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DL_POLY_3: the CCP5 national UK code for molecular-dynamics simulations.

I T Todorov1, W Smith

  • 1Computational Science and Engineering Department, CCLRC Daresbury Laboratory, Daresbury, Warrington WA4 4AD, UK. i.t.todorov@dl.ac.uk

Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
|August 13, 2004
PubMed
Summary

DL_POLY_3 is a molecular-dynamics simulation package featuring efficient domain decomposition (DD) parallelization. It enables large-scale simulations of over a million particles using a novel smoothed particle mesh Ewald method adaptation.

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Area of Science:

  • Computational Physics
  • Materials Science
  • Chemistry

Background:

  • Molecular dynamics simulations are crucial for understanding material properties.
  • Efficient parallelization strategies are needed for large-scale simulations.
  • Existing methods for long-range force calculations can be computationally intensive.

Purpose of the Study:

  • To describe the DL_POLY_3 molecular-dynamics simulation package.
  • To highlight its efficient domain decomposition (DD) parallelization.
  • To detail its capability for simulating large systems.

Main Methods:

  • Utilizes a domain decomposition (DD) parallelization strategy.
  • Incorporates a novel 3D Fast Fourier Transform (the Daresbury Advanced Fourier Transform).

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  • Implements a DD adaptation of the smoothed particle mesh Ewald method for long-range forces.

    • Main Results:

    • DL_POLY_3 supports academic research across various applications.
    • The package runs on diverse computing architectures, from workstations to supercomputers.
    • Enables simulations of systems with one million particles or more.

    Conclusions:

    • DL_POLY_3 offers a powerful and scalable platform for molecular dynamics simulations.
    • Its efficient parallelization and advanced algorithms facilitate large-scale research.
    • The package is designed for broad accessibility and efficient use of computational resources.