dft_tools/python/converters/plovasp/plotools.py

 
################################################################################
#
# 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/>.
#
################################################################################
r"""
    vasp.plotools
    =============

    Set of routines for processing and outputting PLOs.

    This is the main module containing routines responsible for checking
    the consistency of the input data, generation of projected localized
    orbitals (PLOs) out of raw VASP projectors, and outputting data
    required by DFTTools.
"""
import itertools as it
import numpy as np
from proj_group import ProjectorGroup
from proj_shell import ProjectorShell

np.set_printoptions(suppress=True)

# 'simplejson' is supposed to be faster than 'json' in stdlib.
try:
    import simplejson as json
except ImportError:
    import json

def issue_warning(message):
    """
    Issues a warning.
    """
    print
    print "  !!! WARNING !!!: " + message
    print

################################################################################
# check_data_consistency()
################################################################################
def check_data_consistency(pars, el_struct):
    """
    Check the consistency of the VASP data.
    """
# Check that ions inside each shell are of the same sort
    for sh in pars.shells:
        max_ion_index = max([max(gr) for gr in sh['ions']['ion_list']])
        assert max_ion_index < el_struct.natom, "Site index in the projected shell exceeds the number of ions in the structure"
        ion_list = list(it.chain(*sh['ions']['ion_list']))

        sorts = set([el_struct.type_of_ion[io] for io in ion_list])
        assert len(sorts) == 1, "Each projected shell must contain only ions of the same sort"

# Check that ion and orbital lists in shells match those of projectors
        lshell = sh['lshell']
        for ion in ion_list:
            for par in el_struct.proj_params:
                if par['isite'] - 1 == ion and par['l'] == lshell:
                    break
            else:
                errmsg = "Projector for isite = %s, l = %s does not match PROJCAR"%(ion + 1, lshell)
                raise Exception(errmsg)
        
################################################################################
#
# generate_plo()
#
################################################################################
def generate_plo(conf_pars, el_struct):
    """
    Parameters
    ----------

      conf_pars (dict) : dictionary of input parameters (from conf-file)
      el_struct : ElectronicStructure object
    """

    check_data_consistency(conf_pars, el_struct)

    proj_raw = el_struct.proj_raw
    try:
        efermi = conf_pars.general['efermi']
    except (KeyError, AttributeError):
        efermi = el_struct.efermi

# eigvals(nktot, nband, ispin) are defined with respect to the Fermi level
    eigvals = el_struct.eigvals - efermi

    nshell = len(conf_pars.shells)
    print
    print "  Generating %i shell%s..."%(nshell, '' if nshell == 1 else 's')
    pshells = []
    for sh_par in conf_pars.shells:
        pshell = ProjectorShell(sh_par, proj_raw, el_struct.proj_params, el_struct.kmesh, el_struct.structure, el_struct.nc_flag)
        print
        print "    Shell         : %s"%(pshell.user_index)
        print "    Orbital l     : %i"%(pshell.lorb)
        print "    Number of ions: %i"%(pshell.nion)
        print "    Dimension     : %i"%(pshell.ndim)
        pshells.append(pshell)

    pgroups = []
    for gr_par in conf_pars.groups:
        pgroup = ProjectorGroup(gr_par, pshells, eigvals)
        pgroup.orthogonalize()
# DEBUG output
        print "Density matrix:"
        dm_all, ov_all = pshells[pgroup.ishells[0]].density_matrix(el_struct)
        nimp = 0.0
        spin_fac = 2 if dm_all.shape[0] == 1 else 1
        for io in xrange(dm_all.shape[1]):
            print "  Site %i"%(io + 1)
            dm = spin_fac * dm_all[:, io, : ,:].sum(0)
            for row in dm:
                print ''.join(map("{0:12.7f}".format, row))
            ndm = dm.trace()
            nimp += ndm
            print "    trace: ", ndm
        print
        print "  Impurity density:", nimp
        print
        print "Overlap:"
        for io, ov in enumerate(ov_all[0]):
            print "  Site %i"%(io + 1)
            print ov
        print
        print "Local Hamiltonian:"
        loc_ham = pshells[pgroup.ishells[0]].local_hamiltonian(el_struct)
        for io in xrange(loc_ham.shape[1]):
            print "  Site %i"%(io + 1)
            for row in loc_ham[:, io, :, :].sum(0):
                print ''.join(map("{0:12.7f}".format, row))
# END DEBUG output
        if 'dosmesh' in conf_pars.general:
            print
            print "Evaluating DOS..."
            mesh_pars = conf_pars.general['dosmesh']
            if np.isnan(mesh_pars['emin']):
                dos_emin = pgroup.emin
                dos_emax = pgroup.emax
            else:
                dos_emin = mesh_pars['emin']
                dos_emax = mesh_pars['emax']
            n_points = mesh_pars['n_points']

