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Applied Numerical Algorithms Group
Applied Numerical Algorithms Group

David Trebotich

PXL 20230604 0330413064 v2
David Trebotich
Staff Scientist
Phone: +1 510 486 5984
Fax: +1 510 486 6900
1 Cyclotron Road
MS 50A-3123
Berkeley, CA 94720 us

David Trebotich is a staff scientist in the Applied Numerical Algorithms Group at Lawrence Berkeley National Laboratory. His research involves end-to-end development of high resolution algorithms for complex flows in multiscale, multiphysics systems using adaptive, finite volume methods. In particular he has implemented this approach in the hpc suite of application codes known as Chombo-Crunch for solving flow and transport in arbitrarily complex geometries. Current applications of interest revolve around solution to flow and transport equations in complex media--geological (subsurface), engineered (battery electrodes, paper drying felt). Prior to the Berkeley lab, David was staff scientist at the Lawrence Livermore National Laboratory in the Center for Applied Scientific Computing from 2001 to 2009, and before that a post-doc at UC Berkeley after completing his Ph.D. there in 1998.

Chombo-Crunch

»Videos of recent visualizations.

Current Research

  • Exascale Computing Project subsurface application development (ECP)
  • High resolution simulation of pore scale reactive transport processes associated with carbon sequestration (EFRC-NCGC)
  • Dewetting/rewetting in paper manufacturing (AMO HPC4MFG with LLNL and Agenda 2020)
  • Battery manufacturing processes (AMO)
  • Robust embedded boundary methods for science applications
  • Adaptive multiscale, multiphysics, multimodel methods

Journal Articles

David Trebotich, Randolph R Settgast, Terry Ligocki, William Tobin, Gregory H Miller, Sergi Molins, Carl I Steefel, "A multiphysics coupling framework for exascale simulation of subsurface fracture evolution", Frontiers in High Performance Computing, June 30, 2024, 2, doi: 10.3389/fhpcp.2024.1416727

Sergi Molins, David Trebotich, Carl I. Steefel, "Approaches for the simulation of coupled processes in evolving fractured porous media enabled by exascale computing", Computing in Science & Engineering, May 23, 2024, doi: 10.1109/MCSE.2024.3403983

David Trebotich, "Exascale CFD in Heterogeneous Systems", Journal of Fluids Engineering, February 9, 2024, 146(4):041104, doi: 10.1115/1.4064534

T. Groves, N. Ravichandrasekaran, B. Cook, N. Keen, D. Trebotich, N. Wright, B. Alverson, D. Roweth, K. Underwood, "Not All Applications Have Boring Communication Patterns: Profiling Message Matching with BMM", Concurrency and Computation: Practice and Experience, April 26, 2021, doi: 0.1002/cpe.6380

Simulation of mineral dissolution at the pore scale with evolving fluid-solid interfaces: review of approaches and benchmark problem set Thumbnail

Sergi Molins, Cyprien Soulaine, Nikolaos I. Prasianakis, Aida Abbasi, Philippe Poncet, Anthony J. C. Ladd, Vitalii Starchenko, Sophie Roman, David Trebotich, Hamdi Tchelepi, Carl I. Steefel, "Simulation of mineral dissolution at the pore scale with evolving fluid-solid interfaces: review of approaches and benchmark problem set", Computational Geosciences, January 23, 2020, doi: 10.1007/s10596-019-09903-x

Multi-scale Model of Reactive Transport in Fractured Media: Diffusion Limitations on Rates Thumbnail

Sergi Molins, David Trebotich, Bhavna Arora, Carl Steefel, Hang Deng, "Multi-scale Model of Reactive Transport in Fractured Media: Diffusion Limitations on Rates", Transport in Porous Media, March 20, 2019, 128:701-721, doi: 10.1007/s11242-019-01266-2

Pore-scale numerical investigation of the impacts of surface roughness: Up-scaling of reaction rates in rough fractures Thumbnail

Hang Deng, Sergi Molins, David Trebotich, Carl Steefel, Donald DePaolo, "Pore-scale numerical investigation of the impacts of surface roughness: Up-scaling of reaction rates in rough fractures", Geochimica et Cosmochimica Acta, October 15, 2018, 239:374-389, doi: 10.1016/j.gca.2018.08.005

