James: Text replacement - "[pP][bB][sS]" to "SLURM"

2022-10-20T20:38:34Z

Text replacement - "[pP][bB][sS]" to "SLURM"

← Older revision		Revision as of 20:38, 20 October 2022
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	Please refer to the DL_POLY manual for more detailed information on DL_POLY and to the		Please refer to the DL_POLY manual for more detailed information on DL_POLY and to the
	general ~~PBS~~ section in this Wiki for more details on the SLURM queuing system. There are		general SLURM section in this Wiki for more details on the SLURM queuing system. There are
	a number of tutorials and further information to be found online by Googling.		a number of tutorials and further information to be found online by Googling.

James: Created page with "DL_POLY is installed on ANDY under the user applications directory

 /share/apps/dlpoly

The default is currently version 2.20, but users can select the more current version by referencing the 3.10 directory explicitly in their scripts. To run DL_POLY the user needs to provide a set of several files. Those that are '''required''' include: 1) The CONTROL file, which indicates to DL_POLY what kind of simulation you want to run, how much data you want to ga..."

2022-10-20T20:01:23Z

Created page with "DL_POLY is installed on ANDY under the user applications directory <pre> /share/apps/dlpoly </pre> The default is currently version 2.20, but users can select the more current version by referencing the 3.10 directory explicitly in their scripts. To run DL_POLY the user needs to provide a set of several files. Those that are '''required''' include: 1) The CONTROL file, which indicates to DL_POLY what kind of simulation you want to run, how much data you want to ga..."

New page

DL_POLY is installed on ANDY under the user applications directory
<pre>
/share/apps/dlpoly
</pre>

The default is currently version 2.20, but users can select the more current version by
referencing the 3.10 directory explicitly in their scripts.

To run DL_POLY the user needs to provide a set of several files. Those that are '''required''' include:

1) The CONTROL file, which indicates to DL_POLY what kind of simulation you want to run, how
much data you want to gather, and for how long you want the simulation to run.

2) The CONFIG file, which contains the atom positions, and, depending on how the file was created
(e.g. whether this is a configuration created from ‘scratch’ or the end point of another run), the
atom's velocities and forces.

3) The FIELD file, which specifies the nature of the intermolecular interactions, the molecular topology,
and the atomic properties, such as charge and mass.

Sometimes you may require a fourth file: TABLE, which contains short-ranged potential and force
arrays for functional forms not available within DL_POLY (usually because they are too complex
e.g. spline potentials) and/or a fifth file: TABEAM, which contains metal potential arrays for non-
analytic or too complex functional forms and/or a sixth file: REFERENCE, which is similar to the
CONFIG file and contains the ”perfect” crystalline structure of the system.

Several directories are included in the installation tree. The primary executable for DL_POLY and
a number of other supporting scripts are located in the directory:
<pre>
/share/apps/dlpoly/default/bin
</pre>
A collection of example input files that you may use as test cases are located in the directory:
<pre>
/share/apps/dlpoly/default/data
</pre>
The user and installation guide in PDF format are located in the directory:
<pre>
/share/apps/dlpoly/default/man
</pre>
Support utilities and programs are found in:
<pre>
/share/apps/dlpoly/default/utility
/share/apps/dlpoly/default/public
</pre>

To test DL_POLY, copy the files in
<pre>
/share/apps/dlpoly/default/data/TEST10/LF
</pre>
to a working directory (e.g. dlpoly) in your $HOME directory and run the SLURM script provided below
using the SLURM submission command:
<pre>
qsub dlpoly.job
</pre>

<pre>
#!/bin/bash
#SBATCH --partition production
#SBATCH --job-name DLPOLY_mpi
#SBATCH --nodes=8
#SBATCH --ntasks=1
#SBATCH --mem=2880

# Find out name of master execution host (compute node)
echo -n ">>>> SLURM Master compute node is: "
hostname

# You must explicitly change to the working directory in SLURM
cd $SLUM_SUBMIT_DIR

# Use 'mpirun' and point to the MPI parallel executable to run
echo ">>>> Begin DLPOLY MPI Run ..."
mpirun -np 8 dlpoly > dlpoly_mpi.out 2>&1
echo ">>>> Begin DLPOLY MPI Run ..."
</pre>

Please refer to the DL_POLY manual for more detailed information on DL_POLY and to the
general PBS section in this Wiki for more details on the SLURM queuing system. There are
a number of tutorials and further information to be found online by Googling.

DL POLY - Revision history

James: Text replacement - "[pP][bB][sS]" to "SLURM"