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Publications

Phillip Colella

2017

Protonu Basu, Samuel Williams, Brian Van Straalen, Leonid Oliker, Phillip Colella, Mary Hall, "Compiler-Based Code Generation and Autotuning for Geometric Multigrid on GPU-Accelerated Supercomputers", Parallel Computing (PARCO), April 2017, doi: 10.1016/j.parco.2017.04.002

2016

Jared O. Ferguson, Christiane Jablonowski, Hans Johansen, Peter McCorquodale, Phillip Colella, Paul A. Ullrich, "Analyzing the adaptive mesh refinement (AMR) characteristics of a high-order 2D cubed-sphere shallow-water model", Mon. Wea. Rev., November 9, 2016, 144:4641–4666, doi: 10.1175/MWR-D-16-0197.1

Andrew Myers, Phillip Colella, Brian Van Straalen, "A 4th-Order Particle-in-Cell Method with Phase-Space Remapping for the Vlasov-Poisson Equation", submitted to SISC, February 1, 2016,

Andrew Myers, Phillip Colella, Brian Van Straalen, "The Convergence of Particle-in-Cell Schemes for Cosmological Dark Matter Simulations", The Astrophysical Journal, Volume 816, Issue 2, article id. 56, 2016,

2015

Stephen M. Guzik, Xinfeng Gao, Landon D. Owen, Peter McCorquodale, Phillip Colella, "A freestream-preserving fourth-order finite-volume method in mapped coordinates with adaptive-mesh refinement", Computers & Fluids, December 21, 2015, 123:202–217, doi: 10.1016/j.compfluid.2015.10.001

M. Dorf, M. Dorr, J. Hittinger, T. Rognlien, P. Colella, P. Schwartz,R. Cohen, W. Lee, "Modeling Edge Plasma with the Continuum Kinetic Code COGENT", 2015,

P. McCorquodale, P.A. Ullrich, H. Johansen, P. Colella, "An adaptive multiblock high-order finite-volume method for solving the shallow-water equations on the sphere", Comm. App. Math. and Comp. Sci., 2015, 10:121-162, doi: 10.2140/camcos.2015.10.121

Protonu Basu, Samuel Williams, Brian Van Straalen, Mary Hall, Leonid Oliker, Phillip Colella, "Compiler-Directed Transformation for Higher-Order Stencils", International Parallel and Distributed Processing Symposium (IPDPS), May 2015,

P. McCorquodale, M.R. Dorr, J.A.F. Hittinger, P. Colella, "High-order finite-volume methods for hyperbolic conservation laws on mapped multiblock grids", J. Comput. Phys., May 1, 2015, 288:181-195, doi: 10.1016/j.jcp.2015.01.006

Peter Schwartz, Julie Percelay, Terry J. Ligocki, Hans Johansen, Daniel T. Graves, Dharshi Devendran, Phillip Colella, Eli Ateljevich, "High-accuracy embedded boundary grid generation using the divergence theorem", Communications in Applied Mathematics and Computational Science 10-1 (2015), 83--96. DOI 10.2140/camcos.2015.10.83, March 31, 2015,

M. Adams, P. Colella, D. T. Graves, J.N. Johnson, N.D. Keen, T. J. Ligocki. D. F. Martin. P.W. McCorquodale, D. Modiano. P.O. Schwartz, T.D. Sternberg, B. Van Straalen, "Chombo Software Package for AMR Applications - Design Document", Lawrence Berkeley National Laboratory Technical Report LBNL-6616E, January 9, 2015,

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,

2014

J. Ferguson, C. Jablonowski, H. Johansen, R. English, P. McCorquodale, P. Colella, J. Benedict, W. Collins, J. Johnson, P. Ullrich, "Assessing Grid Refinement Strategies in the Chombo Adaptive Mesh Refinement Model", AGU Fall Meeting, San Francisco, CA, December 15, 2014,

Anshu Dubey, Ann Almgren, John Bell, Martin Berzins, Steve Brandt, Greg Bryan, Phillip Colella, Daniel Graves, Michael Lijewski, Frank L\ offler, others, "A survey of high level frameworks in block-structured adaptive mesh refinement packages", Journal of Parallel and Distributed Computing, 2014, 74:3217--3227, doi: 10.1016/j.jpdc.2014.07.001

2013

Daniel T. Graves, Phillip Colella, David Modiano, Jeffrey Johnson, Bjorn Sjogreen, Xinfeng Gao, "A Cartesian Grid Embedded Boundary Method for the Compressible Navier Stokes Equations", Communications in Applied Mathematics and Computational Science, December 23, 2013,

In this paper, we present an unsplit method for the time-dependent
  compressible Navier-Stokes equations in two and three dimensions.
  We use a a conservative, second-order Godunov algorithm.
  We use a Cartesian grid, embedded boundary method to resolve complex
  boundaries.  We solve for viscous and conductive terms with a
  second-order semi-implicit algorithm.  We demonstrate second-order
  accuracy in solutions of smooth problems in smooth geometries and
  demonstrate robust behavior for strongly discontinuous initial
  conditions in complex geometries.

2012

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.

