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A toolbox of equation-free functions in Matlab/Octave for efficient system level simulation

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Abstract

The ‘equation-free toolbox’ empowers the computer-assisted analysis of complex, multiscale systems. Its aim is to enable scientists and engineers to immediately use microscopic simulators to perform macro-scale system level tasks and analysis, because micro-scale simulations are often the best available description of a system. The methodology bypasses the derivation of macroscopic evolution equations by computing the micro-scale simulator only over short bursts in time on small patches in space, with bursts and patches well-separated in time and space respectively. We introduce the suite of coded equation-free functions in an accessible way, link to more detailed descriptions, discuss their mathematical support, and introduce a novel and efficient algorithm for Projective Integration. Some facets of toolbox development of equation-free functions are then detailed. Download the toolbox functions and use to empower efficient and accurate simulation in a wide range of science and engineering problems.

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  1. https://github.com/uoa1184615/EquationFreeGit

  2. https://github.com/uoa1184615/EquationFreeGit

References

  1. Kevrekidis, I.G., Samaey, G.: Equation-free multiscale computation: Algorithms and applications. Annu. Rev. Phys. Chem. 60, 321–44 (2009). https://doi.org/10.1146/annurev.physchem.59.032607.093610

    Article  Google Scholar 

  2. Kevrekidis, I.G., Gear, C.W., Hummer, G.: Equation-free: the computer-assisted analysis of complex, multiscale systems. A. I. Ch. E. Journal 50, 1346–1354 (2004). https://doi.org/10.1002/aic.10106

    Article  Google Scholar 

  3. Kevrekidis, I.G., Gear, C.W., Hyman, J.M., Kevrekidis, P.G., Runborg, O., Theodoropoulos, K.: Equation-free, coarse-grained multiscale computation: enabling microscopic simulators to perform system level tasks. Comm. Math. Sciences 1, 715–762 (2003). https://doi.org/10.4310/CMS.2003.v1.n4.a5

    Article  MATH  Google Scholar 

  4. Roberts, A.J., MacKenzie, T., Bunder, J.E.: A dynamical systems approach to simulating macroscale spatial dynamics in multiple dimensions. J. Engineering Mathematics 86(1), 175–207 (2014). https://doi.org/10.1007/s10665-013-9653-6

    Article  MathSciNet  MATH  Google Scholar 

  5. Roberts, A.J., Kevrekidis, I.G.: General tooth boundary conditions for equation free modelling. SIAM J. Scientific Computing 29(4), 1495–1510 (2007). https://doi.org/10.1137/060654554

    Article  MathSciNet  MATH  Google Scholar 

  6. Saeb, S., Steinmann, P., Javili, A.: Aspects of computational homogenization at finite deformations: a unifying review from Reuss’ to Voigt’s bound. Appl. Mech. Rev. 68(5), 1–33 (2016). https://doi.org/10.1115/1.4034024

    Article  Google Scholar 

  7. Geers, M.G.D., Kouznetsova, V.G., Matouš, K., Yvonnet, J.: Homogenization methods and multiscale modeling: Nonlinear problems. In: Encyclopedia of Computational Mechanics, Second Edition, pp 1–34. Wiley. https://onlinelibrary.wiley.com/doi/abs/10.1002/9781119176817.ecm2107 (2017)

  8. Peterseim, D.: Numerical homogenization beyond scale separation and periodicity. Technical report, AMSI Winter School on Computational Modeling of Heterogeneous Media. https://ws.amsi.org.au/wp-content/uploads/sites/70/2019/06/numhomamsi2019.pdf (2019)

  9. Craster, R.V.: Dynamic homogenization. In: Mityushev, V.V., Ruzhansky, M. (eds.) Springer Proceedings in Mathematics and Statistics, vol 116, pp 41–50. Springer (2015)

  10. Gear, C.W., Kevrekidis, I.G.: Projective methods for stiff differential equations: problems with gaps in their eigenvalue spectrum. SIAM J. Sci. Comput. 24 (4), 1091–1106 (2003). https://doi.org/10.1137/S1064827501388157. http://link.aip.org/link/?SCE/24/1091/1

