Source code for triqs_dft_tools.converters.vasp


################################################################################
#
# TRIQS: a Toolbox for Research in Interacting Quantum Systems
#
# Copyright (C) 2011 by M. Ferrero, O. Parcollet
#
# DFT tools: Copyright (C) 2011 by M. Aichhorn, L. Pourovskii, V. Vildosola
#
# PLOVasp: Copyright (C) 2015 by O. E. Peil
#
# TRIQS is free software: you can redistribute it and/or modify it under the
# terms of the GNU General Public License as published by the Free Software
# Foundation, either version 3 of the License, or (at your option) any later
# version.
#
# TRIQS is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
# details.
#
# You should have received a copy of the GNU General Public License along with
# TRIQS. If not, see <http://www.gnu.org/licenses/>.
#
################################################################################
"""
Vasp converter
"""

from types import *
import numpy
from h5 import *
from .converter_tools import *
import os.path
try:
    import simplejson as json
except ImportError:
    import json

[docs] class VaspConverter(ConverterTools): """ Conversion from VASP output to an hdf5 file that can be used as input for the SumkDFT class. """
[docs] def __init__(self, filename, hdf_filename = None, dft_subgrp = 'dft_input', symmcorr_subgrp = 'dft_symmcorr_input', parproj_subgrp='dft_parproj_input', symmpar_subgrp='dft_symmpar_input', bands_subgrp = 'dft_bands_input', misc_subgrp = 'dft_misc_input', 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. Parameters ---------- filename : string Base name of DFT files. hdf_filename : string, optional Name of hdf5 archive to be created. dft_subgrp : string, optional Name of subgroup storing necessary DFT data. symmcorr_subgrp : string, optional Name of subgroup storing correlated-shell symmetry data. parproj_subgrp : string, optional Name of subgroup storing partial projector data. symmpar_subgrp : string, optional Name of subgroup storing partial-projector symmetry data. bands_subgrp : string, optional Name of subgroup storing band data. misc_subgrp : string, optional Name of subgroup storing miscellaneous DFT data. transp_subgrp : string, optional Name of subgroup storing transport data. repacking : boolean, optional Does the hdf5 archive need to be repacked to save space? proj_or_hk : string, optional Select scheme to convert between KS bands and localized orbitals. """ assert isinstance(filename, str), "Please provide the DFT files' base name as a string." if hdf_filename is None: hdf_filename = filename+'.h5' self.hdf_file = hdf_filename self.basename = filename self.ctrl_file = filename+'.ctrl' # self.pmat_file = filename+'.pmat' self.dft_subgrp = dft_subgrp self.symmcorr_subgrp = symmcorr_subgrp self.parproj_subgrp = parproj_subgrp self.symmpar_subgrp = symmpar_subgrp self.bands_subgrp = bands_subgrp self.misc_subgrp = misc_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'" 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)
# this is to test pull request
[docs] def read_data(self, fh): """ Generator for reading plain data. Parameters ---------- fh : file object file object which is read in. """ for line in fh: line_ = line.strip() if not line or (line_ == '' or line_[0] == '#'): continue for val in map(float, line.split()): yield val
[docs] 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 file name of the file to read. """ fh = open(filename, 'rt') header = "" for line in fh: if not "#END" in line: header += line else: break f_gen = self.read_data(fh) return header, f_gen, fh