S. Guzik, P. McCorquodale, P. Colella, "A Freestream-Preserving High-Order Finite-Volume Method for Mapped Grids with Adaptive-Mesh Refinement", 50th AIAA Aerospace Sciences Meeting Nashville, TN, 2012,

A Mignone, C Zanni, P Tzeferacos, B van Straalen, P Colella, G Bodo, The PLUTO code for adaptive mesh computations in astrophysical fluid dynamics, The Astrophysical Journal Supplement Series, Pages: 7 2012,

2011

B. Wang, G.H. Miller, and P. Colella, "A Particle-in-Cell Method with Adaptive Phase-Space Remapping for Kinetic Plasmas", SIAM J. Sci. Comput, 2011,

B. Van Straalen, P. Colella, D. T. Graves, N. Keen, "Petascale Block-Structured AMR Applications Without Distributed Meta-data", Euro-Par 2011 Parallel Processing - 17th International Conference, Euro-Par 2011, August 29 - September 2, 2011, Proceedings, Part II. Lecture Notes in Computer Science 6853 Springer 2011, ISBN 978-3-642-23396-8, Bordeaux, France, 2011,

P. McCorquodale and P. Colella, "A High-Order Finite-Volume Method for Conservation Laws on Locally Refined Grids", Communications in Applied Mathematics and Computational Science, Vol. 6 (2011), No. 1, 1-25, 2011,

P. Colella, M.R. Dorr, J.A.F. Hittinger, and D.F. Martin, "High-Order Finite-Volume Methods in Mapped Coordinates", Journal of Computational Physics, 230(8):2952-2976 (2011), 2011,

2010

R.H. Cohen, J. Compton, M. Dorr, J. Hittinger, W.M Nevins, T.D. Rognlien, Z.Q. Xu, P. Colella, and D. Martin, "Testing and Plans for the COGENT edge kinetic code", (abstract) submitted to Sherwood 2010, 2010,

E. Ateljevich, P. Colella, D.T. Graves, T.J. Ligocki, J. Percelay, P.O. Schwartz, Q. Shu, "CFD Modeling in the San Francisco Bay and Delta", 2009 Proceedings of the Fourth SIAM Conference on Mathematics for Industry (MI09), pp. 99-107, 2010,

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,

Schwartz, P., and Colella P., "A Second-Order Accurate Method for Solving the Signed Distance Function Equation", Communications in Applied Mathematics and Computational Science, Vol. 5 (2010), No. 1, 81-97, 2010,

Prateek Sharma, Phillip Colella, and Daniel F. Martin, "Numerical Implementation of Streaming Down the Gradient: Application to Fluid Modeling of Cosmic Rays", SIAM Journal on Scientific Computing , Vol 32(6), 3564-3583, 2010,

Q. Zhang, H. Johansen and P. Colella, "A Fourth-Order Accurate Finite-Volume Method with Structured Adaptive Mesh Refinement for Solving the Advection-Diffusion Equation", SIAM Journal on Scientific Computing, Vol. 34, No. 2. (2012), B179, doi:10.1137/110820105, 2010,

R.K. Crockett, P. Colella, and D.T. Graves, "A Cartesian Grid Embedded Boundary Method for Solving the Poisson and Heat Equations with Discontinuous Coefficients in Three Dimensions", Journal of Computational Physics , 230(7):2451-2469, 2010,

2009

P. Colella, M. Dorr, J. Hittinger, D.F. Martin, and P. McCorquodale, "High-Order Finite-Volume Adaptive Methods on Locally Rectangular Grids", 2009 J. Phys.: Conf. Ser. 180 012010, 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,

P. Colella, M. Dorr, J. Hittinger, P.W. McCorquodale, and D.F. Martin, "High-Order Finite-Volume Methods on Locally-Structured Grids", Numerical Modeling of Space Plasma Flows: Astronum 2008 -- Proceedings of the 3rd International Conference, June 8-13, 2008, St John, U.S. Virgin Islands, 2009, pp. 207-216, 2009,

2008

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,

T.J. Ligocki, P.O. Schwartz, J. Percelay, P. Colella, "Embedded Boundary Grid Generation using the Divergence Theorem, Implicit Functions, and Constructive Solid Geometry", 2008 J. Phys.: Conf. Ser. 125 012080, 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,

Colella, P. and Sekora, M. D., "A Limiter for PPM that Preserves Accuracy at Smooth Extrema", Submitted to Journal of Computational Physics, 2008,

Martin, D.F., Colella, P., and Graves, D.T., "A Cell-Centered Adaptive Projection Method for the Incompressible Navier-Stokes Equations in Three Dimensions", Journal of Computational Physics Vol 227 (2008) pp. 1863-1886., 2008, LBNL 62025,

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,

Miniati, F. and Colella, P., "A Modified higher-Order Godunov's Scheme for Stiff Source Conservative Hydrodynamics", Journal of Computational Physics Vol. 224 (2007), pp. 519-538., 2008, LBNL 59902,

2007

Katherine Yelick, Dan Bonachea, Wei-Yu Chen, Phillip Colella, Kaushik Datta, Jason Duell, Susan L. Graham, Paul Hargrove, Paul Hilfinger, Parry Husbands, Costin Iancu, Amir Kamil, Rajesh Nishtala, Jimmy Su, Michael Welcome, Tong Wen, "Productivity and Performance Using Partitioned Global Address Space Languages", Parallel Symbolic Computation (PASCO'07), July 2007,

Partitioned Global Address Space (PGAS) languages combine the programming convenience of shared memory with the locality and performance control of message passing. One such language, Unified Parallel C (UPC) is an extension of ISO C defined by a consortium that boasts multiple proprietary and open source compilers. Another PGAS language, Titanium, is a dialect of Java T M designed for high performance scientific computation. In this paper we describe some of the highlights of two related projects, the Titanium project centered at U.C. Berkeley and the UPC project centered at Lawrence Berkeley National Laboratory. Both compilers use a source-to-source strategy that translates the parallel languages to C with calls to a communication layer called GASNet. The result is portable highperformance compilers that run on a large variety of shared and distributed memory multiprocessors. Both projects combine compiler, runtime, and application efforts to demonstrate some of the performance and productivity advantages to these languages.

