Ready, get set, go

This page tells you how to set DL_POLY up and running.

How to obtain DL_POLY

  • DL_POLY – molecular dynamics simulations (version 4.09 and above).
  • DL_POLY User Manual (PDF) - Version 5.0.0, February 2021.

To be able to use the latest version of DL_POLY you first need to register here. Successful registration will lead to you receiving an email containing instructions on how to download the latest version of DL_POLY. Following the instructions in the email from CCP5-ADMIN should give you an unzipped directory (e.g. dl_poly_4.09). The next step is to compile a dl_poly executable. If you want to compile an executable that runs on more than one core i.e. an mpi version to run on a high performance computing (HPC) system, first transfer the dl_poly directory to the HPC and type the commands below (example given for a bash terminal) adapting if necessary for specific HPC:

$: cd dl_poly_4.09
$: mkdir build-mpi
$: cd build-mpi
$: module load cmake gcc7 openmpi-gcc7
$: FFLAGS="-O3" FC=gfortran cmake ../
$: make –j8    (where 8 is the number of processes used to compile the executable)

Succesful compilation leads to the creation of the dl_poly executable (DLPOLY.Z), which can be found in dl_poly_4.09/build-mpi/bin/.

TIP:

Copy the executable DLPOLY.Z to the directory from where you will run simulations e.g.:

$ cd DL_POLY_SIMULATION
$ cp dl_poly_4.09/build-mpi/bin/DLPOLY.Z .

Note

The exact name of the DL_POLY directory will depend on the version you have downloaded. At the time of writing this, the latest version was dl_poly_4.09.

Continuation runs of simulations

When you need to re-run a simulation make a ‘copy script’ using a text editor that can be used to quickly copy the CONFIG, REVCON and REVIVE files as shown below (in the same order):

$: emacs copy.sh  # this creates a new script file using the emacs text editor

#!/bin/bash

# a simple script file to copy DL_POLY results files to enable a continuation re-run of a simulation

cp CONFIG CONFIG.OLD
cp REVCON CONFIG
cp REVIVE REVOLD


#Renaming the CONTROL file too enables you to retrieve simulation details at a later point if necessary
# -remember to re-number according to the number of the simulation re-run (here it's 'CONTROL0 for the initial simulation for example)

mv CONTROL CONTROL0

Then ensure the script is executable:

$: chmod +x dlpoly_script.sh

and to run it:

$: ./copy.sh