Xyz poscar.pl

#!/usr/bin/perl -w

###############Edit this###############
$title = "Single points"; 
$ncell =  25.832;

#######################################

###Parameters inicialization
$i = $j = $k = $l = $J = $m = 0;
$k = 1;
######
     

###Enter the XYZ file  
chomp($arq_log = <STDIN>);

#open file 
open(ARQ, "<$arq_log") or die "Check the file $arq_log: $!\n";
$arq_xyz = "$arq_log";

#replacing suffix: xyz=>vasp
$arq_xyz =~ s/xyz/vasp/g;

#regular expression, operations
while (<ARQ>){

if (/^\s(\w+)\s+(\-?\d+\.\d+)\s+(\-?\d+\.\d+)\s+(\-?\d+\.\d+)/){ $atom[$i] = $1; $x[$i] = sprintf("%2.16f", $2/$ncell); $y[$i] = sprintf("%2.16f", $3/$ncell); $z[$i] = sprintf("%2.16f", $4/$ncell);

               $line[$i] = "$atom[$i] $x[$i] $y[$i] $z[$i]";
         	#print "$line[$i]\n";

$i++; }

}

#sorting the lines
@sorted_lines = sort @line;

#split sorted lines
foreach (@sorted_lines){
                        if (/^(\w+)\s+(\-?\d+\.\d+)\s+(\-?\d+\.\d+)\s+(\-?\d+\.\d+)/){

$Atom[$j] = $1; $X[$j] = $2;

      		          $Y[$j] = $3;

$Z[$j] = $4;

                         #print "$j $Atom[$j] $X[$j], $Y[$j], $Z[$j]\n";

if ($j == 0){ $l++; $natoms[$l] = $k; #print "$l $k $Atom[$j] $natoms[$l]\n"; $k++; } else { if ($Atom[$j -1] eq $Atom[$j] ){ $natoms[$l] = $k; #print "$l $k $Atom[$j] $natoms[$l]\n"; $k++; } else { $k=1; $l++; $natoms[$l] = $k; #print "$l $k $Atom[$j] $natoms[$l]\n"; $k++ } } $j++; }

} 

##################################
###Generation of the VASP file ###
##################################

#open new file.vasp
open(XYZ, ">$arq_xyz" ) or die "Check the file $arq_xyz : $!\n";

#######################
####Print preambulo####
#######################

#Cell's data
print XYZ " $title \n";
printf XYZ "   % 2.16f \n",$ncell;
printf XYZ "     % 2.16f % 2.16f % 2.16f \n",1.0, 0.0, 0.0;
printf XYZ "     % 2.16f % 2.16f % 2.16f \n",0.0, 1.0, 0.0;
printf XYZ "     % 2.16f % 2.16f % 2.16f \n",0.0, 0.0, 1.0;

#Number of each atom's type N1 N2 N3 ....
for($m = 1; $m <= $l; $m++){
   print XYZ "  $natoms[$m]";
}
print XYZ "\n";
print XYZ "Selective dynamics\n";
print XYZ "Direct\n";
#######################

#print the cartesian to the new file.vasp
for($J = 0; $J < $i; $J++){

printf XYZ " % 2.16f % 2.16f % 2.16f F   F   F \n",$X[$J], $Y[$J], $Z[$J];

} 
$J = 0;

print XYZ "\n"; 

#Print the parameters to dinamics. (by now, only zeros)
for($J = 0; $J < $i; $J++){

printf XYZ " % 2.16f % 2.16f % 2.16f \n",0.0, 0.0, 0.0;

} 

print XYZ "\n";

####Close the XYZ and VASP files

close(ARQ);
close(XYZ);