Editing CRYSDEN (section)

=== XCRYSDEN INPUT ===
 
 #! /usr/bin/perl
 
 #----------------------------------------------------------------
 # PROGRAM FOR  GENERATE XCRYSDEN INPUTS    
 
 # OF VASP POSCAR/CONTCAR FILES   
 #
 # UTILIZATION:
 
 # perl Poscar2xcrysden.pl file1 file2 .... fileN
 #
 # By Javier Carrasco (carrasco@qf.ub.es)
 # Modified By Monica Garcia  (mgarcia@iciq.es)
 #----------------------------------------------------------------
 
 #READ LABELS
 
 
 open(IN,$ARGV[0]);
 
 while (<IN>) {
 if ($.==6){
 
  @at=split(' ');
 };                                                                                                                                                                    };
 close(IN);
 
 
 for ($p=0;$p<@at;$p++){
 
   $k=$p+1;
 
   print "Label $k, $at[$p] atom/s of:\n";
 
   $label[$p]=<STDIN>;chomp($label[$p]);
 
 };
                           
 
 #READ poscar/contcar FILES 
 
 
 for ($r=0; $r<@ARGV;$r++) {
 
 #for ($r=0;$r<$#ARGV+1;$r++) { #$numArgs = $#ARGV + 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);
 
 # DATA PROCESSING
 
 # 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.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]";
 
 };
 
 # 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;
 
 
 #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";
 };