    Article  MathSciNet  MATH  Google Scholar 

  11. Rico-Martinez, R., Gear, C.W., Kevrekidis, I.G.: Coarse projective kMC integration: forward/reverse initial and boundary value problems. J. Comput. Phys. 196(2), 474–489 (2004). https://doi.org/10.1016/j.jcp.2003.11.005. http://www.sciencedirect.com/science/article/B6WHY-4B8B9GY-1/2/e92e0d513d9f01c1a9c449d37d9d1a80

    Article  MATH  Google Scholar 

  12. Erban, R., Kevrekidis, I.G., Othmer, H.G.: An equation-free computational approach for extracting population-level behavior from individual-based models of biological dispersal. Physica D: Nonlinear Phenomena 215(1), 1–24 (2006). https://doi.org/10.1016/j.physd.2006.01.008. http://www.sciencedirect.com/science/article/B6TVK-4JDVNSP-1/2/f31e03e0a32cfcb2a811f41ed6a8dfc6

    Article  MathSciNet  MATH  Google Scholar 

  13. Givon, D., Kevrekidis, I.G., Kupferman, R.: Strong convergence of projective integration schemes for singularly perturbed stochastic differential systems. Comm. Math. Sci. 4(4), 707–729 (2006). https://doi.org/10.4310/CMS.2006.v4.n4.a2

    Article  MathSciNet  MATH  Google Scholar 

  14. Maclean, J., Gottwald, G.A.: On convergence of higher order schemes for the projective integration method for stiff ordinary differential equations. J. Comput. Appl. Math. 288, 44–69 (2015). https://doi.org/10.1016/j.cam.2015.04.004

    Article  MathSciNet  MATH  Google Scholar 

  15. Lafitte, P., Lejon, A., Samaey, G.: A high-order asymptotic-preserving scheme for kinetic equations using projective integration. SIAM Journal on Numerical Analysis 54(1), 1–33 (2016). https://epubs.siam.org/doi/abs/10.1137/140966708, Publisher: Society for Industrial and Applied Mathematics

    Article  MathSciNet  MATH  Google Scholar 

  16. Lafitte, P., Melis, W., Samaey, G.: A high-order relaxation method with projective integration for solving nonlinear systems of hyperbolic conservation laws. J. Comput. Phys. 340, 1–25 (2017). https://doi.org/10.1016/j.jcp.2017.03.027. http://www.sciencedirect.com/science/article/pii/S002199911730222X

    Article  MathSciNet  MATH  Google Scholar 

  17. Zieliński, P., Vandecasteele, H., Samaey, G.: Convergence and stability of a micro–macro acceleration method: Linear slow–fast stochastic differential equations with additive noise. J. Comput. Appl. Math. 9, 112490 (2019). https://doi.org/10.1016/j.cam.2019.112490. http://www.sciencedirect.com/science/article/pii/S0377042719304935

    Article  MathSciNet  MATH  Google Scholar 

  18. Cisternas, J., Gear, C.W., Levin, S., Kevrekidis, I.G.: Equation-free modeling of evolving diseases: Coarse-grained computations with individual-based models. Proc. R. Soc. Lond. A 460, 2761–2779 (2004). https://doi.org/10.1098/rspa.2004.13001471-2946

    Article  MATH  Google Scholar 

  19. Setayeshgar, S., Gear, C.W., Othmer, H.G., Kevrekidis, I.G.: Application of coarse integration to bacterial chemotaxis. SIAM J. Mathematical Modeling and Simulation 4, 307–327 (2005). http://epubs.siam.org/sam-bin/dbq/article/60087

    Article  MathSciNet  Google Scholar 

  20. Roberts, A.J.: Model emergent dynamics in complex systems. SIAM, Philadelphia (2015). http://bookstore.siam.org/mm20/

    MATH  Google Scholar 

  21. Car, R., Parrinello, M.: Unified approach for molecular dynamics and density-functional theory. Phys. Rev. Lett. 55(22), 2471–2474 (1985). https://doi.org/10.1103/PhysRevLett.55.2471. https://link.aps.org/doi/10.1103/PhysRevLett.55.2471, Publisher: American Physical Society