Katherine A. Yelick, Dan Bonachea, Wei-Yu Chen, Phillip Colella, Kaushik Datta, Jason Duell, Susan L. Graham, Paul Hargrove, Paul N. Hilfinger, Parry Husbands, Costin Iancu, Amir Kamil, Rajesh Nishtala, Jimmy Su, Michael L. Welcome, Tong Wen, "Productivity and performance using partitioned global address space languages", Parallel Symbolic Computation (PASCO), 2007,

McCorquodale, P., Colella, P., Balls, G.T., and Baden, S.B., "A Local Corrections Algorithm for Solving Poisson's Equation in Three Dimensions", Communications in Applied Mathematics and Computational Science Vol. 2, No. 1 (2007), pp. 57-81., 2007,

Phillip Colella, John Bell, Noel Keen, Terry Ligocki, Michael Lijewski, Brian van Straalen, "Performance and Scaling of Locally-Structured Grid Methods for Partial Differential Equations", presented at SciDAC 2007 Annual Meeting, 2007,

Miniati, F. and Colella, P., "Block Structured Adaptive Mesh and Time Refinement for Hybrid, Hyperbolic + N-body Systems", Journal of Computational Physics Vol. 227 (2007), pp. 400-430., 2007,

2006

Katherine Yelick, Paul Hilfinger, Susan Graham, Dan Bonachea, Jimmy Su, Amir Kamil, Kaushik Datta, Phillip Colella, and Tong Wen, "Parallel Languages and Compilers: Perspective from the Titanium Experience", The International Journal Of High Performance Computing Applications, June 16, 2006, 21,

We describe the rationale behind the design of key features of Titanium—an explicitly parallel dialect of JavaTM for high-performance scientific programming—and our experiences in building applications with the language. Specifically, we address Titanium’s Partitioned Global Address Space model, SPMD parallelism support, multi-dimensional arrays and array-index calculus, memory management, immutable classes (class-like types that are value types rather than reference types), operator overloading, and generic programming. We provide an overview of the Titanium compiler implementation, covering various parallel analyses and optimizations, Titanium runtime technology and the GASNet network communication layer. We summarize results and lessons learned from implementing the NAS parallel benchmarks, elliptic and hyperbolic solvers using Adaptive Mesh Refinement, and several applications of the Immersed Boundary method. 

Martin, D.F., Colella, P.. and Keen, N., A. Deane, G. Brenner, A. Ecer, D. Emerson, J. McDonough, J. Periaux, N. Satofuka, & D. Tromeur-Dervout (Eds.), "An Incompressible Navier-Stokes with Particles Algorithm and Parallel Implementation", Parallel Computational Fluid Dynamics: Theory and Applications, Proceedings of the 2005 International Conference on Parallel Computational Fluid Dynamics, May 24-27, College Park, MD, USA, Elsevier (2006), p. 461-468., 2006, LBNL 58787,

Gatti-Bono, C., Colella, P., "An Anelastic Allspeed Projection Method for Gravitationally Stratified Flows", J. Comput. Phys. Vol. 216 (2006), pp. 589-615, 2006, LBNL 57158,

Colella, P., Graves, D.T., Keen, B.J., Modiano, D., "A Cartesian Grid Embedded Boundary Method for Hyperbolic Conservation Laws", Journal of Computational Physics. Vol. 211 (2006), pp. 347-366., 2006, LBNL 56420,

Schwartz, P., Barad, M., Colella, P., Ligocki, T.J., "A Cartesian Grid Embedded Boundary Method for the Heat Equation and Poisson's Equation in Three Dimensions", Journal of Computational Physics. Vol. 211 (2006), pp. 531-550., 2006, LBNL 56607,

2005

McCorquodale, P., Colella, P., Balls, G., Baden, S.B., "A Scalable Parallel Poisson Solver with Infinite-Domain Boundary Conditions", Proceedings of the 7th Workshop on High Performance Scientific and Engineering Computing, Oslo, Norway, June 2005,

Ryne, R., Abell, D., Adelmann, A., Admundson, J., Bohn, C., Cary, J., Colella, P., Dechow, D., Decyk, V., Dragt, A., Gerber, R., Habib, S., Higdon, D., Katsouleas, T., Ta, K.L., McCorquodale, P., Mihalcea, D., Mitchell, C., Mori, W., Mottershead, C.T., Neri, F., Pogorelov, I., Quiang, J., Samulyak, R., Serafini, D., Shalf, J., Siegerist, C., Spentzouris, P., Stoltz, P., Terzic, B., Venturini, M., Walstrom, P., "SciDAC Advances and Applications in Computational Beam Dynamics", June 2005, LBNL 58243,

Wen, T., Colella, P., "Adaptive Mesh Refinement in Titanium", Proceedings of the International Parallel and Distributed Processing Symposium, Denver, Colorado, April 2005,

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,

Horst Simon, William Kramer, William Saphir, John Shalf, David Bailey, Leonid Oliker, Michael Banda, C. William McCurdy, John Hules, Andrew Canning, Marc Day, Philip Colella, David Serafini, Michael Wehner, Peter Nugent, "Science-Driven System Architecture: A New Process for Leadership Class Computing", Journal of the Earth Simulator, Volume 2., 2005, LBNL 56545,

Schwartz, P., Adalsteinsson, D., Colella, P., Arkin, A.P., Onsum, M., "A Tightly Coupled Particle-Fluid Model for DNA-laden Flows in Complex Microscale Geometries", Proc. Nat. Acad. Sci. Vol. 102 (2005), pp. 11151-11156, 2005,

Gatti-Bono, C., Colella, P., "A Filtering Method for Gravitationally Stratified Flows", 2005, LBNL 57161,

Martin, D.F., Colella, P., Anghel, M., Alexander, F., "Adaptive Mesh Refinement for Multiscale Nonequilibrium Physics", Computing in Science and Engineering Vol.7 N.3 (2005), pp. 24-31, 2005,

