mirror of
https://github.com/triqs/dft_tools
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416 lines
18 KiB
Python
416 lines
18 KiB
Python
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################################################################################
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#
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# TRIQS: a Toolbox for Research in Interacting Quantum Systems
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#
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# Copyright (C) 2011 by M. Ferrero, O. Parcollet
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#
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# DFT tools: Copyright (C) 2011 by M. Aichhorn, L. Pourovskii, V. Vildosola
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#
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# PLOVasp: Copyright (C) 2015 by O. E. Peil
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#
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# TRIQS is free software: you can redistribute it and/or modify it under the
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# terms of the GNU General Public License as published by the Free Software
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# Foundation, either version 3 of the License, or (at your option) any later
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# version.
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#
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# TRIQS is distributed in the hope that it will be useful, but WITHOUT ANY
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# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
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# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
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# details.
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#
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# You should have received a copy of the GNU General Public License along with
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# TRIQS. If not, see <http://www.gnu.org/licenses/>.
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#
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################################################################################
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from types import *
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import numpy
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from pytriqs.archive import *
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from converter_tools import *
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import os.path
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try:
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import simplejson as json
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except ImportError:
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import json
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class VaspConverter(ConverterTools):
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"""
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Conversion from VASP output to an hdf5 file that can be used as input for the SumkDFT class.
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"""
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def __init__(self, filename, hdf_filename = None,
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dft_subgrp = 'dft_input', symmcorr_subgrp = 'dft_symmcorr_input',
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parproj_subgrp='dft_parproj_input', symmpar_subgrp='dft_symmpar_input',
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bands_subgrp = 'dft_bands_input', misc_subgrp = 'dft_misc_input',
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transp_subgrp = 'dft_transp_input', repacking = False):
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"""
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Init of the class. Variable filename gives the root of all filenames, e.g. case.ctqmcout, case.h5, and so on.
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"""
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assert type(filename)==StringType, "Please provide the DFT files' base name as a string."
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if hdf_filename is None: hdf_filename = filename+'.h5'
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self.hdf_file = hdf_filename
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self.basename = filename
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self.ctrl_file = filename+'.ctrl'
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# self.pmat_file = filename+'.pmat'
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self.dft_subgrp = dft_subgrp
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self.symmcorr_subgrp = symmcorr_subgrp
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self.parproj_subgrp = parproj_subgrp
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self.symmpar_subgrp = symmpar_subgrp
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self.bands_subgrp = bands_subgrp
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self.misc_subgrp = misc_subgrp
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self.transp_subgrp = transp_subgrp
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# Checks if h5 file is there and repacks it if wanted:
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if (os.path.exists(self.hdf_file) and repacking):
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ConverterTools.repack(self)
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def read_data(self, fh):
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"""
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Generator for reading plain data.
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"""
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for line in fh:
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line_ = line.strip()
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if not line or (line_ == '' or line_[0] == '#'):
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continue
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for val in map(float, line.split()):
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yield val
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def read_header_and_data(self, filename):
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"""
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Opens a file and returns a JSON-header and the generator for the plain data.
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"""
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fh = open(filename, 'rt')
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header = ""
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for line in fh:
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if not "#END" in line:
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header += line
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else:
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break
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f_gen = self.read_data(fh)
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return header, f_gen
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def convert_dft_input(self):
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"""
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Reads the input files, and stores the data in the HDFfile
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"""
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energy_unit = 1.0 # VASP interface always uses eV
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k_dep_projection = 1
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# Symmetries are switched off for the moment
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# TODO: implement symmetries
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symm_op = 0 # Use symmetry groups for the k-sum
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# Read and write only on the master node
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if not (mpi.is_master_node()): return
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mpi.report("Reading input from %s..."%self.ctrl_file)
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# R is a generator : each R.Next() will return the next number in the file
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jheader, rf = self.read_header_and_data(self.ctrl_file)
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print jheader
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ctrl_head = json.loads(jheader)
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ng = ctrl_head['ngroups']
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n_k = ctrl_head['nk']
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# Note the difference in name conventions!
