energy-surface

#!/usr/bin/perl
use File::Copy;

$count = 0;

$stepconst = 1550; #first step
$gap = 8; #gap between steps
$numberofsteps = 12; #number of steps

$switch = 0;
$switch2 = 1;
$level = "ground";
$extra = "";

open my $runout, '>', $newfile = "run-nohup" or die "Can't write new file: $!";

print $runout "\#\!/bin/bash

PP=/home/nd/pp

";

while ($switch <= $switch2) {

$step = $stepconst;

        while ($count < $numberofsteps) {

        $rand = $count * $gap;
        $filenumber = $step + $rand;

        print $runout "rm GEO*
rm DENSITY*
rm RESTART*
rm LATEST*
rm WAVEFUNCTION*
nohup cpmd_serial.x sa-$level-$filenumber.in \$\PP > sa-$level-$filenumber.out
";
        $count ++;
        }

        $count = 0;

        # RUN A WHILE LOOP
        while ($count < $numberofsteps) {

                $filenumber = $step;

                $stepnumber = ($filenumber*18)+3;
                $trial = $stepnumber+1;


                open my $in, '<', $file = "TRAJEC.xyz" or die "Can't read old file: $!";
                open my $out, '>', $newfile = "sa-$level-$step.in" or die "Can't write new file: $!";

                print $out "&CPMD
 OPTIMIZE WAVEFUNCTION
 PCG
 CONVERGENCE ORBITAL
 1.D-6
 RHOOUT BANDS
  2
  -26
  -27
  MAXSTEP
  10000
  STORE
  100
&END

&DFT
  FUNCTIONAL BLYP
  GC-CUTOFF
  0.1E-06
&END

&SYSTEM
  ANGSTROM
  POISSON TUCKERMAN
  SYMMETRY
  8
  CELL ABSOLUTE DEGREES
  13. 13 13  90  90  90
  CUTOFF
  70.0$extra
&END

&ATOMS

*C_MT_BLYP  KLEINMAN-BYLANDER
   LMAX=P
   7
";

                while( <$in> )
                {
                next unless $. eq $stepnumber;
                s/\b(C)\b//g;
                s/\b(O)\b//g;
                s/\b(H)\b//g;
                print $out $_;
                }

        open my $in, '<', $file = "TRAJEC.xyz" or die "Can't read old file: $!";

        while( <$in> )
        {
        next unless $. eq $trial;
        s/\b(C)\b//g;
        s/\b(O)\b//g;
        s/\b(H)\b//g;
        print $out $_;
        }

        $trial ++;

        open my $in, '<', $file = "TRAJEC.xyz" or die "Can't read old file: $!";

        while( <$in> )
        {
        next unless $. eq $trial;
        s/\b(C)\b//g;
        s/\b(O)\b//g;
        s/\b(H)\b//g;
        print $out $_;
        }

        $trial ++;

        open my $in, '<', $file = "TRAJEC.xyz" or die "Can't read old file: $!";

        while( <$in> )
        {
        next unless $. eq $trial;
        s/\b(C)\b//g;
        s/\b(O)\b//g;
        s/\b(H)\b//g;
        print $out $_;
        }
        $trial ++;

        open my $in, '<', $file = "TRAJEC.xyz" or die "Can't read old file: $!";

        while( <$in> )
        {
        next unless $. eq $trial;
        s/\b(C)\b//g;
        s/\b(O)\b//g;
        s/\b(H)\b//g;
        print $out $_;
        }
        $trial ++;

        open my $in, '<', $file = "TRAJEC.xyz" or die "Can't read old file: $!";

        while( <$in> )
        {
        next unless $. eq $trial;
        s/\b(C)\b//g;
        s/\b(O)\b//g;
        s/\b(H)\b//g;
        print $out $_;
        }
        $trial ++;

        open my $in, '<', $file = "TRAJEC.xyz" or die "Can't read old file: $!";

        while( <$in> )
        {
        next unless $. eq $trial;
        s/\b(C)\b//g;
        s/\b(O)\b//g;
        s/\b(H)\b//g;
        print $out $_;
        }
        $trial++;

        print $out "
*O_MT_BLYP  KLEINMAN-BYLANDER
   LMAX=P
   3
";

        open my $in, '<', $file = "TRAJEC.xyz" or die "Can't read old file: $!";

        while( <$in> )
        {
        next unless $. eq $trial;
        s/\b(C)\b//g;
        s/\b(O)\b//g;
        s/\b(H)\b//g;
        print $out $_;
        }
        $trial++;
        open my $in, '<', $file = "TRAJEC.xyz" or die "Can't read old file: $!";

        while( <$in> )
        {
        next unless $. eq $trial;
        s/\b(C)\b//g;
        s/\b(O)\b//g;
        s/\b(H)\b//g;
        print $out $_;
        }
        $trial++;
        open my $in, '<', $file = "TRAJEC.xyz" or die "Can't read old file: $!";

        while( <$in> )
        {
        next unless $. eq $trial;
        s/\b(C)\b//g;
        s/\b(O)\b//g;
        s/\b(H)\b//g;
        print $out $_;
        }
        $trial++;

        print $out "
*H_MT_BLYP
   LMAX=S
   6
";

        open my $in, '<', $file = "TRAJEC.xyz" or die "Can't read old file: $!";

        while( <$in> )
        {
        next unless $. eq $trial;
        s/\b(C)\b//g;
        s/\b(O)\b//g;
        s/\b(H)\b//g;
        print $out $_;
        }
        $trial++;
        open my $in, '<', $file = "TRAJEC.xyz" or die "Can't read old file: $!";

        while( <$in> )
        {
        next unless $. eq $trial;
        s/\b(C)\b//g;
        s/\b(O)\b//g;
        s/\b(H)\b//g;
        print $out $_;
        }
        $trial++;
        open my $in, '<', $file = "TRAJEC.xyz" or die "Can't read old file: $!";

        while( <$in> )
        {
        next unless $. eq $trial;
        s/\b(C)\b//g;
        s/\b(O)\b//g;
        s/\b(H)\b//g;
        print $out $_;
        }
        $trial++;

        open my $in, '<', $file = "TRAJEC.xyz" or die "Can't read old file: $!";

        while( <$in> )
        {
        next unless $. eq $trial;
        s/\b(C)\b//g;
        s/\b(O)\b//g;
        s/\b(H)\b//g;
        print $out $_;
        }
        $trial++;
        open my $in, '<', $file = "TRAJEC.xyz" or die "Can't read old file: $!";

        while( <$in> )
        {
        next unless $. eq $trial;
        s/\b(C)\b//g;
        s/\b(O)\b//g;
        s/\b(H)\b//g;
        print $out $_;
        }
        $trial++;
        open my $in, '<', $file = "TRAJEC.xyz" or die "Can't read old file: $!";

        while( <$in> )
        {
        next unless $. eq $trial;
        s/\b(C)\b//g;
        s/\b(O)\b//g;
        s/\b(H)\b//g;
        print $out $_;
        }
        $trial++;

        print $out "
&END";


close $out;

$step = $step + $gap;
$count ++;
        }

$level = "excited";
$extra = "
LOW SPIN EXCITATION ROKS";
$switch ++;
$count = 0;
}

        print $runout "
exit


";

        close $runout;