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RASPA2 / data /scripts /SingleComponentAdsorption-CBMC /script_adsorption.pl
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introvoyz042
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#!/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"