DL POLY

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General

DL_POLY is a general purpose classical molecular dynamics (MD) simulation software. It provides scalable performance from a single processor workstation to a high performance parallel computer. DL_POLY_4 offers fully parallel I/O as well as a NetCDF alternative to the default ASCII trajectory file.

For more on the capabilities, design, and history of DL_POLY, please see the project's web site.

License limitations

To get access to DL_POLY on Compute Canada clusters, register at http://www.scd.stfc.ac.uk/SCD/40526.aspx. Forward the confirmation email to support as proof of your registration. The confirmation email typically begins:

Dear xxxx,
You have registered for a free copy of the DL_POLY_4 program and thus
accepted the terms and conditions of the DL_POLY_4 ACADEMIC LICENCE!
...

Modules

To see which versions of DL_POLY are installed on Compute Canada systems, run module spider dl_poly. See Using modules for more about module subcommands.

One of the options to load the module is:

module load nixpkgs/16.09 intel/2018.3 openmpi/3.1.2 dl_poly4/4.08

We do not currently provide a module for the Java GUI interface.

Getting started

Scripts and examples

The input files shown below (CONTROL and FIELD) were take from example TEST01 that can be downloaded from the page of DL_POLY examples.

To start a simulation, one must have at least three files:

  • CONFIG: simulation box (atomic coordinates),
  • FIELD: force field parameters,
  • CONTROL: simulation parameters (time step, number of MD steps, simulation ensemble, ...etc).


File : CONTROL

SODIUM CHLORIDE WITH (27000 IONS)

restart scale
temperature           500.0
equilibration steps   20
steps                 20
timestep              0.001

cutoff                12.0
rvdw                  12.0
ewald precision       1d-6  

ensemble nvt berendsen 0.01

print every           2
stats every           2
collect
job time              100
close time            10

finish


File : FIELD

SODIUM CHLORIDE WITH EWALD SUM (27000 IONS)
units internal
molecular types 1
SODIUM CHLORIDE
nummols 27
atoms 1000
Na+          22.9898         1.0  500
Cl-           35.453        -1.0  500
finish
vdw    3 
Na+     Na+     bhm      2544.35      3.1545      2.3400   1.0117e+4   4.8177e+3
Na+     Cl-     bhm      2035.48      3.1545      2.7550   6.7448e+4   8.3708e+4
Cl-     Cl-     bhm      1526.61      3.1545      3.1700   6.9857e+5   1.4032e+6
close


File : run_serial_dlp.sh

#!/bin/bash

#SBATCH --account=def-someuser
#SBATCH --ntasks=1
#SBATCH --mem-per-cpu=2500M      # memory; default unit is megabytes.
#SBATCH --time=0-00:30           # time (DD-HH:MM).

# Load the module:

module load nixpkgs/16.09 intel/2018.3 openmpi/3.1.2 dl_poly4/4.08

echo "Starting run at: `date`"

dlp_exec=DLPOLY.Z

${dlp_exec}

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


File : run_mpi_dlp.sh

#!/bin/bash

#SBATCH --account=def-someuser
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=4
#SBATCH --mem-per-cpu=2500M      # memory; default unit is megabytes.
#SBATCH --time=0-00:30           # time (DD-HH:MM).

# Load the module:

module load nixpkgs/16.09 intel/2018.3 openmpi/3.1.2 dl_poly4/4.08

echo "Starting run at: `date`"

dlp_exec=DLPOLY.Z

srun ${dlp_exec}

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



Related software

Message Passing Interface