Dl_poly

DL_POLY

Licensing

DL_POLY_4 is supplied for use by individuals under an academic licence, which is free of cost to academic scientists pursuing scientific research of a non-commercial nature. To obtain the current version of DL_POLY-4 you must complete an on-line registration form from external link: http://www.stfc.ac.uk/SCD/research/app/ccg/software/DL_POLY/40526.aspx . The software is provided under the terms of a licence which may be viewed on this page. You are advised to read the licence before proceeding to registration.

When you complete a Registration Form for the DL_POLY_4 Software and submit it to STFC, your institution (in the Registration Form and the Licence Agreement called "the Licensee") is entering into a contract with The Science & Technology Facilities Council ("STFC") on the terms set out in the Licence Agreement below.

By submitting the Registration Form to STFC, you are confirming that:

  • the institution whose name appears as the Licensee in the Registration Form agrees to the terms of the Licence Agreement;
  • you have authority to agree to the terms of the Licence Agreement and to enter into a contract with STFC on behalf of that institution;
  • the DL_POLY_4 Software will be used only for Academic Purposes (as defined in the Licence Agreement);
  • you will acknowledge the use of DL_POLY_4 when publishing any data obtained with its assistance by including the following reference: "I.T. Todorov, W. Smith, K. Trachenko & M.T. Dove, J. Mater. Chem., 16, 1911-1918 (2006)";
  • the information given on the Registration Form is true; and
  • you agree to your personal data being used for the purpose of managing your institution's licence of the DL_POLY_4 Software, including contacting you to tell you about changes to and error corrections for that software and generally about the software.

Please read the terms of the Licence Agreement carefully. If you do not agree to them, you should not submit the Registration Form.

Acknowledging

Please note: if you have used DL_POLY-4 for a publication you must cite the following paper as a condition of the license agreement.

  1. I.T. Todorov, W. Smith, K. Trachenko and M.T. Dove, J. Mater. Chem., 16, 1911-1918 (2006)

You may also cite the current user manual as follows.

  1. I.T.Todorov and W. Smith "The DL_POLY User Manual" version 4.03 available from external link: http://www.ccp5.ac.uk/DL_POLY/ .

Running on Power-8 Panther or Paragon

This script is part of a 3-part workflow, see example here: Panther 3-step Keras workflow. Module dlpoly/4.08 has been loaded in workflow.sh.

#!/bin/bash
#BSUB -J DLPOLY-4.08
#BSUB -o stdout.DLPOLY.txt
#BSUB -e stderr.DLPOLY.txt
#BSUB -q panther
#BSUB -R "span[ptile=16] affinity[core(1)]"
#BSUB -network "type=sn_all: protocol=mpi: mode=US: usage=shared: instance=1"
#BSUB -x
#BSUB -W 1:19
# workflow step dependency
#BSUB -data "tag:stgin_flag"

# directory should be already created and data copied in previous step
cd /gpfs/panther/local/package_build/build/rja87-build/testing/DLPOLY/gramicidin
rm stdout.DLPOLY.txt
rm stderr.DLPOLY.txt

export myexe=`which DLPOLY.Z`

# count how many processors are allocated
NP=0
for TOKEN in $LSB_HOSTS
do
   ((NP++))
done

# create host file, on disc for testing
rm -rf file.host
for host in $LSB_HOSTS ; do
echo $host >> file.host
done

echo "***** Running DLPOLY *****"
echo "LSB hosts = $NP"

poe $myexe > output.DLPOLY.txt

bstage out -tag stgout_flag -src OUTPUT
bstage out -src output.DLPOLY.txt

Running on Invicta or Napier

DL_POLY v4.07 has been compiled using the default environment. An environment module has been created which can be invoked as follows.

Note, this uses the Intel MPI. A sample job script for DL_POLY might look as follows (change to "ptile=24" for Napier).

This can be submitted to the LSF queue using the bsub command.

Running on Bifort BlueGene/Q

DL_POLY_4.03 to DL_POLY_4.05 have been compiled and installed using the XL compiler suite. Here is a sample job script for a large job.

Further Information

Information about DL_POLY v4 is available here external link: http://www.ccp5.ac.uk/DL_POLY/ . The full user manual is here: external link: http://www.ccp5.ac.uk/DL_POLY/MANUALS/USRMAN4.pdf .