Overview

AMReX

People

Publications

Andy Nonaka

CCSE Group Lead

Contact Information Andy Nonaka MS 50A-3111 Lawrence Berkeley National Lab 1 Cyclotron Rd. Berkeley, CA 94720 (Berkeley Fax) 510-486-6900 [email protected]

Overview

Research

Multiscale Modeling and Stochastic Systems (MuMSS) At macroscopic scales, fluid dynamics is governed by partial differential equations that characterize the behavior of the fluid in terms of smoothly evolving fields that represent density, momentum, and other characteristics of the fluid. However, at atomic scales fluids are discrete systems composed of individual molecules whose dynamics are governed by complex interaction potentials. The discrepancy between these two descriptions is manifest at the mesoscale. While it is possible to model a fluid using macroscopic field variables at the mesoscale, we know that they are no longer smooth fields; instead they fluctuate even for systems that are at thermodynamic equilibrium. The goal of the MuMSS team is to develop models and algorithms that can efficiently and accurately model complex fluids at the mesoscale.

MAESTROeX: Low Mach Number Astrophysical Solver Many astrophysical phenomena of interest occur in the low Mach number regime, where the characteristic fluid velocity is small compared to the speed of sound. Some well-known examples are the convective phase of Type Ia supernovae, classical novae, convection in stars, and Type I X-ray bursts. Such problems require a numerical approach capable of resolving phenomena over time scales much longer than the characteristic time required for an acoustic wave to propagate across the computational domain.

Computational Electrodynamics for Microelectronics We are developing a new time-domain simulation capability for full physical modeling of microelectronic devices. The core Maxwell solver from the WarpX project is being adapted to handle material interfaces, sharp spatial inhomogeneities, and boundary conditions present in such circuitry. We are also interested in coupling schemes for different constitutive models used to describe the relevant physics in various regions of the circuitry. Our initial target applications include spintronic devices and classical modeling of quantum circuitry. .

AMReX: Software Framework for Massively Parallel, Block-structured AMR Applications Our codes utlize AMReX, an ECP co-design center software framework for massively parallel, block-structured adaptive mesh refinement (AMR) applications. AMReX supports hybrid parallelization (MPI/OpenMP and MPI/CUDA) for efficient scaling and parallel communication on leadership-class supercomputers.

M. Polimeno, C. Kim, F. Blanchette, I. Srivastava, A. Garcia, A. Nonaka, and J. Bell, Thermodynamic consistency and fluctuations in mesoscopic stochastic simulations of reactive gas mixtures, submitted for publication, 2024. [arxiv]

J. B. Bell, A. Nonaka, and A. L. Garcia, A Study of Spherical and Sessile Droplet Dynamics by Fluctuating Hydrodynamics, accepted for publication in Physics of Fluids, 2024. [arxiv]

A. L. Garcia, J. B. Bell, A. Nonaka, I. Srivastava, D. Ladiges, C. Kim, An Introduction to Computational Fluctuating Hydrodynamics, 2024. [arxiv]

Y. Tang, R. Chen, M. Lou, J. Fan, C. Yu, A. Nonaka, Z. Yao., W. Gao, Optical Neural Engine for Solving Scientific Partial Differential Equations, submitted for publication, 2024. [arxiv]

S. S. Sawant, F. Leonard, Z. Yao, A. Nonaka, ELEQTRONeX: A GPU-Accelerated Exascale Framework for Non-Equilibrium Quantum Transport in Nanomaterials, submitted for publication, 2024. [arxiv]

J. B. Bell, A. Nonaka, and A. L. Garcia, Brownian motion of droplets induced by thermal noise, submitted for publication, 2024. [arxiv]

P. Kumar, M. Hoffmann, A. Nonaka, S. Salahuddin, and Z. Yao 3D ferroelectric phase field simulations of polycrystalline multi-phase hafnia and zirconia based ultra-thin films, Advanced Electronic Materials, 2400085, 2024. [link]

J. L. Loffeld, A. J. Nonaka, D. R. Reynolds, D. J. Gardner, and C. S. Woodward, Performance of explicit and IMEX MRI multirate methods on complex reactive flow problems within modern parallel adaptive structured grid frameworks, International Journal of High Performance Computing Applications, 10943420241227914, 2024. [link]