Barad, M., Colella, P., "A Fourth-Order Accurate Local Refinement Method for Poisson's Equation", J. Comput. Phys. Vol.209 (2005), pp. 1-18, 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,

Crockett, R.K., Colella, P., Fisher, R., Klein, R.I., McKee, C.F., "An Unsplit, Cell-Centered Godunov Method for Ideal MHD", J. Comput. Phys. Vol.203 (2005), pp. 422-448, 2005,

2004

Simon, H., Kramer, W., Saphir, W., Shalf, J., Bailey, D., Oliker, L., Banda, M., McCurdy, C.W., Hules, J., Canning, A., Day, M., Colella, P., Serafini, D., Wehner, M., Nugent, P., "National Facility for Advanced Computational ScienceL A Sustainable Path to Scientific Discovery", April 2004, LBNL 5500,

McCorquodale, P., Colella, P., Grote, D., Vay, J.L., "A Node-Centered Local Refinement Algorithm for Poisson's Equation in Complex Geometries", J. Comput. Phys. Vol.201 (2004), pp. 34-60, 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,

Vay, J.L., Colella, P., Friedman, A., Grote, D.P., McCorquodale, P., Serafini, D.B., "Implementations of Mesh Refinement Schemes for Particle-in-Cell Plasma Simulations", Computer Physics Communications Vol.164 (2004), pp. 297-305, 2004,

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,

Samtaney, R., Colella, P., Jardin, S.C., Martin, D.F., "3D Adaptive Mesh Refinement Simulations of Pellet Injection in Tokamaks", Computer Physics Communications Vol.164 (2004), pp. 220-228, 2004,

Vay, J.L., Colella, P., Kwan, J.W., McCorquodale, P., Serafini, D.B., Friedman, A., Grote, D.P., Westenskow, G., Adam, J.C., "Application of Adaptive Mesh Refinement to Particle-in-Cell Simulations of Plasmas and Beams", Physics of Plasmas Vol.11 (2004), pp. 2928-2934, 2004,

2003

Balls, G.T., Baden, S.B., Colella, P., "SCALLOP: A Highly Scalable Parallel Poisson Solver in Three Dimensions", Proceedings, SC'03, Phoenix, Arizona, November, 2003, November 2003,

2002

Miller, G.H., Colella, P., "A Conservative Three-Dimensional Eulerian Method for Coupled Solid-Fluid Shock Capturing", J. Comput. Phys. Vol.183 (2002), pp. 26, 2002,

Balls, G., Colella, P., "A Finite Difference Domain Decomposition Method Using Local Corrections for the Solution of Poissons's Equation", J. Comput. Phys. Vol.180 (2002), pp. 25, 2002,

Vay, J.L., Colella, P., McCorquodale, P., Van Straalen, B., Friedman, A., Grote, D.P., "Mesh Refinement for Particle-in-Cell Plasma Simulations: Applications to and Benefits for Heavy Ion Fusion", Laser and Particle Beams. Vol.20 N.4 (2002), pp. 569-575, 2002,

Colella, P., Graves, D.T., Greenough, J.A., "A Second-Order Method for Interface Recontruction in Orthogonal Coordinate Systems", January 2002, LBNL 45244,

2001

McCorquodale, P., Colella, P., Johansen, H., "A Cartesian Grid Embedded Boundary Method for the Heat Equation on Irregular Domains", J. Comput. Phys. Vol.173 (2001), pp. 620-635, 2001,

Miller, G.H., Colella, P., "A Higher-Order Godunov Method for Elastic-Plastic Flow in Solids", J. Comput. Phys. Vol.167 (2001), pp. 131, 2001,

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

2000

Modiano, D., Colella, P., "A Higher-Order Embedded Boundary Method for Time-Dependent Simulation of Hyperbolic Conservation Laws", ASME paper FEDSM00-11220, to appear in Proceedings of the ASME 2000 Fluids Engineering Division Summer Meeting, 2000, LBNL 45239,

Propp, R., Colella, P., Crutchfield, W.Y., Day, M.S., "A Numerical Model for Trickle-Bed Reactors", J. Comput. Phys., 2000, 165:311-333,

Martin D., Colella, P., "A Cell-Centered Adaptive Projection Method for the Incompressible Euler Equations", J. Comput. Phys. Vol.163 (2000), pp. 271-312, 2000,

1999

Colella, P., Graves, D.T., Modiano, D., Puckett, E.G., Sussman, M., "An Embedded Boundary / Volume of Fluid Method for Free Surface Flows in Irregular Geometries", ASME Paper FEDSM99-7108, in Proceedings of the 3rd ASME/JSME Joint Fluids Engineering Conference, 18-23 July, San Francisco, CA, 1999,

Nelson, E.S., Colella, P., "Parametric Study of Reactive Melt Infiltration", R.M. Sullivan, N.J. Salamon, M. Keyhani, and S. White, eds. "Application of porous media methods for engineered materials" AMD-Vol 233, pp 1-11. American Society of Mechanical Engineers (1999). (Presented at the 1999 ASME International Mechanical Engineer, 1999,

Colella, P., Dorr, M.R., Wake, D.D., "A Conservative Finite Difference Method for the Numerical Solution of Plasma Fluid Equations", J. Comput. Phys. Vol.149 (1999), pp. 168-193, 1999,

Colella, P., Dorr, M.R., Wake, D.D., "Numerical Solution of Plasma Fluid Equations Using Locally Refined Grids", J. Comput. Phys. Vol.152 (1999), pp. 550-583, 1999,

Colella, P., Pao, K., "A Projection Method for Low Speed Flows", J. Comput. Phys. Vol.149 (1999), pp. 245-269, 1999,

