ABSTRACT
In coupled molecular-continuum flow simulations, molecular dynamics (MD) simulations exhibit thermal fluctuations. Finding a way to minimize the impact of these fluctuations on the CFD solver, e.g. in terms of stability, and to control the corresponding statistical error plays a key role in order to obtain reliable results.
In this paper, statistical error analysis is employed for MD simulations to determine the statistical error in flow velocities and the number of MD data samples to bound this error. The corresponding error estimator is augmented by a dynamic ensemble handling approach, which allows to couple a variable number of MD simulation instances to a single CFD solver. The ensemble members can be simulated independently from each other over separate coupling time intervals, enabling a high level of (MPI-based) parallelism. Adding or removing MD simulations to/from the ensemble allows to regulate the error and keep it under a prescribed threshold. All functionality is implemented in the massively parallel macro-micro-coupling tool (MaMiCo). We validate our approach by coupled molecular-continuum Couette flow simulation for liquid argon and provide scalability tests on up to 131.072 cores. The computational overhead for handling the dynamic MD ensemble is found to be rather negligible.
- Burkhard Dünweg, Ulf D. Schiller, and Anthony J. C. Ladd. 2007. Statistical Mechanics of the Fluctuating Lattice Boltzmann Equation. Phys. Rev. E 76, 036704 (2007).Google Scholar
- Alexandre Dupuis, Evangelos Kotsalis, and Petros Koumoutsakos. 2007. Coupling lattice Boltzmann and molecular dynamics models for dense fluids. Phys. Rev. E 75, 04704 (2007), 1–8.Google ScholarCross Ref
- Dmitry Fedosov and George Karniadakis. 2009. Triple-decker: Interfacing atomistic-mesoscopic-continuum flow regimes. J. Comput. Phys. 228(2009), 1157–1171.Google ScholarDigital Library
- Nicolas G. Hadjiconstantinou, Alejandro L. Garcia, Martin Z. Bazant, and Gang He. 2003. Statistical error in particle simulations of hydrodynamic phenomena. J. Comput. Phys. 187(2003), 274–297.Google ScholarDigital Library
- Sarwar Hussain and Amir Haji-Akbaria. 2020. Studying rare events using forward-flux sampling: Recent breakthroughs and future outlook. J. Chem. Phys. 152(2020), 060901.Google ScholarCross Ref
- Marco Kalweit and Dimitris Drikakis. 2008. Multiscale Methods for Micro/Nano Flows and Materials. J. Comput. Theor. Nanosci. 5, 9 (2008), 1923–1938.Google ScholarCross Ref
- Andreas Köster, Tao Jiang, Gábor Rutkai, Colin Glass, and Jadran Vrabec. 2016. Automatized determination of fundamental equations of state based on molecular simulations in the cloud. Fluid Phase Equilibria 425 (2016), 84–92.Google ScholarCross Ref
- Evangelos M. Kotsalis, Jens H. Walther, and Petros Koumoutsakos. 2007. Control of density fluctuations in atomistic-continuum simulations of dense liquids. Phys. Rev. E 76(2007), 016709.Google ScholarCross Ref
- Lev D. Landau and Evgeny M. Lifshitz. 1959. Fluid mechanics. Addison-Wesley, Reading.Google Scholar
- Stephan M. Longshaw, Matthew K. Borg, Srinivasa B. Ramisetti, J. Zhang, Duncan A. Lockerby, David R. Emerson, and Jason M. Reese. 2018. mdFoam+: Advanced molecular dynamics in OpenFOAM. Computer Physics Communications 224 (2018), 1–21.Google ScholarCross Ref
- Karsten Meier. 2002. Computer Simulation and Interpretation of the Transport Coefficients of the Lennard-Jones Model Fluid. Ph.D. Dissertation. Helmut-Schmidt-University Hamburg, Shaker.Google Scholar
- Khaled M. Mohamed and Abdulmajeed Mohamad. 2010. A review of the development of hybrid atomistic–continuummethods for dense fluids. Microfluid. Nanofluid. 8(2010), 283–302.Google ScholarCross Ref
- Philipp Neumann and Xin Bian. 2017. MaMiCo: Transient Multi-Instance Molecular-Continuum Flow Simulation on Supercomputers. Comput. Phys. Commun. 220 (2017), 390–402.Google ScholarCross Ref
- Philipp Neumann, Hanno Flohr, Rahul Arora, Piet Jarmatz, Nikola Tchipev, and Hans-Joachim Bungartz. 2016. MaMiCo: Software design for parallel molecular-continuum flow simulations. Comput. Phys. Commun. 200 (2016), 324–335.Google ScholarCross Ref
- Xiaobo Nie, Shiyi Chen, W. E, and Mark Robbins. 2004. A continuum and molecular dynamics hybrid method for micro-and nano-fluid flow. J. Fluid Mech. 500(2004), 55–64.Google ScholarCross Ref
- Weiqing Ren. 2007. Analytical and numerical study of coupled atomistic-continuum methods for fluids. J. Comput. Phys. 227, 2 (2007), 1353–1371.Google ScholarDigital Library
- Xiaoguang Ren, Qian Wang, Li-Yang Xu, Wen-Jing Yang, and Xin-Hai Xu. 2017. HACPar: An efficient parallel multiscale framework for hybrid atomistic–continuum simulation at the micro- and nanoscale. Advances in Mechanical Engineering 9 (2017), 1–13. Issue 8.Google ScholarCross Ref
- Edward R. Smith, D. Trevelyan, and E. Ramos. 2016. cpl-library. https://doi.org/10.5281/zenodo.46573Google ScholarCross Ref
- David Stephenson, James R. Kermode, and Duncan A. Lockerby. 2018. Accelerating multiscale modelling of fluids with on-the-fly Gaussian process regression. Microfluid. Nanofluid. 22 (2018), 139.Google ScholarCross Ref
- Thomas Werder, Jens H. Walther, and Petros Koumoutsakos. 2005. Hybrid atomistic-continuum method for the simulation of dense fluid flows. J. Comput. Phys. 205(2005), 373–390.Google ScholarDigital Library
Index Terms
- Massively Parallel Molecular-Continuum Flow Simulation with Error Control and Dynamic Ensemble Handling
Recommendations
Massively parallel molecular dynamics simulations of lysozyme unfolding
We have performed molecular dynamics simulations for a total duration of more than 10 µs (with most molecular trajectories being 1 µs in duration) to study, the effect of a single mutation on hen lysozyme protein stability and denaturing, using an IBM ...
Fault Tolerance for Ensemble-based Molecular-Continuum Flow Simulations
HPCAsia '23: Proceedings of the International Conference on High Performance Computing in Asia-Pacific RegionMolecular dynamics (MD) simulations exhibit big computational efforts, which makes them very time-consuming. This particularly holds for molecular-continuum simulations in fluid dynamics, which rely on the simulation of MD ensembles that are coupled to ...
Comments