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fixed a index bug that produced empty projectors for a unit cells with multiple shells

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This commit is contained in:
Alexander Hampel 2020-04-01 11:13:28 -04:00
parent bf8bfbe59b
commit 0e05d0687f
1 changed files with 26 additions and 26 deletions
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52
python/converters/vasp_converter.py
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@ -1,4 +1,4 @@
################################################################################
#
# TRIQS: a Toolbox for Research in Interacting Quantum Systems
@ -46,7 +46,7 @@ class VaspConverter(ConverterTools):
transp_subgrp = 'dft_transp_input', repacking = False,
proj_or_hk='proj'):
"""
Init of the class. Variable filename gives the root of all filenames, e.g. case.ctqmcout, case.h5, and so on.
Init of the class. Variable filename gives the root of all filenames, e.g. case.ctqmcout, case.h5, and so on.
Parameters
----------
@ -90,7 +90,7 @@ class VaspConverter(ConverterTools):
self.transp_subgrp = transp_subgrp
assert (proj_or_hk == 'proj') or (proj_or_hk == 'hk'), "proj_or_hk has to be 'proj' of 'hk'"
self.proj_or_hk = proj_or_hk
# Checks if h5 file is there and repacks it if wanted:
if (os.path.exists(self.hdf_file) and repacking):
ConverterTools.repack(self)
@ -99,7 +99,7 @@ class VaspConverter(ConverterTools):
def read_data(self, fh):
"""
Generator for reading plain data.
Parameters
----------
fh : file object
@ -116,7 +116,7 @@ class VaspConverter(ConverterTools):
def read_header_and_data(self, filename):
"""
Opens a file and returns a JSON-header and the generator for the plain data.
Parameters
----------
filename : string
@ -190,7 +190,7 @@ class VaspConverter(ConverterTools):
gr_file = self.basename + '.pg%i'%(ig + 1)
jheader, rf = self.read_header_and_data(gr_file)
gr_head = json.loads(jheader)
nb_max = gr_head['nb_max']
p_shells = gr_head['shells']
@ -224,7 +224,7 @@ class VaspConverter(ConverterTools):
# TODO: check what 'irep' entry does (it seems to be very specific to dmftproj)
pars['irep'] = 0
shells.append(pars)
shion_to_shell[ish].append(ish)
shion_to_shell[ish].append(i)
shorbs_to_globalorbs[ish].append([last_dimension,
last_dimension+sh['ndim']])
last_dimension = last_dimension+sh['ndim']
@ -258,14 +258,14 @@ class VaspConverter(ConverterTools):
n_reps[ish] = 1 # Always 1 in VASP
ineq_first = inequiv_to_corr[ish]
dim_reps[ish] = [corr_shells[ineq_first]['dim']] # Just the dimension of the shell
# The transformation matrix:
# is of dimension 2l+1 without SO, and 2*(2l+1) with SO!
ll = 2 * corr_shells[inequiv_to_corr[ish]]['l']+1
lmax = ll * (corr_shells[inequiv_to_corr[ish]]['SO'] + 1)
# TODO: at the moment put T-matrices to identities
T.append(numpy.identity(lmax, numpy.complex_))
# if nc_flag:
## TODO: implement the noncollinear part
# raise NotImplementedError("Noncollinear calculations are not implemented")
@ -275,7 +275,7 @@ class VaspConverter(ConverterTools):
band_window = [numpy.zeros((n_k, 2), dtype=int) for isp in xrange(n_spin_blocs)]
n_orbitals = numpy.zeros([n_k, n_spin_blocs], numpy.int)
for isp in xrange(n_spin_blocs):
for ik in xrange(n_k):
ib1, ib2 = int(rf.next()), int(rf.next())
@ -285,7 +285,7 @@ class VaspConverter(ConverterTools):
for ib in xrange(nb):
hopping[ik, isp, ib, ib] = rf.next()
f_weights[ik, isp, ib] = rf.next()
if self.proj_or_hk == 'hk':
hopping = numpy.zeros([n_k, n_spin_blocs, n_orbs, n_orbs], numpy.complex_)
# skip header lines
@ -326,7 +326,7 @@ class VaspConverter(ConverterTools):
