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DL_POLY_4 Algorithmic Improvements

DL_POLY is a general purpose package for classical molecular dynamics simulations led by I.T. Todorov at STFC Daresbury Laboratory. The package is used to model the atomistic evolution of the full spectrum of models commonly employed in the materials science, solid state chemistry, biological simulation and soft condensed-matter communities. The main purpose of the software is to enable the exploitation of large scale MD simulations on multi-processor platforms. This was the fifth Distributed Computational Science and Engineering (dCSE) project for improving the effectiveness of DL_POLY_4 on HECToR.

The overall aims of this project were:

  • Implement an extended Verlet neighbour list (VNL) calculation within the linked cells (LC) scheme to improve performance on average by 20%.
  • Implement a symplectic multiple time stepping scheme to enable less frequent calculation of expensive operations such as long-ranged Ewald and short-ranged inter-molecular interactions.

The individual achievements of the project are summarised below:

  • For the VNL work, methods for tracking the motion of atoms between link cells and domains have been implemented.
  • The new code was demonstrated with the DL_POLY_4 standard test cases, and for a value of roughly 0.2-1.0Å for the maximum displacement parameter, a typical improvement of 25% can now be achieved.
  • An improvement of up to a factor of 2 can be observed in favourable cases.
  • A symplectic multiple time stepping algorithm was successfully implemented for the NVE ensemble, and also all the 6 integrators available for the NVT ensemble (i.e. those that employ thermostats for constant temperature simulations).
  • In suitable cases, the whole simulation may now be run up to 2.5 times faster. With a test case for Sodium Chloride, a 20% improvement was demonstrated with up to 2000 cores and for DMPC (a lipid) in water, an improvement of at least 35% was demonstrated with up to 250 cores.
  • This work has been incorporated back into a development branch of the main source code and further work is planned to perform a full optimisation of parameters for the time stepping algorithm.

Please see PDF or HTML for a report which summarises this project.