DL_POLY

Notitle

DL POLY is a package of subroutines, programs and data les, designed to facilitate molecular dynamics simulations of macromolecules, polymers, ionic systems and solutions on a distributed memory parallel computer.

DL_POLY is available as a module on Apocrita.

Usage

To run the latest installed version of DL_POLY, simply load the module:

module load dl_poly

DL_POLY uses openMPI for parallel performance built in and does not require use of the mpirun command

DL_POLY - command line mode

Project Directory

Please ensure that you are in your project directory and the CONTROL, CONFIG and FIELD files are present within your project directory.

An example running DL_POLY within the TEST01 project directory:

$ cd /<full path>/TEST01
$ ls
CONFIG  CONTROL  FIELD
$ DLPOLY.Z

The file 'OUTPUT' containing the execution results will be generated in the project directory.

$ ls
CONFIG  CONTROL  FIELD  OUTPUT  REVCON  REVIVE  STATIS

Additional commands

The following commands can only be run after the DLPOLY.Z job has ran.

  • To restart a previously finished job, execute:
$ copy
'CONFIG' -> 'CONFIG.OLD'
'REVCON' -> 'CONFIG'
'REVIVE' -> 'REVOLD'

This will result in some of the output files being renamed ready for a subsequent run of the program; New output files will be created.

  • To store all files within the project directory from the latest run:
$ store
mkdir: created directory '../data'
mkdir: created directory '../data/TEST'
'CONTROL' -> '../data/TEST/CONTROL'
'CONFIG' -> '../data/TEST/CONFIG'
'FIELD' -> '../data/TEST/FIELD'
'OUTPUT' -> '../data/TEST/OUTPUT'
'STATIS' -> '../data/TEST/STATIS'
'REVOLD' -> '../data/TEST/REVOLD'

This will store all input and output files within the project directory into the data sub-directory (if the directory ../data doesn't exist, it will create it).

  • To clean up the project directory, execute:
$ cleanup
removed 'OUTPUT'
removed 'STATIS'
removed 'REVCON'

This will erase all the output files from the previous run.

Cleanup: Potential Data Loss

Do not use this macro before you have stored all your useful data!

DL_POLY - GUI

X Forwarding Required

Running the GUI requires X Forwarding to be configured correctly.

Running DL_POLY in GUI mode:

module load dl_poly
gui

After a couple of seconds this window should appear:

dl_poly gui

More information on the DL_POLY GUI can be found here.

Example job

Here is an example of a DL_POLY job running 12 cores:

#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 12
#$ -l h_rt=4:0:0
#$ -l h_vmem=2G

module load dl_poly

cd /<full path>/TEST01
DLPOLY.Z

References