str(netcdf_names))
def __init__(self, filepath):
super(ScrReader, self).__init__(filepath)
# Read and store important quantities.
self.structure = self.read_structure()
qred_coords = self.read_value("qpoints_dielectric_function")
self.qpoints = KpointList(self.structure.reciprocal_lattice, qred_coords)
self.wpts = self.read_value("frequencies_dielectric_function", cmode="c")
class ScrReader(ETSF_Reader):
"""
This object reads the results stored in the SCR (Screening) file produced by ABINIT.
It provides helper functions to access the most important quantities.
"""
def __init__(self, filepath):
super(ScrReader, self).__init__(filepath)
# Read and store important quantities.
self.structure = self.read_structure()
qred_coords = self.read_value("qpoints_dielectric_function")
self.qpoints = KpointList(self.structure.reciprocal_lattice, qred_coords)
self.wpts = self.read_value("frequencies_dielectric_function", cmode="c")
#def read_params(self):
# """
# Read the most importan parameters used to generate the data, i.e.
# the parameters that may be subject to convergence studies.
# Returns:
# :class:`AttrDict` a dictionary whose keys can be accessed
# with the dot notation i.e. d.key.
# """
# keys = ["npwwfn_used", "nbands_used",]
# return AttrDict({k: self.read_value(k) for k in keys})
def find_qpoint_fileindex(self, qpoint):
"""
Returns the q-point and the index of in the netcdf file.
Accepts `Kpoint` instance or integer
Raise:
`KpointsError` if qpoint cannot be found.
"""
if isinstance(qpoint, int):
iq = qpoint
else:
iq = self.qpoints.index(qpoint)
return self.qpoints[iq], iq
def read_wggfunc(self, qpoint, cls):
"""
Read data at the given q-point and return an instance
of `cls` where `cls` is a subclass of `WGGFunction`
"""
qpoint, iq = self.find_qpoint_fileindex(qpoint)
# TODO: I don't remember how to slice in python-netcdf
# ecuteps
all_gvecs = self.read_value("reduced_coordinates_plane_waves_dielectric_function")
ecuteps = 2
# TODO: Gpshere.find is very slow if we don't take advantage of shells
gsphere = GSphere(ecuteps, self.structure.reciprocal_lattice, qpoint, all_gvecs[iq])
full_wggmat = self.read_value(cls.etsf_name, cmode="c")
wggmat = full_wggmat[iq]
return cls(qpoint, self.wpts, gsphere, wggmat, inord="F")
def test_kpointlist(self):
"""Test KpointList."""
lattice = self.lattice
frac_coords = [0, 0, 0, 1/2, 1/2, 1/2, 1/3, 1/3, 1/3]
weights = [0.1, 0.2, 0.7]
klist = KpointList(lattice, frac_coords, weights=weights)
self.assertTrue(klist.sum_weights() == 1)
self.assertTrue(len(klist) == 3)
for i, kpoint in enumerate(klist):
self.assertTrue(kpoint in klist)
self.assertTrue(klist.count(kpoint) == 1)
self.assertTrue(klist.find(kpoint) == i)
# Changing the weight of the Kpoint object shoul change the weights of klist.
for kpoint in klist: kpoint.set_weight(1.0)
self.assertTrue(np.all(klist.weights == 1.0))
def test_kpointlist(self):
"""Test KpointList."""
lattice = self.lattice
frac_coords = [0, 0, 0, 1/2, 1/2, 1/2, 1/3, 1/3, 1/3]
weights = [0.1, 0.2, 0.7]
klist = KpointList(lattice, frac_coords, weights=weights)
self.serialize_with_pickle(klist, protocols=[-1])
self.assertMSONable(klist, test_if_subclass=False)
self.assertTrue(klist.sum_weights() == 1)
self.assertTrue(len(klist) == 3)
for i, kpoint in enumerate(klist):
self.assertTrue(kpoint in klist)
self.assertTrue(klist.count(kpoint) == 1)
self.assertTrue(klist.find(kpoint) == i)
# Changing the weight of the Kpoint object should change the weights of klist.
for kpoint in klist: kpoint.set_weight(1.0)
self.assertTrue(np.all(klist.weights == 1.0))
frac_coords = [0, 0, 0, 1/2, 1/3, 1/3]
other_klist = KpointList(lattice, frac_coords)
# Test __add__
add_klist = klist + other_klist
for k in itertools.chain(klist, other_klist):
self.assertTrue(k in add_klist)
self.assertTrue(add_klist.count([0,0,0]) == 2)
# Remove duplicated k-points.
add_klist = add_klist.remove_duplicated()
self.assertTrue(add_klist.count([0,0,0]) == 1)
self.assertTrue(len(add_klist) == 4)
self.assertTrue(add_klist == add_klist.remove_duplicated())
def test_kpointlist(self):
"""Test KpointList."""
lattice = self.lattice
frac_coords = [0, 0, 0, 1 / 2, 1 / 2, 1 / 2, 1 / 3, 1 / 3, 1 / 3]
weights = [0.1, 0.2, 0.7]
klist = KpointList(lattice, frac_coords, weights=weights)
self.serialize_with_pickle(klist, protocols=[-1])
self.assertMSONable(klist, test_if_subclass=False)
assert klist.sum_weights() == 1
assert len(klist) == 3
for i, kpoint in enumerate(klist):
assert kpoint in klist
assert klist.count(kpoint) == 1
assert klist.find(kpoint) == i
# Changing the weight of the Kpoint object should change the weights of klist.
for kpoint in klist:
kpoint.set_weight(1.0)
assert np.all(klist.weights == 1.0)
# Test find_closest
iclose, kclose, dist = klist.find_closest([0, 0, 0])
assert iclose == 0 and dist == 0.
iclose, kclose, dist = klist.find_closest(
Kpoint([0.001, 0.002, 0.003], klist.reciprocal_lattice))
assert iclose == 0
self.assert_almost_equal(dist, 0.001984943324127921)
frac_coords = [0, 0, 0, 1 / 2, 1 / 3, 1 / 3]
other_klist = KpointList(lattice, frac_coords)
# Test __add__
add_klist = klist + other_klist
for k in itertools.chain(klist, other_klist):
assert k in add_klist
assert add_klist.count([0, 0, 0]) == 2
# Remove duplicated k-points.
add_klist = add_klist.remove_duplicated()
self.assertTrue(add_klist.count([0, 0, 0]) == 1)
self.assertTrue(len(add_klist) == 4)
self.assertTrue(add_klist == add_klist.remove_duplicated())
def from_file(cls, filepath):
"""Create the object from a netCDF file."""
with PHBST_Reader(filepath) as r:
structure = r.read_structure()
# Build the list of q-points
qpoints = KpointList(structure.reciprocal_lattice,
frac_coords=r.read_qredcoords(),
weights=r.read_qweights(),
names=None)
return cls(structure=structure,
qpoints=qpoints,
phfreqs=r.read_phfreqs(),
phdispl_cart=r.read_phdispl_cart())
def __init__(self, filepath):
super(DdbFile, self).__init__(filepath)
self._header = self._parse_header()
self._structure = Structure.from_abivars(**self.header)
# Add Spacegroup (needed in guessed_ngkpt)
# FIXME: has_timerev is always True
spgid, has_timerev, h = 0, True, self.header
self._structure.set_spacegroup(SpaceGroup(spgid, h.symrel, h.tnons, h.symafm, has_timerev))
frac_coords = self._read_qpoints()
self._qpoints = KpointList(self.structure.reciprocal_lattice, frac_coords, weights=None, names=None)
# Guess q-mesh
self._guessed_ngqpt = self._guess_ngqpt()
def __init__(self, filepath):
super(ScrReader, self).__init__(filepath)
# Read and store important quantities.
self.structure = self.read_structure()
qfrac_coords = self.read_value("qpoints_dielectric_function")
self.kpoints = KpointList(self.structure.reciprocal_lattice, qfrac_coords)
self.wpoints = self.read_value("frequencies_dielectric_function", cmode="c")
self.ng = self.read_dimvalue("number_of_coefficients_dielectric_function")
# Find number of real/imaginary frequencies.
self.nw = len(self.wpoints)
self.nrew = self.nw
self.nimw = 0
for i, w in enumerate(self.wpoints):
if np.iscomplex(w):
self.nrew = i
break
self.nimw = self.nw - self.nrew
if self.nimw and not np.all(np.iscomplex(self.wpoints[self.nrew+1:])):
raise ValueError("wpoints should contained real points packed in the first positions\n"
"followed by imaginary points but got: %s" % str(self.wpoints))
# Define self.netcdf_name from the data available on file.
nfound = 0
netcdf_names = ["polarizability", "dielectric_function", "inverse_dielectric_function"]
for tryname in netcdf_names:
if tryname in self.rootgrp.variables:
self.netcdf_name = tryname
nfound += 1
if nfound == 0:
raise RuntimeError("Cannot find `%s` in netcdf file" % str(netcdf_names))
if nfound > 1:
raise RuntimeError("Find multiple netcdf arrays (%s) in netcdf file!" % str(netcdf_names))
def test_kpointlist(self):
"""Test KpointList."""
lattice = self.lattice
frac_coords = [0, 0, 0, 1/2, 1/2, 1/2, 1/3, 1/3, 1/3]
weights = [0.1, 0.2, 0.7]
klist = KpointList(lattice, frac_coords, weights=weights)
self.assertTrue(klist.sum_weights() == 1)
self.assertTrue(len(klist) == 3)
for i, kpoint in enumerate(klist):
self.assertTrue(kpoint in klist)
self.assertTrue(klist.count(kpoint) == 1)
self.assertTrue(klist.find(kpoint) == i)
# Changing the weight of the Kpoint object should change the weights of klist.
for kpoint in klist: kpoint.set_weight(1.0)
self.assertTrue(np.all(klist.weights == 1.0))
frac_coords = [0, 0, 0, 1/2, 1/3, 1/3]
other_klist = KpointList(lattice, frac_coords)
# Test __add__
add_klist = klist + other_klist
for k in itertools.chain(klist, other_klist):
self.assertTrue(k in add_klist)
self.assertTrue(add_klist.count([0,0,0]) == 2)
# Remove duplicated k-points.
add_klist = add_klist.remove_duplicated()
self.assertTrue(add_klist.count([0,0,0]) == 1)
self.assertTrue(len(add_klist) == 4)
self.assertTrue(add_klist == add_klist.remove_duplicated())
def qpoints(self):
return KpointList(self.structure.reciprocal_lattice,
frac_coords=self.reader.read_value("qpts"))
class SigresReader(ETSF_Reader):
"""This object provides method to read data from the SIGRES file produced ABINIT.
