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#! /usr/bin/python
# Copyright (C) 2010-2022 ABINIT group
#
# Written by Matthieu Verstraete in python (compatible v1.9).
# This is free software, and you are welcome to redistribute it
# under certain conditions (GNU General Public License,
# see ~abinit/COPYING or http://www.gnu.org/copyleft/gpl.txt).
#
# ABINIT is a project of the Universite Catholique de Louvain,
# Corning Inc. and other collaborators, see ~abinit/doc/developers/contributors.txt.
# Please read ~abinit/doc/biblio/generated_files/bib_acknow.html for suggested
# acknowledgments of the ABINIT effort.
#
# For more information, see https://www.abinit.org .
#
# This script is to be used with the PHON code (or equivalent)
# to calculate frozen phonon frequencies, free energies, etc...
# It takes a DISP file of atomic displacements and an SPOSCAR file
# with a with a supercell structure (VASP/PHON formats), and creates
# the necessary lines for an abinit input file to calculate the
# forces in displaced configurations.
# See http://chianti.geol.ucl.ac.uk/~dario or
# D. Alfe, Computer Physics Communications 180,2622-2633 (2009)
#
# NOTE: the symmetries in the present (1.28 8/2010) version of PHON
# are not functioning properly in some cases. It is your own
# responsibility to check it, and has nothing to do with ABINIT.
#
# How to use:
#
# 1) run abinit for the relaxed structure with prtposcar 1.
# this creates a reference XXX_POSCAR file, which you should rename
# POSCAR.
# 2) run phon with LSUPER=.true. or (e.g.) phonopy -d --dim="2 2 3"
# to create the SPOSCAR and DISP files
# 3) run this script (phondisp2abi.py).
# 4) copy script output to the abinit input file (removing duplicate
# input variables etc...)
# 5) run abinit for each of the given datasets (and prtposcar 1 still)
# 6) concatenate the resulting XXX_FORCES files into one FORCES file
# You also need to include the header lines for each displacement,
# which are given by phondisp2abi.py in comments for each dataset
# 7) run phon again to get the desired phonons and properties.
#
#
import re
import string
import numpy
import numpy.linalg
#
# convert PHON DISP and SPOSCAR files into ABINIT datasets with appropriately displaced atoms
#
fp_disp = open('DISP')
lines_disp = fp_disp.readlines()
fp_sposcar = open('SPOSCAR')
lines_sposcar = fp_sposcar.readlines()
# make unit cell input line
rprimd = numpy.zeros((3,3))
for idir in range(3):
line = lines_sposcar[2+idir]
tokens = map(float,string.split(line))
rprimd[0][idir] = tokens[0]
rprimd[1][idir] = tokens[1]
rprimd[2][idir] = tokens[2]
# get equilibirum positions
equilxred=[]
for line in lines_sposcar[7:]:
equilxred.append(numpy.array(map(float,string.split(line))))
# output unit cell input line
print "# Add this to the abinit input file to do the PHON displacements"
print "# given in the DISP file, with respect to the supercell in SPOSCAR"
print "#"
print "# Remember the POSCAR files have sorted the atomic types so the positions"
print "# and displacements are now type ordered (fix typat, spinat, etc!)"
print "#"
print "ndtset ", len(lines_disp)
print "# supercell lattice vectors "
print "acell 1 1 1 Angstr"
print "rprim"
print " %24.14f %24.14f %24.14f" % (rprimd[0][0], rprimd[1][0], rprimd[2][0])
print " %24.14f %24.14f %24.14f" % (rprimd[0][1], rprimd[1][1], rprimd[2][1])
print " %24.14f %24.14f %24.14f" % (rprimd[0][2], rprimd[1][2], rprimd[2][2])
idtset=1
# for each displacement,
for line in lines_disp:
tokens = string.split(line)
# get displacement in reduced coordinates
iatom = int(tokens[1])
dispred = numpy.array(map(float,tokens[2:5]))
# add displacement to correct atom
xred = list(equilxred)
xred[iatom-1] = xred[iatom-1] + dispred
# output xred for this dataset
print "# add the following line, without the #, to the FORCES file for this dtset, when concatenating"
print "# %d %24.14f %24.14f %24.14f" % (iatom, dispred[0], dispred[1], dispred[2])
print "xred%d" % (idtset,)
for xred_1at in xred:
print " %24.14f %24.14f %24.14f" % (xred_1at[0], xred_1at[1], xred_1at[2])
# increment dataset counter
idtset=idtset+1
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