    Article  Google Scholar 

  22. Coron, F., Perthame, B.: Numerical passage from kinetic to fluid equations. SIAM Journal on Numerical Analysis 28(1), 26–42 (1991). https://doi.org/10.1137/0728002. https://epubs.siam.org/doi/abs/10.1137/0728002, Publisher: Society for Industrial and Applied Mathematics

    Article  MathSciNet  MATH  Google Scholar 

  23. Tao, M., Owhadi, H., Marsden, J.E.: Nonintrusive and structure preserving multiscale integration of stiff ODEs, SDEs, and hamiltonian systems with hidden slow dynamics via flow averaging. Multiscale Modeling & Simulation 8(4), 1269–1324 (2010). https://doi.org/10.1137/090771648. https://epubs.siam.org/doi/10.1137/090771648, Publisher: Society for Industrial and Applied Mathematics

    Article  MathSciNet  MATH  Google Scholar 

  24. E, W., Engquist, B., Li, X., Ren, W., Vanden-Eijnden, E.: Heterogeneous multiscale methods: a review. Communications in Computational Physics 2(3), 367–450 (2007). https://nyu-staging.pure.elsevier.com/en/publications/heterogeneous-multiscale-methods-a-review, Publisher: Global Science Press

    MathSciNet  MATH  Google Scholar 

  25. Abdulle, A., Weinan, E., Engquist, B., Vanden-Eijnden, E.: The heterogeneous multiscale method. Acta Numerica 21, 1–87 (2012). https://doc.rero.ch/record/290539, Publisher: Cambridge University Press

    Article  MathSciNet  Google Scholar 

  26. Roberts, A.J., Maclean, J., Bunder, J.E.: Equation-free function toolbox for Matlab/Octave. Technical report, [https://github.com/uoa1184615/EquationFreeGit] (2020)

  27. Siettos, C.I., Graham, M.D., Kevrekidis, I.G.: Coarse Brownian dynamics for nematic liquid crystals: bifurcation, projective integration, and control via stochastic simulation. J. Chemical Physics 118(22), 10149–10156 (2003). https://doi.org/10.1063/1.1572456

    Article  Google Scholar 

  28. Chuang, C.Y., Han, S.M., Zepeda-Ruiz, L.A., Sinno, T.: On coarse projective integration for atomic deposition in amorphous systems. J. Chem. Phys. 143(13), 134703 (October 2, 2015). https://doi.org/10.1063/1.4931991. https://aip.scitation.org/doi/full/10.1063/1.4931991

    Article  Google Scholar 

  29. Lee, S.L., Gear, C.W.: Second-order accurate projective integrators for multiscale problems. J. Comput. Appl. Math. 201(1), 258–274 (2007)

    Article  MathSciNet  Google Scholar 

  30. E, W.: Analysis of the heterogeneous multiscale method for ordinary differential equations. Commun. Math. Sci. 1(3), 423–436 (2003). https://doi.org/10.4310/CMS.2003.v1.n3.a3

    Article  MathSciNet  MATH  Google Scholar 

  31. Maclean, J.: A note on implementations of the boosting algorithm and heterogeneous multiscale methods. SIAM J. Numer. Anal. 53(5), 2472–2487 (2015). https://doi.org/10.1137/140982374

    Article  MathSciNet  MATH  Google Scholar 

  32. Gear, C.W., Kaper, T.J., Kevrekidis, I.G., Zagaris, A.: Projecting to a slow manifold: singularly perturbed systems and legacy codes. SIAM J. Applied Dynamical Systems 4(3), 711–732 (2005). https://doi.org/10.1137/040608295

    Article  MathSciNet  MATH  Google Scholar 

  33. Gear, C.W., Kevrekidis, I.G.: Constraint-defined manifolds: a legacy code approach to low-dimensional computation. J. Sci. Comput. 25 (1), 17–28 (2005). https://doi.org/10.1007/s10915-004-4630-x

    Article  MathSciNet  MATH  Google Scholar 

  34. Frederix, Y., Samaey, G., Vandekerckhove, C., Roose, D.: Equation-free methods for molecular dynamics: a lifting procedure. Proc. Appl. Meth. Mech. 7, 20100003–20100004 (2007). https://doi.org/10.1002/pamm.200700025