[docs] def convert_dft_input(self): """ Reads the input files, and stores the data in the HDFfile """ energy_unit = 1.0 # VASP interface always uses eV k_dep_projection = 1 # Symmetries are switched off for the moment # TODO: implement symmetries symm_op = 0 # Use symmetry groups for the k-sum # Read and write only on the master node if not (mpi.is_master_node()): return mpi.report("Reading input from %s..."%self.ctrl_file) # R is a generator : each R.Next() will return the next number in the file jheader, rf, fh = self.read_header_and_data(self.ctrl_file) print(jheader) ctrl_head = json.loads(jheader) ng = ctrl_head['ngroups'] n_k = ctrl_head['nk'] # Note the difference in name conventions! SP = ctrl_head['ns'] - 1 SO = ctrl_head['nc_flag'] # load reciprocal basis kpt_basis = numpy.zeros((3,3)) kpt_basis[:,0] = ctrl_head['kvec1'] kpt_basis[:,1] = ctrl_head['kvec2'] kpt_basis[:,2] = ctrl_head['kvec3'] kpts = numpy.zeros((n_k, 3)) kpts_cart = numpy.zeros((n_k, 3)) bz_weights = numpy.zeros(n_k) kpt_weights = numpy.zeros(n_k) try: for ik in range(n_k): kx, ky, kz = next(rf), next(rf), next(rf) kpts[ik, :] = kx, ky, kz bz_weights[ik] = next(rf) # bz_weights soon to be removed, and replaced by kpt_weights kpt_weights[ik] = bz_weights[ik] for ik in range(n_k): kx, ky, kz = next(rf), next(rf), next(rf) kpts_cart[ik, :] = kx, ky, kz except StopIteration: raise "VaspConverter: error reading %s"%self.ctrl_file fh.close() # if nc_flag: # VASP.6. if SO == 1: n_spin_blocs = 1 else: n_spin_blocs = SP + 1 # Read PLO groups # First, we read everything into a temporary data structure # TODO: think about multiple shell groups and how to map them on h5 structures assert ng == 1, "Only one group is allowed at the moment" try: for ig in range(ng): gr_file = self.basename + '.pg%i'%(ig + 1) jheader, rf, fh = self.read_header_and_data(gr_file) gr_head = json.loads(jheader) nb_max = gr_head['nb_max'] p_shells = gr_head['shells'] density_required = gr_head['nelect'] charge_below = 0.0 # This is not defined in VASP interface # Note that in the DftTools convention each site gives a separate correlated shell! n_shells = sum([len(sh['ion_list']) for sh in p_shells]) n_corr_shells = sum([len(sh['ion_list']) for sh in p_shells]) shells = [] corr_shells = [] shion_to_shell = [[] for ish in range(len(p_shells))] cr_shion_to_shell = [[] for ish in range(len(p_shells))] shorbs_to_globalorbs = [[] for ish in range(len(p_shells))] last_dimension = 0 crshorbs_to_globalorbs = [] icsh = 0 for ish, sh in enumerate(p_shells): ion_list = sh['ion_list'] for i, ion in enumerate(ion_list): pars = {} pars['atom'] = ion # We set all sites inequivalent pars['sort'] = sh['ion_sort'][i] pars['l'] = sh['lorb'] #pars['corr'] = sh['corr'] pars['dim'] = sh['ndim'] pars['SO'] = SO # TODO: check what 'irep' entry does (it seems to be very specific to dmftproj) pars['irep'] = 0 shells.append(pars) shorbs_to_globalorbs[ish].append([last_dimension, last_dimension + sh['ndim']]) last_dimension = last_dimension + sh['ndim'] if sh['corr']: shion_to_shell[ish].append(icsh) icsh += 1 corr_shells.append(pars) # TODO: generalize this to the case of multiple shell groups n_corr_shells = len(corr_shells) n_orbs = sum([sh['dim'] for sh in shells]) # FIXME: atomic sorts in Wien2K are not the same as in VASP. # A symmetry analysis from OUTCAR or symmetry file should be used # to define equivalence classes of sites. n_inequiv_shells, corr_to_inequiv, inequiv_to_corr = ConverterTools.det_shell_equivalence(self, corr_shells) mpi.report(f" No. of inequivalent shells: {n_inequiv_shells}") # NB!: these rotation matrices are specific to Wien2K! Set to identity in VASP use_rotations = 1 rot_mat = [numpy.identity(corr_shells[icrsh]['dim'],complex) for icrsh in range(n_corr_shells)] rot_mat_time_inv = [0 for i in range(n_corr_shells)] # TODO: implement transformation matrices n_reps = [1 for i in range(n_inequiv_shells)] dim_reps = [0 for i in range(n_inequiv_shells)] T = [] for ish in range(n_inequiv_shells): 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, complex)) hopping = numpy.zeros([n_k, n_spin_blocs, nb_max, nb_max], complex) f_weights = numpy.zeros([n_k, n_spin_blocs, nb_max], complex) band_window = [numpy.zeros((n_k, 2), dtype=int) for isp in range(n_spin_blocs)] n_orbitals = numpy.zeros([n_k, n_spin_blocs], int) for isp in range(n_spin_blocs): for ik in range(n_k): ib1, ib2 = int(next(rf)), int(next(rf)) band_window[isp][ik, :2] = ib1, ib2 nb = ib2 - ib1 + 1 n_orbitals[ik, isp] = nb for ib in range(nb): hopping[ik, isp, ib, ib] = next(rf) f_weights[ik, isp, ib] = next(rf) if self.proj_or_hk == 'hk': hopping = numpy.zeros([n_k, n_spin_blocs, n_orbs, n_orbs], complex) # skip header lines hk_file = self.basename + '.hk%i'%(ig + 1) f_hk = open(hk_file, 'rt') # skip the header (1 line for n_kpoints, n_electrons, n_shells) # and one line per shell count = 0 while count < 3 + n_shells: f_hk.readline() count += 1 rf_hk = self.read_data(f_hk) for isp in range(n_spin_blocs): for ik in range(n_k): n_orbitals[ik, isp] = n_orbs for ib in range(n_orbs): for jb in range(n_orbs): hopping[ik, isp, ib, jb] = next(rf_hk) for ib in range(n_orbs): for jb in range(n_orbs): hopping[ik, isp, ib, jb] += 1j*next(rf_hk) rf_hk.close() # Projectors proj_mat_csc = numpy.zeros([n_k, n_spin_blocs, sum([sh['dim'] for sh in shells]), numpy.max(n_orbitals)], complex) # TODO: implement reading from more than one projector group # In 'dmftproj' each ion represents a separate correlated shell. # In my interface a 'projected shell' includes sets of ions. # How to reconcile this? Two options: # # 1. Redefine 'projected shell' in my interface to make it correspond to one site only. # In this case the list of ions must be defined at the level of the projector group. # # 2. Split my 'projected shell' to several 'correlated shells' here in the converter. # # 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 range(n_spin_blocs): for ik in range(n_k): for ion in range(len(sh['ion_list'])): for ilm in range(shorbs_to_globalorbs[ish][ion][0],shorbs_to_globalorbs[ish][ion][1]): for ib in range(n_orbitals[ik, isp]): # This is to avoid confusion with the order of arguments pr = next(rf) pi = next(rf) proj_mat_csc[ik, isp, ilm, ib] = complex(pr, pi) # 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)], complex) if self.proj_or_hk == 'proj': for ish, sh in enumerate(p_shells): if sh['corr']: for isp in range(n_spin_blocs): for ik in range(n_k): for ion in range(len(sh['ion_list'])): icsh = shion_to_shell[ish][ion] for iclm,ilm in enumerate(range(shorbs_to_globalorbs[ish][ion][0],shorbs_to_globalorbs[ish][ion][1])): for ib in range(n_orbitals[ik, isp]): proj_mat[ik,isp,icsh,iclm,ib] = proj_mat_csc[ik,isp,ilm,ib] elif self.proj_or_hk == 'hk': for ish, sh in enumerate(p_shells): if sh['corr']: for ion in range(len(sh['ion_list'])): icsh = shion_to_shell[ish][ion] for isp in range(n_spin_blocs): for ik in range(n_k): for iclm,ilm in enumerate(range(shorbs_to_globalorbs[ish][ion][0],shorbs_to_globalorbs[ish][ion][1])): 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'] for it in things_to_set: setattr(self,it,locals()[it]) except StopIteration: raise "VaspConverter: error reading %s"%self.gr_file fh.close() proj_or_hk = self.proj_or_hk #new variable: dft_code - this determines which DFT code the inputs come from. #used for certain routines within dft_tools if treating the inputs differently is required. dft_code = 'vasp' # 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) # 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', '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', 'kpts','kpt_weights', 'kpt_basis', 'dft_code'] if self.proj_or_hk == 'hk' or self.proj_or_hk == True: things_to_save.append('proj_mat_csc') for it in things_to_save: ar[self.dft_subgrp][it] = locals()[it] # Store Fermi weights to 'dft_misc_input' 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]['kpts_cart'] = kpts_cart 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)
