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).