Mineralogical and transport controls on the evolution of porous media texture using direct numerical simulation Thumbnail

Sergi Molins, David Trebotich, Gregory H. Miller, Carl I. Steefel, "Mineralogical and transport controls on the evolution of porous media texture using direct numerical simulation", Water Resources Research, April 7, 2017, doi: 10.1002/2016WR020323

An Adaptive Finite Volume Method for the Incompressible Navier-Stokes Equations in Complex Geometries Thumbnail

David Trebotich, Daniel T. Graves, "An Adaptive Finite Volume Method for the Incompressible Navier-Stokes Equations in Complex Geometries", Communications in Applied Mathematics and Computational Science, January 15, 2015, 10-1:43-82, doi: 10.2140/camcos.2015.10.43

High-Resolution Simulation of Pore-Scale Reactive Transport Processes Associated with Carbon Sequestration Thumbnail

David Trebotich, Mark F. Adams, Sergi Molins, Carl I. Steefel, Chaopeng Shen, "High-Resolution Simulation of Pore-Scale Reactive Transport Processes Associated with Carbon Sequestration", Computing in Science and Engineering, December 2014, 16:22-31, doi: 10.1109/MCSE.2014.77

Pore-Scale Controls on Calcite Dissolution Rates from Flow-through Laboratory and Numerical Experiments Thumbnail

Sergi Molins, David Trebotich, Li Yang, Jonathan B. Ajo-Franklin, Terry J. Ligocki, Chaopeng Shen and Carl Steefel, "Pore-Scale Controls on Calcite Dissolution Rates from Flow-through Laboratory and Numerical Experiments", Environmental Science and Technology, May 27, 2014, 48:7453-7460, doi: 10.1021/es5013438

Pore scale processes associated with subsurface CO2 injection and sequestration”, Reviews in Mineralogy and Geochemistry Thumbnail

C. Steefel, S. Molins, D. Trebotich, "Pore scale processes associated with subsurface CO2 injection and sequestration”, Reviews in Mineralogy and Geochemistry", Reviews in Mineralogy and Geochemistry, November 1, 2013,

B. Kallemov, G. H. Miller, S. Mitran and D. Trebotich, "Calculation of Viscoelastic Bead-Rod Flow Mediated by a Homogenized Kinetic Scale with Holonomic Constraints", Molecular Simulation, 2012, doi: 10.1080/08927022.2011.654206

G. H. Miller and D. Trebotich, "An Embedded Boundary Method for the Navier-Stokes Equations on a Time-Dependent Domain", Communications in Applied Mathematics and Computational Science, 7(1):1-31, 2012,

An Investigation of the Effect of Pore Scale Flow on Average Geochemical Reaction Rates Using Direct Numerical Simulation Thumbnail

S. Molins, D. Trebotich, C. I. Steefel and C. Shen, "An Investigation of the Effect of Pore Scale Flow on Average Geochemical Reaction Rates Using Direct Numerical Simulation", Water Resour. Res., 48(3) W03527, DOI:10.1029/2011WR011404, 2012,

B. Kallemov, G. H. Miller, S. Mitran and D. Trebotich, "Multiscale Rheology: New Results for the Kinetic Scale", NSTI-Nanotech 2011, Vol. 2, pp. 575-578 (2011), 2011,

B. Kallemov, G. H. Miller and D. Trebotich, "A Higher-Order Accurate Fluid-Particle Algorithm for Polymer Flows", Molecular Simulation, 37(8):738-745 (2011), 2011,

Caroline Gatti-Bono, Phillip Colella and David Trebotich, "A Second-Order Accurate Conservative Front-Tracking Method in One Dimension", SIAM J. Sci. Comput., 31(6):4795-4813, 2010,

B. Kallemov, G. H. Miller and D. Trebotich, "A Duhamel Approach for the Langevin Equations with Holonomic Constraints", Molecular Simulation, 35(6):440-447, 2009,

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):57-83, 2009,

D. Trebotich, G. H. Miller and M. D. Bybee, "A Penalty Method to Model Particle Interactions in DNA-laden Flows", J. Nanosci. Nanotechnol., 8(7):3749-3756, 2008,