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SP = ctrl_head['ns'] - 1
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SO = ctrl_head['nc_flag']
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kpts = numpy.zeros((n_k, 3))
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bz_weights = numpy.zeros(n_k)
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try:
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for ik in xrange(n_k):
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kx, ky, kz = rf.next(), rf.next(), rf.next()
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kpts[ik, :] = kx, ky, kz
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bz_weights[ik] = rf.next()
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except StopIteration:
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raise "VaspConverter: error reading %s"%self.ctrl_file
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# if nc_flag:
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## TODO: check this
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# n_spin_blocs = 1
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# else:
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# n_spin_blocs = ns
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n_spin_blocs = SP + 1 - SO
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# Read PLO groups
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# First, we read everything into a temporary data structure
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# TODO: think about multiple shell groups and how to map them on h5 structures
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assert ng == 1, "Only one group is allowed at the moment"
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try:
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for ig in xrange(ng):
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gr_file = self.basename + '.pg%i'%(ig + 1)
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jheader, rf = self.read_header_and_data(gr_file)
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gr_head = json.loads(jheader)
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e_win = gr_head['ewindow']
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nb_max = gr_head['nb_max']
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p_shells = gr_head['shells']
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density_required = gr_head['nelect']
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charge_below = 0.0 # This is not defined in VASP interface
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# Note that in the DftTools convention each site gives a separate correlated shell!
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n_corr_shells = sum([len(sh['ion_list']) for sh in p_shells])
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corr_shells = []
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shion_to_corr_shell = [[] for ish in xrange(len(p_shells))]
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icsh = 0
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for ish, sh in enumerate(p_shells):
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ion_list = sh['ion_list']
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for i, ion in enumerate(ion_list):
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pars = {}
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pars['atom'] = ion
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# We set all sites inequivalent
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# pars['sort'] = sh['ion_sort']
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pars['sort'] = ion
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pars['l'] = sh['lorb']
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pars['dim'] = sh['ndim']
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pars['SO'] = SO
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# TODO: check what 'irep' entry does (it seems to be very specific to dmftproj)
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pars['irep'] = 0
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corr_shells.append(pars)
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shion_to_corr_shell[ish].append(i)
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# TODO: generalize this to the case of multiple shell groups
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n_shells = n_corr_shells # No non-correlated shells at the moment
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shells = corr_shells
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# FIXME: atomic sorts in Wien2K are not the same as in VASP.
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# A symmetry analysis from OUTCAR or symmetry file should be used
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# to define equivalence classes of sites.
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n_inequiv_shells, corr_to_inequiv, inequiv_to_corr = ConverterTools.det_shell_equivalence(self, corr_shells)
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if mpi.is_master_node():
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print " No. of inequivalent shells:", n_inequiv_shells
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# NB!: these rotation matrices are specific to Wien2K! Set to identity in VASP
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use_rotations = 1
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rot_mat = [numpy.identity(corr_shells[icrsh]['dim'],numpy.complex_) for icrsh in range(n_corr_shells)]
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rot_mat_time_inv = [0 for i in range(n_corr_shells)]
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# TODO: implement transformation matrices
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n_reps = [1 for i in range(n_inequiv_shells)]
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dim_reps = [0 for i in range(n_inequiv_shells)]
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T = []
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for ish in range(n_inequiv_shells):
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n_reps[ish] = 1 # Always 1 in VASP
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ineq_first = inequiv_to_corr[ish]
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dim_reps[ish] = [corr_shells[ineq_first]['dim']] # Just the dimension of the shell
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# The transformation matrix:
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# is of dimension 2l+1 without SO, and 2*(2l+1) with SO!
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ll = 2 * corr_shells[inequiv_to_corr[ish]]['l']+1
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lmax = ll * (corr_shells[inequiv_to_corr[ish]]['SO'] + 1)
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# TODO: at the moment put T-matrices to identities
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T.append(numpy.identity(lmax, numpy.complex_))
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# if nc_flag:
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## TODO: implement the noncollinear part
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# raise NotImplementedError("Noncollinear calculations are not implemented")
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# else:
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hopping = numpy.zeros([n_k, n_spin_blocs, nb_max, nb_max], numpy.complex_)
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f_weights = numpy.zeros([n_k, n_spin_blocs, nb_max], numpy.complex_)
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band_window = [numpy.zeros((n_k, 2), dtype=int) for isp in xrange(n_spin_blocs)]
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n_orbitals = numpy.zeros([n_k, n_spin_blocs], numpy.int)
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for isp in xrange(n_spin_blocs):
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for ik in xrange(n_k):
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ib1, ib2 = int(rf.next()), int(rf.next())
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band_window[isp][ik, :2] = ib1, ib2
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nb = ib2 - ib1 + 1
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n_orbitals[ik, isp] = nb
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for ib in xrange(nb):
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hopping[ik, isp, ib, ib] = rf.next()
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f_weights[ik, isp, ib] = rf.next()
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# Projectors
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# print n_orbitals
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# print [crsh['dim'] for crsh in corr_shells]
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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_)
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# TODO: implement reading from more than one projector group
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# In 'dmftproj' each ion represents a separate correlated shell.
