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Attention

The ShARC HPC cluster was decommissioned on the 30th of November 2023 at 17:00. It is no longer possible for users to access that cluster.

DL_POLY

DL_POLY is a general purpose classical molecular dynamics (MD) simulation software developed at Daresbury Laboratory by I.T. Todorov and W. Smith.

Usage

DL_POLY 4.08 can be activated using the module file:

module load apps/dl_poly/4.08/gcc-6.2-openmpi-2.1.1

The DL_POLY executable is DLPOLY.Z. Three DL_POLY input files CONFIG, CONTROL and FIELD are required in the directory where you run your job.

Batch usage

Users are encouraged to write their own batch submission scripts. The following is an example batch submission script, my_job.sh, to run DLPOLY.Z and which is submitted to the queue by typing qsub my_job.sh.

#!/bin/bash
#$ -cwd
#$ -l h_rt=00:30:00
#$ -l rmem=2G
#$ -pe mpi 8

module load apps/dl_poly/4.08/gcc-6.2-openmpi-2.1.1

mpirun DLPOLY.Z

The script requests 8 cores using the MPI parallel environment mpi with a runtime of 30 mins and 2 GB of real memory per core. Note: If your OUTPUT file appears truncated when running a DL_POLY job using MPI, then add the l_scr keyword to your CONTROL file to place the output in the standard output file (see section 5.2.5 Parallel I/O in the user manual).

Installation notes

DL_POLY 4.08 was installed using the install_dl_poly.sh script; the module file is gcc-6.2-openmpi-2.1.1.

During compilation DL_POLY 4.08 was optionally interfaced with the PLUMED 2.3.2 library.

The installation of DL_POLY 4.08 was tested using TEST 28 (see the above installation script and ftp://ftp.dl.ac.uk/ccp5/DL_POLY/DL_POLY_4.0/DATA/ for details).