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A GPU Accelerated Lennard-Jones System for Immersive Molecular Dynamics Simulations in Virtual Reality

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Virtual, Augmented and Mixed Reality. Industrial and Everyday Life Applications (HCII 2020)

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Abstract

Interactive tools and immersive technologies make teaching more engaging and complex concepts easier to comprehend are designed to benefit training and education. Molecular Dynamics (MD) simulations numerically solve Newton’s equations of motion for a given set of particles (atoms or molecules). Improvements in computational power and advances in virtual reality (VR) technologies and immersive platforms may in principle allow the visualization of the dynamics of molecular systems allowing the observer to experience first-hand elusive physical concepts such as vapour-liquid transitions, nucleation, solidification, diffusion, etc. Typical MD implementations involve a relatively large number of particles N = O(\(10^4\)) and the force models imply a pairwise calculation which scales, in case of a Lennard-Jones system, to the order of O(\(N^2\)) leading to a very large number of integration steps. Hence, modelling such a computational system over CPU along with a GPU intensive virtual reality rendering often limits the system size and also leads to a lower graphical refresh rate. In the model presented in this paper, we have leveraged GPU for both data-parallel MD computation and VR rendering thereby building a robust, fast, accurate and immersive simulation medium. We have generated state-points with respect to the data of real substances such as CO\(_2\). In this system the phases of matter viz. solid liquid and gas, and their emergent phase transition can be interactively experienced using an intuitive control panel.

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Change history

  • 10 July 2020

    The original version of this chapter 2 was revised. A video was added to help provide clarity and a visual explanation of the paper.

    The title of the originally published chapter 27 contained a typo. The title was corrected.

References

  1. Abraham, M.J., et al.: GROMACS: high performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX 1, 19–25 (2015)

    Article  Google Scholar 

  2. Anderson, J.A., Lorenz, C.D., Travesset, A.: General purpose molecular dynamics simulations fully implemented on graphics processing units. J. Comput. Phys. 227(10), 5342–5359 (2008)

    Article  Google Scholar 

  3. Buck, I.: High level languages for GPUs. In: SIGGRAPH Courses, p. 109 (2005)

    Google Scholar 

  4. Buckingham, R.A.: The classical equation of state of gaseous helium, neon and argon. Proc. R. Soc. Lond. Ser. A Math. Phys. Sci. 168(933), 264–283 (1938)

    Google Scholar 

  5. Callen, H.B.: Thermodynamics and an Introduction to Thermostatistics, 2nd edn., p. 512. Wiley, New York (1985). ISBN: 978-0-471-86256-7

    Google Scholar 

  6. Duncan, B.S., Olson, A.J.: Approximation and characterization of molecular surfaces. Biopolymers Original Res. Biomol. 33(2), 219–229 (1993)

    Google Scholar 

  7. Elsen, E., Vishal, V., Houston, M., Pande, V., Hanrahan, P., Darve, E.: N-body simulations on GPUs. arXiv preprint arXiv:0706.3060 (2007)

  8. Freina, L., Ott, M.: A literature review on immersive virtual reality in education: state of the art and perspectives. In: The International Scientific Conference eLearning and Software for Education, vol. 1, no. 133, pp. 10–1007 (2015)

    Google Scholar 

  9. Georgii, J., Westermann, R.: Mass-spring systems on the GPU. Simul. Model. Pract. Theory 13(8), 693–702 (2005)

    Article  Google Scholar 

  10. Germann, T.C., Kadau, K.: Trillion-atom molecular dynamics becomes a reality. Int. J. Mod. Phys. C 19(09), 1315–1319 (2008)

    Article  Google Scholar 

  11. Grubmüller, H., Heller, H., Windemuth, A., Schulten, K.: Generalized verlet algorithm for efficient molecular dynamics simulations with long-range interactions. Mol. Simul. 6(1–3), 121–142 (1991)

    Article  Google Scholar 

  12. Harris, M.: Mapping computational concepts to GPUs. In: ACM SIGGRAPH 2005 Courses, p. 50. ACM (2005)

    Google Scholar 

  13. Hirst, J.D., Glowacki, D.R., Baaden, M.: Molecular simulations and visualization: introduction and overview. Faraday Discuss. 169, 9–22 (2014)

