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ab2xsf
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#!/usr/bin/perl
#
# Copyright (C) 2010 ABINIT group
#
# Written by Gian-Marco Rignanese in perl
# 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/users/acknowledgments.html for suggested
# acknowledgments of the ABINIT effort.
#
# For more information, see http://www.abinit.org .
#
$r0=0.5291772083;
$rprim1[0] = 1.0; $rprim1[1] = 0.0; $rprim1[2] = 0.0;
$rprim2[0] = 0.0; $rprim2[1] = 1.0; $rprim2[2] = 0.0;
$rprim3[0] = 0.0; $rprim3[1] = 0.0; $rprim3[2] = 1.0;
$ianimstep = 1;
for($ifil=0;$ifil<=$#ARGV;$ifil++){
@file=`cat $ARGV[$ifil]`;
while($line=shift(@file)){
# print "### ", $line;
if($line =~ / natom =/){
# print "line with natom =\n";
# print $line;
@parts=split(' ',$line);
# print "parts0 = $parts[0] \n";
while ($parts[0] ne "natom") {shift @parts;}
$natom=$parts[2];
#print "natom = ", $natom;
}
if($line =~ / acell[0-9]*/){
@acell = split(' ',$line);
shift (@acell);
@acell[0] *= $r0;
@acell[1] *= $r0;
@acell[2] *= $r0;
#print "acell = ", @acell;
}
if($line =~ / acell=/){
@acell = split(' ',$line);
shift (@acell);
@acell[0] *= $r0;
@acell[1] *= $r0;
@acell[2] *= $r0;
#print "acell = ", @acell;
}
if($line =~ / rprim[0-9]*/){
@tmp=split(' ',$line);
$rprim1[0] = $tmp[1];
$rprim1[1] = $tmp[2];
$rprim1[2] = $tmp[3];
$line=shift(@file);
@tmp=split(' ',$line);
$rprim2[0] = $tmp[0];
$rprim2[1] = $tmp[1];
$rprim2[2] = $tmp[2];
$line=shift(@file);
@tmp=split(' ',$line);
$rprim3[0] = $tmp[0];
$rprim3[1] = $tmp[1];
$rprim3[2] = $tmp[2];
#print "rprim = ", @rprim1,@rprim2,@rprim3;
}
if($line =~ / rprim=/){
@tmp=split(' ',$line);
$rprim1[0] = $tmp[1];
$rprim1[1] = $tmp[2];
$rprim1[2] = $tmp[3];
$line=shift(@file);
@tmp=split(' ',$line);
$rprim2[0] = $tmp[0];
$rprim2[1] = $tmp[1];
$rprim2[2] = $tmp[2];
$line=shift(@file);
@tmp=split(' ',$line);
$rprim3[0] = $tmp[0];
$rprim3[1] = $tmp[1];
$rprim3[2] = $tmp[2];
#print "rprim = ", @rprim1,@rprim2,@rprim3;
}
if($line =~ / typat[0-9]*/){
# for($ii=1;$ii<50;$ii++){
# if($natom>=$ii*20){
# $line=$line.shift(@file);
## print "now line = ", $line
# }
# }
@typ=split(' ',$line);
shift (@typ);
#print "typat 0 = ", @typ, "\n";
}
if($line =~ / type[0-9]*/){
for($ii=1;$ii<50;$ii++){
if($natom>=$ii*20){
$line=$line.shift(@file);
}
}
@typ=split(' ',$line);
shift (@typ);
#print "type 0 = ", $typ;
}
#print $line,$line =~ / xangst /;
if($line =~ / xangst[0-9]* /){
@pos = split (' ', $line);
# print "line ", $line, "\n";
# print "pos ", $pos[0], $pos[1], $pos[2], $pos[3], "\n";
# already in angstroems
$xcoord[0] = $pos[1];
