DL POLY

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General[edit]

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[edit]

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[edit]

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 intel/2020.1.217 openmpi/4.0.3 dl_poly4/4.10.0

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

Getting started[edit]

Scripts and examples[edit]

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 intel/2020.1.217 openmpi/4.0.3 dl_poly4/4.10.0

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 intel/2020.1.217 openmpi/4.0.3 dl_poly4/4.10.0

echo "Starting run at: `date`"

dlp_exec=DLPOLY.Z

srun ${dlp_exec}

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



Related software[edit]