mirror of
https://github.com/triqs/dft_tools
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0ae83d18b3
Now the projectors are defined in agreement with the formulas in Amadon et al. Specifically, the phase exp(-i k Q) for site Q is included.
377 lines
13 KiB
Python
377 lines
13 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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r"""
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vasp.plotools
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=============
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Set of routines for processing and outputting PLOs.
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This is the main module containing routines responsible for checking
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the consistency of the input data, generation of projected localized
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orbitals (PLOs) out of raw VASP projectors, and outputting data
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required by DFTTools.
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"""
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import itertools as it
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import numpy as np
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from proj_group import ProjectorGroup
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from proj_shell import ProjectorShell
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np.set_printoptions(suppress=True)
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# 'simplejson' is supposed to be faster than 'json' in stdlib.
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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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def issue_warning(message):
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"""
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Issues a warning.
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"""
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print
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print " !!! WARNING !!!: " + message
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print
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################################################################################
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# check_data_consistency()
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################################################################################
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def check_data_consistency(pars, el_struct):
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"""
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Check the consistency of the VASP data.
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"""
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# Check that ions inside each shell are of the same sort
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for sh in pars.shells:
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assert max(sh['ion_list']) <= el_struct.natom, "Site index in the projected shell exceeds the number of ions in the structure"
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sorts = set([el_struct.type_of_ion[io] for io in sh['ion_list']])
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assert len(sorts) == 1, "Each projected shell must contain only ions of the same sort"
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# Check that ion and orbital lists in shells match those of projectors
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ion_list = sh['ion_list']
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lshell = sh['lshell']
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for ion in ion_list:
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for par in el_struct.proj_params:
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if par['isite'] - 1 == ion and par['l'] == lshell:
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break
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else:
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errmsg = "Projector for isite = %s, l = %s does not match PROJCAR"%(ion + 1, lshell)
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raise Exception(errmsg)
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################################################################################
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#
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# generate_plo()
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#
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################################################################################
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def generate_plo(conf_pars, el_struct):
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"""
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Parameters
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----------
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conf_pars (dict) : dictionary of input parameters (from conf-file)
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el_struct : ElectronicStructure object
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"""
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check_data_consistency(conf_pars, el_struct)
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proj_raw = el_struct.proj_raw
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try:
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efermi = conf_pars.general['efermi']
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except (KeyError, AttributeError):
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efermi = el_struct.efermi
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# eigvals(nktot, nband, ispin) are defined with respect to the Fermi level
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eigvals = el_struct.eigvals - efermi
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nshell = len(conf_pars.shells)
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print
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print " Generating %i shell%s..."%(nshell, '' if nshell == 1 else 's')
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pshells = []
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for sh_par in conf_pars.shells:
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pshell = ProjectorShell(sh_par, proj_raw, el_struct.proj_params, el_struct.kmesh, el_struct.structure, el_struct.nc_flag)
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print
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print " Shell : %s"%(pshell.user_index)
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print " Orbital l : %i"%(pshell.lorb)
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print " Number of ions: %i"%(len(pshell.ion_list))
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print " Dimension : %i"%(pshell.ndim)
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pshells.append(pshell)
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pgroups = []
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for gr_par in conf_pars.groups:
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pgroup = ProjectorGroup(gr_par, pshells, eigvals)
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pgroup.orthogonalize()
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# DEBUG output
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print "Density matrix:"
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dm_all, ov_all = pshells[pgroup.ishells[0]].density_matrix(el_struct)
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nimp = 0.0
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spin_fac = 2 if dm_all.shape[0] == 1 else 1
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for io in xrange(dm_all.shape[1]):
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print " Site %i"%(io + 1)
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dm = spin_fac * dm_all[:, io, : ,:].sum(0)
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for row in dm:
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print ''.join(map("{0:12.7f}".format, row))
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ndm = dm.trace()
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nimp += ndm
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print " trace: ", ndm
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print
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print " Impurity density:", nimp
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print
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print "Overlap:"
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for io, ov in enumerate(ov_all[0]):
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print " Site %i"%(io + 1)
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print ov
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print
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print "Local Hamiltonian:"
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loc_ham = pshells[pgroup.ishells[0]].local_hamiltonian(el_struct)
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for io in xrange(loc_ham.shape[1]):
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print " Site %i"%(io + 1)
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for row in loc_ham[:, io, :, :].sum(0):
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print ''.join(map("{0:12.7f}".format, row))
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# END DEBUG output
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if 'dosmesh' in conf_pars.general:
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print
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print "Evaluating DOS..."
