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use IBZ kpoint list for writing GAMMA vaspgamma.h5

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* use IBZ kpoint list for writing GAMMA vaspgamma.h5
* make vaspgamma.h5 default
* write n_k_ibz into dft_misc_input so in can be used inside of sumk
* write n_k_ibz into seed.ctrl json file
* change ref h5 files for VASP tests by adding n_k_ibz
* add new svo converter test
This commit is contained in:
the-hampel 2024-11-19 12:15:49 +01:00
parent 13d975bdf7
commit 6a893840ee
12 changed files with 101 additions and 11 deletions
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6
python/triqs_dft_tools/converters/plovasp/elstruct.py
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@ -39,6 +39,7 @@ class ElectronicStructure:
- *natom* (int) : total number of atoms
- *nktot* (int) : total number of `k`-points
- *nkibz* (int) : number of `k`-points in IBZ
- *nband* (int) : total number of bands
- *nspin* (int) : spin-polarization
- *nc_flag* (True/False) : non-collinearity flag
@ -58,8 +59,9 @@ class ElectronicStructure:
self.natom = vasp_data.poscar.nq
self.type_of_ion = vasp_data.poscar.type_of_ion
self.nktot = vasp_data.kpoints.nktot
self.nkibz = vasp_data.kpoints.nkibz
self.kmesh = {'nktot': self.nktot}
self.kmesh = {'nktot': self.nktot, 'nkibz': self.nkibz}
self.kmesh['kpoints'] = vasp_data.kpoints.kpts
# VASP.6.
self.nc_flag = vasp_data.plocar.nc_flag
@ -86,7 +88,7 @@ class ElectronicStructure:
# Check that the number of k-points is the same in all files
_, ns_plo, nk_plo, nb_plo = vasp_data.plocar.plo.shape
assert nk_plo == self.nktot, "PLOCAR is inconsistent with IBZKPT (number of k-points)"
assert nk_plo == self.nktot, "PLOCAR is inconsistent with IBZKPT (number of k-points). If you run VASP with symmetry make sure to use the h5 interface of the converter, i.e. have the locproj information written to vaspout.h5"
# FIXME: Reading from EIGENVAL is obsolete and should be
# removed completely.

3
python/triqs_dft_tools/converters/plovasp/plotools.py
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@ -289,6 +289,8 @@ def ctrl_output(conf_pars, el_struct, ng):
* *nk*: number of `k`-points
* *nkibz*: number of `k`-points in IBZ
* *ns*: number of spin channels
* *nc_flag*: collinear/noncollinear case (False/True)
@ -309,6 +311,7 @@ def ctrl_output(conf_pars, el_struct, ng):
# Construct the header dictionary
head_dict['ngroups'] = ng
head_dict['nk'] = el_struct.kmesh['nktot']
head_dict['nkibz'] = el_struct.kmesh['nkibz']
head_dict['ns'] = el_struct.nspin
head_dict['kvec1'] = list(el_struct.structure['kpt_basis'][:,0])
head_dict['kvec2'] = list(el_struct.structure['kpt_basis'][:,1])