    Article  Google Scholar 

  35. Bold, K.A., Rajendran, K., Rath, B., Kevrekidis, I.G.: An equation-free approach to coarse-graining the dynamics of networks. Technical report, [1202.5618v1] (2012)

  36. Sieber, J., Marschler, C., Starke, J.: Convergence of equation-free methods in the case of finite time scale separation with application to deterministic and stochastic systems. SIAM J. Appl. Dyn. Syst. 17(4), 2574–2614 (January 2018). https://doi.org/10.1137/17M1126084

    Article  MathSciNet  MATH  Google Scholar 

  37. Roose, D., Nies, E., Li, T., Vandekerckhove, C., Samaey, G., Frederix, Y.: Lifting in equation-free methods for molecular dynamics simulations of dense fluids. Discrete and Continuous Dynamical Systems—Series B 11(4), 855–874 (April 2009). https://doi.org/10.3934/dcdsb.2009.11.855

    Article  MathSciNet  MATH  Google Scholar 

  38. Samaey, G., Roberts, A.J., Kevrekidis, I.G.: Equation-free computation: an overview of patch dynamics. In: Fish, J (ed.) Multiscale Methods: Bridging the Scales in Science and Engineering, pp 216–246. Oxford University Press (2010)

  39. Bunder, J.E., Roberts, A.J., Kevrekidis, I.G.: Good coupling for the multiscale patch scheme on systems with microscale heterogeneity. J. Computational Physics 337, 154–174 (2017). https://doi.org/10.1016/j.jcp.2017.02.004

    Article  MathSciNet  MATH  Google Scholar 

  40. Cao, M., Roberts, A.J.: Multiscale modelling couples patches of nonlinear wave-like simulations. IMA J. Applied Maths. 81(2), 228–254 (2016). https://doi.org/10.1093/imamat/hxv034

    Article  MATH  Google Scholar 

  41. Cao, M., Roberts, A.J.: Multiscale modelling couples patches of wave-like simulations. In: McCue, S, Moroney, T, Mallet, D, Bunder, J (eds.) Proceedings of the 16th Biennial Computational Techniques and Applications Conference, CTAC-2012, vol 54 of ANZIAM J., pp C153–C170 (May 2013)

  42. Geers, M.G.D., Kouznetsova, V.G., Brekelmans, W.A.M.: Multi-scale computational homogenization: trends and challenges. J. Comput. Appl. Math. 234(7), 2175–2182 (August 2010). https://doi.org/10.1016/j.cam.2009.08.077

    Article  MATH  Google Scholar 

  43. Owhadi, H.: Bayesian numerical homogenization. Multiscale Modeling & Simulation 13(3), 812–828 (2015). https://doi.org/10.1137/140974596

    Article  MathSciNet  MATH  Google Scholar 

  44. Maier, R., Peterseim, D.: Explicit computational wave propagation in micro-heterogeneous media. BIT Numer. Math. 59(2), 443–462 (June 2019). https://doi.org/10.1007/s10543-018-0735-8

    Article  MathSciNet  MATH  Google Scholar 

  45. Gear, C.W., Kevrekidis, I.G.: Computing in the past with forward integration. Phys. Lett. A 321, 335–343 (2003). https://doi.org/10.1016/j.physleta.2003.12.041

    Article  MathSciNet  MATH  Google Scholar 

  46. Kutz, J.N., Brunton, S.L., Brunton, B.W., Proctor, J.L.: Dynamic mode decomposition: data-driven modeling of complex systems. Number 149 in Other titles in applied mathematics. SIAM, Philadelphia (2016)

    Book  Google Scholar 

  47. Kutz, J.N., Proctor, J.L., Brunton, S.L.: Applied koopman theory for partial differential equations and data-driven modeling of spatio-temporal systems. Complexity 6010634, 1–16 (2018). https://doi.org/10.1155/2018/6010634

    Article  MATH  Google Scholar 

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This project is supported by the Australian Research Council via grants DP150102385 and DP180100050.

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Correspondence to John Maclean.

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Maclean, J., Bunder, J.E. & Roberts, A.J. A toolbox of equation-free functions in Matlab/Octave for efficient system level simulation. Numer Algor 87, 1729–1748 (2021). https://doi.org/10.1007/s11075-020-01027-z

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