# See 70gw/m_sigma_results.F90
# Name of the diagonal matrix elements stored in the file.
# b1gw:b2gw,nkibz,nsppol*nsig_ab))
#_DIAGO_MELS = [
# "sigxme",
# "vxcme",
# "vUme",
# "dsigmee0",
# "sigcmee0",
# "sigxcme",
# "ze0",
#]
integer :: b1gw,b2gw ! min and Max gw band indeces over spin and k-points (used to dimension)
integer :: gwcalctyp ! Flag defining the calculation type.
integer :: nkptgw ! No. of points calculated
integer :: nkibz ! No. of irreducible k-points.
integer :: nbnds ! Total number of bands
integer :: nomega_r ! No. of real frequencies for the spectral function.
integer :: nomega_i ! No. of frequencies along the imaginary axis.
integer :: nomega4sd ! No. of real frequencies to evaluate the derivative of $\Sigma(E)$.
integer :: nsig_ab ! 1 if nspinor=1,4 for noncollinear case.
integer :: nsppol ! No. of spin polarizations.
integer :: usepawu ! 1 if we are using LDA+U as starting point (only for PAW)
real(dp) :: deltae ! Frequency step for the calculation of d\Sigma/dE
real(dp) :: maxomega4sd ! Max frequency around E_ks for d\Sigma/dE.
real(dp) :: maxomega_r ! Max frequency for spectral function.
real(dp) :: scissor_ene ! Scissor energy value. zero for None.
integer,pointer :: maxbnd(:,:)
! maxbnd(nkptgw,nsppol)
! Max band index considered in GW for this k-point.
integer,pointer :: minbnd(:,:)
! minbnd(nkptgw,nsppol)
! Min band index considered in GW for this k-point.
real(dp),pointer :: degwgap(:,:)
! degwgap(nkibz,nsppol)
! Difference btw the QPState and the KS optical gap.
real(dp),pointer :: egwgap(:,:)
! egwgap(nkibz,nsppol))
! QPState optical gap at each k-point and spin.
real(dp),pointer :: en_qp_diago(:,:,:)
! en_qp_diago(nbnds,nkibz,nsppol))
! QPState energies obtained from the diagonalization of the Hermitian approximation to Sigma (QPSCGW)
real(dp),pointer :: e0(:,:,:)
! e0(nbnds,nkibz,nsppol)
! KS eigenvalues for each band, k-point and spin. In case of self-consistent?
real(dp),pointer :: e0gap(:,:)
! e0gap(nkibz,nsppol),
! KS gap at each k-point, for each spin.
real(dp),pointer :: omega_r(:)
! omega_r(nomega_r)
! real frequencies used for the self energy.
real(dp),pointer :: kptgw(:,:)
! kptgw(3,nkptgw)
! ! TODO there is a similar array in sigma_parameters
! List of calculated k-points.
real(dp),pointer :: sigxme(:,:,:)
! sigxme(b1gw:b2gw,nkibz,nsppol*nsig_ab))
! Diagonal matrix elements of $\Sigma_x$ i.e $\<nks|\Sigma_x|nks\>$
real(dp),pointer :: vxcme(:,:,:)
! vxcme(b1gw:b2gw,nkibz,nsppol*nsig_ab))
! $\<nks|v_{xc}[n_val]|nks\>$ matrix elements of vxc (valence-only contribution).
real(dp),pointer :: vUme(:,:,:)
! vUme(b1gw:b2gw,nkibz,nsppol*nsig_ab))
! $\<nks|v_{U}|nks\>$ for LDA+U.
complex(dpc),pointer :: degw(:,:,:)
! degw(b1gw:b2gw,nkibz,nsppol))
! Difference between the QPState and the KS energies.
complex(dpc),pointer :: dsigmee0(:,:,:)
! dsigmee0(b1gw:b2gw,nkibz,nsppol*nsig_ab))
! Derivative of $\Sigma_c(E)$ calculated at the KS eigenvalue.
complex(dpc),pointer :: egw(:,:,:)
! egw(nbnds,nkibz,nsppol))
! QPState energies, $\epsilon_{nks}^{QPState}$.
complex(dpc),pointer :: eigvec_qp(:,:,:,:)
! eigvec_qp(nbnds,nbnds,nkibz,nsppol))
! Expansion of the QPState amplitude in the KS basis set.
complex(dpc),pointer :: hhartree(:,:,:,:)
! hhartree(b1gw:b2gw,b1gw:b2gw,nkibz,nsppol*nsig_ab)
! $\<nks|T+v_H+v_{loc}+v_{nl}|mks\>$
complex(dpc),pointer :: sigcme(:,:,:,:)
! sigcme(b1gw:b2gw,nkibz,nomega_r,nsppol*nsig_ab))
! $\<nks|\Sigma_{c}(E)|nks\>$ at each nomega_r frequency
complex(dpc),pointer :: sigmee(:,:,:)
! sigmee(b1gw:b2gw,nkibz,nsppol*nsig_ab))
! $\Sigma_{xc}E_{KS} + (E_{QPState}- E_{KS})*dSigma/dE_KS
complex(dpc),pointer :: sigcmee0(:,:,:)
! sigcmee0(b1gw:b2gw,nkibz,nsppol*nsig_ab))
! Diagonal mat. elements of $\Sigma_c(E)$ calculated at the KS energy $E_{KS}$
complex(dpc),pointer :: sigcmesi(:,:,:,:)
! sigcmesi(b1gw:b2gw,nkibz,nomega_i,nsppol*nsig_ab))
! Matrix elements of $\Sigma_c$ along the imaginary axis.
! Only used in case of analytical continuation.
complex(dpc),pointer :: sigcme4sd(:,:,:,:)
! sigcme4sd(b1gw:b2gw,nkibz,nomega4sd,nsppol*nsig_ab))
! Diagonal matrix elements of \Sigma_c around the zeroth order eigenvalue (usually KS).
complex(dpc),pointer :: sigxcme(:,:,:,:)
! sigxme(b1gw:b2gw,nkibz,nomega_r,nsppol*nsig_ab))
! $\<nks|\Sigma_{xc}(E)|nks\>$ at each real frequency frequency.
complex(dpc),pointer :: sigxcmesi(:,:,:,:)
! sigxcmesi(b1gw:b2gw,nkibz,nomega_i,nsppol*nsig_ab))
! Matrix elements of $\Sigma_{xc}$ along the imaginary axis.
! Only used in case of analytical continuation.
complex(dpc),pointer :: sigxcme4sd(:,:,:,:)
! sigxcme4sd(b1gw:b2gw,nkibz,nomega4sd,nsppol*nsig_ab))
! Diagonal matrix elements of \Sigma_xc for frequencies around the zeroth order eigenvalues.
complex(dpc),pointer :: ze0(:,:,:)
! ze0(b1gw:b2gw,nkibz,nsppol))
! renormalization factor. $(1-\dfrac{\partial\Sigma_c} {\partial E_{KS}})^{-1}$
complex(dpc),pointer :: omega_i(:)
! omegasi(nomega_i)
! Frequencies along the imaginary axis used for the analytical continuation.
complex(dpc),pointer :: omega4sd(:,:,:,:)
! omega4sd(b1gw:b2gw,nkibz,nomega4sd,nsppol).
! Frequencies used to evaluate the Derivative of Sigma.
"""
def __init__(self, path):
self.ks_bands = ElectronBands.from_file(path)
self.nsppol = self.ks_bands.nsppol
super(SigresReader, self).__init__(path)
try:
self.nomega_r = self.read_dimvalue("nomega_r")
except self.Error:
self.nomega_r = 0
#self.nomega_i = self.read_dim("nomega_i")
# Save important quantities needed to simplify the API.
self.structure = self.read_structure()
self.gwcalctyp = self.read_value("gwcalctyp")
self.usepawu = self.read_value("usepawu")
# 1) The K-points of the homogeneous mesh.
self.ibz = self.ks_bands.kpoints
# 2) The K-points where QPState corrections have been calculated.
gwred_coords = self.read_redc_gwkpoints()
self.gwkpoints = KpointList(self.structure.reciprocal_lattice, gwred_coords)
# minbnd[nkptgw,nsppol] gives the minimum band index computed
# Note conversion between Fortran and python convention.
self.gwbstart_sk = self.read_value("minbnd") - 1
self.gwbstop_sk = self.read_value("maxbnd")
# min and Max band index for GW corrections.
self.min_gwbstart = np.min(self.gwbstart_sk)
self.max_gwbstart = np.max(self.gwbstart_sk)
self.min_gwbstop = np.min(self.gwbstop_sk)
self.max_gwbstop = np.max(self.gwbstop_sk)
self._egw = self.read_value("egw", cmode="c")
# Read and save important matrix elements.
# All these arrays are dimensioned
# vxcme(b1gw:b2gw,nkibz,nsppol*nsig_ab))
self._vxcme = self.read_value("vxcme")
self._sigxme = self.read_value("sigxme")
self._hhartree = self.read_value("hhartree", cmode="c")
self._vUme = self.read_value("vUme")
#if self.usepawu == 0: self._vUme.fill(0.0)
# Complex arrays
self._sigcmee0 = self.read_value("sigcmee0", cmode="c")
self._ze0 = self.read_value("ze0", cmode="c")
# Frequencies for the spectral function.
if self.has_spfunc:
self._omega_r = self.read_value("omega_r")
self._sigcme = self.read_value("sigcme", cmode="c")
self._sigxcme = self.read_value("sigxcme", cmode="c")
# Self-consistent case
self._en_qp_diago = self.read_value("en_qp_diago")
# <KS|QPState>
self._eigvec_qp = self.read_value("eigvec_qp", cmode="c")
#self._mlda_to_qp
#def is_selfconsistent(self, mode):
# return self.gwcalctyp
@property
def has_spfunc(self):
"""True if self contains the spectral function."""
return self.nomega_r
def kpt2fileindex(self, kpoint):
"""
Helper function that returns the index of kpoint in the netcdf file.