Howell, L.H., Pember, R.B., Colella, P., Fiveland, W.A., Jessee, J.P., "A Conservative Adaptive-Mesh Algorithm for Unsteady, Combined-Mode Heat Transfer Using the Discrete Ordinates Method", Numerical Heat Transfer, Part B: Fundamentals , Vol.35, (1999), pp. 407-430, 1999,

Colella, P., Trebotich, D., "Numerical Simulation of Incompressible Viscous flow in Deforming Domains", Proceedings of the National Academy of Sciences of the United States of America Vol.96, (1999), pp. 5378-5381, 1999,

Sussman, M.M., Almgren, A.S., Bell, J.B., Colella, P., Howell, L.H., Welcome, M., "An Adaptive Level Set Approach for Incompressible Two-Phase Flows", J. Comp. Phys. Vol.148, pp. 81-124, 1999, LBNL 40327,

1998

Johansen, H., Colella, P., "A Cartesian Grid Embedded Boundary Method for Poisson's Equation on Irregular Domains", J. Comput. Physics, Vol.147, No.1, pp. 60-85, November 1998,

Vegas-Landeau, M.A., Propp, R., Patzek, T.W., Colella, P., "A Sequential Semi-Implicit Algorithm for Computing Discontinuous Flows in Porous Media", SPE Journal, June 1998,

Yelick, K., Semenzato, L., Pike, G., Miyamoto, C., Liblit, B., Krishnamurthy, A., Hilfinger, P., Graham, S., Gay, D., Colella, P., Aiken, A., "Titanium: A High-Performance Java Dialect", ACM 1998 workshop on Java for high-performance computing, Stanford, CA, February 1998,

Pember, R.P., Howell, L.H., Bell, J.B., Colella, P., Crutchfield, W.Y., Fiveland, W.A., Jessee, J.P., "An Adaptive Projection Method For Unsteady Low-Mach Number Combustion", Comb. Sci. Tech., 1998, 140:123-168,

Almgren, A.S., Bell, J.B., Colella, P., Howell, L.H., Welcome, M.L., "A Conservative Adaptive Projection Method for the Variable Density Incompressible Navier-Stokes Equations", J. Comp. Phys., 1998, 142:1-46, LBNL 39075,

M.S. Day, P. Colella, M. Lijewski, C.A. Rendleman and D.L. Marcus, "Embedded Boundry Algorithms for Solving the Poisson Equation on Complex Domains", 1998, LBNL 41811,

Dudek, S., Colella, P., "Steady-State Solution-Adaptive Euler Computations on Structured Grids", AIAA paper 98-0543, AIAA Aerospace Sciences meeting, Reno, NV, January 1998,

Jessee, J.P., Fiveland, W.A., Howell, L.H., Colella, P., Pember, R., "An Adaptive Mesh Refinement Algorithm for the Radiative Transport Equation", J. Comput. Phys. Vol.139, (1998), pp. 380-398, 1998,

1997

Tallio, K.V., Colella, P., "A Multifluid CFD Turbulent Entrainment Combustion Model: Formulation and One-Dimensional Results", Society of Automotive Engineers Fuels and Lubricants Meeting, November 1997, LBNL 40806,

Sussman, M.M., Almgren, A.S., Bell, J.B., Colella, P., Howell, L.H., Welcome, M., "An Adaptive Level Set Approach for Incompressible Two-Phase Flows", April 1997, LBNL 40327,

Dudek, S., Colella, P., "A Godunov Steady-State Solver for Structured Grids", AIAA Aerospace Sciences meeting, AIAA paper 97-0875, Reno, NV, January 1997,

Helmsen, J., Colella, P., Puckett, E.G., "Non-Convex Profile Evolution in Two Dimensions Using Volume of Fluids", 1997, LBNL 40693,

Hilditch, J., Colella, P., "A Projection Method for Low-Mach Number Fast Chemistry Reacting Flow", AIAA Aerospace Sciences meeting, AIAA paper 97-0263, Reno, NV, January 1997,

Almgren, A.S., Bell, J.B., Colella, P., Marthaler, T., "A Cartesian Grid Projection Method for the Incompressible Euler Equations in Complex Geometries", SIAM J. Sci. Comp., 1997, 18(5):1289-1309,

J.A. Greenough, J.B. Bell, P. Colella, E.G. Puckett, "A Numerical Study of Shock-Induced Mixing of a Helium Cylinder: Comparison with Experiment", Proceedings of the 20th International Symposium on Shock Waves, 1997,

1996

Jesse, J.P., Howell, L.H., Fiveland, W.A., Colella, P., Pember, R.B., "An Adaptive Mesh Refinement Algorithm for the Discrete Ordinates Methods", Proceedings, ASME 1996 National Heat Transfer Conference, August 1996,

Mark. M. Sussman, Ann S. Almgren, John B. Bell, Phillip Colella, Louis H. Howell, Michael Welcome, "An Adaptive Level Set Approach for Incompressible Two-Phase Flows", Proceedings of the ASME Fluids Engineering Summer Meeting: Forum on Advances in Numerical Modeling of Free Surface and Interface Fluid Dynamics, July 1996,

Helmsen, J., Puckett, E.G., Colella, P., Dorr, M., "Two New Methods for Simulating Photolithography Development in 3D", Proceedings of the SPIE - The International Society for Optical Engineering Optical Microlithography IX, Santa Clara, CA, March 1996,

R.B. Pember, P. Colella, L.H. Howell, A.S. Almgren, J.B. Bell, W.Y. Crutchfield, V.E. Beckner, K.C. Kaufman, W.A. Fiveland, and J.P. Jessee, "The Modeling of a Laboratory Natural Gas-Fired Furnace with a Higher-Order Projection Method for Unsteady Combustion", UCRL-JC123244, February 1996,

