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_4

DL_POLY_4 is a general purpose classical molecular dynamics (MD) simulation software developed at Daresbury Laboratory by I.T. Todorov, W. Smith, A.M. Elena and others.

Interactive Usage

After connecting to Bessemer (see Establishing a SSH connection), start an interactive session with the srun --pty bash -i command.

The latest version of DL_POLY_4 (currently version 5.0.0) is made available with the command:

$ module load DL_POLY_4_PLUMED_INTEG/5.0.0-intel-2020b

After this the DL_POLY_4 command can be run from the terminal prompt

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 sbatch my_job.sh.

#!/bin/bash
#SBATCH --job-name=DL_POLY_4_test
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=8
#SBATCH --mem=2000
#SBATCH --time=00:30:00
#SBATCH --mail-user=a.person@sheffield.ac.uk
#SBATCH --mail-type=ALL

module load DL_POLY_4_PLUMED_INTEG/5.0.0-intel-2020b
# Get Example 2 from the DL_POLY website.
# ftp://ftp.dl.ac.uk/ccp5/DL_POLY/DL_POLY_4.0/TUTORIAL/Tutorial_Notes.pdf
wget ftp://ftp.dl.ac.uk/ccp5/DL_POLY/DL_POLY_4.0/TUTORIAL/Exercise2.tar.gz
tar -xvf Exercise2.tar.gz
cd Exercise2
mpirun -np $SLURM_NTASKS DLPOLY.Z

Installation notes

Installation method

DL_POLY_4 version 5.0.0 was installed using Easybuild 4.4.0 and was optionally interfaced with the PLUMED 2.6.2 library. build details can be found in /usr/local/packages/live/eb/DL_POLY_4_PLUMED_INTEG/5.0.0-intel-2020b/easybuild

Installation was tested as with the above batch script with example 2 directly taken from ftp://ftp.dl.ac.uk/ccp5/DL_POLY/DL_POLY_4.0/TUTORIAL/) with the following decomposeParDict: https://openfoamwiki.net/index.php/DecomposePar