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introvoyz042
/

RASPA2

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RASPA2 / data /scripts /FitToVLE /script_fit_Gibbs.pl

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74e10df verified about 2 months ago

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

# framework-information
@Forcefield=("Dubbeldam2007FlexibleIRMOF-1");

@epsilon=(10,11,12,13,14,15,16);
@sigma=(4.65,4.66,4.67,4.68,4.69);

$FitAtom="CH";

# temperature-information
@temperature = (300.0,450.0); # list of temperatures
@molecule = ("isobutane"); # list of molecules
@idealgas = ([1.0],[1.0]); # list of IG Rosenbluth weights for each temperature

# simulation-information
$SimulationType="MonteCarlo";
$NumberOfCycles="50000";
$NumberOfInitializationCycles="20000";
$PrintEvery="5000";
$RestartFile="no";

# system and queuing information
$divide_into_batches="no"; # combine serial run in larger blocks
$batches = 12; # combine into an 8-core job
$queue = "VASP"; # the queue type
$job_name = "MC_GIBBS_FIT"; # name of the job
@file_list = ("force_field_mixing_rules.def"); # list of files copied to all the directories

# get cluster-name
chomp($cluster = `hostname -s`);

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

$index_batches=0;
$count=0;

$index_molecule=0;
foreach (@molecule)
{
  $index_temperature=0;
  foreach (@temperature)
  {
    $index_sigma=0;
    foreach (@sigma)
    {
      $index_epsilon=0;
      foreach (@epsilon)
      {
        $dir_press="$molecule[$index_molecule]/$temperature[$index_temperature]/$sigma[$index_sigma]/$epsilon[$index_epsilon]";
        mkpath($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: $!";
        }

        # read in the forcefield file
        open(FILE,"$dir_press/force_field_mixing_rules.def") || die("Cannot Open File");
        my(@fcont) = <FILE>;
        close FILE;
       
        # replace atom LJ paramters by the trial ones 
        open(FOUT,">$dir_press/force_field_mixing_rules.def") || die("Cannot Open File");
        foreach $line (@fcont)
        {
          if($line =~ /$FitAtom/)
          {
              $line = "$FitAtom        Lennard-jones     $epsilon[$index_epsilon]       $sigma[$index_sigma]\n";
          }
          print FOUT $line;
        }
        close FOUT;

        if(($cluster eq "login3") || ($cluster eq "login4"))
        {
          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($cluster eq "carbon")
        {
          open(DATw1, ">$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";
        }
        elsif($cluster eq "kraken")
        {
          open(DATw1, ">$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 $job_name\n";
          printf DATw1 "#\$ -V\n";
          printf DATw1 "#\$ -cwd\n";
          printf DATw1 "#\$ -notify\n";
          printf DATw1 "\n";
          printf DATw1 "# set path for intel compiler libraries\n";
          printf DATw1 "source /opt/intel/cce/10.1.018/bin/iccvars.sh\n";
          printf DATw1 "\n";
          printf DATw1 "echo \$JOB_ID > jobid\n";
          printf DATw1 "export RASPA_DIR=\${HOME}/RASPA/simulations/\n";
          printf DATw1 "\${RASPA_DIR}/bin/simulate \$1\n";
          close(DATw1);
          chmod 0755, "$dir_press/bsub.job";
        }
        else
        {
          die("Unknown cluster!");
        }