Accepts `Kpoint` instance or integer
Raise:
`KpointsError` if kpoint cannot be found.
.. note::
This function is needed since arrays in the netcdf file are dimensioned
with the total number of k-points in the IBZ.
"""
if isinstance(kpoint, int):
return kpoint
#kpoint = self.gwkpoints[kpoint]
try:
return self.ibz.index(kpoint)
except:
raise
def gwkpt2seqindex(self, gwkpoint):
"""
This function returns the index of the GW k-point in (0:nkptgw)
Used to access data in the arrays that are dimensioned [0:nkptgw] e.g. minbnd.
"""
if isinstance(gwkpoint, int):
return gwkpoint
else:
return self.gwkpoints.index(gwkpoint)
def read_redc_gwkpoints(self):
return self.read_value("kptgw")
def read_allqps(self):
qps_spin = self.nsppol * [None]
for spin in range(self.nsppol):
qps = []
for gwkpoint in self.gwkpoints:
ik = self.gwkpt2seqindex(gwkpoint)
bands = range(self.gwbstart_sk[spin,ik], self.gwbstop_sk[spin,ik])
for band in bands:
qps.append(self.read_qp(spin, gwkpoint, band))
qps_spin[spin] = QPList(qps)
return tuple(qps_spin)
def read_qplist_sk(self, spin, kpoint):
ik = self.gwkpt2seqindex(kpoint)
bstart, bstop = self.gwbstart_sk[spin, ik], self.gwbstop_sk[spin, ik]
return QPList([self.read_qp(spin, kpoint, band) for band in range(bstart, bstop)])
#def read_qpene(self, spin, kpoint, band)
def read_qpenes(self):
return self._egw[:, :, :]
def read_qp(self, spin, kpoint, band):
ik_file = self.kpt2fileindex(kpoint)
ib_file = band - self.gwbstart_sk[spin, self.gwkpt2seqindex(kpoint)]
return QPState(
spin=spin,
kpoint=kpoint,
band=band,
e0=self.read_e0(spin, ik_file, band),
qpe=self._egw[spin, ik_file, band],
qpe_diago=self._en_qp_diago[spin, ik_file, band],
vxcme=self._vxcme[spin, ik_file, ib_file],
sigxme=self._sigxme[spin, ik_file, ib_file],
sigcmee0=self._sigcmee0[spin, ik_file, ib_file],
vUme=self._vUme[spin, ik_file, ib_file],
ze0=self._ze0[spin, ik_file, ib_file],
)
def read_qpgaps(self):
"""Read the QP gaps. Returns ndarray with shape [nsppol, nkibz] in eV"""
return self.read_value("egwgap")
def read_e0(self, spin, kfile, band):
return self.ks_bands.eigens[spin, kfile, band]
def read_sigmaw(self, spin, kpoint, band):
"""Returns the real and the imaginary part of the self energy."""
if not self.has_spfunc:
raise ValueError("%s does not contain spectral function data" % self.path)
ik = self.kpt2fileindex(kpoint)
return self._omega_r, self._sigxcme[spin,:,ik,band]
def read_spfunc(self, spin, kpoint, band):
"""
Returns the spectral function.
one/pi * ABS(AIMAG(Sr%sigcme(ib,ikibz,io,is))) /
( (REAL(Sr%omega_r(io)-Sr%hhartree(ib,ib,ikibz,is)-Sr%sigxcme(ib,ikibz,io,is)))**2 &
+(AIMAG(Sr%sigcme(ib,ikibz,io,is)))**2) / Ha_eV,&
"""
if not self.has_spfunc:
raise ValueError("%s does not contain spectral function data" % self.path)
ik = self.kpt2fileindex(kpoint)
ib = band - self.gwbstart_sk[spin, self.gwkpt2seqindex(kpoint)]
aim_sigc = np.abs(self._sigcme[spin,:,ik,ib].imag)
den = np.zeros(self.nomega_r)
for (io, omega) in enumerate(self._omega_r):
den[io] = (omega - self._hhartree[spin,ik,ib,ib].real - self._sigxcme[spin,io,ik,ib].real) ** 2 + \
self._sigcme[spin,io,ik,ib].imag ** 2
return self._omega_r, 1./np.pi * (aim_sigc/den)
def read_eigvec_qp(self, spin, kpoint, band=None):
"""
Returns <KS|QPState> for the given spin, kpoint and band. If band is None, <KS_b|QP_{b'}> is returned.
"""
ik = self.kpt2fileindex(kpoint)
if band is not None:
return self._eigvec_qp[spin,ik,:,band]
else:
return self._eigvec_qp[spin,ik,:,:]
def read_params(self):
"""
Read the parameters of the calculation.
Returns :class:`AttrDict` instance with the value of the parameters.
"""
param_names = [
"ecutwfn",
"ecuteps",
"ecutsigx",
"scr_nband",
"sigma_nband",
"gwcalctyp",
"scissor_ene",
]
params = AttrDict()
for pname in param_names:
params[pname] = self.read_value(pname, default=None)
# Other quantities that might be subject to convergence studies.
params["nkibz"] = len(self.ibz)
return params
def print_qps(self, spin=None, kpoints=None, bands=None, fmt=None, stream=sys.stdout):
"""
Args:
spin: Spin index, if None all spins are considered
kpoints: List of k-points to select. Default: all kpoints
bands: List of bands to select. Default is all bands
fmt: Format string passe to `to_strdict`
stream: file-like object.
Returns
List of tables.
"""
spins = range(self.nsppol) if spin is None else [spin]
kpoints = self.gwkpoints if kpoints is None else [kpoints]
if bands is not None: bands = [bands]
header = QPState.get_fields(exclude=["spin", "kpoint"])
tables = []
for spin in spins:
for kpoint in kpoints:
table_sk = PrettyTable(header)
if bands is None:
ik = self.gwkpt2seqindex(kpoint)
bands = range(self.gwbstart_sk[spin,ik], self.gwbstop_sk[spin,ik])
for band in bands:
qp = self.read_qp(spin, kpoint, band)
d = qp.to_strdict(fmt=fmt)
table_sk.add_row([d[k] for k in header])
stream.write("\nkpoint: %s, spin: %s, energy units: eV (NB: bands start from zero)\n" % (kpoint, spin))
print(table_sk, file=stream)
stream.write("\n")
# Add it to tables.
tables.append(table_sk)
return tables
class Fold2BlochNcfile(AbinitNcFile, Has_Header, Has_Structure, Has_ElectronBands, NotebookWriter):
"""
Netcdf file with output data produced by Fold2Bloch.
Usage example:
.. code-block:: python
with Fold2BlochNcfile("foo_FOLD2BLOCH.nc") as fb:
fb.plot_unfolded()
.. rubric:: Inheritance Diagram
.. inheritance-diagram:: Fold2BlochNcfile
"""
@classmethod
def from_wfkpath(cls, wfkpath, folds, workdir=None, manager=None, mpi_procs=1, verbose=0):
"""
Run fold2bloch in workdir.
Args:
wfkpath:
folds:
workdir: Working directory of the fake task used to compute the ibz. Use None for temporary dir.
manager: :class:`TaskManager` of the task. If None, the manager is initialized from the config file.
mpi_procs: Number of MPI processors to use.
verbose: Verbosity level.
"""
# Build a simple manager to run the job in a shell subprocess
from abipy import flowtk
manager = flowtk.TaskManager.as_manager(manager).to_shell_manager(mpi_procs=mpi_procs)
fold2bloch = flowtk.Fold2Bloch(manager=manager, verbose=verbose)
# Create temporary directory and link to the WFK file
import tempfile
workdir = tempfile.mkdtemp() if workdir is None else workdir
wfkpath = os.path.abspath(wfkpath)
link = os.path.join(workdir, os.path.basename(wfkpath))
os.symlink(wfkpath, link)
# Run fold2bloch
ncpath = fold2bloch.unfold(link, folds, workdir=workdir)
return cls(ncpath)
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 __str__(self):
return self.to_string()
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)
@property
def ebands(self):
"""|ElectronBands| object with folded band energies."""
return self._ebands
@property
def structure(self):
"""|Structure| object defining the supercell."""
return self.ebands.structure
def close(self):
"""Close the file."""
self.reader.close()
@lazy_property
def params(self):
""":class:`OrderedDict` with parameters that might be subject to convergence studies."""
od = self.get_ebands_params()
return od
@lazy_property
def uf_eigens(self):
"""[nsppol, nk_unfolded, nband] |numpy-array| with unfolded eigenvalues in eV."""
# nctkarr_t("unfolded_eigenvalues", "dp", "max_number_of_states, nk_unfolded, number_of_spins")
return self.reader.read_value("unfolded_eigenvalues") * units.Ha_to_eV
@lazy_property
def uf_weights(self):
"""[nss, nk_unfolded, nband] array with spectral weights. nss = max(nspinor, nsppol)."""
# nctkarr_t("spectral_weights", "dp", "max_number_of_states, nk_unfolded, nsppol_times_nspinor")
return self.reader.read_value("spectral_weights")
def get_spectral_functions(self, step=0.01, width=0.02):
"""
Args:
step: Energy step (eV) of the linear mesh.
width: Standard deviation (eV) of the gaussian.
Return:
mesh, sfw, int_sfw
"""
# Compute linear mesh.
epad = 3.0 * width
e_min = self.uf_eigens.min() - epad
e_max = self.uf_eigens.max() + epad
nw = int(1 + (e_max - e_min) / step)
mesh, step = np.linspace(e_min, e_max, num=nw, endpoint=True, retstep=True)
sfw = np.zeros((self.nss, self.uf_nkpt, nw))
for spin in range(self.nss):
for ik in range(self.uf_nkpt):
for band in range(self.nband):
e = self.uf_eigens[spin, ik, band]
sfw[spin, ik] += self.uf_weights[spin, ik, band] * gaussian(mesh, width, center=e)
from scipy.integrate import cumtrapz
int_sfw = cumtrapz(sfw, x=mesh, initial=0.0)
return dict2namedtuple(mesh=mesh, sfw=sfw, int_sfw=int_sfw)
@add_fig_kwargs
def plot_unfolded(self, kbounds, klabels, ylims=None, dist_tol=1e-12, verbose=0,
colormap="afmhot", facecolor="black", ax=None, fontsize=12, **kwargs):
r"""
Plot unfolded band structure with spectral weights.