1995

Pember, R.B., Almgren, A.S., Bell, J.B., Colella, P., Howell, L., Lai, M., "A Higher-Order Projection Method for the Simulation of Unsteady Turbulent Nonpremixed Combustion in an Industrial Burner", Proceedings of the 8th International Symposium on Transport Phenomena in Combustion, San Francisco, CA, July 1995,

Steinthorsson, E., Modiano, D., Crutchfield, W.Y., Bell, J.B., Colella, P., "An Adaptive Semi-Implicit Scheme for Simulations of Unsteady Viscous Compressible Flow", AIAA Paper 95-1727-CP, in Proceedings of the 12th AIAA CFD Conference, June 1995,

Bell, J.B., Colella, P., Greenough, J.A., Marcus, D.L., "A Multi-Fluid Algorithm for Compressible, Reacting Flow", AIAA 95-1720, 12th AIAA Computational Fluid Dynamics Conference, San Diego, CA, June 1995,

Greenough, J.A., Beckner, V., Pember, R.B., Crutchfield, W.Y., Bell, J.B.,Colella, P., "An Adaptive Multifluid Interface-Capturing Method for Compressible Flow in Complex Geometries", AIAA-95-1718, Proceedings of 26th AIAA Fluid Dynamics Conference, San Diego, CA, June 1995,

Almgren, A.S., Bell, J.B., Colella, P., Marthaler, T., "A Cell-Centered Cartesian Grid Projection Method for the Incompressible Euler Equations in Complex Geometries", AIAA paper 95-1924, Proceedings, AIAA 12th Computational Fluid Dynamics Conference, San Diego, CA, June 1995,

Pember, R.B., Bell, J.B., Colella, P., Crutchfield, W.Y., Welcome, M.L., "An Adaptive Cartesian Grid Method for Unsteady Compressible Flow in Irregular Regions", J. Comp. Phys., 1995, 120(2):278-304,

Hilditch, J., Colella, P., "A Front Tracking Method for Compressible Flames in One Dimension", SIAM Journal on Scientific Computing, Vol.16 No.4 (1995), pp. 755-772, 1995,

Chien, K.Y., Ferguson, R.E., Kuhl, A.L., Glaz, H.M., Colella, P., "Inviscid Dynamics of Two-Dimensional Shear Layers", International Journal of Computational Fluid Dynamics, Vol.5 No.1-2, pp. 59+, 1995,

Collins, J.P., Colella, P., Glaz, H.M., "An Implicit-Explicit Eulerian Godunov Scheme for Compressible Flow", J. Comp. Phys., Vol.116 No.2, pp. 195-211, 1995,

Ann S. Almgren, John B. Bell, Phillip Colella, Louis H. Howell, Michael Welcome, "A High-Resolution Adaptive Projection Method for Regional Atmospheric Modeling", Proceedings of the NGEMCOM Conference sponsored by the U.S. EPA, August 7-9, Bay City, MI, 1995,

Richard B. Pember, Ann S. Almgren, John B. Bell, Phillip Colella, Louis Howell, and Mindy Lai, "A Higher-Order Projection Method for the Simulation of Unsteady Turbulent Nonpremixed Combustion in an Industrial Burner", Proceedings of the 8th International Symposium on Transport Phenomena in Combustion, July 16-20, San Francisco, CA, 1995,

R.B. Pember, A.S. Almgren, W.Y. Crutchfield, L.H. Howell, J.B. Bell, P. Colella, and V.E. Beckner, "An Embedded Boundry Method for the Modeling of Unsteady Combustion in an Industrial Gas-Fired Furnace", WSS/CI 95F-165, 1995 Fall Meeting of the Western united States Section of the Comustion Institute, Stanford University, October 30-31, 1995,

1994

P. Colella and W.Y. Crutchfield, "A Parallel Adaptive Mesh Refinement Algorithm on the C-90", Energy Research Power Users Symposium, July 12, 1994,

Steinthorsson, E., Modiano, D., Colella, P., "Computations of Unsteady Viscous Compressible Flows Using Adaptive Mesh Refinement in Curvilinear Body-Fitted Grid Systems", NASA technical memorandum 106704, ICOMP report no. 94-17, 1994,

Ann S. Almgren, John B. Bell, Louis H. Howell and Phillip Colella, "An Adaptive Projection Method for the Incompressible Navier-Stokes Equations", Proceedings of the 14th IMACS World Congress, July 11-15, pp. 537-540, Atlanta, Georgia, 1994,

Colella, P., Crutchfield, W.Y., "A Parallel Adaptive Mesh Refinement Algorithm on the C-90", Energy Research Power Users Symposium, 1994,

Almgren, A.S., Buttke, T., Colella, P., "A Fast Adaptive Vortex Method In Three Dimensions", J. Comp. Phys., Vol.113 No.2, pp. 177-200, 1994,

Zachary, A.L., Malagoli, A., Colella, P., "A Higher-Order Godunov Method for Multidimensional Ideal Magnetohydrodynamics", SIAM Journal on Scientific Computing, Vol.15 No.2, pp. 263-284, 1994,

Liu, J.C., Colella, P., Peterson, P.F., Schrock, V.E., "Modeling Supersonic Flows Through a Gas-Continuous 2-Fluid Medium", Nuclear Engineering and Design, Vol.146 No.1-3, pp. 337-348, 1994,

Klein, R.I., McKee, C.F., Colella, P., "On the Hydrodynamic Interaction of Shock Waves with Interstellar Clouds .1. Nonradiative Shocks in Small Clouds", Astrophysical Journal, Vol.420 No.1, pp. 213-236, 1994,