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mesh_pars = conf_pars.general['dosmesh']
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if np.isnan(mesh_pars['emin']):
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dos_emin = pgroup.emin
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dos_emax = pgroup.emax
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else:
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dos_emin = mesh_pars['emin']
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dos_emax = mesh_pars['emax']
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n_points = mesh_pars['n_points']
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emesh = np.linspace(dos_emin, dos_emax, n_points)
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dos = pshells[pgroup.ishells[0]].density_of_states(el_struct, emesh)
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de = emesh[1] - emesh[0]
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ntot = (dos[1:,...] + dos[:-1,...]).sum(0) / 2 * de
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print " Total number of states:", ntot
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for io in xrange(dos.shape[2]):
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np.savetxt('pdos_%i.dat'%(io), np.vstack((emesh.T, dos[:, 0, io, :].T)).T)
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pgroups.append(pgroup)
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return pshells, pgroups
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################################################################################
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#
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# output_as_text
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#
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################################################################################
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def output_as_text(pars, el_struct, pshells, pgroups):
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"""
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Output all information necessary for the converter as text files.
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"""
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ctrl_output(pars, el_struct, len(pgroups))
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plo_output(pars, el_struct, pshells, pgroups)
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# TODO: k-points with weights should be stored once and for all
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################################################################################
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#
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# kpoints_output
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#
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################################################################################
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def kpoints_output(basename, el_struct):
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"""
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Outputs k-point data into a text file.
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"""
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kmesh = el_struct.kmesh
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fname = basename + '.kpoints'
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with open(fname, 'wt') as f:
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f.write("# Number of k-points: nktot\n")
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nktot = kmesh['nktot']
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f.write("%i\n"%(nktot))
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# TODO: add the output of reciprocal lattice vectors
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f.write("# List of k-points with weights\n")
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for ik in xrange(nktot):
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kx, ky, kz = kmesh['kpoints'][ik, :]
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kwght = kmesh['kweights'][ik]
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f.write("%15.10f%15.10f%15.10f%20.10f\n"%(kx, ky, kz, kwght))
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# Check if there are tetrahedra defined and if they are, output them
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try:
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ntet = kmesh['ntet']
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volt = kmesh['volt']
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f.write("\n# Number of tetrahedra and volume: ntet, volt\n")
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f.write("%i %s\n"%(ntet, volt))
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f.write("# List of tetrahedra: imult, ik1, ..., ik4\n")
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for it in xrange(ntet):
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f.write(' '.join(map("{0:d}".format, *kmesh['itet'][it, :])) + '\n')
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except KeyError:
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pass
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################################################################################
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#
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# ctrl_output
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#
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################################################################################
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def ctrl_output(conf_pars, el_struct, ng):
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"""
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Outputs a ctrl-file.
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"""
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ctrl_fname = conf_pars.general['basename'] + '.ctrl'
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head_dict = {}
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# TODO: Add output of tetrahedra
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# Construct the header dictionary
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head_dict['ngroups'] = ng
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head_dict['nk'] = el_struct.kmesh['nktot']
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head_dict['ns'] = el_struct.nspin
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head_dict['nc_flag'] = 1 if el_struct.nc_flag else 0
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# head_dict['efermi'] = conf_pars.general['efermi'] # We probably don't need Efermi
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header = json.dumps(head_dict, indent=4, separators=(',', ': '))
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print " Storing ctrl-file..."
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with open(ctrl_fname, 'wt') as f:
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f.write(header + "\n")
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f.write("#END OF HEADER\n")
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f.write("# k-points and weights\n")
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labels = ['kx', 'ky', 'kz', 'kweight']
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out = "".join(map(lambda s: s.center(15), labels))
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f.write("#" + out + "\n")
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for ik, kp in enumerate(el_struct.kmesh['kpoints']):
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tmp1 = "".join(map("{0:15.10f}".format, kp))
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out = tmp1 + "{0:16.10f}".format(el_struct.kmesh['kweights'][ik])
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f.write(out + "\n")
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################################################################################
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#
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# plo_output
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#
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################################################################################
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def plo_output(conf_pars, el_struct, pshells, pgroups):
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"""
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Outputs PLO groups into text files.