        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_molecule]\n";
        print DATw3 "\n";
        print DATw3 "Box 0\n";
        print DATw3 "BoxLengths 30 30 30\n";
        print DATw3 "BoxAngles 90 90 90\n";
        print DATw3 "ExternalTemperature $temperature[$index_temperature]\n";
        print DATw3 "\n";
        print DATw3 "Box 1\n";
        print DATw3 "BoxLengths 50 50 50\n";
        print DATw3 "BoxAngles 90 90 90\n";
        print DATw3 "ExternalTemperature $temperature[$index_temperature]\n";
        print DATw3 "\n";
        print DATw3 "GibbsVolumeChangeProbability 1.0\n";
        print DATw3 "\n";

        print DATw3 "Component 0 MoleculeName              $molecule[$index_molecule]\n";
        print DATw3 "            StartingBead              0\n";
        print DATw3 "            MoleculeDefinition        ExampleDefinitions\n";
        print DATw3 "            IdealGasRosenbluthWeight  $idealgas[$index_temperature][$index_molecule]\n";
        print DATw3 "            FugacityCoefficient       1.0\n";
        print DATw3 "            TranslationProbability    1.0\n";
        print DATw3 "            RotationProbability       1.0\n";
        print DATw3 "            ReinsertionProbability    1.0\n";
        print DATw3 "            CBMCProbability           1.0\n";
        print DATw3 "            GibbsSwapProbability      1.0\n";
        print DATw3 "            CreateNumberOfMolecules   200 75\n";
        close(DATw3);

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

            if(($cluster eq "login3") || ($cluster eq "login4"))
            {
              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($cluster eq "carbon")
            {
              open(DATw4, ">submit_$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 $batches\n";
              printf DATw4 "\n";
              close(DATw4);
              chmod 0755, "$dir_press/bsub.job";
            }
            elsif($cluster eq "kraken")
            {
              open(DATw4, ">submit_$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 $batches\n";
              printf DATw4 "\n";
              printf DATw4 "# set path for intel compiler libraries\n";
              printf DATw4 "source /opt/intel/cce/10.1.018/bin/iccvars.sh\n";
              printf DATw4 "\n";
              close(DATw4);
              chmod 0755, "$dir_press/bsub.job";
            }
            else
            {
              die("Unknown cluster!");
            }

            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);
        }
        $index_epsilon=$index_epsilon+1;
      }
      $index_sigma=$index_sigma+1;
    }
    $index_temperature=$index_temperature+1;
  }
  $index_molecule=$index_molecule+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"

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

	# framework-information
	@Forcefield=("Dubbeldam2007FlexibleIRMOF-1");

	@epsilon=(10,11,12,13,14,15,16);
	@sigma=(4.65,4.66,4.67,4.68,4.69);

	$FitAtom="CH";

	# temperature-information
	@temperature = (300.0,450.0); # list of temperatures
	@molecule = ("isobutane"); # list of molecules
	@idealgas = ([1.0],[1.0]); # list of IG Rosenbluth weights for each temperature

	# simulation-information
	$SimulationType="MonteCarlo";
	$NumberOfCycles="50000";
	$NumberOfInitializationCycles="20000";
	$PrintEvery="5000";
	$RestartFile="no";

	# system and queuing information
	$divide_into_batches="no"; # combine serial run in larger blocks
	$batches = 12; # combine into an 8-core job
	$queue = "VASP"; # the queue type
	$job_name = "MC_GIBBS_FIT"; # name of the job
	@file_list = ("force_field_mixing_rules.def"); # list of files copied to all the directories

	# get cluster-name
	chomp($cluster = `hostname -s`);

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

	$index_batches=0;
	$count=0;

	$index_molecule=0;
	foreach (@molecule)
	{
	$index_temperature=0;
	foreach (@temperature)
	{
	$index_sigma=0;
	foreach (@sigma)
	{
	$index_epsilon=0;
	foreach (@epsilon)
	{
	$dir_press="$molecule[$index_molecule]/$temperature[$index_temperature]/$sigma[$index_sigma]/$epsilon[$index_epsilon]";
	mkpath($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: $!";
	}

	# read in the forcefield file
	open(FILE,"$dir_press/force_field_mixing_rules.def") \|\| die("Cannot Open File");
	my(@fcont) = <FILE>;
	close FILE;

