Poscar2xcrysden.pl

#! /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 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]); }; #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"; }; <nowiki><nowiki>Insert non-formatted text here</nowiki></nowiki>