LCPQ/dft_tools
3
0
Fork 0
mirror of https://github.com/triqs/dft_tools synced 2024-11-19 04:22:29 +01:00
Code Issues Releases Wiki Activity

Fixed small bugs and typos in vasp_converter

Browse Source 
VaspConverter is fixed to run and successfully produce some *.h5-file.
Consistency of this file is to be determined later.
This commit is contained in:
Oleg E. Peil 2015-09-21 20:18:37 +02:00 committed by Michel Ferrero
parent fada2af703
commit 77a169d242
2 changed files with 28 additions and 19 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

1
python/converters/vasp/examples/simple/conv_example.py
View File

@ -3,4 +3,5 @@ from vasp_converter import VaspConverter
if __name__ == '__main__': if __name__ == '__main__':
conv = VaspConverter('vasp') conv = VaspConverter('vasp')
conv.convert_dft_input()

46
python/converters/vasp/python/vasp_converter.py
View File

@ -70,7 +70,7 @@ class VaspConverter(ConverterTools):
""" """
for line in fh: for line in fh:
line_ = line.strip() line_ = line.strip()
if line_[0] == '#' or line_ == '': if not line or (line_ == '' or line_[0] == '#'):
continue continue
for val in map(float, line.split()): for val in map(float, line.split()):
@ -83,7 +83,7 @@ class VaspConverter(ConverterTools):
fh = open(filename, 'rt') fh = open(filename, 'rt')
header = "" header = ""
for line in fh: for line in fh:
if not "# END" in line: if not "#END" in line:
header += line header += line
else: else:
break break
@ -104,22 +104,23 @@ class VaspConverter(ConverterTools):
# Read and write only on the master node # Read and write only on the master node
if not (mpi.is_master_node()): return if not (mpi.is_master_node()): return
mpi.report("Reading input from %s..."%self.dft_file) mpi.report("Reading input from %s..."%self.ctrl_file)
# R is a generator : each R.Next() will return the next number in the file # R is a generator : each R.Next() will return the next number in the file
jheader, rf = self.read_header_and_data(self.ctrl_file) jheader, rf = self.read_header_and_data(self.ctrl_file)
print jheader
ctrl_head = json.loads(jheader) ctrl_head = json.loads(jheader)
ng = ctrl_head['ngroups'] ng = ctrl_head['ngroups']
n_k = ctrl_head['nk'] n_k = ctrl_head['nk']
# Note the difference in name conventions! # Note the difference in name conventions!
SP = ctrl_head['ns'] SP = ctrl_head['ns'] - 1
SO = ctrl_head['nc_flag'] SO = ctrl_head['nc_flag']
kpts = numpy.zeros((nk, 3)) kpts = numpy.zeros((n_k, 3))
bz_weights = numpy.zeros(nk) bz_weights = numpy.zeros(n_k)
try: try:
for ik in xrange(nk): for ik in xrange(n_k):
kx, ky, kz = rf.next(), rf.next(), rf.next() kx, ky, kz = rf.next(), rf.next(), rf.next()
kpts[ik, :] = kx, ky, kz kpts[ik, :] = kx, ky, kz
bz_weights[ik] = rf.next() bz_weights[ik] = rf.next()
@ -150,9 +151,6 @@ class VaspConverter(ConverterTools):
density_required = gr_head['nelect'] density_required = gr_head['nelect']
charge_below = 0.0 # This is not defined in VASP interface charge_below = 0.0 # This is not defined in VASP interface
# TODO: generalize this to the case of multiple shell groups
n_shells = 0 # No non-correlated shells at the moment
# Note that in the DftTools convention each site gives a separate correlated shell! # Note that in the DftTools convention each site gives a separate correlated shell!
n_corr_shells = sum([len(sh['ion_list']) for sh in p_shells]) n_corr_shells = sum([len(sh['ion_list']) for sh in p_shells])
@ -173,6 +171,10 @@ class VaspConverter(ConverterTools):
corr_shells.append(pars) corr_shells.append(pars)
shion_to_corr_shell[ish].append(i) shion_to_corr_shell[ish].append(i)
