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dc.contributor.advisorAckland, Graeme
dc.contributor.advisorLeimkuhler, Benedict
dc.contributor.authorBethune, Iain Arthur
dc.date.accessioned2021-08-02T13:23:14Z
dc.date.available2021-08-02T13:23:14Z
dc.date.issued2021-07-31
dc.identifier.urihttps://hdl.handle.net/1842/37849
dc.identifier.urihttp://dx.doi.org/10.7488/era/1125
dc.description.abstractThe main contribution of this thesis is MIST, the Molecular Integration Simula- tion Toolkit, a lightweight and efficient software library written in C++ which provides an abstract interface to common Molecular Dynamics codes, enabling rapid and portable development of new integration schemes for Molecular Dynamics. The initial release provides plug-in interfaces to NAMD-Lite, GROMACS, Amber and LAMMPS and includes several standard integration schemes, a constraint solver, temperature control using Langevin Dynamics, temperature and pressure control using Nosé-Hoover chains, and five advanced sampling schemes. I describe the architecture, functionality and internal details of the library and the C and Fortran APIs which can be used to interface additional MD codes to MIST. As an example to future developers, each of the existing plug-ins and the integrators that are included with MIST are described. Brief instructions for compilation and use of the library are also given as a reference to users. The library is designed to be expressive, portable and performant, and I show via a range of test systems that MIST introduces negligible overheads for serial, parallel, and GPU-accelerated cases, except for Amber where the native integrators run directly on the GPU itself, but only run on the CPU in MIST. The capabilities of MIST for production-quality simulations are demonstrated through the use of a simulated tempering simulation to study the free energy landscape of Alanine-12 in both vacuum and detailed solvent conditions. I also present the evaluation and application of force-field and ab initio Molecular Dynamics to study the structural properties and behaviour of olivine melts. Three existing classical potentials for fayalite are tested and found to give lattice parameters and Radial Distribution Functions in good agreement with experimental data. For forsterite, lattice parameters at ambient pressure and temperature are slightly over-predicted by simulation (similar to other reported results in the literature). Likewise, higher-than expected thermal expansion coefficients and heat capacities are obtained from both ab initio and classical methods. The structure of both the crystal and melt are found to be in good agreement with experimental data. Several methodological improvements which could improve the accuracy of melting point determination and the thermal expansion coefficients are discussed.en
dc.contributor.sponsorEngineering and Physical Sciences Research Council (EPSRC)en
dc.language.isoenen
dc.publisherThe University of Edinburghen
dc.relation.hasversionBethune, I. “Improving the performance of CP2K on HECToR.” Technical report, 2009. http://www.hector.ac.uk/cse/distributedcse/ reports/cp2k/cp2k_final_report.pdf.en
dc.relation.hasversionBethune, I., “Improving the performance of CP2K on multi-core systems.” Technical report, 2010. http://www.hector.ac.uk/cse/ distributedcse/reports/cp2k02/cp2k02_final_report.pdf.en
dc.relation.hasversionBethune, I., R. Banisch, E. Breitmoser, A. B. Collis, G. Gibb, G. Gobbo, C. Matthews, G. J. Ackland, and B. J. Leimkuhler. “MIST: A simple and efficient molecular dynamics abstraction library for integrator development.” Computer Physics Communications 236: (2019) 224 – 236. https://doi.org/10.1016/j.cpc.2018.10.006.en
dc.relation.hasversionBethune, I., E. Breitmoser, A. B. K. Collis, G. Gobbo, and B. J. Leimkuhler. “Interfacing novel integrators and existing Molecular Dynamics codes with the MIST library.” In Producing High Performance and Sustainable Software for Molecular Simulation Workshop, Supercomputing 2015. 2015. https://www.era.lib.ed.ac.uk/bitstream/handle/1842/16531/ 04-Bethune-Interfacing_integrators_MD_codes_MIST_library.pdf.en
dc.relation.hasversionBethune, I., E. Breitmoser, G. Gobbo, C. Matthews, and B. J. Leimkuhler. “MIST: Molecular Integration Simulation Toolkit.” In Computational Molecular Science 2015. 2015. https://ibethune.github.io/files/ MIST-CMS2015.pdf.en
dc.relation.hasversionBethune, I., E. Breitmoser, and B. J. Leimkuhler. “Molecular Integration Simulation Toolkit: Interfacing novel integrators with Molecular Dynamics codes.” In International Society of Quantum Biology and Pharmacology (ISQBP) President’s Meeting 2016. 2016. https://ibethune.github.io/ files/MIST_ISQBP.pdf.en
dc.relation.hasversionBethune, I., F. Reid, and A. Lazzaro. “CP2K Performance from Cray XT3 to XC30.” In Proceedings of the Cray User Group (CUG). 2014.en
dc.relation.hasversionBethune, I., S. Wheeler, S. Genheden, and J. W. Essex. “Implementation of Dual Resolution Simulation Methodology in LAMMPS.” Technical report, 2016. https://www.archer.ac.uk/documentation/white-papers/ lammps-elba/lammps-ecse.pdf.en
dc.relation.hasversionK¨uhne, T. D., M. Iannuzzi, M. Del Ben, V. V. Rybkin, P. Seewald, F. Stein, T. Laino, R. Z. Khaliullin, O. Sch¨utt, F. Schiffmann, D. Golze, J. Wilhelm, S. Chulkov, M. H. Bani-Hashemian, V. Weber, U. Borˇstnik, M. Taillefumier, A. S. Jakobovits, A. Lazzaro, H. Pabst, T. M¨uller, R. Schade, M. Guidon, S. Andermatt, N. Holmberg, G. K. Schenter, A. Hehn, A. Bussy, F. Belleflamme, G. Tabacchi, A. Gl¨oß, M. Lass, I. Bethune, C. J. Mundy, C. Plessl, M. Watkins, J. VandeVondele, M. Krack, and J. Hutter. “CP2K: An electronic structure and molecular dynamics software package - Quickstep: Efficient and accurate electronic structure calculations.” The Journal of Chemical Physics 152, 19: (2020) 194,103. https://doi.org/10.1063/5.0007045.en
dc.relation.hasversionMisic, M., I. Bethune, and M. Tomasevic. “Automated regression testing and code coverage analysis of the CP2K application.” In Proceedings of the 2014 IEEE Seventh International Conference on Software Testing, Verification and Validation. 2014. https://doi.org/10.1109/ICST.2014. 21.en
dc.relation.hasversionShkurti, A., I. Styliari, V. Balasubramanian, I. Bethune, C. Pedebos, S. Jha, and C. Laughton. “CoCo-MD: A Simple and Effective Method for the Enhanced Sampling of Conformational Space.” Journal of Chemical Theory and Computation 15, 4: (2019) 2587–2596. https://doi.org/10.1021/ acs.jctc.8b00657.en
dc.subjectMolecular Dynamicsen
dc.subjectMolecular Integration Simulation Toolkiten
dc.subjectMISTen
dc.subjectMD algorithmsen
dc.subjectperformance overheadsen
dc.subjectreliabilityen
dc.titleMIST: a portable and efficient toolkit for molecular dynamics integration algorithm developmenten
dc.typeThesis or Dissertationen
dc.type.qualificationlevelDoctoralen
dc.type.qualificationnamePhD Doctor of Philosophyen


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