Args:
klabels: dictionary whose keys are tuple with the reduced coordinates of the k-points.
The values are the labels. e.g. ``klabels = {(0.0,0.0,0.0): "$\Gamma$", (0.5,0,0): "L"}``.
ylims: Set the data limits for the y-axis. Accept tuple e.g. ``(left, right)``
or scalar e.g. ``left``. If left (right) is None, default values are used
dist_tol: A point is considered to be on the path if its distance from the line
is less than dist_tol.
verbose: Verbosity level.
colormap: Have a look at the colormaps here and decide which one you like:
http://matplotlib.sourceforge.net/examples/pylab_examples/show_colormaps.html
facecolor:
ax: |matplotlib-Axes| or None if a new figure should be created.
fontsize: Legend and title fontsize.
Returns: |matplotlib-Figure|
"""
cart_bounds = [self.pc_lattice.reciprocal_lattice.get_cartesian_coords(c)
for c in np.reshape(kbounds, (-1, 3))]
uf_cart = self.uf_kpoints.get_cart_coords()
p = find_points_along_path(cart_bounds, uf_cart, dist_tol)
if len(p.ikfound) == 0:
cprint("Warning: find_points_along_path returned zero points along the path. Try to increase dist_tol.", "yellow")
return None
if verbose:
uf_frac_coords = np.reshape([k.frac_coords for k in self.uf_kpoints], (-1, 3))
fcoords = uf_frac_coords[p.ikfound]
print("Found %d points along input k-path" % len(fcoords))
print("k-points of path in reduced coordinates:")
print(fcoords)
fact = 8.0
e0 = self.ebands.fermie
ax, fig, plt = get_ax_fig_plt(ax=ax)
ax.set_facecolor(facecolor)
xs = np.tile(p.dist_list, self.nband)
marker_spin = {0: "^", 1: "v"} if self.nss == 2 else {0: "o"}
for spin in range(self.nss):
ys = self.uf_eigens[spin, p.ikfound, :] - e0
ws = self.uf_weights[spin, p.ikfound, :]
s = ax.scatter(xs, ys.T, s=fact * ws.T, c=ws.T,
marker=marker_spin[spin], label=None if self.nss == 1 else "spin %s" % spin,
linewidth=1, edgecolors='none', cmap=plt.get_cmap(colormap))
plt.colorbar(s, ax=ax, orientation='vertical')
ax.set_xticks(p.path_ticks, minor=False)
ax.set_xticklabels(klabels, fontdict=None, minor=False, size=kwargs.pop("klabel_size", "large"))
ax.grid(True)
ax.set_ylabel('Energy (eV)')
set_axlims(ax, ylims, "y")
if self.nss == 2: ax.legend(loc="best", fontsize=fontsize, shadow=True)
return fig
def yield_figs(self, **kwargs): # pragma: no cover
"""
This function *generates* a predefined list of matplotlib figures with minimal input from the user.
"""
print("TODO: Add call to plot_unfolded")
yield self.ebands.plot(show=False)
def write_notebook(self, nbpath=None):
"""
Write a jupyter_ notebook to nbpath. If `nbpath` is None, a temporay file in the current
working directory is created. Return path to the notebook.
"""
nbformat, nbv, nb = self.get_nbformat_nbv_nb(title=None)
nb.cells.extend([
nbv.new_code_cell("f2b = abilab.abiopen('%s')" % self.filepath),
nbv.new_code_cell("print(f2b)"),
nbv.new_code_cell("f2b.ebands.plot();"),
nbv.new_code_cell("#f2b.unfolded_kpoints.plot();"),
nbv.new_code_cell(r"""\
# kbounds = [0, 1/2, 0, 0, 0, 0, 0, 0, 1/2]
# klabels = ["Y", "$\Gamma$", "X"]
# f2b.plot_unfolded(kbounds, klabels);"""),
])
return self._write_nb_nbpath(nb, nbpath)
def test_kpointlist(self):
"""Test KpointList."""
lattice = self.lattice
frac_coords = [0, 0, 0, 1 / 2, 1 / 2, 1 / 2, 1 / 3, 1 / 3, 1 / 3]
weights = [0.1, 0.2, 0.7]
klist = KpointList(lattice, frac_coords, weights=weights)
repr(klist)
str(klist)
self.serialize_with_pickle(klist, protocols=[-1])
self.assertMSONable(klist, test_if_subclass=False)
self.assert_equal(klist.frac_coords.flatten(), frac_coords)
self.assert_equal(klist.get_cart_coords(),
np.reshape([k.cart_coords for k in klist], (-1, 3)))
assert klist.sum_weights() == 1
assert len(klist) == 3
for i, kpoint in enumerate(klist):
assert kpoint in klist
assert klist.count(kpoint) == 1
assert klist.find(kpoint) == i
# Changing the weight of the Kpoint object should change the weights of klist.
for kpoint in klist:
kpoint.set_weight(1.0)
assert np.all(klist.weights == 1.0)
# Test find_closest
iclose, kclose, dist = klist.find_closest([0, 0, 0])
assert iclose == 0 and dist == 0.
iclose, kclose, dist = klist.find_closest(
Kpoint([0.001, 0.002, 0.003], klist.reciprocal_lattice))
assert iclose == 0
self.assert_almost_equal(dist, 0.001984943324127921)
# Compute mapping k_index --> (k + q)_index, g0
k2kqg = klist.get_k2kqg_map((0, 0, 0))
assert all(ikq == ik for ik, (ikq, g0) in k2kqg.items())
k2kqg = klist.get_k2kqg_map((1 / 2, 1 / 2, 1 / 2))
assert len(k2kqg) == 2
assert k2kqg[0][0] == 1 and np.all(k2kqg[0][1] == 0)
assert k2kqg[1][0] == 0 and np.all(k2kqg[1][1] == 1)
frac_coords = [0, 0, 0, 1 / 2, 1 / 3, 1 / 3]
other_klist = KpointList(lattice, frac_coords)
# Test __add__
add_klist = klist + other_klist
for k in itertools.chain(klist, other_klist):
assert k in add_klist
assert add_klist.count([0, 0, 0]) == 2
# Remove duplicated k-points.
add_klist = add_klist.remove_duplicated()
assert add_klist.count([0, 0, 0]) == 1
assert len(add_klist) == 4
assert add_klist == add_klist.remove_duplicated()
def __init__(self, path):
self.ks_bands = ElectronBands.from_file(path)
self.nsppol = self.ks_bands.nsppol
super(SigresReader, self).__init__(path)
try:
self.nomega_r = self.read_dimvalue("nomega_r")
except self.Error:
self.nomega_r = 0
#self.nomega_i = self.read_dim("nomega_i")
# Save important quantities needed to simplify the API.
self.structure = self.read_structure()
self.gwcalctyp = self.read_value("gwcalctyp")
self.usepawu = self.read_value("usepawu")
# 1) The K-points of the homogeneous mesh.
self.ibz = self.ks_bands.kpoints
# 2) The K-points where QPState corrections have been calculated.
gwred_coords = self.read_redc_gwkpoints()
self.gwkpoints = KpointList(self.structure.reciprocal_lattice, gwred_coords)
# minbnd[nkptgw,nsppol] gives the minimum band index computed
# Note conversion between Fortran and python convention.
self.gwbstart_sk = self.read_value("minbnd") - 1
self.gwbstop_sk = self.read_value("maxbnd")
# min and Max band index for GW corrections.
self.min_gwbstart = np.min(self.gwbstart_sk)
self.max_gwbstart = np.max(self.gwbstart_sk)
self.min_gwbstop = np.min(self.gwbstop_sk)
self.max_gwbstop = np.max(self.gwbstop_sk)
self._egw = self.read_value("egw", cmode="c")
# Read and save important matrix elements.
# All these arrays are dimensioned
# vxcme(b1gw:b2gw,nkibz,nsppol*nsig_ab))
self._vxcme = self.read_value("vxcme")
self._sigxme = self.read_value("sigxme")
self._hhartree = self.read_value("hhartree", cmode="c")
self._vUme = self.read_value("vUme")
#if self.usepawu == 0: self._vUme.fill(0.0)
# Complex arrays
self._sigcmee0 = self.read_value("sigcmee0", cmode="c")
self._ze0 = self.read_value("ze0", cmode="c")
# Frequencies for the spectral function.
if self.has_spfunc:
self._omega_r = self.read_value("omega_r")
self._sigcme = self.read_value("sigcme", cmode="c")
self._sigxcme = self.read_value("sigxcme", cmode="c")
# Self-consistent case
self._en_qp_diago = self.read_value("en_qp_diago")
# <KS|QPState>
self._eigvec_qp = self.read_value("eigvec_qp", cmode="c")
class Fold2BlochNcfile(AbinitNcFile, Has_Header, Has_Structure,
Has_ElectronBands, NotebookWriter):
"""
Netcdf file with output data produced by Fold2Bloch.
Usage example:
.. code-block:: python
with Fold2BlochNcfile("foo_FOLD2BLOCH.nc") as fb:
fb.plot_unfolded()
.. rubric:: Inheritance Diagram
.. inheritance-diagram:: Fold2BlochNcfile
"""
@classmethod
def from_wfkpath(cls,
wfkpath,
folds,
workdir=None,
manager=None,
mpi_procs=1,
verbose=0):
"""
Run fold2bloch in workdir.
Args:
wfkpath:
folds:
workdir: Working directory of the fake task used to compute the ibz. Use None for temporary dir.
manager: :class:`TaskManager` of the task. If None, the manager is initialized from the config file.
mpi_procs: Number of MPI processors to use.
verbose: Verbosity level.
