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2021 | OriginalPaper | Chapter

MaMiCo: Non-Local Means Filtering with Flexible Data-Flow for Coupling MD and CFD

Authors : Piet Jarmatz, Felix Maurer, Philipp Neumann

Published in: Computational Science – ICCS 2021

Publisher: Springer International Publishing

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Abstract

When a molecular dynamics (MD) simulation and a computational fluid dynamics (CFD) solver are coupled together to create a multiscale, molecular-continuum flow simulation, thermal noise fluctuations from the particle system can be a critical issue, so that noise filtering methods are required. Noise filters are one option to significantly reduce these fluctuations.

We present a modified variant of the Non-Local Means (NLM) algorithm for MD data. Originally developed for image processing, we extend NLM to a space-time formulation and discuss its implementation details.

The space-time NLM algorithm is incorporated into the Macro-Micro-Coupling tool (MaMiCo), a C++ molecular-continuum coupling framework, together with a novel flexible filtering subsystem. The latter can be used to configure and efficiently execute arbitrary data-flow chains of simulation data analytics modules or noise filters at runtime on an HPC system, even including python functions. We employ a coupling to a GPU-based Lattice Boltzmann solver running a vortex street scenario to show the benefits of our approach. Our results demonstrate that NLM has an excellent signal-to-noise ratio gain and is a superior method for extraction of macroscopic flow information from noisy fluctuating particle ensemble data.

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previous chapter MsFEM Upscaling for the Coupled Thermo-Mechanical Problem

https://github.com/HSU-HPC/MaMiCo.

https://www.scipy.org/.

Bauer, M., Köstler, H., Rüde, U.: lbmpy: automatic code generation for efficient parallel lattice boltzmann methods. J. Comput. Sci. 49, 101269 (2021)MathSciNetCrossRef

Borg, M.K., Lockerby, D.A., Reese, J.M.: A hybrid molecular-continuum method for unsteady compressible multiscale flows. J. Fluid Mech. 768, 388–414 (2015)CrossRef

Buades, A., Coll, B., Morel, J.M.: On image denoising methods. CMLA. Preprint, vol. 5 (2004)

Buades, A., Coll, B., Morel, J.M.: Non-local means denoising. Image Process. OnLine 1, 208–212 (2011)CrossRef

Coupé, P., Yger, P., Barillot, C.: Fast non local means denoising for 3D MR images. In: Larsen, R., Nielsen, M., Sporring, J. (eds.) MICCAI 2006. LNCS, vol. 4191, pp. 33–40. Springer, Heidelberg (2006). https://doi.org/10.1007/11866763_5CrossRef

Delgado-Buscalioni, R., Coveney, P.: USHER an algorithm for particle insertion in dense fluids. J. Chem. Phys. 119(2), 978 (2003)CrossRef

Gonnet, P.: A simple algorithm to accelerate the computation of non-bonded interactions in cell-based molecular dynamics simulations. J. Comput. Chem. 28(2), 570–573 (2007)MathSciNetCrossRef

Grinberg, L.: Proper orthogonal decomposition of atomistic flow simulations. J. Comput. Phys. 231(16), 5542–5556 (2012)CrossRef

Grinberg, L., Yakhot, A., Karniadakis, G.E.: Analyzing transient turbulence in a stenosed carotid artery by proper orthogonal decomposition. Ann. Biomed. Eng. 37(11), 2200–2217 (2009)CrossRef

10.

Jakob, W., Rhinelander, J., Moldovan, D.: pybind11-seamless operability between C++ 11 and Python. https://github.com/pybind/pybind11 (2017)

11.

Jarmatz, P., Neumann, P.: MaMiCo: parallel noise reduction for multi-instance molecular-continuum flow simulation. In: Rodrigues, J.M.F., et al. (eds.) ICCS 2019. LNCS, vol. 11539, pp. 451–464. Springer, Cham (2019). https://doi.org/10.1007/978-3-030-22747-0_34CrossRef

12.

Ling, H., Bovik, A.C.: Smoothing low-SNR molecular images via anisotropic median-diffusion. IEEE Trans. Med. Imaging 21(4), 377–384 (2002)CrossRef

13.

Neumann, P., Bian, X.: Mamico: transient multi-instance molecular-continuum flow simulation on supercomputers. Comput. Phys. Commun. 220, 390–402 (2017)CrossRef

14.

Neumann, P., Flohr, H., Arora, R., Jarmatz, P., Tchipev, N., Bungartz, H.J.: Mamico: software design for parallel molecular-continuum flow simulations. Comput. Phys. Commun. 200, 324–335 (2016), ISSN 0010–4655

15.

Nie, X., Chen, S., Robbins, M.O., et al.: A continuum and molecular dynamics hybrid method for micro-and nano-fluid flow. J. Fluid Mech. 500, 55–64 (2004)CrossRef

16.

Niethammer, C., et al.: ls1 mardyn: the massively parallel molecular dynamics code for large systems. J. Chem. Theory Comput. 10(10), 4455–4464 (2014)CrossRef

17.

Páll, S., Abraham, M.J., Kutzner, C., Hess, B., Lindahl, E.: Tackling exascale software challenges in molecular dynamics simulations with GROMACS. In: Markidis, S., Laure, E. (eds.) EASC 2014. LNCS, vol. 8759, pp. 3–27. Springer, Cham (2015). https://doi.org/10.1007/978-3-319-15976-8_1CrossRef

18.

Plimpton, S.: Fast parallel algorithms for short-range molecular dynamics. J. Comput. Phys. 117(1), 1–19 (1995). ISSN 0021–9991

19.

Schäfer, M., Turek, S., Durst, F., Krause, E., Rannacher, R.: Benchmark computations of laminar flow around a cylinder. In: Flow Simulation with High-Performance Computers II, pp. 547–566. Springer, Cham (1996). https://doi.org/10.1007/978-3-322-89849-4_39

20.

Zhou, W., Luan, H., He, Y., Sun, J., Tao, W.: A study on boundary force model used in multiscale simulations with non-periodic boundary condition. Microfluidics Nanofluidics 16(3), 1 (2014)CrossRef

21.

Zimoń, M., et al.: An evaluation of noise reduction algorithms for particle-based fluid simulations in multi-scale applications. J. Comput. Phys. 325, 380–394 (2016)MathSciNetCrossRef

Title: MaMiCo: Non-Local Means Filtering with Flexible Data-Flow for Coupling MD and CFD
Authors: Piet Jarmatz
Felix Maurer
Philipp Neumann
Publisher: Springer International Publishing
Book: Computational Science – ICCS 2021
Print ISBN: 978-3-030-77976-4

Electronic ISBN: 978-3-030-77977-1

Copyright Year: 2021
DOI: https://doi.org/10.1007/978-3-030-77977-1_46

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