L. Esclapez, M. Day, J. Bell, A. Felden, C. Gilet, R. Grout, M. Henry de Frahan, E. Motheau, A. Nonaka, L. Owen, B. Perry, J. Rood, N. Wimer, and W. Zhang, PeleLMeX: an AMR Low Mach Number Reactive Flow Simulation Code without level sub-cycling, Journal of Open Source Software, 8, 2023. [link]

J. G. Wang, D. R. Ladiges, I. Srivastava, S. P. Carney, A. J. Nonaka, A. L. Garcia, J. B. Bell, Steric effects in induced-charge electro-osmosis for strong electric fields, Physical Review Fluids, 8, 083702, 2023. [arxiv] [doi]

R. Jambunathan, Z. Yao, R. Lombardini, A. Rodriguez, and A. Nonaka, Two-Fluid Physical Modeling of Superconducting Resonators in the ARTEMIS Framework, Computer Physics Communications, 291, 2023. [arxiv] [doi]

E. Mercado, H. T. Jung, C. Kim, A. L. Garcia, A. J. Nonaka, and J. B. Bell, Surface Coverage Dynamics for Reversible Dissociative Adsorption on Finite Linear Lattices, J. Chem. Phys., 159, 2023. [doi] [arxiv]

P. Kumar, A. Nonaka, R. Jambunathan, G. Pahwa, S. Salahuddin, and Z. Yao, FerroX: A GPU-accelerated, 3D Phase-Field Simulation Framework for Modeling Ferroelectric Devices, Computer Physics Communications, 108757, 2023 [link]

I. Srivastava, D. R. Ladiges, A. Nonaka, A. L. Garcia, J. B. Bell, A Staggered Scheme for the Compressible Fluctuating Hydrodynamics of Multispecies Fluid Mixtures, Physical Review E, 107, 015305, 2023. [link]

D. R. Ladiges, J. G. Wang, I. Srivastava, S. P. Carney, A. Nonaka, A. L. Garcia, A. Donev and J. B. Bell, Modeling Electrokinetic Flows with the Discrete Ion Stochastic Continuum Overdamped Solvent Algorithm, Physical Review E, 106, 035104, 2022. [link]

S. Sawant, Z. Yao, R. Jambunathan, and A. Nonaka, Characterization of Transmission Lines in Microelectronics Circuits using the ARTEMIS Solver, IEEE J. on Multiscale and Multiphysics Comp. Tech., 8, 2022. [link]

D. Fan, D. E. Willcox, C. DeGrendele, M. Zingale, and A. Nonaka, Neural Networks for Nuclear Reactions in MAESTROeX, The Astrophysical Journal, 940, 2, 2022. [link]

M. Zingale, M. P. Katz, A. Nonaka, and M. Rasmussen, An Improved Method for Coupling Hydrodynamics with Astrophysical Reaction Networks, Astrophysical Journal, 936, 6, 2022. [link]

John Bell, Andrew Nonaka, Alejandro L. Garcia, Gregory Eyink, Thermal Fluctuations in the Dissipation Range of Homogeneous Isotropic Turbulence, J. Fluid Mech., 939, 2022. [link]

Z. Yao, R. Jambunathan, Y. Zeng, and A. Nonaka, A Massively Parallel Time-Domain Coupled Electrodynamics-Micromagnetics Solver, International Journal of High Performance Computing Applications, 10943420211057906, 2021. [link]

D. R. Ladiges, S. P. Carney, A. Nonaka, K. Kymko, G. C. Moore, A. L. Garcia, S. R. Natesh, A. Donev and J. B. Bell, A Discrete Ion Stochastic Continuum Overdamped Solvent Algorithm for Modeling Electrolytes, Phys. Rev. Fluids, 6, 4, 2021. [link]

K. Klymko, S. P. Carney, A. Nonaka, A. L. Garcia, and J. B. Bell, A Low Mach Number Fluctuating Hydrodynamics Model For Ionic Liquids, Phys. Rev. Fluids, 5, 9, 2020. [arxiv]

A. Harpole, D. Fan, M. P. Katz, A. J. Nonaka, D. E. Willcox, and M. Zingale, Modelling low Mach number stellar hydrodynamics with MAESTROeX proceedings of Astronum 2019, Paris, July 1-5, 2019.