"""
# Build a simple manager to run the job in a shell subprocess
from abipy import flowtk
manager = flowtk.TaskManager.as_manager(manager).to_shell_manager(
mpi_procs=mpi_procs)
fold2bloch = flowtk.Fold2Bloch(manager=manager, verbose=verbose)
# Create temporary directory and link to the WFK file
import tempfile
workdir = tempfile.mkdtemp() if workdir is None else workdir
wfkpath = os.path.abspath(wfkpath)
link = os.path.join(workdir, os.path.basename(wfkpath))
os.symlink(wfkpath, link)
# Run fold2bloch
ncpath = fold2bloch.unfold(link, folds, workdir=workdir)
return cls(ncpath)
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 __str__(self):
return self.to_string()
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)
@property
def ebands(self):
"""|ElectronBands| object with folded band energies."""
return self._ebands
@property
def structure(self):
"""|Structure| object defining the supercell."""
return self.ebands.structure
def close(self):
"""Close the file."""
self.reader.close()
@lazy_property
def params(self):
""":class:`OrderedDict` with parameters that might be subject to convergence studies."""
od = self.get_ebands_params()
return od
@lazy_property
def uf_eigens(self):
"""[nsppol, nk_unfolded, nband] |numpy-array| with unfolded eigenvalues in eV."""
# nctkarr_t("unfolded_eigenvalues", "dp", "max_number_of_states, nk_unfolded, number_of_spins")
return self.reader.read_value("unfolded_eigenvalues") * units.Ha_to_eV
@lazy_property
def uf_weights(self):
"""[nss, nk_unfolded, nband] array with spectral weights. nss = max(nspinor, nsppol)."""
# nctkarr_t("spectral_weights", "dp", "max_number_of_states, nk_unfolded, nsppol_times_nspinor")
return self.reader.read_value("spectral_weights")
def get_spectral_functions(self, step=0.01, width=0.02):
"""
Args:
step: Energy step (eV) of the linear mesh.
width: Standard deviation (eV) of the gaussian.
Return:
mesh, sfw, int_sfw
"""
# Compute linear mesh.
epad = 3.0 * width
e_min = self.uf_eigens.min() - epad
e_max = self.uf_eigens.max() + epad
nw = int(1 + (e_max - e_min) / step)
mesh, step = np.linspace(e_min,
e_max,
num=nw,
endpoint=True,
retstep=True)
sfw = np.zeros((self.nss, self.uf_nkpt, nw))
for spin in range(self.nss):
for ik in range(self.uf_nkpt):
for band in range(self.nband):
e = self.uf_eigens[spin, ik, band]
sfw[spin,
ik] += self.uf_weights[spin, ik, band] * gaussian(
mesh, width, center=e)
from scipy.integrate import cumtrapz
int_sfw = cumtrapz(sfw, x=mesh, initial=0.0)
return dict2namedtuple(mesh=mesh, sfw=sfw, int_sfw=int_sfw)
@add_fig_kwargs
def plot_unfolded(self,
kbounds,
klabels,
ylims=None,
dist_tol=1e-12,
verbose=0,
colormap="afmhot",
facecolor="black",
ax=None,
fontsize=12,
**kwargs):
r"""
Plot unfolded band structure with spectral weights.
Args:
klabels: dictionary whose keys are tuple with the reduced coordinates of the k-points.
The values are the labels. e.g. ``klabels = {(0.0,0.0,0.0): "$\Gamma$", (0.5,0,0): "L"}``.
ylims: Set the data limits for the y-axis. Accept tuple e.g. ``(left, right)``
or scalar e.g. ``left``. If left (right) is None, default values are used
dist_tol: A point is considered to be on the path if its distance from the line
is less than dist_tol.
verbose: Verbosity level.
colormap: Have a look at the colormaps here and decide which one you like:
http://matplotlib.sourceforge.net/examples/pylab_examples/show_colormaps.html
facecolor:
ax: |matplotlib-Axes| or None if a new figure should be created.
fontsize: Legend and title fontsize.
Returns: |matplotlib-Figure|
"""
cart_bounds = [
self.pc_lattice.reciprocal_lattice.get_cartesian_coords(c)
for c in np.reshape(kbounds, (-1, 3))
]
uf_cart = self.uf_kpoints.get_cart_coords()
p = find_points_along_path(cart_bounds, uf_cart, dist_tol)
if len(p.ikfound) == 0:
cprint(
"Warning: find_points_along_path returned zero points along the path. Try to increase dist_tol.",
"yellow")
return None
if verbose:
uf_frac_coords = np.reshape(
[k.frac_coords for k in self.uf_kpoints], (-1, 3))
fcoords = uf_frac_coords[p.ikfound]
print("Found %d points along input k-path" % len(fcoords))
print("k-points of path in reduced coordinates:")
print(fcoords)
fact = 8.0
e0 = self.ebands.fermie
ax, fig, plt = get_ax_fig_plt(ax=ax)
ax.set_facecolor(facecolor)
xs = np.tile(p.dist_list, self.nband)
marker_spin = {0: "^", 1: "v"} if self.nss == 2 else {0: "o"}
for spin in range(self.nss):
ys = self.uf_eigens[spin, p.ikfound, :] - e0
ws = self.uf_weights[spin, p.ikfound, :]
s = ax.scatter(xs,
ys.T,
s=fact * ws.T,
c=ws.T,
marker=marker_spin[spin],
label=None if self.nss == 1 else "spin %s" % spin,
linewidth=1,
edgecolors='none',
cmap=plt.get_cmap(colormap))
plt.colorbar(s, ax=ax, orientation='vertical')
ax.set_xticks(p.path_ticks, minor=False)
ax.set_xticklabels(klabels,
fontdict=None,
minor=False,
size=kwargs.pop("klabel_size", "large"))
ax.grid(True)
ax.set_ylabel('Energy (eV)')
set_axlims(ax, ylims, "y")
if self.nss == 2: ax.legend(loc="best", fontsize=fontsize, shadow=True)
return fig
def yield_figs(self, **kwargs): # pragma: no cover
"""
This function *generates* a predefined list of matplotlib figures with minimal input from the user.
"""
print("TODO: Add call to plot_unfolded")
yield self.ebands.plot(show=False)
def write_notebook(self, nbpath=None):
"""
Write a jupyter_ notebook to nbpath. If `nbpath` is None, a temporay file in the current
working directory is created. Return path to the notebook.
"""
nbformat, nbv, nb = self.get_nbformat_nbv_nb(title=None)
nb.cells.extend([
nbv.new_code_cell("f2b = abilab.abiopen('%s')" % self.filepath),
nbv.new_code_cell("print(f2b)"),
nbv.new_code_cell("f2b.ebands.plot();"),
nbv.new_code_cell("#f2b.unfolded_kpoints.plot();"),
nbv.new_code_cell(r"""\
# kbounds = [0, 1/2, 0, 0, 0, 0, 0, 0, 1/2]
# klabels = ["Y", "$\Gamma$", "X"]
# f2b.plot_unfolded(kbounds, klabels);"""),
])
return self._write_nb_nbpath(nb, nbpath)
def __init__(self, path):
self.ks_bands = ElectronBands.from_file(path)
self.nsppol = self.ks_bands.nsppol
super(SigresReader, self).__init__(path)
try:
self.nomega_r = self.read_dimvalue("nomega_r")
except self.Error:
self.nomega_r = 0
#self.nomega_i = self.read_dim("nomega_i")
# Save important quantities needed to simplify the API.
self.structure = self.read_structure()
self.gwcalctyp = self.read_value("gwcalctyp")
self.usepawu = self.read_value("usepawu")
# 1) The K-points of the homogeneous mesh.
self.ibz = self.ks_bands.kpoints
# 2) The K-points where QPState corrections have been calculated.
gwred_coords = self.read_redc_gwkpoints()
self.gwkpoints = KpointList(self.structure.reciprocal_lattice, gwred_coords)
# minbnd[nkptgw,nsppol] gives the minimum band index computed
# Note conversion between Fortran and python convention.
self.gwbstart_sk = self.read_value("minbnd") - 1
self.gwbstop_sk = self.read_value("maxbnd")
# min and Max band index for GW corrections.
self.min_gwbstart = np.min(self.gwbstart_sk)
self.max_gwbstart = np.max(self.gwbstart_sk)
self.min_gwbstop = np.min(self.gwbstop_sk)
self.max_gwbstop = np.max(self.gwbstop_sk)
self._egw = self.read_value("egw", cmode="c")
# Read and save important matrix elements.
# All these arrays are dimensioned
# vxcme(b1gw:b2gw,nkibz,nsppol*nsig_ab))
self._vxcme = self.read_value("vxcme")
self._sigxme = self.read_value("sigxme")
self._hhartree = self.read_value("hhartree", cmode="c")
self._vUme = self.read_value("vUme")
#if self.usepawu == 0: self._vUme.fill(0.0)
# Complex arrays
self._sigcmee0 = self.read_value("sigcmee0", cmode="c")
self._ze0 = self.read_value("ze0", cmode="c")
# Frequencies for the spectral function.
if self.has_spfunc:
self._omega_r = self.read_value("omega_r")
self._sigcme = self.read_value("sigcme", cmode="c")
self._sigxcme = self.read_value("sigxcme", cmode="c")
# Self-consistent case
self._en_qp_diago = self.read_value("en_qp_diago")
# <KS|QPState>
self._eigvec_qp = self.read_value("eigvec_qp", cmode="c")
class ScrReader(ETSF_Reader):
"""
This object reads the results stored in the SCR (Screening) file produced by ABINIT.
