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DL_POLY

Introduction

DL_POLY is a suite of programs developed at Daresbury Laboratory for molecular dynamics simulations of a variety of systems, including "macromolecules, polymers, ionic systems and solutions".

DL_POLY 4.02, DL_POLY 4.03 and DL_POLY CLASSIC 1.7 have been installed on Lattice and Parallel under /global/software/dl_poly, along with all of the test files for these programs.   DL_POLY 4.04 is available on Jasper, where the environment to use it is initialized using module load application/dl_poly/4.04 . Please note that Lattice and Parallel accounts are not activated automatically, but, can be requested as explained in the Lattice QuickStart Guide and the Parallel QuickStart Guide.

Restrictions / License Information

The software is licensed for academic, non-commercial use to individual researchers. In accordance with section 2.3 of the license agreement, WestGrid makes the software available only to researchers who have registered at http://www.stfc.ac.uk/SCD/research/app/ccg/software/DL_POLY/40526.aspx , agreeing to the license terms given there. Please note that this is a new registration for DL_POLY 4.  If you have previously registered to use DL_POLY 2, you should reregister for DL_POLY 4.

If you have completed that registration and would like to use the DL_POLY software on WestGrid systems, please send a signed email to support@westgrid.ca with the subject line: "DL_POLY access request (user name)", substituting your WestGrid user name. In your request, please confirm that you have registered for DL_POLY 4. In response, a request will be sent to the WestGrid system administrators to add your user name to the UNIX group wg-dlpol. Only members of that group have access to the directory in which the DL_POLY software is located. It may take a day or two for the request to be processed.  Please note that registration is not required to use DL_POLY CLASSIC.

Users are expected to be generally familiar with DL_POLY capabilities and input file formats. In particular, you must decide whether DL_POLY 2 or DL_POLY 3 is most appropriate for your work. DL_POLY 3 can handle much larger systems than DL_POLY 2 due to a different parallelization strategy. In some cases, benchmarking with both versions may be needed to make the best choice. DL_POLY 4 will likely be the only registered version of DL_POLY installed on WestGrid systems going forward.

Running DL_POLY on Lattice or Parallel

Look in /global/software/dl_poly for versions of DL_POLY installed on Lattice and Parallel.

Like other jobs on WestGrid systems, DL_POLY jobs are run by submitting an appropriate script for batch scheduling using the qsub command.  Details of scheduling and job management are explained on the Running Jobs page, but, a simple example is given below.

The following command submits a DL_POLY 4 job script, dlpoly403.pbs, to run on 16 cores on Lattice.

qsub -l nodes=2:ppn=8,mem=22gb dlpoly403.pbs

or 24 cores on Parallel:

qsub -l nodes=2:ppn=12,mem=44gb dlpoly403.pbs

where dlpoly403.pbs is:

#!/bin/bash
#PBS -S /bin/bash

# 2014-02-28 DSP - DL_POLY batch job script example for Lattice

# Put the script in the directory in which you have placed
# DL_POLY CONFIG, CONTROL and other input files.

# Specify the DL_POLY binary to use:
DLPOLY=/global/software/dl_poly/dl_poly_4.03/execute/DLPOLY.Z

cd $PBS_O_WORKDIR
echo "Current directory: `pwd`"

echo "Node file: $PBS_NODEFILE :"
echo "---------------------"
cat $PBS_NODEFILE
echo "---------------------"

echo "Running on $PBS_NP cores."
echo "Starting run at: `date`"

mpiexec $DLPOLY

echo "Job finished with exit code $? at: `date`"

 The example script is available on Lattice and Parallel as /global/software/dl_poly/examples/test1/dlpoly403.pbs.

For More Information

Updated:

2014-02-11 - Removed Checkers reference.
2014-02-28 - Removed Matrix example and added one for Lattice/Parallel.