    Article  Google Scholar 

  14. HTC: HTC Vive product page. https://www.vive.com. Accessed 20 Sept 2019

  15. Jo, J.C., Kim, B.C.: Determination of proper time step for molecular dynamics simulation. Bull. Korean Chem. Soc. 21(4), 419–424 (2000)

    Google Scholar 

  16. Johnson, J.K., Mueller, E.A., Gubbins, K.E.: Equation of state for Lennard-Jones chains. J. Phys. Chem. 98(25), 6413–6419 (1994)

    Article  Google Scholar 

  17. Jones, L.L., Jordan, K.D., Stillings, N.A.: Molecular visualization in chemistry education: the role of multidisciplinary collaboration. Chem. Educ. Res. Pract. 6(3), 136–149 (2005)

    Article  Google Scholar 

  18. Kolb, A., Latta, L., Rezk-Salama, C.: Hardware-based simulation and collision detection for large particle systems. In: Proceedings of the ACM SIGGRAPH/EUROGRAPHICS Conference on Graphics Hardware, pp. 123–131. ACM (2004)

    Google Scholar 

  19. Kruger, J., Kipfer, P., Konclratieva, P., Westermann, R.: A particle system for interactive visualization of 3D flows. IEEE Trans. Visual. Comput. Graphics 11(6), 744–756 (2005)

    Article  Google Scholar 

  20. Lammers, K.: Unity Shaders and Effects Cookbook. Packt Publishing Ltd, Birmingham (2013)

    Google Scholar 

  21. Luebke, D., Harris, M.: General-purpose computation on graphics hardware. In: Workshop, SIGGRAPH, vol. 33 (2004)

    Google Scholar 

  22. Luebke, D., et al.: GPGPU: general-purpose computation on graphics hardware. In: Proceedings of the 2006 ACM/IEEE Conference on Supercomputing, p. 208. ACM (2006)

    Google Scholar 

  23. Luebke, D., Humphreys, G.: How GPUs work. Computer 40(2), 96–100 (2007)

    Article  Google Scholar 

  24. Mecke, M., Winkelmann, J., Fischer, J.: Molecular dynamics simulation of the liquid-vapor interface: the Lennard-Jones fluid. J. Chem. Phys. 107(21), 9264–9270 (1997)

    Article  Google Scholar 

  25. Mezey, P.G.: Shape in Chemistry: An Introduction to Molecular Shape and Topology. Wiley-VCH, Weinheim (1993)

    Google Scholar 

  26. Microsoft: Microsoft Hololens product page. https://www.microsoft.com/en-us/hololens. Accessed 20 Sept 2019

  27. Müller, E.A., Gubbins, K.E.: Molecular-based equations of state for associating fluids: a review of saft and related approaches. Ind. Eng. Chem. Res. 40(10), 2193–2211 (2001)

    Article  Google Scholar 

  28. Oculus: Asynchronous Spacewarp blog post. https://developer.oculus.com/blog/asynchronous-spacewarp. Accessed 20 Sept 2019

  29. Oculus: Oculus Rift product page. https://www.oculus.com/rift. Accessed 20 Sept 2019

  30. Owens, J.D., et al.: A survey of general-purpose computation on graphics hardware. Comput. Graph. Forum 26(1), 80–113 (2007)

    Article  MathSciNet  Google Scholar 

  31. Purawat, S., et al.: A Kepler workflow tool for reproducible AMBER GPU molecular dynamics. Biophys. J. 112(12), 2469–2474 (2017)

    Article  Google Scholar 

  32. Rapaport, D.: Molecular dynamics simulation. Comput. Sci. Eng. 1(1), 70–71 (1999)

    Article  Google Scholar 

  33. Schroeder, D.V.: Interactive molecular dynamics. Am. J. Phys. 83(3), 210–218 (2015)

    Article  Google Scholar 

  34. Steinfeld, J.I., Francisco, J.S., Hase, W.L.: Chemical Kinetics and Dynamics, vol. 3. Prentice Hall, Englewood Cliffs (1989)

    Google Scholar 

  35. Stone, J.E., Gullingsrud, J., Schulten, K.: A system for interactive molecular dynamics simulation. In: Proceedings of the 2001 Symposium on Interactive 3D Graphics, pp. 191–194 (2001)