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# In my interface a 'projected shell' includes sets of ions.
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# How to reconcile this? Two options:
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#
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# 1. Redefine 'projected shell' in my interface to make it correspond to one site only.
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# In this case the list of ions must be defined at the level of the projector group.
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#
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# 2. Split my 'projected shell' to several 'correlated shells' here in the converter.
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#
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# At the moment I choose i.2 for its simplicity. But one should consider possible
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# use cases and decide which solution is to be made permanent.
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#
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for ish, sh in enumerate(p_shells):
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for isp in xrange(n_spin_blocs):
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for ik in xrange(n_k):
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for ion in xrange(len(sh['ion_list'])):
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icsh = shion_to_corr_shell[ish][ion]
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for ilm in xrange(sh['ndim']):
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for ib in xrange(n_orbitals[ik, isp]):
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# This is to avoid confusion with the order of arguments
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pr = rf.next()
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pi = rf.next()
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proj_mat[ik, isp, icsh, ilm, ib] = complex(pr, pi)
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things_to_set = ['n_shells','shells','n_corr_shells','corr_shells','n_spin_blocs','n_orbitals','n_k','SO','SP','energy_unit']
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for it in things_to_set:
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# print "%s:"%(it), locals()[it]
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setattr(self,it,locals()[it])
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except StopIteration:
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raise "VaspConverter: error reading %s"%self.gr_file
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rf.close()
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# Save it to the HDF:
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ar = HDFArchive(self.hdf_file,'a')
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if not (self.dft_subgrp in ar): ar.create_group(self.dft_subgrp)
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# The subgroup containing the data. If it does not exist, it is created. If it exists, the data is overwritten!
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things_to_save = ['energy_unit','n_k','k_dep_projection','SP','SO','charge_below','density_required',
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'symm_op','n_shells','shells','n_corr_shells','corr_shells','use_rotations','rot_mat',
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'rot_mat_time_inv','n_reps','dim_reps','T','n_orbitals','proj_mat','bz_weights','hopping',
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'n_inequiv_shells', 'corr_to_inequiv', 'inequiv_to_corr']
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for it in things_to_save: ar[self.dft_subgrp][it] = locals()[it]
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# Store Fermi weights to 'dft_misc_input'
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if not (self.misc_subgrp in ar): ar.create_group(self.misc_subgrp)
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ar[self.misc_subgrp]['dft_fermi_weights'] = f_weights
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ar[self.misc_subgrp]['band_window'] = band_window
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del ar
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# Symmetries are used, so now convert symmetry information for *correlated* orbitals:
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self.convert_symmetry_input(ctrl_head, orbits=self.corr_shells, symm_subgrp=self.symmcorr_subgrp)
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# TODO: Implement misc_input
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# self.convert_misc_input(bandwin_file=self.bandwin_file,struct_file=self.struct_file,outputs_file=self.outputs_file,
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# misc_subgrp=self.misc_subgrp,SO=self.SO,SP=self.SP,n_k=self.n_k)
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def convert_misc_input(self, bandwin_file, struct_file, outputs_file, misc_subgrp, SO, SP, n_k):
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"""
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Reads input for the band window from bandwin_file, which is case.oubwin,
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structure from struct_file, which is case.struct,
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symmetries from outputs_file, which is case.outputs.
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"""
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if not (mpi.is_master_node()): return
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things_to_save = []
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# Read relevant data from .oubwin/up/dn files
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#############################################
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# band_window: Contains the index of the lowest and highest band within the
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# projected subspace (used by dmftproj) for each k-point.