16
python/triqs_dft_tools/converters/plovasp/vaspio.py
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@ -40,6 +40,7 @@ import logging
import numpy as np
import re
import os
import time
from h5 import HDFArchive
log = logging.getLogger('plovasp.vaspio')
@ -79,6 +80,10 @@ class VaspData:
if vasph5:
log.warning("Reading from vaspout.h5")
h5path = os.path.join(vasp_dir, 'vaspout.h5')
# give VASP some time to write the file
with HDFArchive(h5path, 'r') as archive:
if 'locproj' not in archive['results']:
time.sleep(2)
self.plocar = h5Plocar(h5path)
self.poscar = h5Poscar(h5path)
self.kpoints = h5Kpoints(h5path)
@ -401,7 +406,8 @@ class Kpoints:
Class describing k-points and optionally tetrahedra.
Properties:
- nktot (int) : total number of k-points in the IBZ
- nktot (int) : total number of k-points in the BZ
- nkibz (int) : number of k-points in the IBZ
- kpts (numpy.array((nktot, 3), dtype=float)) : k-point vectors (fractional coordinates)
- ntet (int) : total number of k-point tetrahedra
- itet (numpy.array((ntet, 5), dtype=float) : array of tetrahedra
@ -412,6 +418,7 @@ class Kpoints:
def __init__(self):
self.kpts = None
self.nktot = None
self.nkibz = None
self.kwghts = None
#
@ -441,6 +448,9 @@ class Kpoints:
# Number of k-points
line = next(ibz_file)
self.nktot = int(line.strip().split()[0])
# when reading from IBZKPT file we do not know the full number of k-points, i.e.
# works only ISYM=-1
self.nkibz = self.nktot
print()
print(" {0:>26} {1:d}".format("Total number of k-points:", self.nktot))
@ -716,7 +726,7 @@ class h5Kpoints:
# h5path = './vasptriqs.h5'
with HDFArchive(h5path, 'a') as archive:
kpoints = archive['results/electron_eigenvalues']
self.nkred = kpoints['kpoints']
self.nkibz = kpoints['kpoints']
self.kpts = kpoints['kpoint_coords_full']
self.nktot = len(self.kpts)
self.kwghts = kpoints['kpoints_symmetry_weight_full']
@ -731,7 +741,7 @@ class h5Kpoints:
self.ntet = 0
print()
print(" {0:>26} {1:d}".format("Reduced number of k-points:", self.nkred))
print(" {0:>26} {1:d}".format("Reduced number of k-points:", self.nkibz))
print(" {0:>26} {1:d}".format("Total number of k-points:", self.nktot))
print(" {0:>26} {1:d}".format("Total number of tetrahedra:", self.ntet))

6
python/triqs_dft_tools/converters/vasp.py
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@ -158,6 +158,8 @@ class VaspConverter(ConverterTools):
ng = ctrl_head['ngroups']
n_k = ctrl_head['nk']
n_k_ibz = ctrl_head['nkibz']
# Note the difference in name conventions!
SP = ctrl_head['ns'] - 1
SO = ctrl_head['nc_flag']
@ -387,7 +389,7 @@ class VaspConverter(ConverterTools):
with HDFArchive(self.hdf_file,'a') as ar:
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',
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',
'rot_mat_time_inv','n_reps','dim_reps','T','n_orbitals','proj_mat','bz_weights',
'hopping','n_inequiv_shells', 'corr_to_inequiv', 'inequiv_to_corr','proj_or_hk',
@ -401,6 +403,8 @@ class VaspConverter(ConverterTools):
ar[self.misc_subgrp]['dft_fermi_weights'] = f_weights
ar[self.misc_subgrp]['kpts_cart'] = kpts_cart
ar[self.misc_subgrp]['band_window'] = band_window
if n_k_ibz is not None:
ar[self.misc_subgrp]['n_k_ibz'] = n_k_ibz
# 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)