D. T. Graves, D Trebotich, G. H. Miller, P. Colella, "An Efficient Solver for the Equations of Resistive MHD with Spatially-Varying Resistivity", Journal of Computational Physics Vol 227 (2008) pp.4797-4804., 2008,

G. H. Miller and D. Trebotich, "Toward a Mesoscale Model for the Dynamics of Polymer Solutions", J. Comput. Theoret. Nanosci. 4(4):797-801, 2007,

D. Trebotich, G. H. Miller and M. D. Bybee, "A Hard Constraint Algorithm to Model Particle Interactions in DNA-laden Flows", Nanoscale and Microscale Thermophysical Engineering 11(1):121-128, 2007,

D. Trebotich, "Toward a Solution to the High Weissenberg Number Problem", Proc. Appl. Math. Mech. 7(1):2100073-2100074, 2007,

D. Trebotich, "Simulation of Biological Flow and Transport in Complex Geometries using Embedded Boundary / Volume-of-Fluid Methods", Journal of Physics: Conference Series 78 (2007) 012076, 2007,

D. Trebotich, "Modeling Complex Biological Flows in Multi-Scale Systems Using the APDEC Framework", Journal of Physics: Conference Series 46 (2006) 316-321., 2006,

Trebotich, D., Miller, G.H., Colella, P., Graves, D.T., Martin, D.F., Schwartz, P.O., "A Tightly Coupled Particle-Fluid Model for DNA-Laden Flows in Complex Microscale Geometries", Computational Fluid and Solid Mechanics 2005, pp. 1018-1022, Elsevier (K. J. Bathe editor), 2005,

Trebotich, D., Colella, P., Miller, G.H., "A Stable and Convergent Scheme for Viscoelastic Flow in Contraction Channels", J. Comput. Phys. Vol.205 (2005), pp. 315-342, 2005,

David Trebotich, Phil Colella, "A Projection Method for Incompressible Viscous Flow on Moving Quadrilateral Grids", J. Comput. Phys. Vol.166 (2001), pp. 191-217, 2001,

Phil Colella, David Trebotich, "Numerical Simulation of Incompressible Viscous flow in Deforming Domains", Proceedings of the National Academy of Sciences of the United States of America, 1999, 96:5378-5381,

Conference Papers

Andrey Ovsyannikov, Melissa Romanus, Brian Van Straalen, Gunther H. Weber, David Trebotich, "Scientific Workflows at DataWarp-Speed: Accelerated Data-Intensive Science using NERSC s Burst Buffer", Proceedings of the 1st Joint International Workshop on Parallel Data Storage & Data Intensive Scalable Computing Systems, IEEE Press, 2016, 1--6, doi: 10.1109/PDSW-DISCS.2016.005

Ushizima, D.M., Weber, G.H., Ajo-Franklin, J., Kim, Y., Macdowell, A., Morozov, D., Nico, P., Parkinson, D., Trebotich, D., Wan, J., and Bethel E.W., "Analysis and visualization for multiscale control of geologic CO2", Journal of Physics: Conference Series, Proceedings of SciDAC 2011, July 2011, LBNL Denver, CO, USA,

Chaopeng Shen, David Trebotich, Sergi Molins, Daniel T Graves, BV Straalen, DT Graves, T Ligocki, CI Steefel, "High performance computations of subsurface reactive transport processes at the pore scale", Proceedings of SciDAC, 2011,

B. Kallemov, G. H. Miller and D. Trebotich, "Numerical Simulation of Polymer Flow in Microfluidic Devices", 009 Proceedings of the Fourth SIAM Conference on Mathematics for Industry (MI09) pp. 93-98, 2010,

P. Colella, D. Graves, T. Ligocki, D. Trebotich and B.V. Straalen, "Embedded Boundary Algorithms and Software for Partial Differential Equations", 2008 J. Phys.: Conf. Ser. 125 012084, 2008,

D. Trebotich, B.V. Straalen, D. Graves and P. Colella, "Performance of Embedded Boundary Methods for CFD with Complex Geometry", 2008 J. Phys.: Conf. Ser. 125 012083, 2008,

D. Trebotich and G. H. Miller, "Simulation of Flow and Transport at the Micro (Pore) Scale", Proceedings of the 2nd International Conference on Porous Media and its Applications in Science and Engineering, ICPM2 June 17-21, Kauai, Hawaii, USA, 2007,