    Google Scholar 

  36. Store, U.A.: Paint booth UAA business. https://assetstore.unity.com/packages/3d/environments/uaa-business-paint-booth-120410. Accessed 20 Sept 2019

  37. Technologies, U.: Graphics. DrawMeshInstancedIndirect function description. https://docs.unity3d.com/ScriptReference/Graphics.DrawMeshInstancedIndirect.html. Accessed 20 Sept 2019

  38. Technologies, U.: XR Plugin Architecture unity. https://docs.unity3d.com/Manual/XRPluginArchitecture.html. Accessed 20 Sept 2019

  39. Thorsteinsson, G., Shavinina, L.: Developing an understanding of the pedagogy of using a virtual reality learning environment (VRLE) to support innovation education. In: Shavinina, L.V. (ed.) The Routledge International Handbook of Innovation Education, pp. 456–470. Routledge, Oxford (2013). ISBN-10 415682215

    Google Scholar 

  40. Vormoor, O.: Quick and easy interactive molecular dynamics using Java3D. Comput. Sci. Eng. 3(5), 98–104 (2001)

    Article  Google Scholar 

  41. Yeh, I.C., Hummer, G.: System-size dependence of diffusion coefficients and viscosities from molecular dynamics simulations with periodic boundary conditions. J. Phys. Chem. B 108(40), 15873–15879 (2004)

    Article  Google Scholar 

  42. Zyda, M.: From visual simulation to virtual reality to games. Computer 38(9), 25–32 (2005)

    Article  Google Scholar 

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Acknowledgements

Funding through Imperial College London Pedagogy Transformation programme is gratefully acknowledged.

Author information

Authors and Affiliations

  1. Imperial College London, South Kensington, London, SW7 2AZ, UK

    Nitesh Bhatia, Erich A. Müller & Omar Matar

Authors
  1. Nitesh Bhatia
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  2. Erich A. Müller
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  3. Omar Matar
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Corresponding author

Correspondence to Nitesh Bhatia .

Editor information

Editors and Affiliations

  1. U.S. Army Research Laboratory, Aberdeen Proving Ground, MD, USA

    Jessie Y. C. Chen

  2. U.S. Army Combat Capabilities Development Command, Orlando, FL, USA

    Gino Fragomeni

Appendices

A Appendix: VR System Configurations Used for Performance Computations

For teaching chemical engineering through virtual reality, we acquired several Oculus VR headsets and computers under pedagogy transformation funding. For computing the performance of MD VR system, we have used Oculus Rift VR Headset tethered to two different systems, one laptop class GPU and one desktop-class GPU. The hardware and software configurations are described below.

Hardware Configuration 1

  • HP Omen 15t Laptop

  • Oculus Rift with Controllers

  • Intel Core i7 8750H Processor

  • Nvidia Geforce GTX1070 Max-Q GPU

  • 16 GB RAM

Hardware Configuration 2

  • HP EliteDesk 800 G3 Desktop

  • Oculus Rift with Controllers

  • Intel Core i7 7700 Processor

  • Nvidia Geforce GTX1080 GPU

  • 64 GB RAM

Software Configuration

  • Microsoft Windows 10 Build 1803

  • DirectX 11 supported GPU drivers

  • Oculus Runtime and SDK

  • Unity 2018 with Education Licence

  • Microsoft Visual Studio 2017 Community Edition

B Appendix: Demo video

Demo video is available at https://www.youtube.com/watch?v=HgkOREay5JY

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Bhatia, N., Müller, E.A., Matar, O. (2020). A GPU Accelerated Lennard-Jones System for Immersive Molecular Dynamics Simulations in Virtual Reality. In: Chen, J.Y.C., Fragomeni, G. (eds) Virtual, Augmented and Mixed Reality. Industrial and Everyday Life Applications. HCII 2020. Lecture Notes in Computer Science(), vol 12191. Springer, Cham. https://doi.org/10.1007/978-3-030-49698-2_2

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  • DOI: https://doi.org/10.1007/978-3-030-49698-2_2

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-030-49697-5

  • Online ISBN: 978-3-030-49698-2

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