It provides helper functions to access the most important quantities.
double inverse_dielectric_function(number_of_qpoints_dielectric_function,
number_of_frequencies_dielectric_function, number_of_spins, number_of_spins,
number_of_coefficients_dielectric_function, number_of_coefficients_dielectric_function, complex)
.. rubric:: Inheritance Diagram
.. inheritance-diagram:: ScrReader
"""
def __init__(self, filepath):
super(ScrReader, self).__init__(filepath)
# Read and store important quantities.
self.structure = self.read_structure()
qfrac_coords = self.read_value("qpoints_dielectric_function")
self.kpoints = KpointList(self.structure.reciprocal_lattice,
qfrac_coords)
self.wpoints = self.read_value("frequencies_dielectric_function",
cmode="c")
self.ng = self.read_dimvalue(
"number_of_coefficients_dielectric_function")
# Find number of real/imaginary frequencies.
self.nw = len(self.wpoints)
self.nrew = self.nw
self.nimw = 0
for i, w in enumerate(self.wpoints):
if np.iscomplex(w):
self.nrew = i
break
self.nimw = self.nw - self.nrew
if self.nimw and not np.all(np.iscomplex(
self.wpoints[self.nrew + 1:])):
raise ValueError(
"wpoints should contained real points packed in the first positions\n"
"followed by imaginary points but got: %s" % str(self.wpoints))
# Define self.netcdf_name from the data available on file.
nfound = 0
netcdf_names = [
"polarizability", "dielectric_function",
"inverse_dielectric_function"
]
for tryname in netcdf_names:
if tryname in self.rootgrp.variables:
self.netcdf_name = tryname
nfound += 1
if nfound == 0:
raise RuntimeError("Cannot find `%s` in netcdf file" %
str(netcdf_names))
if nfound > 1:
raise RuntimeError(
"Find multiple netcdf arrays (%s) in netcdf file!" %
str(netcdf_names))
def read_params(self):
"""
Read the most important parameters used to compute the screening i.e.
the parameters that may be subject to convergence studies.
Returns:
|AttrDict| a dictionary whose keys can be accessed with the dot notation i.e. ``d.key``.
"""
# TODO: ecuteps is missing!
keys = [
"ikxc", "inclvkb", "gwcalctyp", "nbands_used", "npwwfn_used",
"spmeth", "test_type", "tordering", "awtr", "icutcoul", "gwcomp",
"gwgamma", "mbpt_sciss", "spsmear", "zcut", "gwencomp"
]
def convert(arr):
"""Convert to scalar if size == 1"""
return np.asscalar(arr) if arr.size == 1 else arr
return AttrDict({k: convert(self.read_value(k)) for k in keys})
def read_emacro_lf(self, kpoint=(0, 0, 0)):
"""
Read the macroscopic dielectric function *with* local field effects 1 / em1_{0,0)(kpoint, omega).
Return: |Function1D| object.
"""
if self.netcdf_name == "inverse_dielectric_function":
em1 = self.read_wslice(kpoint, ig1=0, ig2=0)
emacro = 1 / em1[:self.nrew]
else:
raise NotImplementedError(
"emacro_lf with netcdf != InverseDielectricFunction")
return Function1D(np.real(self.wpoints[:self.nrew]).copy(), emacro)
def read_emacro_nlf(self, kpoint=(0, 0, 0)):
"""
Read the macroscopic dielectric function *without* local field effects e_{0,0)(kpoint, omega).
Return: |Function1D|
.. warning::
This function performs the inversion of e-1 to get e.
that can be quite expensive and memory demanding for large matrices!
"""
if self.netcdf_name == "inverse_dielectric_function":
em1 = self.read_wggmat(kpoint)
e = np.linalg.inv(em1.wggmat[:self.nrew, :, :])
else:
raise NotImplementedError(
"emacro_nlf with netcdf != InverseDielectricFunction")
return Function1D(np.real(self.wpoints[:self.nrew]).copy(), e[:, 0, 0])
def read_eelf(self, kpoint=(0, 0, 0)):
"""
Read electron energy loss function
- Im(1/ emacro)
Return: |Function1D| object.
"""
# eelf = -Im(1 / eM)
emacro_lf = self.read_emacro_lf(kpoint=kpoint)
#emacro_lf = self.read_emacro_nlf(kpoint=kpoint)
values = (-1 / emacro_lf.values).imag
return Function1D(emacro_lf.mesh.copy(), values)
def read_wggmat(self, kpoint, spin1=0, spin2=0, cls=None):
"""
Read data at the given k-point and return an instance of ``cls`` where
``cls`` is a subclass of :class:`_AwggMatrix`
"""
cls = _AwggMatrix.class_from_netcdf_name(
self.netcdf_name) if cls is None else cls
var = self.rootgrp.variables[
"reduced_coordinates_plane_waves_dielectric_function"]
# Use ik=0 because the basis set is not k-dependent.
ik0 = 0
gvecs = var[ik0, :]
#print("gvecs", gvecs)
kpoint, ik = self.find_kpoint_fileindex(kpoint)
# FIXME ecuteps is missing
# TODO: Gpshere.find is very slow if we don't take advantage of shells
ecuteps = 2
gsphere = GSphere(ecuteps, self.structure.reciprocal_lattice, kpoint,
gvecs)
# Exchange spin due to F --> C
values = self.rootgrp.variables[self.netcdf_name][ik, :, spin2,
spin1, :, :, :]
wggmat = values[:, :, :, 0] + 1j * values[:, :, :, 1]
return cls(self.wpoints, gsphere, wggmat, inord="F")
def find_kpoint_fileindex(self, kpoint):
"""
Returns the k-point and the index of the k-point in the netcdf file.
Accepts |Kpoint| instance or integer.
"""
if duck.is_intlike(kpoint):
ik = int(kpoint)
else:
ik = self.kpoints.index(kpoint)
return self.kpoints[ik], ik
def read_wslice(self, kpoint, ig1=0, ig2=0, spin1=0, spin2=0):
"""Read slice along the frequency dimension."""
kpoint, ik = self.find_kpoint_fileindex(kpoint)
var = self.rootgrp.variables[self.netcdf_name]
values = var[ik, :, spin2, spin1, ig2,
ig1, :] # Exchange G indices F --> C
return values[:, 0] + 1j * values[:, 1]
class ScrReader(ETSF_Reader):
"""
This object reads the results stored in the SCR (Screening) file produced by ABINIT.
It provides helper functions to access the most important quantities.
"""
def __init__(self, filepath):
super(ScrReader, self).__init__(filepath)
# Read and store important quantities.
self.structure = self.read_structure()
qred_coords = self.read_value("qpoints_dielectric_function")
self.qpoints = KpointList(self.structure.reciprocal_lattice,
qred_coords)
self.wpts = self.read_value("frequencies_dielectric_function",
cmode="c")
#def read_params(self):
# """
# Read the most importan parameters used to generate the data, i.e.
# the parameters that may be subject to convergence studies.
# Returns:
# :class:`AttrDict` a dictionary whose keys can be accessed
# with the dot notation i.e. d.key.
# """
# keys = ["npwwfn_used", "nbands_used",]
# return AttrDict({k: self.read_value(k) for k in keys})
def find_qpoint_fileindex(self, qpoint):
"""
Returns the q-point and the index of in the netcdf file.
Accepts `Kpoint` instance or integer
Raise:
`KpointsError` if qpoint cannot be found.
"""
if isinstance(qpoint, int):
iq = qpoint
else:
iq = self.qpoints.index(qpoint)
return self.qpoints[iq], iq
def read_wggfunc(self, qpoint, cls):
"""
Read data at the given q-point and return an instance
of `cls` where `cls` is a subclass of `WGGFunction`
"""
qpoint, iq = self.find_qpoint_fileindex(qpoint)
# TODO: I don't remember how to slice in python-netcdf
# ecuteps
all_gvecs = self.read_value(
"reduced_coordinates_plane_waves_dielectric_function")
ecuteps = 2
# TODO: Gpshere.find is very slow if we don't take advantage of shells
gsphere = GSphere(ecuteps, self.structure.reciprocal_lattice, qpoint,
all_gvecs[iq])
full_wggmat = self.read_value(cls.etsf_name, cmode="c")
wggmat = full_wggmat[iq]
return cls(qpoint, self.wpts, gsphere, wggmat, inord="F")
class ScrReader(ETSF_Reader):
"""
This object reads the results stored in the SCR (Screening) file produced by ABINIT.
It provides helper functions to access the most important quantities.
double inverse_dielectric_function(number_of_qpoints_dielectric_function,
number_of_frequencies_dielectric_function, number_of_spins, number_of_spins,
number_of_coefficients_dielectric_function, number_of_coefficients_dielectric_function, complex)
.. rubric:: Inheritance Diagram
.. inheritance-diagram:: ScrReader
"""
def __init__(self, filepath):
super(ScrReader, self).__init__(filepath)
# Read and store important quantities.
self.structure = self.read_structure()
qfrac_coords = self.read_value("qpoints_dielectric_function")
self.kpoints = KpointList(self.structure.reciprocal_lattice, qfrac_coords)
self.wpoints = self.read_value("frequencies_dielectric_function", cmode="c")
self.ng = self.read_dimvalue("number_of_coefficients_dielectric_function")
# Find number of real/imaginary frequencies.
self.nw = len(self.wpoints)
self.nrew = self.nw
self.nimw = 0
for i, w in enumerate(self.wpoints):
if np.iscomplex(w):
self.nrew = i
break
self.nimw = self.nw - self.nrew
if self.nimw and not np.all(np.iscomplex(self.wpoints[self.nrew+1:])):
raise ValueError("wpoints should contained real points packed in the first positions\n"
"followed by imaginary points but got: %s" % str(self.wpoints))
# Define self.netcdf_name from the data available on file.
nfound = 0
netcdf_names = ["polarizability", "dielectric_function", "inverse_dielectric_function"]
for tryname in netcdf_names:
if tryname in self.rootgrp.variables:
self.netcdf_name = tryname
nfound += 1
if nfound == 0:
raise RuntimeError("Cannot find `%s` in netcdf file" % str(netcdf_names))
if nfound > 1:
raise RuntimeError("Find multiple netcdf arrays (%s) in netcdf file!" % str(netcdf_names))
def read_params(self):
"""
Read the most important parameters used to compute the screening i.e.
the parameters that may be subject to convergence studies.
Returns:
|AttrDict| a dictionary whose keys can be accessed with the dot notation i.e. ``d.key``.
"""
# TODO: ecuteps is missing!
keys = ["ikxc", "inclvkb", "gwcalctyp", "nbands_used", "npwwfn_used",
"spmeth", "test_type", "tordering", "awtr", "icutcoul", "gwcomp",
"gwgamma", "mbpt_sciss", "spsmear", "zcut", "gwencomp"]
def convert(arr):
"""Convert to scalar if size == 1"""
return np.asscalar(arr) if arr.size == 1 else arr
return AttrDict({k: convert(self.read_value(k)) for k in keys})
def read_emacro_lf(self, kpoint=(0, 0, 0)):
"""
Read the macroscopic dielectric function *with* local field effects 1 / em1_{0,0)(kpoint, omega).
