Running

Input file

An input-file describing the type of simulation and the parameters. In the same directory as the 'run'-file, there needs to be a file called simulation.json. An example file is:

{
    "SimulationType" : "MonteCarlo",
    "NumberOfCycles" : 100000,
    "NumberOfInitializationCycles" : 1000,
    "NumberOfEquilibrationCycles" : 10000,
    "PrintEvery" : 1000,
 
    "Systems" :
    [
    {
        "Type" : "Box",
        "BoxLengths" : [30.0, 30.0, 30.0],
        "ExternalTemperature" : 300.0,
        "ChargeMethod" : "None",
        "OutputPDBMovie" : true,
        "SampleMovieEvery" : 10
    }
    ],
 
    "Components" :
    [
    {
        "Name" : "methane",
        "MoleculeDefinition" : "ExampleDefinitions",
        "TranslationProbability" : 1.0,
        "CreateNumberOfMolecules" : 100
    }
    ]
}

This tells RASPA to run a Monte-Carlo simulation of 100 methane molecules in a $30\times30\times30$ Å cubic box (with 90$^\circ$ angles) at 300 Kelvin. It will start with 1000 cycles to initialize the system, 10000 cycles to equilibrate the system, and will use 100000 cycle to obtain thermodynamic properties of interest. Every 1000 cycles a status-report is printed to the output. The Monte-Carlo program will use only the 'translation move' where a particle is given a random translation and the move is accepted or rejected based on the energy difference.

Further settings for writing input files can be found in the section.

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RASPA_DIR

The RASPA_DIR should be linked, as many of the default .cif and force field files are given there. Make sure the the environment variable RASPA_DIR is set up correctly or run using the run file, which automatically includes the right path after building.

run file:

#! /bin/sh -f
export RASPA_DIR=/usr/share/raspa3
/usr/bin/raspa3

This type of file is know as a 'shell script'. RASPA needs the variable 'RASPA_DIR' to be set in order to look up the molecules, frameworks, etc. The scripts sets the variable and runs RASPA. RASPA can then be run from any directory you would like.

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Run job on cluster

In order to run it on a cluster using a queuing system one needs an additional file 'bsub.job' (arbitrary name)

• 'gridengine'

       #!/bin/bash
       # Serial sample script for Grid Engine
       # Replace items enclosed by {}
       #$ -S /bin/bash
       #$ -N Test
       #$ -V
       #$ -cwd
       echo $PBS_JOBID > jobid
       export RASPA_DIR=/usr/share/raspa3
       /usr/bin/raspa3
  

  The job can be submitted using 'qsub bsub.job'.
• 'torque'

       #!/bin/bash
       #PBS -N Test
       #PBS -o pbs.out
       #PBS -e pbs.err
       #PBS -r n
       #PBS -V
       #PBS -mba
       cd $PBS_O_WORKDIR
       echo $PBS_JOBID > jobid
       export RASPA_DIR=/usr/share/raspa3
       /usr/bin/raspa3
  

  The job can be submitted using 'qsub bsub.job'.
• 'slurm'

    #!/bin/bash 
    #SBATCH -N 1
    #SBATCH --job-name=Test
    #SBATCH --export=ALL
    echo $SLURM_JOBID > jobid
    valhost=$SLURM_JOB_NODELIST
    echo $valhost > hostname
    module load slurm
    export RASPA_DIR=/usr/share/raspa3
    /usr/bin/raspa3
  

  The job can be submitted using 'sbatch bsub.job'.