D L _ P O L Y

Valinomycin/Membrane Simulation Detail from a DL_POLY simulation

Overview

DL_POLY is a general purpose molecular dynamics simulation package developed at STFC Daresbury Laboratory by W. Smith, T.R. Forester and I.T. Todorov. The package was developed under the auspices of the Engineering and Physical Sciences Research Council (EPSRC) for the EPSRC’s Collaborative Computational Project for the Computer Simulation of Condensed Phases (CCP5), the Computational Chemistry Group (CCG) at Daresbury Laboratory and the Natural Environment Research Council (NERC) for the NERC’s eScience project Computational Chemistry in the Environment (eMinerals).

DL_POLY can be used to simulate a wide variety of molecular systems including:

• Simple atomic systems and mixtures, e.g. Ne, Ar, Kr, etc.
• Simple unpolarisable point ions, e.g. NaCl, KCl, etc.
• Polarisable point ions and molecules, e.g. MgO, H₂O etc.
• Polymers with rigid bonds, e.g. C_nH_2n+2
• Polymers with rigid bonds and point charges, e.g. proteins, macromolecules etc.
• Silicate glasses and zeolites
• Simple metals and metal alloys, e.g. Al, Ni, Cu, Cu₃Au etc.
• Hydro-carbons and transition elements, e.g. C, Si, Ge, SiC, SiGe, ets.

There are two versions of DL_POLY packages - DL_POLY_2 and DL_POLY_3. They are written in modularised, free formatted F90 (+MPI) with rigorous code syntax (FORCHECK and NAGWare verified) and no external library dependencies. Both versions use MPI1.1 for interprocessor communication. However, the most up-to-date version of DL_POLY_3 requires MPI-I/O (MPI2) for its parallel printing functionality.

Although both versions serve the same purpose, they implement parallelisation in a different manner. This ultimately leads to difference in performance with regard to system size and complexity between the two vesrions as well as some differences in functionality due to the specificity of the technical constraints in either parallelisation strategy. A summary of the major differences between DL_POLY_2 and DL_POLY_3 is given below:

DL_POLY_2 (version 18)

• Replicated Data parallelisation (algorithmic), limits up to 30,000 atoms with good parallelisation up to 32/64 (system dependent) processors (with no restriction on the processor count)
• Full force field and molecular description
• Features not ported from DL_POLY_3:
  • Andersen, Langevin and Martina-Tuckerman-Klein ensembles
  • variable timestep
  • defects detection
  • system replication
  • full exlectrostatics exclusion
  • RDF lookup specification in FIELD

DL_POLY_3 (version 09)

• Domain Decomposition parallelisation (spatial), limits up to 2.1*10⁹ atoms with inherent parallelisation (to any high processor count, N as long as the system can be distrubuted equi-spatially well on N = k * l * m, if SPM Electrostics is used N is restricted to the power of 2 series)
• Full force field and molecular description but no rigid bodies
• Features not ported from DL_POLY_2:
  • Truncated octahedral (IMCON=4), Rhombic dodecahedral (IMCON=5) and Hexagonal prism (IMCON=7) periodic boundaries
  • Hautman-Klein (z-dimention aperiodic) Electrosatics

Restarting simulations between DL_POLY_2 and DL_POLY_3 is not possible! However, either package will handle the other's input with the exception of cases when a non-ported feature is used.

Accessing DL_POLY on the HPCx system

Please note that the source code for the package is not publicly available on the machine but is available to each individual researcher under a licence. In order to run DL_POLY on HPCx you will need to apply for a DL_POLY licence. If you require a licence then visit the DL_POLY official webpage.

DL_POLY_2 executable is named DLPOLY.X whereas DL_POLY_3 one DLPOLY.Y. As either executable is available only in parallel mode it can be invoked on nproc processors using the poe command as shown below:

poe -procs <nproc> /usr/local/packages/dlpoly/DLPOLY.Z

Further Information

This is avalable through the DL_POLY official webpage which contains links to

• DL_POLY FAQ Section (basic how-tos)
• DL_POLY Java GUI (available under the standard release to help visualise structures, prepare input files and analyse simulation results)
• DL_POLY Manuals (self-referencing PDF documents)
• DL_POLY On-line Licensing (terms)
• DL_POLY On-line Forum (discussion board facility to post scientific, engineering and general help questions and answers on DL_POLY codes and simulations)
• DL_POLY Benchmark Reports
• DL_POLY Tutorial
• DL_POLY Exercises
• Past DL_POLY Mail Shots