LCPQ/dft_tools
3
0
Fork 0
mirror of https://github.com/triqs/dft_tools synced 2025-04-16 13:39:25 +02:00
Code Issues Releases Wiki Activity

Merge pull request #135 from the-hampel/unstable

Browse Source 
Fixing a bug in the vasp converter for multiple sites per unit cell
This commit is contained in:
Markus Aichhorn 2020-04-02 12:49:35 +02:00 committed by GitHub
commit 8e8ce2b67b
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
2 changed files with 26 additions and 26 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

52
python/converters/vasp_converter.py
View File

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

BIN
test/plovasp/converter/lunio3.out.h5
View File

Binary file not shown.