# TODO: Implement misc_input # self.convert_misc_input(bandwin_file=self.bandwin_file,struct_file=self.struct_file,outputs_file=self.outputs_file, # misc_subgrp=self.misc_subgrp,SO=self.SO,SP=self.SP,n_k=self.n_k)
[docs] def convert_misc_input(self, bandwin_file, struct_file, outputs_file, misc_subgrp, SO, SP, n_k): """ 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 filename of .oubwin/up/dn file. struct_file : string filename of .struct file. outputs_file : string filename of .outputs file. misc_subgrp : string name of the subgroup in which to save SO : boolean spin-orbit switch SP : int spin n_k : int number of k-points """ if not (mpi.is_master_node()): return things_to_save = [] # Read relevant data from .oubwin/up/dn files ############################################# # band_window: Contains the index of the lowest and highest band within the # projected subspace (used by dmftproj) for each k-point. if (SP == 0 or SO == 1): files = [self.bandwin_file] elif SP == 1: 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): mpi.report("Reading input from %s..."%f) R = ConverterTools.read_fortran_file(self, f, self.fortran_to_replace) assert int(next(R)) == n_k, "convert_misc_input: Number of k-points is inconsistent in oubwin file!" assert int(next(R)) == SO, "convert_misc_input: SO is inconsistent in oubwin file!" for ik in range(n_k): next(R) band_window[isp][ik,0] = next(R) # lowest band band_window[isp][ik,1] = next(R) # highest band next(R) things_to_save.append('band_window') R.close() # Reading done! # Read relevant data from .struct file ###################################### # lattice_type: bravais lattice type as defined by Wien2k # lattice_constants: unit cell parameters in a. u. # lattice_angles: unit cell angles in rad 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() lattice_type = R.readline().split()[0] R.readline() temp = R.readline() # print temp lattice_constants = numpy.array([float(temp[0+10*i:10+10*i].strip()) for i in range(3)]) lattice_angles = numpy.array([float(temp[30+10*i:40+10*i].strip()) for i in range(3)]) * numpy.pi / 180.0 things_to_save.extend(['lattice_type', 'lattice_constants', 'lattice_angles']) except IOError: raise "convert_misc_input: reading file %s failed" %self.struct_file # 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: while 1: temp = R.readline().strip(' ').split() if (temp[0] =='PGBSYM:'): n_symmetries = int(temp[-1]) break for i in range(n_symmetries): while 1: if (R.readline().strip().split()[0] == 'Symmetry'): break sym_i = numpy.zeros((3, 3), dtype = float) for ir in range(3): temp = R.readline().strip().split() for ic in range(3): sym_i[ir, ic] = float(temp[ic]) R.readline() rot_symmetries.append(sym_i) things_to_save.extend(['n_symmetries', 'rot_symmetries']) things_to_save.append('rot_symmetries') except IOError: raise "convert_misc_input: reading file %s failed" %self.outputs_file # Save it to the HDF: with HDFArchive(self.hdf_file,'a') as ar: if not (misc_subgrp in ar): ar.create_group(misc_subgrp) for it in things_to_save: ar[misc_subgrp][it] = locals()[it]
[docs] 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 symm_subgrp : name of symmetry group in h5 archive """ # In VASP interface the symmetries are read directly from *.ctrl file # For the moment the symmetry parameters are just stubs n_symm = 0 n_atoms = 1 perm = [0] n_orbits = len(orbits) SP = ctrl_head['ns'] SO = ctrl_head['nc_flag'] time_inv = [0] mat = [numpy.identity(1)] mat_tinv = [numpy.identity(1)] # Save it to the HDF: with HDFArchive(self.hdf_file,'a') as ar: 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'] for it in things_to_save: ar[symm_subgrp][it] = locals()[it]