DL POLY: Difference between revisions

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DL POLY (view source)

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= General =
= General =


* Project web site: [https://www.scd.stfc.ac.uk/Pages/DL_POLY.aspx DL_POLY4]
* Project web site: [https://www.scd.stfc.ac.uk/Pages/DL_POLY.aspx DL_POLY4]
* Documentation: [http://lammps.sandia.gov/doc/Manual.html Online Manual].
* Documentation: [ftp://ftp.dl.ac.uk/ccp5/DL_POLY/DL_POLY_4.0/DOCUMENTS/USRMAN4.pdf PDF manual].
* [https://www.jiscmail.ac.uk/cgi-bin/webadmin?A0=DLPOLY Mailing list.]
* [https://www.jiscmail.ac.uk/cgi-bin/webadmin?A0=DLPOLY 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.
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.


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 [http://www.ccp5.ac.uk/DL_POLY_C/ DL_POLY_Classic] and available as open source under the [https://opensource.org/licenses/bsd-license.php BSD] at [http://ccpforge.cse.rl.ac.uk/gf/project/dl_poly_classic/ CCPForge].
For more on the capabilities, design, and history of DL_POLY, please see the [https://www.scd.stfc.ac.uk/Pages/DL_POLY.aspx project's web site].
 
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 =
= License limitations =


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 [[Technical_support | support]].  
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:
 
The confirmation email should include:<br />


::Dear xxxx,<br />
::Dear xxxx,<br />
::You have registered for a free copy of the DL_POLY_4 program and thus<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 />
::accepted the terms and conditions of the DL_POLY_4 ACADEMIC LICENCE! <br />
::You have provided the following details at registration:<br />
::...<br />
::Department: xxx<br />
::Institution: xxx<br />
::Address: xxx<br />
::Town/City: xxx<br />
::Post Code: xxx<br />
::Country: xxx<br />
::Science Domain: xxx<br />


= Modules =
= Modules =
To see which versions of DL_POLY are installed on Compute Canada systems, run <code>module spider dl_poly4</code>. See [[Using modules]] for more about <code>module</code> subcommands.
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.


On of the options to load the module is:  
One of the options to load the module is:  


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


'''Note:''' The Java GUI interface is not supported in this module.
We do not currently provide a module for the Java GUI interface.


= Getting started =
= Getting started =
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= Scripts and examples =
= Scripts and examples =


The input files (CONTROL and FIELD) were take from the 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 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].


To start a simulation, one need to have at least 3 files:
To start a simulation, one must have at least three files:


* '''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).
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= Related software =
= Related software =
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* [[VMD]]
* [[VMD]]
* [[LAMMPS]]
* [[LAMMPS]]
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