DL_MESO_DPD: development and use of mesoscale modelling software

ABSTRACT

DL_MESO is a highly-scalable general purpose software package for mesoscale modelling. Created and developed at Daresbury Laboratory for the UK Collaborative Computational Project CCP5, it was intended to be a companion package to the flagship molecular dynamics code DL_POLY. One of DL_MESO component codes, DL_MESO_DPD, is based on dissipative particle dynamics, a mesoscale modelling technique with many similarities to classical molecular dynamics. While this code and DL_POLY were created with different applications in mind, they share a significant amount of functionality and development history. This article gives an overview on how DL_MESO_DPD has been developed, including its shared history with DL_POLY and information on its current performance, and a selection of applications for which the code has been used.

KEYWORDS:

• DL_MESO
• mesoscale modelling
• dissipative particle dynamics
• software development
• DL_POLY

Acknowledgments

Many thanks are especially due to Rongshan Qin (currently at The Open University) and William Smith, the originators and original developers of DL_MESO.

Specifically for DL_MESO_DPD, the author would like to thank Ilian Todorov, Richard Anderson, David Bray, Annalaura Del Regno and Silvia Chiacchiera (all at STFC Daresbury Laboratory), Ard van Bergen (Novidec Ltd) and William Swope (IBM Research) for practical suggestions that have led to code improvements. Many thanks are due to Michael Johnston and Leopold Grinberg (IBM Research) for their general-purpose and IBM-specific optimisations of DL_MESO_DPD, as well as Luke Mason and Stephen Pickles (STFC Hartree Centre) for optimisations of DL_MESO_DPD for Intel Xeon Phi systems.

Thanks to Nidhi Raj for carrying out the drug loading/release simulations on the Hartree Centre's Blue Wonder machine with DL_MESO_DPD version 2.6 (Figure 8) in August 2016.

Many thanks are due to the many past and current users of DL_MESO_DPD who have helped to improve the code by reporting bugs and making suggestions for new features.

Disclosure statement

No potential conflict of interest was reported by the author.

Notes

1 Advanced users can modify the relevant force and potential calculation routines to use their own MDPD models.

2 All of these changes were made to versions 2.5 and 2.6 of DL_MESO_DPD: these will be standard features in the upcoming version (2.7).

Additional information

Funding

The author is grateful to a number of funding bodies, particularly EPSRC via the Computational Science Centre for Research Communities (CoSeC), whose financial support led to the creation of DL_MESO under the auspices of CCP5 and continues to support its further development via CCP5 and the High End Computing consortium UKCOMES.