#!/usr/bin/perl -w
use File::Copy;
use File::Path;

# framework-information
@Framework = ("ITQ-29");  # list of structures
@BlockPockets = ("yes");
@BlockPocketsFilename = ("ITQ-29");  # list of blocking pockets filenames
@HeliumVoidFraction = ("0.401506");  # list of helium-voidfractions for the structures
@UnitCells = ("2 2 2"); # list of sizes of the unit cells for the structures
@Forcefield=("ExampleZeolitesForceField");
@UseChargesFromCIFFile=("yes");
@RemoveAtomNumberCodeFromLabel=("yes");
@CutOff=("11.8");

# temperature-information
@Temperature = (300.0); # list of temperatures
@Molecule = ("CO2"); # list of molecules
@MoleculeStartingBead = (0);
@MoleculeDefinition = ("ExampleDefinitions");
@Idealgas = ([1.0]); # list of IG Rosenbluth weights for each temperature

# pressure-information
$pressure_type = "fugacity";     # "pressure" or "fugacity"
$pressure_start = 1e2;          # lowest pressure
$pressure_end = 1e8;            # highest pressure
$number_of_pressure_points = 4; # number of points equally spaced in log-scale or linear scale
$pressure_unit="Pa";             # "bar", "kPa", or "Pa"
$pressure_scale="log";           # "log" or "linear"

# simulation-information
$SimulationType="MonteCarlo";
$NumberOfCycles="2000";
$NumberOfInitializationCycles="2000";
$PrintEvery="5000";
$RestartFile="no";

# system and queuing information
$queueing_system="gridengine";    # gridengine or torque
$divide_into_batches="no"; # combine serial run in larger blocks
$batches = 4; # combine into an 8-core job
$queue = "mof4,mof5,VASP"; # the queue type
$job_name = "Adsorption"; # name of the job
@file_list = (); # list of files copied to all the directories

sub log10 {
  my $n = shift;
  return log($n)/log(10);
}

if($pressure_scale eq "log")
{
  for($i = 0; $i < $number_of_pressure_points; $i++)
  {
    $pressure[$i]=10**(((log10($pressure_end)-log10($pressure_start))*($i/($number_of_pressure_points-1)))+log10($pressure_start));
  }
}
else
{
  for($i = 0; $i < $number_of_pressure_points; $i++)
  {
    $pressure[$i]=($pressure_end-$pressure_start)*($i/($number_of_pressure_points-1))+$pressure_start;
  }
}

# empty 'submit-file'
open(DATw4, ">submit") || die("Could not open file!");
close(DATw4);

$index_batches=0;
$count=0;

$index_framework=0;
foreach (@Framework)
{
  $dir_fr=$Framework[$index_framework];
  mkpath($dir_fr);

  $index_temperature=0;
  foreach (@Temperature)
  {
    $index_molecule=0;
    foreach (@Molecule)
    {
      $dir_molecule="$dir_fr/$Temperature[$index_temperature]K/$Molecule[$index_molecule]";
      mkpath($dir_molecule);

      $index_pressure=0;
      foreach (@pressure)
      {
        $dir_press="$dir_molecule/$pressure[$index_pressure]$pressure_unit";
        mkpath($dir_press);

        open(DATw1, ">$dir_press/run") || die("Could not open file!");
        printf DATw1 "#! /bin/sh -f\n";
        printf DATw1 "export RASPA_DIR=\${HOME}/RASPA/simulations/\n";
        printf DATw1 "\${RASPA_DIR}/bin/simulate \$1\n";
        close(DATw1);
        chmod 0755, "$dir_press/run";

