DL POLY: Difference between revisions
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<tabs> | <tabs> | ||
<tab name="CONTROL"> | <tab name="CONTROL"> | ||
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SODIUM CHLORIDE WITH (27000 IONS) | SODIUM CHLORIDE WITH (27000 IONS) | ||
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restart scale | restart scale | ||
temperature 500.0 | temperature 500.0 | ||
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timestep 0.001 | timestep 0.001 | ||
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cutoff 12.0 | cutoff 12.0 | ||
rvdw 12.0 | rvdw 12.0 | ||
ewald precision 1d-6 | ewald precision 1d-6 | ||
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ensemble nvt berendsen 0.01 | ensemble nvt berendsen 0.01 | ||
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print every 2 | print every 2 | ||
stats every 2 | stats every 2 | ||
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close time 10 | close time 10 | ||
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finish | finish | ||
}} | }} | ||
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#!/bin/bash | #!/bin/bash | ||
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#SBATCH --account=def-someuser | #SBATCH --account=def-someuser | ||
#SBATCH --ntasks=1 | #SBATCH --ntasks=1 | ||
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#SBATCH --time=0-00:30 # time (DD-HH:MM). | #SBATCH --time=0-00:30 # time (DD-HH:MM). | ||
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# Load the module: | # Load the module: | ||
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module load intel/2020.1.217 openmpi/4.0.3 dl_poly4/4.10.0 | module load intel/2020.1.217 openmpi/4.0.3 dl_poly4/4.10.0 | ||
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echo "Starting run at: `date`" | echo "Starting run at: `date`" | ||
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dlp_exec=DLPOLY.Z | dlp_exec=DLPOLY.Z | ||
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${dlp_exec} | ${dlp_exec} | ||
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echo "Program finished with exit code $? at: `date`" | echo "Program finished with exit code $? at: `date`" | ||
}} | }} | ||
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#!/bin/bash | #!/bin/bash | ||
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#SBATCH --account=def-someuser | #SBATCH --account=def-someuser | ||
#SBATCH --nodes=1 | #SBATCH --nodes=1 | ||
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#SBATCH --time=0-00:30 # time (DD-HH:MM). | #SBATCH --time=0-00:30 # time (DD-HH:MM). | ||
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# Load the module: | # Load the module: | ||
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module load intel/2020.1.217 openmpi/4.0.3 dl_poly4/4.10.0 | module load intel/2020.1.217 openmpi/4.0.3 dl_poly4/4.10.0 | ||
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echo "Starting run at: `date`" | echo "Starting run at: `date`" | ||
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dlp_exec=DLPOLY.Z | dlp_exec=DLPOLY.Z | ||
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srun ${dlp_exec} | srun ${dlp_exec} | ||
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echo "Program finished with exit code $? at: `date`" | echo "Program finished with exit code $? at: `date`" | ||
}} | }} | ||
Revision as of 21:58, 8 July 2022
General[edit]
- Project web site: DL_POLY4
- Documentation: PDF manual.
- Mailing list.
DL_POLY is a general purpose classical molecular dynamics (MD) simulation software. It provides scalable performance from a single processor workstation to a high performance parallel computer. DL_POLY_4 offers fully parallel I/O as well as a NetCDF alternative to the default ASCII trajectory file.
For more on the capabilities, design, and history of DL_POLY, please see the project's web site.
License limitations[edit]
To get access to DL_POLY on our clusters, register at http://www.scd.stfc.ac.uk/SCD/40526.aspx. Forward the confirmation email to support as proof of your registration. The confirmation email typically begins:
- 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!
- ...
- Dear xxxx,
Modules[edit]
To see which versions of DL_POLY are installed on our systems, run module spider dl_poly. See Using modules for more about module subcommands.
One of the options to load the module is:
module load intel/2020.1.217 openmpi/4.0.3 dl_poly4/4.10.0
We do not currently provide a module for the Java GUI interface.
Getting started[edit]
- DL_POLY tutorial and exercises
- DL_POLY4 examples
- DL_POLY FAQs
- DL_Software User Community
- Useful Resources for DL_POLY Users
Scripts and examples[edit]
The input files shown below (CONTROL and FIELD) were taken from example TEST01 that can be downloaded from the page of DL_POLY examples.
To start a simulation, one must have at least three 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 intel/2020.1.217 openmpi/4.0.3 dl_poly4/4.10.0
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 intel/2020.1.217 openmpi/4.0.3 dl_poly4/4.10.0
echo "Starting run at: `date`"
dlp_exec=DLPOLY.Z
srun ${dlp_exec}
echo "Program finished with exit code $? at: `date`"