1993

Almgren, A.S., Bell, J.B., Colella, P., Howell, L.H., "An Adaptive Projection Method for the Incompressible Euler Equations", Proceedings of the AIAA 11th Computational Fluid Dynamics Conference, Orlando, FL, July 1993,

Lai, M., Colella, P., Bell, J., "A Projection Method for Combustion in the Zero Mach Number Limit", AIAA paper 93-3369, Proceedings of the AIAA 11th Computational Fluid Dynamics Conference, Orlando, FL, July 1993,

Pember, R.B., Bell, J.B., Colella, P., Crutchfield, W.Y., Welcome, M.L., "Adaptive Cartesian Grid Methods for Representing Geometry in Inviscid Compressible Flow", Proceedings of the 11th AAIA CFD Conference, Orlando, Florida, July 1993,

Hilfinger, P.N., Colella, P., "FIDIL Reference Manual", UC Berkeley Computer Science Division Report, UCB/CSD-93-759, May 1993,

  • Download File: B17.pdf (pdf: 1.7 MB)

Ann S. Almgren, John B. Bell,Phillip Colella, Louis H. Howell, "An Adaptive Projection Method for the Incompressible Euler Equations", Proceedings of the AIAA 11th Computational Fluid Dynamics Conference, July 6-9, Orlando, FL, 1993,

1992

Chen, X.M., Schrock, V.E., Peterson, P.F., Colella, P., "Gas Dynamics in the Central Cavity of the Hylife-II Reactor", Fusion Technology, Vol.21 No.3, pp. 1520-1524., 1992,

Zachary, A.L., Colella, P., "A Higher-Order Godunov Method for the Equations of Ideal Magnetohydrodynamics", Journal of Computational Physics, Vol.99 No.2, pp. 341-347., 1992,

1991

Chien, KY., Ferguson, R.E., Kuhl, A.L., Glaz, H.M., Colella P., "Inviscid Dynamics of Two-Dimensional Shear Layers", Proceedings, 22nd AIAA Fluid Dynamics, Plasma Dynamics, and Lasers Conference, Honolulu, Hawaii, June 1991,

Bell, J.B., Colella P., Welcome, M., "Conservative Front-Tracking for Inviscid Compressible Flow", Proceedings, 10th AIAA Computational Fluid Dynamics Conference, pp. 814-822., Honolulu, Hawaii, June 1991,

Bell, J.B., Colella P., Howell, L., "An Efficient Second-Order Projection Method for Viscous Incompressible Flow", Proceedings, 10th AIAA Computational Fluid Dynamics Conference, pp. 360-367., Honolulu, Hawaii, June 1991,

Henderson L.F., Colella P., Puckett E.G., "On the Refraction of Shock Waves at a Slow Fast Gas Interface", Journal of Fluid Mechanics, Vol.224 MAR:1+., 1991,

Trangenstein J.A., Colella P., "A Higher-Order Godunov Method for Modeling Finite Deformation in Elastic-Plastic Solids", Communications on Pure and Applied Mathematics, Vol.44 No.1, pp. 41-100, 1991,

1990

Colella, P., "Multidimensional Upwind Methods for Hyperbolic Conservation Laws", J. Comp. Phys., Vol.87 No.1, pp. 171-200, 1990,

Kuhl, A.L., Ferguson, R.E., Chien, K.Y., Glowacki, W., Collins, P. Glaz, H., Colella P., "Turbulent Wall Jet in a Mach Reflection Flow", Progress in Aeronautics and Astronautics, Vol.13, pp. 201-232, 1990,

Colella, P., Henderson, L.F., "The von Neumann Paradox for the Diffraction of Weak Shock Waves", Journal of Fluid Mechanics, Vol.213, pp. 71-94., 1990,

1989

Colella, P., Henderson, L.F., Puckett, E.G., "A Numerical Study of Shock Wave Refractions at a Gas Interface", Proceedings, 9th AIAA Computational Fluid Dynamics Conference, pp. 426-439, Buffalo, NY, 1989,

Bell, J.B., Colella P., Trangenstein, J. A., Welcome, M., "Adaptive Mesh Refinement on Moving Quadrilateral Grids", Proceedings, 9th AIAA Computational Fluid Dynamics Conference, pp. 471-479, Buffalo, NY, 1989,

Bell, J.B., Colella, P., Glaz, H.M., "A Second-Order Projection Method for the Incompressible Navier Stokes Equations", J. Comp. Phys,, Vol.85 No.2, pp. 257-283., 1989,

Bell, J.B., Colella, P,, Trangenstein, J.A., "Higher Order Godunov Methods for General Systems of Hyperbolic Conservation Laws", Journal of Computational Physics, Vol.82 No.2, pp. 362-397, 1989,

Berger M.J., Colella P., "Local Adaptive Mesh Refinement for Shock Hydrodynamics", J. Comp. Phys., Vol.82 No.1, pp. 64-84, 1989,

Sakurai, A., Henderson, L.F., Takayama, K., Walenta, Z., Colella P., "On the Von Neumann Paradox of Weak Mach Reflection", Fluid Dynamics Research, Vol.4, pp. 333-346, 1989,

1988

Bell, J.B., Colella, P. Trangenstein, J.A., Welcome, M., "Godunov Methods and Adaptive Algorithms for Unsteady Fluid Dynamics", Proceedings, 11th International Conference on Numerical Methods in Fluid Dynamics, Springer Lecture Notes in Physics Vol.323, pp. 137-141, Williamsburg, Virginia, June 1988,

Glaz, H.M., Colella, P., Collins, J.P., Ferguson, R.E., "Nonequilibrium Effects in Oblique Shock-Wave Reflection", AIAA Journal, Vol.26, pp. 698-705., 1988,