        # copy files to the dir
        for($i = 0; $i < scalar @file_list; $i++)
        {
          copy("$file_list[$i]","$dir_press/$file_list[$i]") or die "Copy failed: $!";
        }

        if($queueing_system eq "torque")
        {
          open(DATw1, ">$dir_press/bsub.job") || die("Could not open file!");
          printf DATw1 "#!/bin/bash\n";
          printf DATw1 "#PBS -S /bin/bash\n";
          printf DATw1 "#PBS -l nodes=1\n";
          printf DATw1 "#PBS -N $job_name\n";
          printf DATw1 "#PBS -l walltime=120:00:00\n";
          printf DATw1 "#PBS -o pbs.out\n";
          printf DATw1 "#PBS -e pbs.err\n";
          printf DATw1 "#PBS -r n\n";
          printf DATw1 "#PBS -V\n";
          printf DATw1 "#PBS -mba\n";
          printf DATw1 "\n";
          printf DATw1 "cd \${PBS_O_WORKDIR}\n";
          printf DATw1 "\n";
          printf DATw1 "echo \$PBS_JOBID > jobid\n";
          printf DATw1 "export RASPA_DIR=\${HOME}/RASPA/simulations/\n";
          printf DATw1 "\${RASPA_DIR}/bin//simulate \$1\n";
          close(DATw1);
          chmod 0755, "$dir_press/bsub.job";
        }
        elsif($queueing_system eq "gridengine")
        {
          open(DATw1, ">$dir_press/bsub.job") || die("Could not open file!");
          printf DATw1 "#!/bin/bash\n";
          printf DATw1 "# script for Grid Engine\n";
          printf DATw1 "#\$ -S /bin/bash\n";
          printf DATw1 "#\$ -q $queue\n";
          printf DATw1 "#\$ -N $job_name\n";
          printf DATw1 "#\$ -V\n";
          printf DATw1 "#\$ -cwd\n";
          printf DATw1 "#\$ -notify\n";
          printf DATw1 "\n";
          printf DATw1 "echo \$JOB_ID > jobid\n";
          printf DATw1 "export RASPA_DIR=\${HOME}/RASPA/simulations/\n";
          printf DATw1 "\${RASPA_DIR}/bin/simulate \$1\n";
          close(DATw1);
          chmod 0755, "$dir_press/bsub.job";
        }
        else
        {
          die("Unknown queueing system!");
        }
 
        open(DATw3, ">$dir_press/simulation.input") || die("Could not open file!");
        print DATw3 "SimulationType                $SimulationType\n";
        print DATw3 "NumberOfCycles                $NumberOfCycles\n";
        print DATw3 "NumberOfInitializationCycles  $NumberOfInitializationCycles\n";
        print DATw3 "PrintEvery                    $PrintEvery\n";
        print DATw3 "RestartFile                   $RestartFile\n";
        print DATw3 "\n";
        print DATw3 "ContinueAfterCrash no\n";
        print DATw3 "WriteBinaryRestartFileEvery 5000\n";
        print DATw3 "\n";
        print DATw3 "ChargeMethod                  Ewald\n";
        print DATw3 "Forcefield                    $Forcefield[$index_framework]\n";
        print DATw3 "CutOffVDW                     $CutOff[$index_framework]\n";
        print DATw3 "RemoveAtomNumberCodeFromLabel $RemoveAtomNumberCodeFromLabel[$index_framework]\n";
        print DATw3 "\n";
        print DATw3 "Framework             0\n";
        print DATw3 "FrameworkName         $Framework[$index_framework]\n";
        print DATw3 "UseChargesFromCIFFile $UseChargesFromCIFFile[$index_framework]\n";
        print DATw3 "UnitCells             $UnitCells[$index_framework]\n";
        print DATw3 "HeliumVoidFraction    $HeliumVoidFraction[$index_framework]\n";
        print DATw3 "ExternalTemperature   $Temperature[$index_temperature]\n";
        if($pressure_unit eq "bar") {printf DATw3 "ExternalPressure    %g\n", $pressure[$index_pressure]*1e5}
        elsif($pressure_unit eq "kPa") {printf DATw3 "ExternalPressure    %g\n", $pressure[$index_pressure]*1e3}
        elsif($pressure_unit eq "Pa")  {printf DATw3 "ExternalPressure    %g\n", $pressure[$index_pressure]}
        print DATw3 "\n";