#
# At the moment I choose i.2 for its simplicity. But one should consider possible
# use cases and decide which solution is to be made permanent.
#
#
for ish, sh in enumerate(p_shells):
for isp in xrange(n_spin_blocs):
for ik in xrange(n_k):
@ -340,7 +340,7 @@ class VaspConverter(ConverterTools):
# now save only projectors with flag 'corr' to proj_mat
proj_mat = numpy.zeros([n_k, n_spin_blocs, n_corr_shells, max([crsh['dim'] for crsh in corr_shells]), numpy.max(n_orbitals)], numpy.complex_)
if self.proj_or_hk == 'proj':
if self.proj_or_hk == 'proj':
for ish, sh in enumerate(p_shells):
if sh['corr']:
for isp in xrange(n_spin_blocs):
@ -362,7 +362,7 @@ class VaspConverter(ConverterTools):
proj_mat[ik,isp,icsh,iclm,ilm] = 1.0
#corr_shell.pop('ion_list')
things_to_set = ['n_shells','shells','n_corr_shells','corr_shells','n_spin_blocs','n_orbitals','n_k','SO','SP','energy_unit']
things_to_set = ['n_shells','shells','n_corr_shells','corr_shells','n_spin_blocs','n_orbitals','n_k','SO','SP','energy_unit']
for it in things_to_set:
# print "%s:"%(it), locals()[it]
setattr(self,it,locals()[it])
@ -374,10 +374,10 @@ class VaspConverter(ConverterTools):
proj_or_hk = self.proj_or_hk
# Save it to the HDF:
with HDFArchive(self.hdf_file,'a') as ar:
if not (self.dft_subgrp in ar): ar.create_group(self.dft_subgrp)
if not (self.dft_subgrp in ar): ar.create_group(self.dft_subgrp)
# The subgroup containing the data. If it does not exist, it is created. If it exists, the data is overwritten!
things_to_save = ['energy_unit','n_k','k_dep_projection','SP','SO','charge_below','density_required',
'symm_op','n_shells','shells','n_corr_shells','corr_shells','use_rotations','rot_mat',
@ -391,7 +391,7 @@ class VaspConverter(ConverterTools):
if not (self.misc_subgrp in ar): ar.create_group(self.misc_subgrp)
ar[self.misc_subgrp]['dft_fermi_weights'] = f_weights
ar[self.misc_subgrp]['band_window'] = band_window
# Symmetries are used, so now convert symmetry information for *correlated* orbitals:
self.convert_symmetry_input(ctrl_head, orbits=self.corr_shells, symm_subgrp=self.symmcorr_subgrp)
@ -405,7 +405,7 @@ class VaspConverter(ConverterTools):
Reads input for the band window from bandwin_file, which is case.oubwin,
structure from struct_file, which is case.struct,
symmetries from outputs_file, which is case.outputs.
Parameters
----------
bandwin_file : string
@ -422,7 +422,7 @@ class VaspConverter(ConverterTools):
spin
n_k : int
number of k-points
"""
if not (mpi.is_master_node()): return
@ -439,7 +439,7 @@ class VaspConverter(ConverterTools):
files = [self.bandwin_file+'up', self.bandwin_file+'dn']
else: # SO and SP can't both be 1
assert 0, "convert_transport_input: Reding oubwin error! Check SP and SO!"
band_window = [numpy.zeros((n_k, 2), dtype=int) for isp in range(SP + 1 - SO)]
for isp, f in enumerate(files):
if os.path.exists(f):
@ -464,7 +464,7 @@ class VaspConverter(ConverterTools):
if (os.path.exists(self.struct_file)):
mpi.report("Reading input from %s..."%self.struct_file)
with open(self.struct_file) as R:
try:
R.readline()
@ -481,10 +481,10 @@ class VaspConverter(ConverterTools):
# Read relevant data from .outputs file
#######################################
# rot_symmetries: matrix representation of all (space group) symmetry operations
if (os.path.exists(self.outputs_file)):
mpi.report("Reading input from %s..."%self.outputs_file)
rot_symmetries = []
with open(self.outputs_file) as R:
try:
@ -517,15 +517,15 @@ class VaspConverter(ConverterTools):
def convert_symmetry_input(self, ctrl_head, orbits, symm_subgrp):
"""
Reads input for the symmetrisations from symm_file, which is case.sympar or case.symqmc.
Parameters
----------
ctrl_head : dict
dictionary of header of .ctrl file
orbits : list of shells
contains all shells
contains all shells
symm_subgrp : name of symmetry group in h5 archive
"""
# In VASP interface the symmetries are read directly from *.ctrl file