M. Zingale, A. S. Almgren, M. Barrios Sazo, J. B. Bell, K. Eiden, A. Harpole, M. P. Katz, A. J. Nonaka, D. E. Willcox, and W. Zhang, The Castro AMR Simulation Code: Current and Future Developments proceedings of Astronum 2019, Paris, July 1-5, 2019.

D. Fan, A. Nonaka, A. S. Almgren, D. E. Willcox, A. Harpole, and M. Zingale, MAESTROeX: A Massively Parallel Low Mach Number Astrophysical Solver Journal of Open Source Software, 4, 44, 1757, 2019. [link]

D. Fan, A. Nonaka, A. S. Almgren, A. Harpole, and M. Zingale, MAESTROeX: A Massively Parallel Low Mach Number Astrophysical Solver Astrophysical Journal, 887, 2, 2019. [link]

M. Zingale, M. P. Katz, J. B. Bell, M. L. Minion, A. J. Nonaka, W. Zhang, Improved Coupling of Hydrodynamics and Nuclear Reactions via Spectral Deferred Corrections, Astrophysical Journal, 886, 2, 2019 [arxiv]

W. Zhang, A. Almgren, V. Beckner, J. Bell, J. Blaschke, C Chan, M. Day, B. Friesen, K. Gott, D. Graves, M. Katz, A. Myers T. Nguyen, A. Nonaka, M. Rosso, S. Williams and M. Zingale, AMReX: a framework for block-structured adaptive mesh refinement, Journal of Open Source Software, 4, 37, 1370, 2019. [doi]

D. R. Ladiges, A. J. Nonaka, J. B. Bell, and A. L. Garcia "On the Suppression and Distortion of Non-Equilibrium Fluctuations by Transpiration," Phys. Fluids, 31, 5, 2019. [link]

A. Donev, A. J. Nonaka, C. Kim, A. L. Garcia, and J. B. Bell, "Fluctuating hydrodynamics of electrolytes at electroneutral scales," Phys. Rev. Fluids. 4, 4, 2019. [link]

A. Donev, A. L. Garcia, J. Peraud, A. Nonaka, J. B. Bell, "Fluctuating hydrodynamics and Debye-Hückel-Onsager theory for electrolytes," Current Opinion in Electrochemistry, 13, 2019. [link]

M. Zingale, K. Eiden, Y. Cavecchi, A. Harpole, J. B. Bell, M. Chang, I. Hawke, M. P. Katz, C.M. Malone, A. J. Nonaka, D. E. Willcox, and W. Zhang, "Toward resolved simulations of burning fronts in thermonuclear X-ray bursts," Journal of Physics: Conference Series, 1225, 1, 2019 [link]

C. Kim, A. Nonaka, J. B. Bell, A .L. Garcia, and A. Donev, "Fluctuating hydrodynamics of reactive liquid mixtures," J. Chem. Phys.,, 149, 084113, 2018. [link]

A. Nonaka, M. S. Day, and J. B. Bell, "A conservative, thermodynamically consistent numerical approach for low Mach number combustion. I. Single-level integration," Combust. Theor. Model., 22, 1, 2018. [link]

M. Zingale, A. S. Almgren, M. G. Barrios Sazo, V. E. Beckner, J. B. Bell, B. Friesen, A. M. Jacobs, M. P. Katz, C. M. Malone, A. J. Nonaka, D. E. Willcox, and W. Zhang, "Meeting the Challenges of Modeling Astrophysical Thermonuclear Explosions: Castro, Maestro, and the AMReX Astrophysics Suite", J. Phys. Conf. Ser., 1031, 1, 2018. [link]

J-P. Péraud, A. Nonaka, J. B. Bell, A. Donev, and A. L. Garcia, "Fluctuation-enhanced electric conductivity in electrolyte solutions", P. Natl. Acad. Sci. USA, 114, 41, 2017. [link]