23
python/triqs_dft_tools/sumk_dft.py
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@ -2207,8 +2207,7 @@ class SumkDFT(object):
filename = 'dens_mat.dat'
elif dm_type == 'vasp':
# use new h5 interface to vasp by default, if not wanted specify dm_type='vasp' + filename='GAMMA'
# filename = 'vaspgamma.h5'
filename = 'GAMMA'
filename = 'vaspgamma.h5'
elif dm_type == 'elk':
filename = 'DMATDMFT.OUT'
elif dm_type == 'qe':
@ -2229,12 +2228,17 @@ class SumkDFT(object):
if dm_type in ['vasp', 'qe']:
fermi_weights = 0
band_window = 0
n_k_ibz = self.n_k
if mpi.is_master_node():
with HDFArchive(self.hdf_file, 'r') as ar:
fermi_weights = ar['dft_misc_input']['dft_fermi_weights']
band_window = ar['dft_misc_input']['band_window']
if 'n_k_ibz' in ar['dft_misc_input']:
n_k_ibz = ar['dft_misc_input']['n_k_ibz']
fermi_weights = mpi.bcast(fermi_weights)
band_window = mpi.bcast(band_window)
n_k_ibz = mpi.bcast(n_k_ibz)
# Convert Fermi weights to a density matrix
dens_mat_dft = {}
@ -2349,8 +2353,13 @@ class SumkDFT(object):
fout.write("\n")
fout.close()
elif dm_type == 'vasp':
if kpts_to_write is None:
if kpts_to_write is None and self.n_k == n_k_ibz:
kpts_to_write = np.arange(self.n_k)
elif kpts_to_write is None and n_k_ibz < self.n_k:
# If the number of IBZ k-points is less than the total number of k-points,
# then we only write the IBZ k-points, which are the first n_k_ibz k-points
# in VASP
kpts_to_write = np.arange(n_k_ibz)
else:
assert np.min(kpts_to_write) >= 0 and np.max(kpts_to_write) < self.n_k
@ -2359,8 +2368,12 @@ class SumkDFT(object):
if mpi.is_master_node():
if filename == 'vaspgamma.h5':
with HDFArchive('vaspgamma.h5', 'w') as vasp_h5:
vasp_h5['band_window'] = band_window
vasp_h5['deltaN'] = deltaN
# only store the ibz kpoints in the h5
bnd_win_towrite = [band_window[0][:n_k_ibz,:]]
vasp_h5['band_window'] = bnd_win_towrite
vasp_h5.create_group('deltaN')
vasp_h5['deltaN']['up'] = deltaN['up'][:n_k_ibz]
vasp_h5['deltaN']['down'] = deltaN['down'][:n_k_ibz]
else:
with open(filename, 'w') as f:
f.write(" -1 -1 ! Number of k-points, default number of bands\n") # % len(kpts_to_write))

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test/python/plovasp/converter/lunio3.ref.h5
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test/python/plovasp/converter/nio.ref.h5
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test/python/plovasp/converter/pg_output.ref.h5
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16
test/python/plovasp/converter/svo.cfg Normal file
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@ -0,0 +1,16 @@
[General]
BASENAME = converter/svo
[Group 1]
SHELLS = 1
NORMALIZE = True
EWINDOW = -1.4 2.0
[Shell 1]
LSHELL = 2
IONS = 2
TRANSFORM = 1.0 0.0 0.0 0.0 0.0
0.0 1.0 0.0 0.0 0.0
0.0 0.0 0.0 1.0 0.0

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test/python/plovasp/converter/svo.ref.h5 Normal file
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test/python/plovasp/converter/svo/vaspout.h5 Normal file
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42
test/python/plovasp/converter/test_converter_svo.py Normal file
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@ -0,0 +1,42 @@
import os
import rpath
_rpath = os.path.dirname(rpath.__file__) + '/'
from triqs_dft_tools.converters.plovasp.converter import generate_and_output_as_text
from triqs_dft_tools.converters import VaspConverter
import mytest
################################################################################
#
# TestConverterOneSite
#
################################################################################
class TestConverterSVO(mytest.MyTestCase):
"""
Function:
def generate_and_output_as_text(pars, el_struct)
and
VaspConverter
Scenarios:
- Parse config file and produce a correct converted h5-file
"""
# Scenario 1
def test_convert_svo(self):
generate_and_output_as_text(_rpath + 'svo.cfg', _rpath + 'svo/')
test_file = _rpath + 'svo.test.h5'
converter = VaspConverter(filename=_rpath + 'svo',
hdf_filename=test_file)
converter.convert_dft_input()
expected_file = _rpath + 'svo.ref.h5'
self.assertH5FileEqual(test_file, expected_file)
if __name__ == '__main__':
import unittest
unittest.main(verbosity=2, buffer=False)