$ycoord[0] = $pos[2];
$zcoord[0] = $pos[3];
$iat=1;
while(!($line =~ / xcart[0-9]* /)){
# print "in xangst clause ", $line;
$line=shift(@file);
@pos=split(' ',$line);
# already in angstroems
$xcoord[$iat] = $pos[0];
$ycoord[$iat] = $pos[1];
$zcoord[$iat] = $pos[2];
$iat++;
}
}
if($line =~ /Cartesian coordinates \(bohr\)/){
$line=shift(@file);
# print "zatnum = ", $zatnum;
print $acell;
print $rprim1,$rprim2,$rprim3;
$iat=0;
while(!($line =~ /Cartesian force/)){
@pos=split(' ',$line);
$xcoord[$iat] = $pos[0]*$r0;
$ycoord[$iat] = $pos[1]*$r0;
$zcoord[$iat] = $pos[2]*$r0;
$iat++;
$line=shift(@file);
}
print "DIM-GROUP\n";
print "3 1\n";
print "PRIMVEC\n";
printf ("%20.10f %20.10f %20.10f \n",
$rprim1[0]*$acell[0], $rprim1[1]*$acell[0], $rprim1[2]*$acell[0]);
printf ("%20.10f %20.10f %20.10f \n",
$rprim2[0]*$acell[1], $rprim2[1]*$acell[1], $rprim2[2]*$acell[1]);
printf ("%20.10f %20.10f %20.10f \n",
$rprim3[0]*$acell[2], $rprim3[1]*$acell[2], $rprim3[2]*$acell[2]);
print "PRIMCOORD\n";
$ianimstep++;
printf ("$natom 1 \n");
for ($iatom=0; $iatom<$natom; $iatom++)
{
printf ("%d %20.10f %20.10f %20.10f\n", $zatnum[$typ[$iatom]],
$xcoord[$iatom], $ycoord[$iatom], $zcoord[$iatom]);
}
# print "ATOMS\n";
# for ($iatom=0; $iatom<$natom; $iatom++)
# {
# printf ("%d %20.10f %20.10f %20.10f\n", $zatnum[$typ[$iatom]],
# $xcoord[$iatom], $ycoord[$iatom], $zcoord[$iatom]);
# }
}
if($line =~ / zatnum / || $line =~ / znucl /){
@zatnum=split(' ',$line);
# print "zatnum 0 = ", $zatnum, $line;
# print "xcoord ", $xcoord[0], $xcoord[1], $xcoord[2];
# print "ycoord ", $ycoord[0], $ycoord[1], $ycoord[2];
# print "zcoord ", $zcoord[0], $zcoord[1], $zcoord[2];
#
print "DIM-GROUP\n";
print "3 1\n";
print "PRIMVEC\n";
printf ("%20.10f %20.10f %20.10f \n",
$rprim1[0]*$acell[0], $rprim1[1]*$acell[0], $rprim1[2]*$acell[0]);
printf ("%20.10f %20.10f %20.10f \n",
$rprim2[0]*$acell[1], $rprim2[1]*$acell[1], $rprim2[2]*$acell[1]);
printf ("%20.10f %20.10f %20.10f \n",
$rprim3[0]*$acell[2], $rprim3[1]*$acell[2], $rprim3[2]*$acell[2]);
print "PRIMCOORD\n";
$ianimstep++;
printf ("$natom 1 \n");
for ($iatom=0; $iatom<$natom; $iatom++)
{
printf ("%d %20.10f %20.10f %20.10f\n", $zatnum[$typ[$iatom]],
$xcoord[$iatom], $ycoord[$iatom], $zcoord[$iatom]);
}
# print "ATOMS\n";
# for ($iatom=0; $iatom<$natom; $iatom++)
# {
# printf ("%d %20.10f %20.10f %20.10f\n", $zatnum[$typ[$iatom]],
# $xcoord[$iatom], $ycoord[$iatom], $zcoord[$iatom]);
# }
#
}
}
}
#***************************************************8