C. Kim, A. Nonaka, J. B. Bell, A. L. Garcia, and A. Donev, "Stochastic simulation of reaction-diffusion systems: A fluctuating-hydrodynamics approach," J. Chem. Phys. 146, 12, 2017. [link]

J. Peraud, A. Nonaka, A. Chaudhri, J. B. Bell, A. Donev, and A. L. Garcia, "Low Mach Number Fluctuating Hydrodynamics for Electrolytes," Phys. Rev. Fluids, 1, 7, 2016. [link]

W. Pazner, A. Nonaka, J. B. Bell, M. S. Day, and M. L. Minion, "A High-Order Spectral Deferred Correction Strategy for Low Mach Number Flow With Complex Chemistry," Combust. Theor. Model., 20, 3, 2016. [link]

A.M. Jacobs, M. Zingale, A. Nonaka, A.S. Almgren, J.B. Bell, "Low Mach Number Modeling of Convection in Helium Shells on Sub-Chandrasekhar White Dwarfs II: Bulk Properties of Simple Models," Astrophys. J., 827, 84, 2016. [iop].

A. Nonaka, Y. Sun, J. B. Bell, and A. Donev, "Low Mach Number Fluctuating Hydrodynamics of Binary Liquid Mixtures," Comm. App. Math. and Comp. Sci., 10, 2, 2015. [pdf].

M. Zingale, A. Jacobs, A. Almgren, J. Bell, A. Nonaka, C. Malone, S. Woosley, "Understanding Ignition in Type Ia Supernovae", 25rd International Colloquium on the Dynamics of Explosions and Reactive Systems, Leeds, UK, August 2-7, 2015.

A. Donev, A. Nonaka, A. K. Bhattacharjee, A. L. Garcia, and J. B. Bell, "Low Mach Number Fluctuating Hydrodynamics of Multispecies Liquid Mixtures", Phys. Fluids, 27, 3, 2015. [pdf]

M. Zingale, C. M. Malone, A. Nonaka, A. S. Almgren, and J. B. Bell, "Comparisons of Two- and Three-Dimensional Convection in Type I X-ray Bursts," Astrophys. J., 807, 60, 2015 [link].

M. Cai, A. Nonaka, B. E. Griffith, J. B. Bell, and A. Donev, "Efficient Variable-Coefficient Finite-Volume Stokes Solvers", Commun. Comput. Phys., 16, 1263-1297, 2014. [link]

Ann Almgren, John Bell, Andy Nonaka and Michael Zingale, "Low Mach Number Modeling of Stratified Flows," Finite Volumes for Complex Applications VII -- Methods and Theoretical Aspects, Springer Proceedings in Mathematics and Statistics, eds. J. Fuhrmann, M. Ohlberger, C. Rohde, Berlin, June 2014. [link]

A. Donev, A. Nonaka, Y. Sun, T. Fai, A. Garcia and J. Bell, "Low Mach Number Fluctuating Hydrodynamics of Diffusively Mixing Fluids" Comm. App. Math. and Comp. Sci, 9, 1, 2014. [pdf]

C. M. Malone, M. Zingale, A. Nonaka, A. S. Almgren, and J. B. Bell, "Multidimensional Modeling of Type I X-ray Bursts. II. Two-Dimensional Convection in a Mixed H/He Accretor", Astrophys. J., 788, 115, 2014. [link]

C. M. Malone, A. Nonaka, S. E. Woosley, A. S. Almgren, J. B. Bell, S. Dong, and M. Zingale, "The Deflagration Stage of Chandrasekhar Mass Models for Type Ia Supernovae:I. Early Evolution", Astrophys. J., 782, 11, 2014. [iop].