        print DATw3 "\n";
        print DATw3 "Component 0 MoleculeName              $Molecule[$index_molecule]\n";
        print DATw3 "            StartingBead              $MoleculeStartingBead[$index_molecule]\n";
        print DATw3 "            MoleculeDefinition        $MoleculeDefinition[$index_molecule]\n";
        print DATw3 "            IdealGasRosenbluthWeight  $Idealgas[$index_temperature][$index_molecule]\n";
        if($pressure_type eq "fugacity") {printf DATw3 "            FugacityCoefficient       1.0\n";}
        print DATw3 "            TranslationProbability    1.0\n";
        print DATw3 "            RotationProbability       1.0\n";
        print DATw3 "            BlockPockets              $BlockPockets[$index_framework]\n";
        print DATw3 "            BlockPocketsFilename      $BlockPocketsFilename[$index_framework]\n";
        print DATw3 "            ReinsertionProbability    1.0\n";
        print DATw3 "            CBMCProbability           1.0\n";
        print DATw3 "            IdentityChangeProbability 0.0\n";
        print DATw3 "            SwapProbability           1.0\n";
        print DATw3 "            CreateNumberOfMolecules   0\n";
        close(DATw3);

        if($divide_into_batches eq "yes")
        {
          if($count%$batches==0)
          {
            $index_batches=$index_batches+1;

            if($queueing_system eq "torque")
            {
              open(DATw4, ">submit_$index_batches") || die("Could not open file!");
              print DATw4 "\#\!/bin/bash\n";
              print DATw4 "#PBS -S /bin/bash\n";
              print DATw4 "#PBS -l nodes=1\n";
              print DATw4 "#PBS -N $job_name\n";
              print DATw4 "#PBS -l walltime=120:00:00\n";
              print DATw4 "#PBS -o pbs.out\n";
              print DATw4 "#PBS -e pbs.err\n";
              print DATw4 "#PBS -r n\n";
              print DATw4 "#PBS -V\n";
              print DATw4 "#PBS -mba\n";
              print DATw4 "\n";
              print DATw4 "cd \$\{PBS_O_WORKDIR\}\n";
              print DATw4 "\n";
              close(DATw4);
              chmod 0755, "submit_$index_batches"
            }
            elsif($queueing_system eq "gridengine")
            {
              open(DATw4, ">submit_$index_batches") || die("Could not open file!");
              printf DATw4 "#!/bin/bash\n";
              printf DATw4 "# script for Grid Engine\n";
              printf DATw4 "#\$ -S /bin/bash\n";
              printf DATw4 "#\$ -q $queue\n";
              printf DATw4 "#\$ -N $job_name\n";
              printf DATw4 "#\$ -V\n";
              printf DATw4 "#\$ -cwd\n";
              printf DATw4 "#\$ -pe orte $batches\n";
              printf DATw4 "#\$ -notify\n";
              printf DATw4 "\n";
              close(DATw4);
              chmod 0755, "$dir_press/bsub.job";
            }
            else
            {
              die("Unknown queueing system!");
            }

            open(DATw5, ">>submit") || die("Could not open file!");
            print DATw5 "qsub ./submit_$index_batches\n";
            close(DATw5);
          }

          open(DATw5, ">>submit_$index_batches") || die("Could not open file!");
          print DATw5 "cd \"$dir_press\"\n";
          print DATw5 ".\/run > out 2\>\&1\&\n";
          print DATw5 "cd -\n";

          if(($count+1)%$batches==0) {print DATw5 "wait\n";}
          close(DATw5);

          $count=$count+1;
        }
        else
        {
          open(DATw4, ">>submit") || die("Could not open file!");
          print DATw4 "cd \"$dir_press\"\n";
          print DATw4 "qsub bsub.job\n";
          print DATw4 "cd -\n";
          close(DATw4);
        }

        $index_pressure=$index_pressure+1;
      }
      $index_molecule=$index_molecule+1;
    }
    $index_temperature=$index_temperature+1;
  }
  $index_framework=$index_framework+1;
}

# put a "wait" on the last submit which (probably) is not a full batch
if($divide_into_batches eq "yes")
{
  open(DATw5, ">>submit_$index_batches") || die("Could not open file!");
  if(($count)%$batches!=0) {print DATw5 "wait\n";}
  close(DATw5);
}

chmod 0755, "submit"