            emesh = np.linspace(dos_emin, dos_emax, n_points)
            dos = pshells[pgroup.ishells[0]].density_of_states(el_struct, emesh)
            de = emesh[1] - emesh[0]
            ntot = (dos[1:,...] + dos[:-1,...]).sum(0) / 2 * de
            print "  Total number of states:", ntot
            for io in xrange(dos.shape[2]):
                np.savetxt('pdos_%i.dat'%(io), np.vstack((emesh.T, dos[:, 0, io, :].T)).T)

        pgroups.append(pgroup)

    return pshells, pgroups

################################################################################
#
# output_as_text
#
################################################################################
def output_as_text(pars, el_struct, pshells, pgroups):
    """
    Output all information necessary for the converter as text files.
    """
    ctrl_output(pars, el_struct, len(pgroups))
    plo_output(pars, el_struct, pshells, pgroups)


# TODO: k-points with weights should be stored once and for all
################################################################################
#
# kpoints_output
#
################################################################################
def kpoints_output(basename, el_struct):
    """
    Outputs k-point data into a text file.
    """
    kmesh = el_struct.kmesh
    fname = basename + '.kpoints'
    with open(fname, 'wt') as f:
        f.write("# Number of k-points: nktot\n")
        nktot = kmesh['nktot']
        f.write("%i\n"%(nktot))
# TODO: add the output of reciprocal lattice vectors
        f.write("# List of k-points with weights\n")
        for ik in xrange(nktot):
            kx, ky, kz = kmesh['kpoints'][ik, :]
            kwght = kmesh['kweights'][ik]
            f.write("%15.10f%15.10f%15.10f%20.10f\n"%(kx, ky, kz, kwght))

# Check if there are tetrahedra defined and if they are, output them
        try:
            ntet = kmesh['ntet']
            volt = kmesh['volt']
            f.write("\n# Number of tetrahedra and volume: ntet, volt\n")
            f.write("%i %s\n"%(ntet, volt))
            f.write("# List of tetrahedra: imult, ik1, ..., ik4\n")
            for it in xrange(ntet):
                f.write('  '.join(map("{0:d}".format, *kmesh['itet'][it, :])) + '\n')
        except KeyError:
            pass


################################################################################
#
# ctrl_output
#
################################################################################
def ctrl_output(conf_pars, el_struct, ng):
    """
    Outputs a ctrl-file.
    """
    ctrl_fname = conf_pars.general['basename'] + '.ctrl'
    head_dict = {}

# TODO: Add output of tetrahedra
# Construct the header dictionary
    head_dict['ngroups'] = ng
    head_dict['nk'] = el_struct.kmesh['nktot']
    head_dict['ns'] = el_struct.nspin
    head_dict['nc_flag'] = 1 if el_struct.nc_flag else 0
#    head_dict['efermi'] = conf_pars.general['efermi']  # We probably don't need Efermi

    header = json.dumps(head_dict, indent=4, separators=(',', ': '))

    print "  Storing ctrl-file..."
    with open(ctrl_fname, 'wt') as f:
        f.write(header + "\n")
        f.write("#END OF HEADER\n")

        f.write("# k-points and weights\n")
        labels = ['kx', 'ky', 'kz', 'kweight']
        out = "".join(map(lambda s: s.center(15), labels))
        f.write("#" + out + "\n")
        for ik, kp in enumerate(el_struct.kmesh['kpoints']):
            tmp1 = "".join(map("{0:15.10f}".format, kp))
            out = tmp1 + "{0:16.10f}".format(el_struct.kmesh['kweights'][ik])
            f.write(out + "\n")


################################################################################
#
# plo_output
#
################################################################################
def plo_output(conf_pars, el_struct, pshells, pgroups):
    """
    Outputs PLO groups into text files.