C. Gilet, A.S. Almgren, J.B. Bell, A. Nonaka, S.E. Woosley and M. Zingale, "Low-Mach Number Modeling of Core Convection in Massive Stars", Astrophys. J., 773, 137, 2013. [pdf]

M. Zingale, A. Nonaka, A. S. Almgren, J. B. Bell, C. Malone, and R. Orvedahl, "Low Mach Number Modeling of Convection in Helium Shells on Sub-Chandrasekhar White Dwarfs. I. Methodology", Astrophys. J., 764, 97, 2013. [pdf]

A. Nonaka, J. B. Bell, M. S. Day, C. Gilet, A. S. Almgren, and M. L. Minion, "A Deferred Correction Coupling Strategy for Low Mach Number Flow with Complex Chemistry", Combust. Theor. Model., 16, 6, 2012. [pdf]

R. Sisneros, C. Malone, A. Nonaka, and S. Woosley, "Investigation of Turbulence in the Early Stages of a High Resolution Supernova Simulation", Proceedings of the Supercomputing 2012 Conference, Salt Lake City, UT, November 2012. [pdf]

A. Nonaka, A. J. Aspden, M. Zingale, A. S. Almgren, J. B. Bell, and S. E. Woosley, "High-Resolution Simulations of Convection Preceding Ignition in Type Ia Supernovae Using Adaptive Mesh Refinement", Astrophys. J., 745, 73, 2012. [pdf]

M. Zingale, A. Nonaka, A. S. Almgren, J. B. Bell, C. M. Malone, and S. E. Woosley, "The Convective Phase Preceding Type Ia Supernovae", Astrophys. J., 740, 8, 2011. [pdf]

A. Nonaka, S. May, A. S. Almgren, and J. B. Bell, "A Three-Dimensional, Unsplit Godunov Method for Scalar Conservation Laws", SIAM J. Sci. Comput., 33, 4, 2011. [pdf]

A. Nonaka, A. S. Almgren, J. B. Bell, H. Ma, S. E. Woosley, and M. Zingale, "From Convection to Explosion: End-to-End Simulation of Type Ia Supernovae," Proceedings of SciDAC 2011, Denver, CO, July 2011. [pdf]

S. May, A. Nonaka, A. S. Almgren, and J. B. Bell, "An Unsplit, Higher-Order Godunov Method Using Quadratic Reconstruction for Advection in Two Dimensions", Comm. App. Math. and Comp. Sci., 6, 1, 2011. [pdf]

C. M. Malone, A. Nonaka, A. S. Almgren, J. B. Bell, and M. Zingale, "Multidimensional Modeling of Type I X-ray Bursts. I. Two-Dimensional Convection Prior to the Outburst of a pure ⁴He Accretor", Astrophys. J., 728, 118, 2011. [pdf]

A. Almgren, J. Bell, D. Kasen, M. Lijewski, A. Nonaka, P. Nugent, C. Rendleman, R. Thomas, and M. Zingale, "MAESTRO, CASTRO and SEDONA -- Petascale Codes for Astrophysical Applications," Proceedings of SciDAC 2010, Chattanooga, TN, July 2010. [pdf]

H. Ma, M. Zingale, S. E. Woosley, A. J. Aspden, J. B. Bell, A. S. Almgren, A. Nonaka, and S. Dong, "Type Ia Supernovae: Advances in Large Scale Simulation," Proceedings of SciDAC 2010, Chattanooga, TN, July 2010. [pdf]

A. Nonaka, A. S. Almgren, J. B. Bell, M. J. Lijewski, C. M. Malone, and M. Zingale, "MAESTRO: An Adaptive Low Mach Number Hydrodynamics Algorithm for Stellar Flows", Astrophys. J. Supplement Series, 188, 358, 2010. [pdf]

M. Zingale, A. S. Almgren, J. B. Bell, A. Nonaka, and S. E. Woosley, "Low Mach Number Modeling of Type Ia Supernovae. IV. White Dwarf Convection", Astrophys. J., 704, 196, 2009. [pdf]

S.E. Woosley, A. S. Almgren, A.J. Aspden, J. B. Bell, D. Kasen, A.R. Kerstein, H. Ma, A. Nonaka, and M. Zingale, "Type Ia Supernovae: Advances in Large Scale Simulation ", SciDAC 2009, J. Phys. Conf. Ser., 180, San Diego, CA, July 2009. [pdf]

A. Nonaka, D. Trebotich, G. H. Miller, D. T. Graves, and P. Colella, "A Higher-Order Upwind Method for Viscoelastic Flow", Comm. App. Math. and Comp. Sci., 4, 1, 2009. [pdf]

A. S. Almgren, J. B. Bell, A. Nonaka, and M. Zingale, "A New Low Mach Number Approach in Astrophysics", Comput. Sci. Eng., 11, 2, 2009. [link]