Return: |Function1D| object.
"""
if self.netcdf_name == "inverse_dielectric_function":
em1 = self.read_wslice(kpoint, ig1=0, ig2=0)
emacro = 1 / em1[:self.nrew]
else:
raise NotImplementedError("emacro_lf with netcdf != InverseDielectricFunction")
return Function1D(np.real(self.wpoints[:self.nrew]).copy(), emacro)
def read_emacro_nlf(self, kpoint=(0, 0, 0)):
"""
Read the macroscopic dielectric function *without* local field effects e_{0,0)(kpoint, omega).
Return: |Function1D|
.. warning::
This function performs the inversion of e-1 to get e.
that can be quite expensive and memory demanding for large matrices!
"""
if self.netcdf_name == "inverse_dielectric_function":
em1 = self.read_wggmat(kpoint)
e = np.linalg.inv(em1.wggmat[:self.nrew, :, :])
else:
raise NotImplementedError("emacro_nlf with netcdf != InverseDielectricFunction")
return Function1D(np.real(self.wpoints[:self.nrew]).copy(), e[:, 0, 0])
def read_eelf(self, kpoint=(0, 0, 0)):
"""
Read electron energy loss function
- Im(1/ emacro)
Return: |Function1D| object.
"""
# eelf = -Im(1 / eM)
emacro_lf = self.read_emacro_lf(kpoint=kpoint)
#emacro_lf = self.read_emacro_nlf(kpoint=kpoint)
values = (-1 / emacro_lf.values).imag
return Function1D(emacro_lf.mesh.copy(), values)
def read_wggmat(self, kpoint, spin1=0, spin2=0, cls=None):
"""
Read data at the given k-point and return an instance of ``cls`` where
``cls`` is a subclass of :class:`_AwggMatrix`
"""
cls = _AwggMatrix.class_from_netcdf_name(self.netcdf_name) if cls is None else cls
var = self.rootgrp.variables["reduced_coordinates_plane_waves_dielectric_function"]
# Use ik=0 because the basis set is not k-dependent.
ik0 = 0
gvecs = var[ik0, :]
#print("gvecs", gvecs)
kpoint, ik = self.find_kpoint_fileindex(kpoint)
# FIXME ecuteps is missing
# TODO: Gpshere.find is very slow if we don't take advantage of shells
ecuteps = 2
gsphere = GSphere(ecuteps, self.structure.reciprocal_lattice, kpoint, gvecs)
# Exchange spin due to F --> C
values = self.rootgrp.variables[self.netcdf_name][ik, :, spin2, spin1, :, :, :]
wggmat = values[:, :, :, 0] + 1j * values[:, :, :, 1]
return cls(self.wpoints, gsphere, wggmat, inord="F")
def find_kpoint_fileindex(self, kpoint):
"""
Returns the k-point and the index of the k-point in the netcdf file.
Accepts |Kpoint| instance or integer.
"""
if duck.is_intlike(kpoint):
ik = int(kpoint)
else:
ik = self.kpoints.index(kpoint)
return self.kpoints[ik], ik
def read_wslice(self, kpoint, ig1=0, ig2=0, spin1=0, spin2=0):
"""Read slice along the frequency dimension."""
kpoint, ik = self.find_kpoint_fileindex(kpoint)
var = self.rootgrp.variables[self.netcdf_name]
values = var[ik, :, spin2, spin1, ig2, ig1, :] # Exchange G indices F --> C
return values[:, 0] + 1j * values[:, 1]
def qpoints(self):
"""List of q-points (ndarray)."""
# Read the fractional coordinates and convert them to KpointList.
return KpointList(self.structure.reciprocal_lattice,
frac_coords=self.read_value("qpoints"))
class SigresReader(ETSF_Reader):
"""This object provides method to read data from the SIGRES file produced ABINIT.
# See 70gw/m_sigma_results.F90
# Name of the diagonal matrix elements stored in the file.
# b1gw:b2gw,nkibz,nsppol*nsig_ab))
#_DIAGO_MELS = [
# "sigxme",
# "vxcme",
# "vUme",
# "dsigmee0",
# "sigcmee0",
# "sigxcme",
# "ze0",
#]
integer :: b1gw,b2gw ! min and Max gw band indeces over spin and k-points (used to dimension)
integer :: gwcalctyp ! Flag defining the calculation type.
integer :: nkptgw ! No. of points calculated
integer :: nkibz ! No. of irreducible k-points.
integer :: nbnds ! Total number of bands
integer :: nomega_r ! No. of real frequencies for the spectral function.
integer :: nomega_i ! No. of frequencies along the imaginary axis.
integer :: nomega4sd ! No. of real frequencies to evaluate the derivative of $\Sigma(E)$.
integer :: nsig_ab ! 1 if nspinor=1,4 for noncollinear case.
integer :: nsppol ! No. of spin polarizations.
integer :: usepawu ! 1 if we are using LDA+U as starting point (only for PAW)
real(dp) :: deltae ! Frequency step for the calculation of d\Sigma/dE
real(dp) :: maxomega4sd ! Max frequency around E_ks for d\Sigma/dE.
real(dp) :: maxomega_r ! Max frequency for spectral function.
real(dp) :: scissor_ene ! Scissor energy value. zero for None.
integer,pointer :: maxbnd(:,:)
! maxbnd(nkptgw,nsppol)
! Max band index considered in GW for this k-point.
integer,pointer :: minbnd(:,:)
! minbnd(nkptgw,nsppol)
! Min band index considered in GW for this k-point.
real(dp),pointer :: degwgap(:,:)
! degwgap(nkibz,nsppol)
! Difference btw the QPState and the KS optical gap.
real(dp),pointer :: egwgap(:,:)
! egwgap(nkibz,nsppol))
! QPState optical gap at each k-point and spin.
real(dp),pointer :: en_qp_diago(:,:,:)
! en_qp_diago(nbnds,nkibz,nsppol))
! QPState energies obtained from the diagonalization of the Hermitian approximation to Sigma (QPSCGW)
real(dp),pointer :: e0(:,:,:)
! e0(nbnds,nkibz,nsppol)
! KS eigenvalues for each band, k-point and spin. In case of self-consistent?
real(dp),pointer :: e0gap(:,:)
! e0gap(nkibz,nsppol),
! KS gap at each k-point, for each spin.
real(dp),pointer :: omega_r(:)
! omega_r(nomega_r)
! real frequencies used for the self energy.
real(dp),pointer :: kptgw(:,:)
! kptgw(3,nkptgw)
! ! TODO there is a similar array in sigma_parameters
! List of calculated k-points.
real(dp),pointer :: sigxme(:,:,:)
! sigxme(b1gw:b2gw,nkibz,nsppol*nsig_ab))
! Diagonal matrix elements of $\Sigma_x$ i.e $\<nks|\Sigma_x|nks\>$
real(dp),pointer :: vxcme(:,:,:)
! vxcme(b1gw:b2gw,nkibz,nsppol*nsig_ab))
! $\<nks|v_{xc}[n_val]|nks\>$ matrix elements of vxc (valence-only contribution).
real(dp),pointer :: vUme(:,:,:)
! vUme(b1gw:b2gw,nkibz,nsppol*nsig_ab))
! $\<nks|v_{U}|nks\>$ for LDA+U.
complex(dpc),pointer :: degw(:,:,:)
! degw(b1gw:b2gw,nkibz,nsppol))
! Difference between the QPState and the KS energies.
complex(dpc),pointer :: dsigmee0(:,:,:)
! dsigmee0(b1gw:b2gw,nkibz,nsppol*nsig_ab))
! Derivative of $\Sigma_c(E)$ calculated at the KS eigenvalue.
complex(dpc),pointer :: egw(:,:,:)
! egw(nbnds,nkibz,nsppol))
! QPState energies, $\epsilon_{nks}^{QPState}$.
complex(dpc),pointer :: eigvec_qp(:,:,:,:)
! eigvec_qp(nbnds,nbnds,nkibz,nsppol))
! Expansion of the QPState amplitude in the KS basis set.
complex(dpc),pointer :: hhartree(:,:,:,:)
! hhartree(b1gw:b2gw,b1gw:b2gw,nkibz,nsppol*nsig_ab)
! $\<nks|T+v_H+v_{loc}+v_{nl}|mks\>$
complex(dpc),pointer :: sigcme(:,:,:,:)
! sigcme(b1gw:b2gw,nkibz,nomega_r,nsppol*nsig_ab))
! $\<nks|\Sigma_{c}(E)|nks\>$ at each nomega_r frequency
complex(dpc),pointer :: sigmee(:,:,:)
! sigmee(b1gw:b2gw,nkibz,nsppol*nsig_ab))
! $\Sigma_{xc}E_{KS} + (E_{QPState}- E_{KS})*dSigma/dE_KS
complex(dpc),pointer :: sigcmee0(:,:,:)
! sigcmee0(b1gw:b2gw,nkibz,nsppol*nsig_ab))
! Diagonal mat. elements of $\Sigma_c(E)$ calculated at the KS energy $E_{KS}$
complex(dpc),pointer :: sigcmesi(:,:,:,:)
! sigcmesi(b1gw:b2gw,nkibz,nomega_i,nsppol*nsig_ab))
! Matrix elements of $\Sigma_c$ along the imaginary axis.
! Only used in case of analytical continuation.
complex(dpc),pointer :: sigcme4sd(:,:,:,:)
! sigcme4sd(b1gw:b2gw,nkibz,nomega4sd,nsppol*nsig_ab))
! Diagonal matrix elements of \Sigma_c around the zeroth order eigenvalue (usually KS).
complex(dpc),pointer :: sigxcme(:,:,:,:)
! sigxme(b1gw:b2gw,nkibz,nomega_r,nsppol*nsig_ab))
! $\<nks|\Sigma_{xc}(E)|nks\>$ at each real frequency frequency.
complex(dpc),pointer :: sigxcmesi(:,:,:,:)
! sigxcmesi(b1gw:b2gw,nkibz,nomega_i,nsppol*nsig_ab))
! Matrix elements of $\Sigma_{xc}$ along the imaginary axis.
