Hugging Face's logo

Datasets:
introvoyz042
/
RASPA2

License:
Dataset card Files
xet
 Community
RASPA2 / data /scripts /MixtureMD /script_md_mixture.pl
introvoyz042's picture
introvoyz042
Migrated from GitHub
74e10df verified
Raw History Blame Contribute Delete
10.7 kB
#!/usr/bin/perl -w
use File::Copy;
use File::Path;
# framework-information
@framework = ("MOF-1-Dybtsev-dmol"); # list of structures
@HeliumVoidFraction = ("0.627073"); # list of helium-voidfractions for the structures
@UnitCells = ("3 3 3"); # list of sizes of the unit cells for the structures
@Forcefield=("ExampleMOFsForceField");
# temperature-information
@temperature = (313.0); # list of temperatures
@molecule = ("hexane","3-methylpentane","22-dimethylbutane"); # list of molecules
@mol_fraction = (1.0/3.0,1.0/3.0,1.0/3.0);
# loading-information
$loading_start = 1;
$loading_end = 80;
$number_of_loading_points = 32; # 32 point equally spaced
# simulation-information
$SimulationType="MolecularDynamics";
$NumberOfCycles="100000000000";
$NumberOfInitializationCycles="10000";
$NumberOfEquilibrationCycles="100000";
$PrintEvery="10000";
$RestartFile="no";
# system and queuing information
$divide_into_batches="yes"; # combine serial run in larger blocks
$batches = 8; # combine into an 8-core job
$queue = "mof1"; # the queue type
$job_name = "MD"; # name of the job
for($i=0;$i<$number_of_loading_points;$i++)
{
$loading[$i]=($loading_end-$loading_start)*($i/($number_of_loading_points-1))+$loading_start;
}
# get cluster-name
chomp($cluster = `hostname -s`);
# empty 'submit-file'
open(DATw4, ">submit") || die("Could not open file!");
close(DATw4);
$index_batches=0;
$count=0;
$index_framework=0;
foreach (@framework)
{
$dir_fr=$framework[$index_framework];
mkpath($dir_fr);
$index_temperature=0;
foreach (@temperature)
{
$dir_temp="$dir_fr/$temperature[$index_temperature]K";
mkpath($dir_temp);
# concat the molecule names with "-" between them
$molecule_list = join("-",@molecule);
$dir_mol="$dir_temp/$molecule_list";
mkpath($dir_mol);
$index_loading=0;
foreach (@loading)
{
$dir_loading="$dir_mol/$loading[$index_loading]_mol_per_cell";
mkpath($dir_loading);
open(DATw1, ">$dir_loading/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";
close(DATw1);
chmod 0755, "$dir_loading/run";
if(($cluster eq "login3") || ($cluster eq "login4"))
{
open(DATw1, ">$dir_loading/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 $job_name\n";
printf DATw1 "#PBS -l walltime=120:00:00\n";
printf DATw1 "#PBS -o pbs.out\n";
printf DATw1 "#PBS -e pbs.err\n";
printf DATw1 "#PBS -r n\n";
printf DATw1 "#PBS -V\n";
printf DATw1 "#PBS -mba\n";
printf DATw1 "\n";
printf DATw1 "cd \${PBS_O_WORKDIR}\n";
printf DATw1 "\n";
printf DATw1 "echo \$JOB_ID > jobid\n";
printf DATw1 "export RASPA_DIR=\${HOME}/RASPA/simulations/\n";
printf DATw1 "\${RASPA_DIR}/bin//simulate \$1\n";
close(DATw1);
chmod 0755, "$dir_loading/bsub.job";
}
elsif($cluster eq "carbon")
{
open(DATw1, ">$dir_loading/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_loading/bsub.job";
}
elsif($cluster eq "kraken")
{
open(DATw1, ">$dir_loading/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_loading/bsub.job";
}
open(DATw3, ">$dir_loading/simulation.input") || die("Could not open file!");
print DATw3 "SimulationType $SimulationType\n";
print DATw3 "NumberOfCycles $NumberOfCycles\n";
print DATw3 "NumberOfInitializationCycles $NumberOfInitializationCycles\n";
print DATw3 "NumberOfEquilibrationCycles $NumberOfEquilibrationCycles\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 "Ensemble NVT\n";
print DATw3 "\n";
print DATw3 "ChargeMethod Ewald\n";
print DATw3 "Forcefield $Forcefield[$index_framework]\n";
print DATw3 "EwaldPrecision 1e-6\n";
print DATw3 "TimeStep 0.0005\n";
print DATw3 "\n";
print DATw3 "Framework 0\n";
print DATw3 "FrameworkName $framework[$index_framework]\n";
print DATw3 "UnitCells $UnitCells[$index_framework]\n";
print DATw3 "HeliumVoidFraction $HeliumVoidFraction[$index_framework]\n";
print DATw3 "ExternalTemperature $temperature[$index_temperature]\n";
print DATw3 "ExternalPressure 0\n";
print DATw3 "\n";
$index_molecule=0;
foreach (@molecule)
{
print DATw3 "\n";
print DATw3 "Component $index_molecule MoleculeName $molecule[$index_molecule]\n";
print DATw3 " StartingBead 0\n";
print DATw3 " MoleculeDefinition ExampleDefinitions\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 " SwapProbability 0.0\n";
printf DATw3 " CreateNumberOfMolecules %d\n",$loading[$index_loading]*$mol_fraction[$index_molecule];
$index_molecule=$index_molecule+1;
}
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 $batches\n";
printf DATw4 "#\$ -notify\n";
printf DATw4 "\n";
close(DATw4);
chmod 0755, "$dir_loading/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 $batches\n";
printf DATw4 "#\$ -notify\n";
printf DATw4 "\n";
printf DATw4 "# set path for intel compiler libraries\n";
printf DATw4 "source /opt/intel/cce/10.1.018/bin/iccvars.sh\n";
printf DATw4 "\n";
close(DATw4);
chmod 0755, "$dir_loading/bsub.job";
}
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 \"$dir_loading\"\n";
print DATw5 ".\/run > out 2\>\&1\&\n";
print DATw5 "cd -\n";
if(($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_loading\"\n";
print DATw4 "qsub bsub.job\n";
print DATw4 "cd -\n";
close(DATw4);
}
$index_loading=$index_loading+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"