M. Zingale, A. S. Almgren, J. B. Bell, C. M. Malone, and A. Nonaka, "Astrophysical Applications of the MAESTRO Code", SciDAC 2008, J. Phys. Conf. Ser., 125, Seattle, WA, July 2008. [pdf]

A. S. Almgren, J. B. Bell, A. Nonaka, and M. Zingale, "Low Mach Number Modeling of Type Ia Supernovae. III. Reactions", Astrophys. J., 684, 449, 2008. [pdf]

A. Nonaka, "A Higher-Order Upwind Method for Viscoelastic Flow", PhD Thesis, UC Davis, 2007. [pdf]

A. Nonaka, S. Gulati, D. Trebotich, G. H. Miller, S. J. Muller, and D. Liepmann, "A Computational Model with Experimental Validation for DNA Flow in Microchannels", Technical Proceedings of the 2005 NSTI Nanotechnology Conference and Trade Show, 3, 10, Anaheim, CA, May 2005. [pdf]

D. Trebotich, P. Colella, G. H. Miller, A. Nonaka, T. Marshall, S. Gulati, and D. Liepmann, "A Numerical Algorithm for Complex Biological Flow in Irregular Microdevice Geometries", Technical Proceedings of the 2004 NSTI Nanotechnology Conference and Trade Show, 2, 8, Boston, MA, March 2004. [pdf]

3/2/2017: "Stochastic Simulation of Reaction-Diffusion Systems: A Fluctuating-Hydrodynamics Approach". This talk discusses a new approach for stochastic reaction-diffusion systems that combines the efficiency of fluctuating hydrodynamics for diffusive fluxes and the rigor of Poisson noise treatment for reactions. Presented at the 2017 SIAM CSE Confererence in Atlanta.. [pdf]

2/27/2017: "From Microscale Flow to Exploding Stars - Fluid Simulation at Lawrence Berkeley Lab". This talk discusses various fluid simulation efforts in CCSE, in particular, how low Mach number models can be applied to astrophysics, combustion, and mesoscopic flow. Presented at the UC Berkeley Fluids Seminar. [pdf]

6/11/2015: "Using Math and Computing to Model Supernovae". This talk discusses results from end-to-end Type Ia supernovae simulations using both MAESTRO and CASTRO. Presented at the 2015 Computing Sciences Summer Student Lecture Series at LBNL. [pdf]

11/24/2014: "Efficient Modeling of Multicomponent Diffusive Mixing". This talk discusses a new efficient low Mach number model and algorithm suitable for diffusive mixing of fluids at length scales where thermal fluctuations are important. Presented at the American Physical Society 67th Annual DFD Meeting in San Francisco. [pdf]

10/18/2011: "A Deferred Correction Strategy for Advection-Diffusion-Reaction Systems with Complex Chemistry". This talk gives an overview of a new iterative coupling strategy for multiphysics applications with widely varying timescales. Presented at the DOE Applied Mathematics Program Meeting in Washington, D.C. [pdf]

7/26/2011: "How to Thread a Hydro Code with OpenMP". A 2-hour short course introducing the basics of OpenMP, including downloadable tutorials available at NERSC. Presented at the UC High-Performance AstroComputing Center Summer School on Computational Explosive Astrophysics at UC Berkeley / LBNL. [pdf]

5/8/2011: "Petascale Simulations of Type Ia Supernovae". This talk gives an overview of the importance of Type Ia supernovae and the role of MAESTRO in understanding the physics of such events, and also includes the latest scientific results. Presented at the Bay Area Scientific Computing Day at Stanford University. [pdf]

3/4/2011: "MAESTRO and CASTRO: Petascale AMR Codes for Astrophysical Applications". This talk includes a discussion of the parallel implementation of MAESTRO and CASTRO. Presented at the SIAM Conference on Computational Science and Engineering in Reno, NV. [pdf]

1/19/2011: "Numerical Simulations of Type Ia Supernovae". This talk includes a discussion of the development of MAESTRO, particularly the treatment of time-dependent stratification in an AMR framework. Presented at Lawrence Berkeley National Laboratory. [pdf]