    Filenames are defined by <basename> that is passed from config-file.
    All necessary general parameters are stored in a file '<basename>.ctrl'.

    Each group is stored in a '<basename>.plog<Ng>' file. The format is the
    following:

    # Energy window: emin, emax
    ib_min, ib_max
    nelect
    # Eigenvalues
    isp, ik1, kx, ky, kz, kweight
    ib1, ib2
    eig1
    eig2
    ...
    eigN
    ik2, kx, ky, kz, kweight
    ...

    # Projected shells
    Nshells
    # Shells: <shell indices>
    # Shell <1>
    Shell 1
    ndim
    # complex arrays: plo(ns, nion, ndim, nb)
    ...
    # Shells: <shell indices>
    # Shell <2>
    Shell 2
    ...

    """
    for ig, pgroup in enumerate(pgroups):
        plo_fname = conf_pars.general['basename'] + '.pg%i'%(ig + 1)
        print "  Storing PLO-group file '%s'..."%(plo_fname)
        head_dict = {}

        head_dict['ewindow'] = (pgroup.emin, pgroup.emax)
        head_dict['nb_max'] = pgroup.nb_max

# Number of electrons within the window
        head_dict['nelect'] = pgroup.nelect_window(el_struct)
        print "  Density within window:", head_dict['nelect']

        head_shells = []
        for ish in pgroup.ishells:
            shell = pgroup.shells[ish]
            sh_dict = {}
            sh_dict['shell_index'] = ish
            sh_dict['lorb'] = shell.lorb
            sh_dict['ndim'] = shell.ndim
# Convert ion indices from the internal representation (starting from 0)
# to conventional VASP representation (starting from 1)
            ion_output = [io + 1 for io in shell.ion_list]
# Derive sorts from equivalence classes
            sh_dict['ion_list'] = ion_output
            sh_dict['ion_sort'] = shell.ion_sort

# TODO: add the output of transformation matrices

            head_shells.append(sh_dict)

        head_dict['shells'] = head_shells

        header = json.dumps(head_dict, indent=4, separators=(',', ': '))

        with open(plo_fname, 'wt') as f:
            f.write(header + "\n")
            f.write("#END OF HEADER\n")
            
# Eigenvalues within the window
            f.write("# Eigenvalues within the energy window: %s, %s\n"%(pgroup.emin, pgroup.emax))
            nk, nband, ns_band = el_struct.eigvals.shape
            for isp in xrange(ns_band):
                f.write("# is = %i\n"%(isp + 1))
                for ik in xrange(nk):
                    ib1, ib2 = pgroup.ib_win[ik, isp, 0], pgroup.ib_win[ik, isp, 1]
# Output band indices in Fortran convention!
                    f.write(" %i  %i\n"%(ib1 + 1, ib2 + 1))
                    for ib in xrange(ib1, ib2 + 1):
                        eigv_ef = el_struct.eigvals[ik, ib, isp] - el_struct.efermi
                        f_weight = el_struct.ferw[isp, ik, ib]
                        f.write("%13.8f %12.7f\n"%(eigv_ef, f_weight))

# Projected shells
            f.write("# Projected shells\n")
            f.write("# Shells: %s\n"%(pgroup.ishells))
            for ish in pgroup.ishells:
                shell = pgroup.shells[ish]
                f.write("# Shell %i\n"%(ish))

                nion, ns, nk, nlm, nb = shell.proj_win.shape
                for isp in xrange(ns):
                    f.write("# is = %i\n"%(isp + 1))
                    for ik in xrange(nk):
                        f.write("# ik = %i\n"%(ik + 1))
                        for ion in xrange(nion):
                            for ilm in xrange(nlm):
                                ib1, ib2 = pgroup.ib_win[ik, isp, 0], pgroup.ib_win[ik, isp, 1]
                                ib_win = ib2 - ib1 + 1
                                for ib in xrange(ib_win):
                                    p = shell.proj_win[ion, isp, ik, ilm, ib]
                                    f.write("{0:16.10f}{1:16.10f}\n".format(p.real, p.imag))
                                f.write("\n")