	# replace atom LJ paramters by the trial ones
	open(FOUT,">$dir_press/force_field_mixing_rules.def") \|\| die("Cannot Open File");
	foreach $line (@fcont)
	{
	if($line =~ /$FitAtom/)
	{
	$line = "$FitAtom Lennard-jones $epsilon[$index_epsilon] $sigma[$index_sigma]\n";
	}
	print FOUT $line;
	}
	close FOUT;

	if(($cluster eq "login3") \|\| ($cluster eq "login4"))
	{
	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($cluster eq "carbon")
	{
	open(DATw1, ">$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";
	}
	elsif($cluster eq "kraken")
	{
	open(DATw1, ">$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 $job_name\n";
	printf DATw1 "#\$ -V\n";
	printf DATw1 "#\$ -cwd\n";
	printf DATw1 "#\$ -notify\n";
	printf DATw1 "\n";
	printf DATw1 "# set path for intel compiler libraries\n";
	printf DATw1 "source /opt/intel/cce/10.1.018/bin/iccvars.sh\n";
	printf DATw1 "\n";
	printf DATw1 "echo \$JOB_ID > jobid\n";
	printf DATw1 "export RASPA_DIR=\${HOME}/RASPA/simulations/\n";
	printf DATw1 "\${RASPA_DIR}/bin/simulate \$1\n";
	close(DATw1);
	chmod 0755, "$dir_press/bsub.job";
	}
	else
	{
	die("Unknown cluster!");
	}

	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_molecule]\n";
	print DATw3 "\n";
	print DATw3 "Box 0\n";
	print DATw3 "BoxLengths 30 30 30\n";
	print DATw3 "BoxAngles 90 90 90\n";
	print DATw3 "ExternalTemperature $temperature[$index_temperature]\n";
	print DATw3 "\n";
	print DATw3 "Box 1\n";
	print DATw3 "BoxLengths 50 50 50\n";
	print DATw3 "BoxAngles 90 90 90\n";
	print DATw3 "ExternalTemperature $temperature[$index_temperature]\n";
	print DATw3 "\n";
	print DATw3 "GibbsVolumeChangeProbability 1.0\n";
	print DATw3 "\n";

	print DATw3 "Component 0 MoleculeName $molecule[$index_molecule]\n";
	print DATw3 " StartingBead 0\n";
	print DATw3 " MoleculeDefinition ExampleDefinitions\n";
	print DATw3 " IdealGasRosenbluthWeight $idealgas[$index_temperature][$index_molecule]\n";
	print DATw3 " FugacityCoefficient 1.0\n";
	print DATw3 " TranslationProbability 1.0\n";
	print DATw3 " RotationProbability 1.0\n";
	print DATw3 " ReinsertionProbability 1.0\n";
	print DATw3 " CBMCProbability 1.0\n";
	print DATw3 " GibbsSwapProbability 1.0\n";
	print DATw3 " CreateNumberOfMolecules 200 75\n";
	close(DATw3);

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

	if(($cluster eq "login3") \|\| ($cluster eq "login4"))
	{
	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($cluster eq "carbon")
	{
	open(DATw4, ">submit_$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 $batches\n";
	printf DATw4 "\n";
	close(DATw4);
	chmod 0755, "$dir_press/bsub.job";
	}
	elsif($cluster eq "kraken")
	{
	open(DATw4, ">submit_$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 $batches\n";
	printf DATw4 "\n";
	printf DATw4 "# set path for intel compiler libraries\n";
	printf DATw4 "source /opt/intel/cce/10.1.018/bin/iccvars.sh\n";
	printf DATw4 "\n";
	close(DATw4);
	chmod 0755, "$dir_press/bsub.job";
	}
	else
	{
	die("Unknown cluster!");
	}

	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);
	}
	$index_epsilon=$index_epsilon+1;
	}
	$index_sigma=$index_sigma+1;
	}
	$index_temperature=$index_temperature+1;
	}
	$index_molecule=$index_molecule+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"