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if (SP == 0 or SO == 1):
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files = [self.bandwin_file]
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elif SP == 1:
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files = [self.bandwin_file+'up', self.bandwin_file+'dn']
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else: # SO and SP can't both be 1
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assert 0, "convert_transport_input: Reding oubwin error! Check SP and SO!"
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band_window = [numpy.zeros((n_k, 2), dtype=int) for isp in range(SP + 1 - SO)]
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for isp, f in enumerate(files):
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if os.path.exists(f):
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mpi.report("Reading input from %s..."%f)
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R = ConverterTools.read_fortran_file(self, f, self.fortran_to_replace)
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assert int(R.next()) == n_k, "convert_misc_input: Number of k-points is inconsistent in oubwin file!"
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assert int(R.next()) == SO, "convert_misc_input: SO is inconsistent in oubwin file!"
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for ik in xrange(n_k):
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R.next()
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band_window[isp][ik,0] = R.next() # lowest band
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band_window[isp][ik,1] = R.next() # highest band
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R.next()
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things_to_save.append('band_window')
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R.close() # Reading done!
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# Read relevant data from .struct file
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######################################
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# lattice_type: bravais lattice type as defined by Wien2k
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# lattice_constants: unit cell parameters in a. u.
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# lattice_angles: unit cell angles in rad
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if (os.path.exists(self.struct_file)):
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mpi.report("Reading input from %s..."%self.struct_file)
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with open(self.struct_file) as R:
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try:
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R.readline()
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lattice_type = R.readline().split()[0]
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R.readline()
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temp = R.readline()
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# print temp
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lattice_constants = numpy.array([float(temp[0+10*i:10+10*i].strip()) for i in range(3)])
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lattice_angles = numpy.array([float(temp[30+10*i:40+10*i].strip()) for i in range(3)]) * numpy.pi / 180.0
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things_to_save.extend(['lattice_type', 'lattice_constants', 'lattice_angles'])
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except IOError:
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raise "convert_misc_input: reading file %s failed" %self.struct_file
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# Read relevant data from .outputs file
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#######################################
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# rot_symmetries: matrix representation of all (space group) symmetry operations
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if (os.path.exists(self.outputs_file)):
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mpi.report("Reading input from %s..."%self.outputs_file)
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rot_symmetries = []
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with open(self.outputs_file) as R:
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try:
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while 1:
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temp = R.readline().strip(' ').split()
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if (temp[0] =='PGBSYM:'):
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n_symmetries = int(temp[-1])
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break
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for i in range(n_symmetries):
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while 1:
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if (R.readline().strip().split()[0] == 'Symmetry'): break
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sym_i = numpy.zeros((3, 3), dtype = float)
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for ir in range(3):
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temp = R.readline().strip().split()
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for ic in range(3):
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sym_i[ir, ic] = float(temp[ic])
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R.readline()
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rot_symmetries.append(sym_i)
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things_to_save.extend(['n_symmetries', 'rot_symmetries'])
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things_to_save.append('rot_symmetries')
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except IOError:
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raise "convert_misc_input: reading file %s failed" %self.outputs_file
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# Save it to the HDF:
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ar=HDFArchive(self.hdf_file,'a')
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if not (misc_subgrp in ar): ar.create_group(misc_subgrp)
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for it in things_to_save: ar[misc_subgrp][it] = locals()[it]
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del ar
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def convert_symmetry_input(self, ctrl_head, orbits, symm_subgrp):
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"""
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Reads input for the symmetrisations from symm_file, which is case.sympar or case.symqmc.
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"""
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# In VASP interface the symmetries are read directly from *.ctrl file
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# For the moment the symmetry parameters are just stubs
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n_symm = 0
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n_atoms = 1
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perm = [0]
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n_orbits = len(orbits)
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SP = ctrl_head['ns']
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SO = ctrl_head['nc_flag']
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time_inv = [0]
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mat = [numpy.identity(1)]
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mat_tinv = [numpy.identity(1)]
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# Save it to the HDF:
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ar=HDFArchive(self.hdf_file,'a')
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if not (symm_subgrp in ar): ar.create_group(symm_subgrp)
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things_to_save = ['n_symm','n_atoms','perm','orbits','SO','SP','time_inv','mat','mat_tinv']
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for it in things_to_save:
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# print "%s:"%(it), locals()[it]
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ar[symm_subgrp][it] = locals()[it]
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del ar
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