DL POLY: Difference between revisions
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m (Updated the scripts to use the last module from StdEnv/2023 environment.) |
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'''DL_POLY''' is now [https://gitlab.com/DL%20POLY%20Classic/dl%20poly open source] and it does not require registration. A new module '''dl_poly4/5.1.0''' is already installed under '''StdEnv/2023''' and it is accessible for all users. However, if you would like to use the previous versions ('''dl_poly4/4.10.0''' and/or '''dl_poly4/4.08'''), you should contact [[Technical_support | support]] and ask to be added to the POSIX group that controls access to DL_POLY4. There is no need to register on DL_POLY website. | |||
= Modules = <!--T:8--> | = Modules = <!--T:8--> | ||
To see which versions of DL_POLY are installed on our systems, run <code>module spider | To see which versions of DL_POLY are installed on our systems, run <code>module spider dl_poly4</code>. See [[Using modules]] for more about <code>module</code> subcommands. | ||
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To load the version '''5.x''', use: | |||
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<code>module load StdEnv/2023 intel/2023.2.1 openmpi/4.1.5 dl_poly4/5.1.0</code> | |||
<!--T:10--> | <!--T:10--> | ||
<code>module load intel/2020.1.217 openmpi/4.0.3 dl_poly4/4.10.0</code> | To load the previous version 4.10.0, use: | ||
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<code>module load StdEnv/2023 intel/2020.1.217 openmpi/4.0.3 dl_poly4/4.10.0</code> | |||
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Note that this version requires to be added to a POSIX group as explained above in [[#License limitations | License limitations]]. | |||
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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 | ||
<!--T:24--> | |||
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: | ||
module load intel/ | <!--T:28--> | ||
module load StdEnv/2023 | |||
module load intel/2023.2.1 openmpi/4.1.5 dl_poly4/5.1.0 | |||
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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: | ||
module load intel/ | <!--T:35--> | ||
module load StdEnv/2023 | |||
module load intel/2023.2.1 openmpi/4.1.5 dl_poly4/5.1.0 | |||
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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 | ||
<!--T:38--> | |||
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`" | ||
}} | }} | ||
</tab> | </tab> | ||
</tabs> | </tabs> | ||
= Related software = <!--T:18--> | = Related software = <!--T:18--> | ||
Latest revision as of 14:42, 3 April 2024
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]
DL_POLY is now open source and it does not require registration. A new module dl_poly4/5.1.0 is already installed under StdEnv/2023 and it is accessible for all users. However, if you would like to use the previous versions (dl_poly4/4.10.0 and/or dl_poly4/4.08), you should contact support and ask to be added to the POSIX group that controls access to DL_POLY4. There is no need to register on DL_POLY website.
Modules[edit]
To see which versions of DL_POLY are installed on our systems, run module spider dl_poly4. See Using modules for more about module subcommands.
To load the version 5.x, use:
module load StdEnv/2023 intel/2023.2.1 openmpi/4.1.5 dl_poly4/5.1.0
To load the previous version 4.10.0, use:
module load StdEnv/2023 intel/2020.1.217 openmpi/4.0.3 dl_poly4/4.10.0
Note that this version requires to be added to a POSIX group as explained above in License limitations.
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.)
File : CONTROL
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
File : FIELD
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
File : run_serial_dlp.sh
#!/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 StdEnv/2023
module load intel/2023.2.1 openmpi/4.1.5 dl_poly4/5.1.0
echo "Starting run at: `date`"
dlp_exec=DLPOLY.Z
${dlp_exec}
echo "Program finished with exit code $? at: `date`"
File : run_mpi_dlp.sh
#!/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 StdEnv/2023
module load intel/2023.2.1 openmpi/4.1.5 dl_poly4/5.1.0
echo "Starting run at: `date`"
dlp_exec=DLPOLY.Z
srun ${dlp_exec}
echo "Program finished with exit code $? at: `date`"