Trebotich, D., Colella, P., Miller, G.H., Nonaka, A., Marshall, T., Gulati, S., Liepmann, D., "A Numerical Algorithm for Complex Biological Flow in Irregular Microdevice Geometries", Technical Proceedings of the 2004 Nanotechnology Conference and Trade Show Vol.2 (2004), pp. 470-473, 2004,

Deschamps, T., Schwartz, P., Trebotich, D., Colella, P., Malladi, R., Saloner, D., "Vessel Segmentation and Blood Flow Simulation Using Level Sets and Embedded Boundary Methods", Elsevier International Congress Series, 1268, pp. 75-80. Presented at the 18th Conference and Exhibition for Computer Assisted Radiology and Surgery, June, 2004, 2004,

Book Chapters

Tim Kneafsey, David Trebotich, Terry Ligocki, "Direct Numerical Simulation of Flow Through Nanoscale Shale Pores in a Mesoscale Sample", Album of Porous Media, edited by E.F. Médici, A.D. Otero, (Springer Cham: April 14, 2023) Pages: 87 doi: https://doi.org/10.1007/978-3-031-23800-0_69

Sergi Molins, David Trebotich, "Pore-Scale Controls on Calcite Dissolution using Direct Numerical Simulations", Album of Porous Media, edited by E.F. Médici, A.D. Otero, (Springer Cham: April 14, 2023) Pages: 135 doi: https://doi.org/10.1007/978-3-031-23800-0_112

David Trebotich, Terry Ligocki, "High Resolution Simulation of Fluid Flow in Press Felts Used in Paper Manufacturing", Album of Porous Media, edited by E.F. Médici, A.D. Otero, (Springer Cham: April 14, 2023) Pages: 132 doi: https://doi.org/10.1007/978-3-031-23800-0_109

B. Van Straalen, D. Trebotich, A. Ovsyannikov and D.T. Graves, "Scalable Structured Adaptive Mesh Refinement with Complex Geometry", Exascale Scientific Applications: Programming Approaches for Scalability, Performance, and Portability, edited by Straatsma, T., Antypas, K., Williams, T., (Chapman and Hall/CRC: November 9, 2017)

Reports

P. Colella, D. T. Graves, T. J. Ligocki, G.H. Miller , D. Modiano, P.O. Schwartz, B. Van Straalen, J. Pillod, D. Trebotich, M. Barad, "EBChombo Software Package for Cartesian Grid, Embedded Boundary Applications", Lawrence Berkeley National Laboratory Technical Report LBNL-6615E, January 9, 2015,

Brian Van Straalen, David Trebotich, Terry Ligocki, Daniel T. Graves, Phillip Colella, Michael Barad, "An Adaptive Cartesian Grid Embedded Boundary Method for the Incompressible Navier Stokes Equations in Complex Geometry", LBNL Report Number: LBNL-1003767, 2012, LBNL LBNL Report Numb,

We present a second-order accurate projection method to solve the
  incompressible Navier-Stokes equations on irregular domains in two
  and three dimensions.  We use a finite-volume discretization
  obtained from intersecting the irregular domain boundary with a
  Cartesian grid.  We address the small-cell stability problem
  associated with such methods by hybridizing a conservative
  discretization of the advective terms with a stable, nonconservative
  discretization at irregular control volumes, and redistributing the
  difference to nearby cells.  Our projection is based upon a
  finite-volume discretization of Poisson's equation.  We use a
  second-order, $L^\infty$-stable algorithm to advance in time.  Block
  structured local refinement is applied in space.  The resulting
  method is second-order accurate in $L^1$ for smooth problems.  We
  demonstrate the method on benchmark problems for flow past a
  cylinder in 2D and a sphere in 3D as well as flows in 3D geometries
  obtained from image data.

Thesis/Dissertations

A Projection Method for Incompressible Viscous Flow on a Deformable Domain, Trebotich, D.P., 1998,

Annual Reports

Others

Massively-Parallel Simulations Verify Carbon Dioxide Sequestration Experiments, FY15 DOE ASCR Budget Request to Congress, May 1, 2014,

Last edited: 01/17/2024
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