DL POLY
General[edit]
- Project web site: DL_POLY4
- Documentation: Online Manual.
- Mailing list.
DL_POLY is a general purpose classical molecular dynamics (MD) simulation software developed at Daresbury Laboratory by I.T. Todorov and W. Smith.
Currently, only one version of the DL_POLY software is available under an STFC licence, DL_POLY_4, and with support provisioned to the UK's academia only. The former DL_POLY_2 version (authored by W. Smith, T.R. Forester and I.T. Todorov) is now transformed into DL_POLY_Classic and available as open source under the BSD at CCPForge.
DL_POLY_4 general design provides scalable performance from a single processor workstation to a high performance parallel computer. It is supplied in source form under license and can be compiled as a serial application code, using only a Fortran90 compiler, or as a parallel application code, provided an MPI2 instrumentation is available on the parallel machine. DL_POLY_4 offers fully parallel I/O as well as a netCDF alternative (HDF5 library dependence) to the default ASCII trajectory file.
License limitations[edit]
To get access to DL_POLY on Compute Canada clusters, users need first to register at http://www.scd.stfc.ac.uk/SCD/40526.aspx and send proof of registration by forwarding the confirmation email to support.
The confirmation email should include:
- 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!
- You have provided the following details at registration:
- Department: xxx
- Institution: xxx
- Address: xxx
- Town/City: xxx
- Post Code: xxx
- Country: xxx
- Science Domain: xxx
- Dear xxxx,
Modules[edit]
To see which versions of DL_POLY are installed on Compute Canada systems, run module spider dl_poly4. See Using modules for more about module subcommands.
On of the options to load the module is:
module load nixpkgs/16.09 intel/2018.3 openmpi/3.1.2 dl_poly4/4.08
Note: The Java GUI interface is not supported in this module.
Getting started[edit]
- DL_POLY Tutorial and Exercises
- DL_POLY4 examples
- DL_POLY Frequently Asked Questions
- DL_Software User Community
- Useful Resources for DL_POLY Users
Scripts and examples[edit]
The input files (CONTROL and FIELD) were take from the example TEST01 that can be downloaded from the page of DL_POLY examples.
To start a simulation, one need to have at least 3 files:
- CONFIG: simulation box (atomic coordinates).
- FIELD: force field parameters.
- CONTROL: simulation parameters (time step, number of MD steps, simulation ensemble, ...etc).
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
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
#!/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 nixpkgs/16.09 intel/2018.3 openmpi/3.1.2 dl_poly4/4.08
echo "Starting run at: `date`"
dlp_exec=DLPOLY.Z
${dlp_exec}
echo "Program finished with exit code $? at: `date`"
#!/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 nixpkgs/16.09 intel/2018.3 openmpi/3.1.2 dl_poly4/4.08
echo "Starting run at: `date`"
dlp_exec=DLPOLY.Z
srun ${dlp_exec}
echo "Program finished with exit code $? at: `date`"