Poscar2xcrysden.pl

1. ! /usr/bin/perl

1. ----------------------------------------------------------------
2. PROGRAM FOR GENERATE XCRYSDEN INPUTS

1. OF VASP POSCAR/CONTCAR FILES
3. UTILIZATION:

1. perl Poscar2xcrysden.pl file1 file2 .... fileN
3. By Javier Carrasco (carrasco@qf.ub.es)
4. Modified By Monica Garcia (mgarcia@iciq.es)
5. ----------------------------------------------------------------

1. READ PARAMETERS FOR GENERATE OUTPUT

print "Insert the atoms number of each specie\n"; print "For finish Ctrl+D:\n";

@at=<STDIN>;

print "\n"; print "Insert the species labels\n";

for ($p=0;$p<@at;$p++){

  $k=$p+1;
        print "Label $k, $at[$p] atom/s de:\n";
                 $label[$p]=<STDIN>;chomp($label[$p]);

                          };
                          

1. READ poscar/contcar FILES

for ($r=0; $r<@ARGV;$r++) {

1. for ($r=0;$r<$#ARGV+1;$r++) { #$numArgs = $#ARGV + 1;

1. print "$ARGV[$r] : $ENV{$ARGV[$r]}\n";

open (IN,$ARGV[$r]);

$i=0;

       @at=();               

while (<IN>) {

 		if ($. ==1){ $name=$_;chomp($name);};
 		if ($. ==2) { $escala=$_;chomp($escala);};
 		if ($. ==3) {

     			@fields=split(' ');

     			$ax=$fields[0];
     			$ay=$fields[1];
     			$az=$fields[2];

 		};

  		if ($.==4){

     			@fields=split(' ');

     			$bx=$fields[0];
      			$by=$fields[1];
     			$bz=$fields[2];

 		};

  		if ($.==5){

     			@fields=split(' ');

     			$cx=$fields[0];
      			$cy=$fields[1];
     			$cz=$fields[2];

		 };

 		if ($.==6){

     			@at=split(' ');
                       #print "@at";
                       $NAT=0;
      			$suma=0;
      			$sum=0;

      			for ($j=0;$j<@at;$j++){

         			$at[$j]=$at[$j];
         			$sum=$sum+1;
         			$NAT=$NAT+$at[$j];

      			};

                       #print "$NAT";

 		};

 		if (($.>8)&&($.<$NAT+9)){

     			@fields=split (' ');

     			$x[$i]=$fields[0];$y[$i]=$fields[1];$z[$i]=$fields[2];

     			$optx[$i]=$fields[3];$opty[$i]=$fields[4];$optz[$i]=$fields[5];

     			$i++;

 		};

};

close (IN);

1. DATA PROCESSING

1. Convert fractional coordinates to positive values

for ($p=0;$p<$NAT;$p++){

  if ($x[$p]<0.0) {

     $x[$p]=$x[$p]+1;

  };

  if ($y[$p]<0.0) {

     $y[$p]=$y[$p]+1;

  };

  if ($z[$p]<0.0) {

     $z[$p]=$z[$p]+1;

  };

};

1. 1.Transformation to cartesian coordinates

for ($i=0;$i<$NAT;$i++){

  $xc[$i]=($escala)*($x[$i]*$ax+$y[$i]*$bx+$z[$i]*$cx);
  #print "$xc[$i]";

  $yc[$i]=($escala)*($x[$i]*$ay+$y[$i]*$by+$z[$i]*$cy);
  #print "$yc[$i]";

  $zc[$i]=($escala)*($x[$i]*$az+$y[$i]*$bz+$z[$i]*$cz);
  #print "$zc[$i]";

};

1. 2.Write results in suitable format

@output=<$ARGV[$r].xcrysden>; chomp(@output);

open (OUT1, ">@output");

print OUT1 "set xsfStructure {\n";

print OUT1 " DIM-GROUP\n";

print OUT1 " 3 1\n";

print OUT1 " PRIMVEC\n";

$eax=$escala*$ax;$eay=$escala*$ay;$eaz=$escala*$az;

printf OUT1 "%3.10f %3.10f %3.10f\n",$eax,$eay,$eaz;

$ebx=$escala*$bx;$eby=$escala*$by;$ebz=$escala*$bz;

printf OUT1 "%3.10f %3.10f %3.10f\n",$ebx,$eby,$ebz;

$ecx=$escala*$cx;$ecy=$escala*$cy;$ecz=$escala*$cz;

printf OUT1 "%3.10f %3.10f %3.10f\n",$ecx,$ecy,$ecz;

print OUT1 " PRIMCOORD\n";

printf OUT1 "%5.0f 1\n",$NAT;

1. Initialization $index

$index=0;

for ($p=0;$p<@at;$p++){

  for ($i=$index;$i<$index+$at[$p];$i++){

  printf OUT1 "$label[$p] %2.8f %2.8f %2.8f\n",$xc[$i],$yc[$i],$zc[$i];

  };

  $index=$index+$at[$p];

};

print OUT1 "}\n";

print OUT1 "WriteFile \$system(SCRDIR)/xc_tmp.\$system(PID) \$xsfStructure w\n";

print OUT1 "catch {exec \$system(BINDIR)/xsf2xsf \$system(SCRDIR)/xc_tmp.\$system(PID) \$system(SCRDIR)/xc_struc.\$system(PID)}\n";

print OUT1 "xc_openstr xcr \$system(SCRDIR)/xc_struc.\$system(PID) .mesa PL\n";

print OUT1 "UpdateWMTitle tempest.xcrysden\n";

print OUT1 "set working_XSF_file \$system(SCRDIR)/xc_struc.\$system(PID)\n";

print OUT1 "Get_sInfoArray\n";

print OUT1 "DisplayDefaultMode\n";

print OUT1 " xcAppendState render\n";

print OUT1 " xcUpdateState\n";

print OUT1 "SetWatchCursor\n";

print OUT1 " set xcCursor(dont_update) 1\n";

print OUT1 "set nxdir 1\n";

print OUT1 "set nydir 1\n";

print OUT1 "set nzdir 1\n";

print OUT1 "array set radio {space {SpaceFill based on covalent radii} .mesa,bg #000000 cellmode prim frames rods unitrep cell hexamode parapipedal ball {Balls based on covalent radii}}\n";

print OUT1 "CellMode 1\n";

print OUT1 "DispFramesAs\n";

print OUT1 "xc_newvalue .mesa 2\n";

print OUT1 "xc_newvalue .mesa 0\n";

print OUT1 "set xcCursor(dont_update) 0\n";

print OUT1 "ResetCursor\n";

close (OUT1);

print "\n";

print "Result in @output\n";

print "\n";

print " J.C.R\n"; };