# TODO: generalize this to the case of multiple shell groups
n_shells = n_corr_shells # No non-correlated shells at the moment
shells = corr_shells
# FIXME: atomic sorts in Wien2K are not the same as in VASP. # FIXME: atomic sorts in Wien2K are not the same as in VASP.
# A symmetry analysis from OUTCAR or symmetry file should be used # A symmetry analysis from OUTCAR or symmetry file should be used
# to define equivalence classes of sites. # to define equivalence classes of sites.
@ -190,7 +192,7 @@ class VaspConverter(ConverterTools):
for ish in range(n_inequiv_shells): for ish in range(n_inequiv_shells):
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_shell[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!
@ -217,6 +219,8 @@ class VaspConverter(ConverterTools):
hopping[ik, isp, ib, ib] = rf.next() hopping[ik, isp, ib, ib] = rf.next()
# Projectors # Projectors
print n_orbitals
print [crsh['dim'] for crsh in corr_shells]
proj_mat = numpy.zeros([n_k, n_spin_blocs, n_corr_shells, max([crsh['dim'] for crsh in corr_shells]), 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]), max(n_orbitals)], numpy.complex_)
# TODO: implement reading from more than one projector group # TODO: implement reading from more than one projector group
@ -237,7 +241,7 @@ class VaspConverter(ConverterTools):
for ik in xrange(n_k): for ik in xrange(n_k):
for ion in xrange(len(sh['ion_list'])): for ion in xrange(len(sh['ion_list'])):
icsh = shion_to_corr_shell[ish][ion] icsh = shion_to_corr_shell[ish][ion]
for ilm in xrange(sh['dim']): for ilm in xrange(sh['ndim']):
for ib in xrange(n_orbitals[ik, isp]): for ib in xrange(n_orbitals[ik, isp]):
# This is to avoid confusion with the order of arguments # This is to avoid confusion with the order of arguments
pr = rf.next() pr = rf.next()
@ -245,7 +249,9 @@ class VaspConverter(ConverterTools):
proj_mat[ik, isp, icsh, ilm, ib] = complex(pr, pi) proj_mat[ik, isp, icsh, ilm, ib] = complex(pr, pi)
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: setattr(self,it,locals()[it]) for it in things_to_set:
print "%s:"%(it), locals()[it]
setattr(self,it,locals()[it])
except StopIteration: except StopIteration:
raise "VaspConverter: error reading %s"%self.gr_file raise "VaspConverter: error reading %s"%self.gr_file
@ -719,14 +725,14 @@ class VaspConverter(ConverterTools):
# In VASP interface the symmetries are read directly from *.ctrl file # In VASP interface the symmetries are read directly from *.ctrl file
# For the moment the symmetry parameters are just stubs # For the moment the symmetry parameters are just stubs
n_symm = 0 n_symm = 0
n_atoms = 0 n_atoms = 1
perm = [] perm = [0]
n_orbits = len(orbits) n_orbits = len(orbits)
SP = ctrl_head['ns'] SP = ctrl_head['ns']
SO = ctrl_head['nc_flag'] SO = ctrl_head['nc_flag']
time_inv = [] time_inv = [0]
mat = [] mat = [numpy.identity(1)]
mat_tinv = [] mat_tinv = [numpy.identity(1)]
# if not (mpi.is_master_node()): return # if not (mpi.is_master_node()): return
# mpi.report("Reading input from %s..."%symm_file) # mpi.report("Reading input from %s..."%symm_file)
# #
@ -774,5 +780,7 @@ class VaspConverter(ConverterTools):
ar=HDFArchive(self.hdf_file,'a') ar=HDFArchive(self.hdf_file,'a')
if not (symm_subgrp in ar): ar.create_group(symm_subgrp) if not (symm_subgrp in ar): ar.create_group(symm_subgrp)
things_to_save = ['n_symm','n_atoms','perm','orbits','SO','SP','time_inv','mat','mat_tinv'] things_to_save = ['n_symm','n_atoms','perm','orbits','SO','SP','time_inv','mat','mat_tinv']
for it in things_to_save: ar[symm_subgrp][it] = locals()[it] for it in things_to_save:
print "%s:"%(it), locals()[it]
ar[symm_subgrp][it] = locals()[it]
del ar del ar