! Only used in case of analytical continuation.
complex(dpc),pointer :: sigxcme4sd(:,:,:,:)
! sigxcme4sd(b1gw:b2gw,nkibz,nomega4sd,nsppol*nsig_ab))
! Diagonal matrix elements of \Sigma_xc for frequencies around the zeroth order eigenvalues.
complex(dpc),pointer :: ze0(:,:,:)
! ze0(b1gw:b2gw,nkibz,nsppol))
! renormalization factor. $(1-\dfrac{\partial\Sigma_c} {\partial E_{KS}})^{-1}$
complex(dpc),pointer :: omega_i(:)
! omegasi(nomega_i)
! Frequencies along the imaginary axis used for the analytical continuation.
complex(dpc),pointer :: omega4sd(:,:,:,:)
! omega4sd(b1gw:b2gw,nkibz,nomega4sd,nsppol).
! Frequencies used to evaluate the Derivative of Sigma.
"""
def __init__(self, path):
self.ks_bands = ElectronBands.from_file(path)
self.nsppol = self.ks_bands.nsppol
super(SigresReader, self).__init__(path)
try:
self.nomega_r = self.read_dimvalue("nomega_r")
except self.Error:
self.nomega_r = 0
#self.nomega_i = self.read_dim("nomega_i")
# Save important quantities needed to simplify the API.
self.structure = self.read_structure()
self.gwcalctyp = self.read_value("gwcalctyp")
self.usepawu = self.read_value("usepawu")
# 1) The K-points of the homogeneous mesh.
self.ibz = self.ks_bands.kpoints
# 2) The K-points where QPState corrections have been calculated.
gwred_coords = self.read_redc_gwkpoints()
self.gwkpoints = KpointList(self.structure.reciprocal_lattice, gwred_coords)
# minbnd[nkptgw,nsppol] gives the minimum band index computed
# Note conversion between Fortran and python convention.
self.gwbstart_sk = self.read_value("minbnd") - 1
self.gwbstop_sk = self.read_value("maxbnd")
# min and Max band index for GW corrections.
self.min_gwbstart = np.min(self.gwbstart_sk)
self.max_gwbstart = np.max(self.gwbstart_sk)
self.min_gwbstop = np.min(self.gwbstop_sk)
self.max_gwbstop = np.max(self.gwbstop_sk)
self._egw = self.read_value("egw", cmode="c")
# Read and save important matrix elements.
# All these arrays are dimensioned
# vxcme(b1gw:b2gw,nkibz,nsppol*nsig_ab))
self._vxcme = self.read_value("vxcme")
self._sigxme = self.read_value("sigxme")
self._hhartree = self.read_value("hhartree", cmode="c")
self._vUme = self.read_value("vUme")
#if self.usepawu == 0: self._vUme.fill(0.0)
# Complex arrays
self._sigcmee0 = self.read_value("sigcmee0", cmode="c")
self._ze0 = self.read_value("ze0", cmode="c")
# Frequencies for the spectral function.
if self.has_spfunc:
self._omega_r = self.read_value("omega_r")
self._sigcme = self.read_value("sigcme", cmode="c")
self._sigxcme = self.read_value("sigxcme", cmode="c")
# Self-consistent case
self._en_qp_diago = self.read_value("en_qp_diago")
# <KS|QPState>
self._eigvec_qp = self.read_value("eigvec_qp", cmode="c")
#self._mlda_to_qp
#def is_selfconsistent(self, mode):
# return self.gwcalctyp
@property
def has_spfunc(self):
"""True if self contains the spectral function."""
return self.nomega_r
def kpt2fileindex(self, kpoint):
"""
Helper function that returns the index of kpoint in the netcdf file.
Accepts `Kpoint` instance of integer
Raise:
`KpointsError` if kpoint cannot be found.
.. note::
This function is needed since arrays in the netcdf file are dimensioned
with the total number of k-points in the IBZ.
"""
if isinstance(kpoint, int):
kpoint = self.gwkpoints[kpoint]
try:
return self.ibz.index(kpoint)
except:
raise
def gwkpt2seqindex(self, gwkpoint):
"""
This function returns the index of the GW k-point in (0:nkptgw)
Used to access data in the arrays that are dimensioned [0:nkptgw] e.g. minbnd.
"""
if isinstance(gwkpoint, int):
return gwkpoint
else:
return self.gwkpoints.index(gwkpoint)
def read_redc_gwkpoints(self):
return self.read_value("kptgw")
def read_allqps(self):
qps_spin = self.nsppol * [None]
for spin in range(self.nsppol):
qps = []
for gwkpoint in self.gwkpoints:
ik = self.gwkpt2seqindex(gwkpoint)
bands = range(self.gwbstart_sk[spin,ik], self.gwbstop_sk[spin,ik])
for band in bands:
qps.append(self.read_qp(spin, gwkpoint, band))
qps_spin[spin] = QPList(qps)
return tuple(qps_spin)
def read_qplist_sk(self, spin, kpoint):
ik = self.gwkpt2seqindex(kpoint)
bstart, bstop = self.gwbstart_sk[spin, ik], self.gwbstop_sk[spin, ik]
return QPList([self.read_qp(spin, kpoint, band) for band in range(bstart, bstop)])
#def read_qpene(self, spin, kpoint, band)
def read_qpenes(self):
return self._egw[:, :, :]
def read_qp(self, spin, kpoint, band):
ik_file = self.kpt2fileindex(kpoint)
ib_file = band - self.gwbstart_sk[spin, self.gwkpt2seqindex(kpoint)]
return QPState(
spin=spin,
kpoint=kpoint,
band=band,
e0=self.read_e0(spin, ik_file, band),
qpe=self._egw[spin, ik_file, band],
qpe_diago=self._en_qp_diago[spin, ik_file, band],
vxcme=self._vxcme[spin, ik_file, ib_file],
sigxme=self._sigxme[spin, ik_file, ib_file],
sigcmee0=self._sigcmee0[spin, ik_file, ib_file],
vUme=self._vUme[spin, ik_file, ib_file],
ze0=self._ze0[spin, ik_file, ib_file],
)
def read_qpgaps(self):
"""Read the QP gaps. Returns ndarray with shape [nsppol, nkibz] in eV"""
return self.read_value("egwgap")
def read_e0(self, spin, kfile, band):
return self.ks_bands.eigens[spin, kfile, band]
def read_sigmaw(self, spin, kpoint, band):
"""Returns the real and the imaginary part of the self energy."""
if not self.has_spfunc:
raise ValueError("%s does not contain spectral function data" % self.path)
ik = self.kpt2fileindex(kpoint)
return self._omega_r, self._sigxcme[spin,:,ik,band]
def read_spfunc(self, spin, kpoint, band):
"""
Returns the spectral function.
one/pi * ABS(AIMAG(Sr%sigcme(ib,ikibz,io,is))) /
( (REAL(Sr%omega_r(io)-Sr%hhartree(ib,ib,ikibz,is)-Sr%sigxcme(ib,ikibz,io,is)))**2 &
+(AIMAG(Sr%sigcme(ib,ikibz,io,is)))**2) / Ha_eV,&
"""
if not self.has_spfunc:
raise ValueError("%s does not contain spectral function data" % self.path)
ik = self.kpt2fileindex(kpoint)
ib = band - self.gwbstart_sk[spin, self.gwkpt2seqindex(kpoint)]
aim_sigc = np.abs(self._sigcme[spin,:,ik,ib].imag)
den = np.zeros(self.nomega_r)
for (io, omega) in enumerate(self._omega_r):
den[io] = (omega - self._hhartree[spin,ik,ib,ib].real - self._sigxcme[spin,io,ik,ib].real) ** 2 + \
self._sigcme[spin,io,ik,ib].imag ** 2
return self._omega_r, 1./np.pi * (aim_sigc/den)
def read_eigvec_qp(self, spin, kpoint, band=None):
"""
Returns <KS|QPState> for the given spin, kpoint and band. If band is None, <KS_b|QP_{b'}> is returned.
"""
ik = self.kpt2fileindex(kpoint)
if band is not None:
return self._eigvec_qp[spin,ik,:,band]
else:
return self._eigvec_qp[spin,ik,:,:]
def read_params(self):
"""
Read the parameters of the calculation.
Returns :class:`AttrDict` instance with the value of the parameters.
"""
param_names = [
"ecutwfn",
"ecuteps",
"ecutsigx",
"scr_nband",
"sigma_nband",
"gwcalctyp",
"scissor_ene",
]
params = AttrDict()
for pname in param_names:
params[pname] = self.read_value(pname, default=None)
# Other quantities that might be subject to convergence studies.
params["nkibz"] = len(self.ibz)
return params
def print_qps(self, spin=None, kpoints=None, bands=None, fmt=None, stream=sys.stdout):
"""
Args:
spin: Spin index, if None all spins are considered
kpoints: List of k-points to select. Default: all kpoints
bands: List of bands to select. Default is all bands
fmt: Format string passe to `to_strdict`
stream: file-like object.
Returns
List of tables.
"""
spins = range(self.nsppol) if spin is None else [spin]
kpoints = self.gwkpoints if kpoints is None else [kpoints]
if bands is not None: bands = [bands]
header = QPState.get_fields(exclude=["spin", "kpoint"])
tables = []
for spin in spins:
for kpoint in kpoints:
table_sk = PrettyTable(header)
if bands is None:
ik = self.gwkpt2seqindex(kpoint)
bands = range(self.gwbstart_sk[spin,ik], self.gwbstop_sk[spin,ik])
for band in bands:
qp = self.read_qp(spin, kpoint, band)
d = qp.to_strdict(fmt=fmt)
table_sk.add_row([d[k] for k in header])
stream.write("\nkpoint: %s, spin: %s, energy units: eV (NB: bands start from zero)\n" % (kpoint, spin))
print(table_sk, file=stream)
stream.write("\n")
# Add it to tables.
tables.append(table_sk)
return tables