DL POLY: Difference between revisions

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To get access to DL_POLY on Compute Canada clusters, register at http://www.scd.stfc.ac.uk/SCD/40526.aspx. Forward the confirmation email to [[Technical_support | support]] as proof of your registration.  The confirmation email typically begins:
'''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.
 
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::Dear xxxx,<br />
::You have registered for a free copy of the DL_POLY_4 program and thus<br />
::accepted the terms and conditions of the DL_POLY_4 ACADEMIC LICENCE! <br />
::...<br />


= Modules = <!--T:8-->
= Modules = <!--T:8-->
To see which versions of DL_POLY are installed on Compute Canada systems, run <code>module spider dl_poly</code>. See [[Using modules]] for more about <code>module</code> subcommands.
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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One of the options to load the module is:
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>


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<code>module load nixpkgs/16.09  intel/2018.3 openmpi/3.1.2 dl_poly4/4.08</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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The input files shown below (CONTROL and FIELD) were take from example TEST01 that can be downloaded from the page of [ftp://ftp.dl.ac.uk/ccp5/DL_POLY/DL_POLY_4.0/DATA/ DL_POLY examples].
The input files shown below (CONTROL and FIELD) were taken from example TEST01 that can be downloaded from the page of [ftp://ftp.dl.ac.uk/ccp5/DL_POLY/DL_POLY_4.0/DATA/ DL_POLY examples].


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* '''CONFIG''': simulation box (atomic coordinates),
* '''CONFIG''': simulation box (atomic coordinates)
* '''FIELD''': force field parameters,
* '''FIELD''': force field parameters
* '''CONTROL''': simulation parameters (time step, number of MD steps, simulation ensemble, ...etc).
* '''CONTROL''': simulation parameters (time step, number of MD steps, simulation ensemble, ...etc.)


</translate>


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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   


<!--T:23-->
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:


module load nixpkgs/16.09 intel/2018.3 openmpi/3.1.2 dl_poly4/4.08
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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 nixpkgs/16.09 intel/2018.3 openmpi/3.1.2 dl_poly4/4.08
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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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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>
<translate>


= Related software = <!--T:18-->
= Related software = <!--T:18-->

Latest revision as of 14:42, 3 April 2024

Other languages:

General[edit]

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]

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`"


Related software[edit]

Message Passing Interface

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