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Filenames are defined by <basename> that is passed from config-file.
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All necessary general parameters are stored in a file '<basename>.ctrl'.
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Each group is stored in a '<basename>.plog<Ng>' file. The format is the
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following:
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# Energy window: emin, emax
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ib_min, ib_max
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nelect
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# Eigenvalues
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isp, ik1, kx, ky, kz, kweight
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ib1, ib2
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eig1
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eig2
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...
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eigN
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ik2, kx, ky, kz, kweight
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...
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# Projected shells
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Nshells
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# Shells: <shell indices>
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# Shell <1>
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Shell 1
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ndim
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# complex arrays: plo(ns, nion, ndim, nb)
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...
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# Shells: <shell indices>
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# Shell <2>
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Shell 2
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...
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"""
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for ig, pgroup in enumerate(pgroups):
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plo_fname = conf_pars.general['basename'] + '.pg%i'%(ig + 1)
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print " Storing PLO-group file '%s'..."%(plo_fname)
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head_dict = {}
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head_dict['ewindow'] = (pgroup.emin, pgroup.emax)
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head_dict['nb_max'] = pgroup.nb_max
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# Number of electrons within the window
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head_dict['nelect'] = pgroup.nelect_window(el_struct)
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print " Density within window:", head_dict['nelect']
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head_shells = []
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for ish in pgroup.ishells:
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shell = pgroup.shells[ish]
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sh_dict = {}
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sh_dict['shell_index'] = ish
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sh_dict['lorb'] = shell.lorb
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sh_dict['ndim'] = shell.ndim
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# Convert ion indices from the internal representation (starting from 0)
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# to conventional VASP representation (starting from 1)
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ion_output = [io + 1 for io in shell.ion_list]
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sh_dict['ion_list'] = ion_output
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sh_dict['ion_sort'] = el_struct.type_of_ion[shell.ion_list[0]]
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# TODO: add the output of transformation matrices
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head_shells.append(sh_dict)
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head_dict['shells'] = head_shells
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header = json.dumps(head_dict, indent=4, separators=(',', ': '))
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with open(plo_fname, 'wt') as f:
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f.write(header + "\n")
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f.write("#END OF HEADER\n")
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# Eigenvalues within the window
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f.write("# Eigenvalues within the energy window: %s, %s\n"%(pgroup.emin, pgroup.emax))
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nk, nband, ns_band = el_struct.eigvals.shape
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for isp in xrange(ns_band):
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f.write("# is = %i\n"%(isp + 1))
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for ik in xrange(nk):
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ib1, ib2 = pgroup.ib_win[ik, isp, 0], pgroup.ib_win[ik, isp, 1]
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# Output band indices in Fortran convention!
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f.write(" %i %i\n"%(ib1 + 1, ib2 + 1))
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for ib in xrange(ib1, ib2 + 1):
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eigv_ef = el_struct.eigvals[ik, ib, isp] - el_struct.efermi
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f_weight = el_struct.ferw[isp, ik, ib]
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f.write("%13.8f %12.7f\n"%(eigv_ef, f_weight))
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# Projected shells
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f.write("# Projected shells\n")
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f.write("# Shells: %s\n"%(pgroup.ishells))
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for ish in pgroup.ishells:
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shell = pgroup.shells[ish]
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f.write("# Shell %i\n"%(ish))
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nion, ns, nk, nlm, nb = shell.proj_win.shape
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for isp in xrange(ns):
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f.write("# is = %i\n"%(isp + 1))
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for ik in xrange(nk):
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f.write("# ik = %i\n"%(ik + 1))
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for ion in xrange(nion):
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for ilm in xrange(nlm):
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ib1, ib2 = pgroup.ib_win[ik, isp, 0], pgroup.ib_win[ik, isp, 1]
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ib_win = ib2 - ib1 + 1
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for ib in xrange(ib_win):
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p = shell.proj_win[ion, isp, ik, ilm, ib]
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f.write("{0:16.10f}{1:16.10f}\n".format(p.real, p.imag))
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f.write("\n")
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