Hilfinger, P.N., Colella P., "FIDIL: A Language for Scientific Programming", Symbolic Computation: Applications to Scientific Computing, SIAM Frontiers in Applied Mathematics, Vol.5, pp. 97-138, 1988,

1987

Chern, I.L., Colella P., "A Conservative Front Tracking Method for Hyperbolic Conservation Laws", Lawrence Livermore National Laboratory Report UCRL-97200, July 1987,

Bell, J.B., Colella P., Trangenstein, J., Welcome, M., "Adaptive Methods for High Mach Number Reactig Flow", Proceedings, AIAA 8th Computational Fluid Dynamics Conference, pp. 717-725, Honolulu, Hawaii, June 1987,

Glaz, H.M., Colella, P., Collins, J.P., Ferguson, R.E., "High Resolution Calculations of Unsteady, Two-Dimensional Non-Equilibrium Gas Dynamics with Experimental Comparisons", AIAA paper 87-1293, Proceedings, AIAA 8th Computational Fluid Dynamics Conference, Honolulu, Hawaii, June 1987,

Bell, J.B., Colella P., Glaz, H.M., "A Second Order Projection Method for Viscous Incompressible Flow", AIAA paper 87-1176-CP, Proceedings, AIAA 8th Computational Fluid Dynamics Conference, pp. 789-794, Honolulu, Hawaii, June 1987,

1986

Colella, P., Majda, A., Roytburd, V., "Theoretical and Numerical Structure for Reacting Shock Waves", SIAM Journal of Sci. Stat. Computing, Vol.7 No.4, pp. 1059-1080, 1986,

Fryxell, B.A., Woodward, P.R., Colella, P., Winkler, K.H., "An Implicit-Explicit Hybrid Method for Lagrangian Hydrodynamics", Journal of Computational Physics, Vol.62, pp. 283-310., 1986,

Glaz, H.M., Colella P., Glass, I.I., Deschambault, R.L., "Mach Reflection from an HE-Driven Blast Wave", Progress in Aeronautics and Astronautics, Vol.106, pp. 388-421., 1986,

1985

Glaz, H.M., Colella P., Glass, I.I., Deschambault, R.L., "A Numerical Study of Oblique Shock-Wave Reflections with Experimental Comparisons", Proceedings, Royal Society of London A, Vol. 398, pp. 117-140, 1985,

  • Download File: A18.pdf (pdf: 1.3 MB)

Colella, P., Glaz, H.M., "Efficient Solution Algorithms for the Riemann Problem for Real Gases", J. Comp. Phys., Vol.59 No.2, pp. 264-289., 1985,

  • Download File: A17.pdf (pdf: 565 KB)

Colella, P., "A Direct Eulerian MUSCL Scheme for Gas Dynamics", SIAM Journal for Sci. Stat. Computing, Vol.6 No.1, pp. 104-117., 1985,

  • Download File: A16.pdf (pdf: 716 KB)

1984

Eidelman, S., Colella P., Shreeve, R.P., "Application of the Godunov Method and its Second-Order Extension to Cascade Flow Modeling", AIAA Journal, Vol.22 No.11 (1984), pp. 1609-1615, 1984,

  • Download File: A15.pdf (pdf: 1.1 MB)

Colella P., Glaz, H.M., "Numerical Calculation of Complex Shock Reflections in Gases", Proceedings, 9th International Conference on Numerical Methods in Fluid Dynamics, Saclay, France, June, 1984, Springer Lecture Notes in Physics, Vol.218, pp. 154-158, 1984,

Woodward, P.R., Colella, P., "The Numerical Simulation of Two-Dimensional Fluid Flow with Strong Shocks", J. Comp. Phys., Vol.54 No.1 (1984), pp. 115-173, 1984,

Colella P., Woodward, P.R., "The Piecewise Parabolic Method (PPM) for Gas-Dynamical Simulations", J. Comp. Phys., Vol.54 No.1 (1984), pp. 174-201, 1984,

1982

Colella P., Glaz, H.M., "Numerical Modelling of Inviscid Shocked Flows of Real Gases", Proceedings, 8th International Conference on Numerical Methods in Fluid Dynamics,Springer Lecture Notes in Physics, Vol.170, pp. 175-182, Aachen, Germany, June 1982,

Colella P., "Glimm's Method for Gas Dynamics", SIAM Journal for Sci. Stat. Computing, Vol.3 No.1, pp. 76-110, 1982,

  • Download File: A12.pdf (pdf: 852 KB)

1980

Woodward, P.R., Colella P., "High Resolution Difference Schemes for Compressible Gas Dynamics", Proceedings, 7th International Conference on Numerical Methods in Fluid Dynamics, Stanford, CA, June, 1980, Springer Lecture Notes in Physics, Vol.142, pp. 434-441, June 1980,

1973

Colella P., Lanford, O.E., "Sample Field Behavior for the Free Markov Random Field", 1973,

  • Download File: B21.pdf (pdf: 903 KB)

Anshu Dubey

2016

Anshu Dubey, Hajime Fujita, Daniel T. Graves, Andrew Chien Devesh Tiwari, "Granularity and the Cost of Error Recovery in Resilient AMR Scientific Applications", SuperComputing 2016, August 10, 2016,

2015

Anshu Dubey, Daniel T. Graves, "A Design Proposal for a Next Generation Scientific Software Framework", EuroPar 2015, July 31, 2015,

A Chien, P Balaji, P Beckman, N Dun, A Fang, H Fujita, K Iskra, Z Rubenstein, Z Zheng, R Schreiber, others, "Versioned Distributed Arrays for Resilience in Scientific Applications: Global View Resilience", Journal of Computational Science, 2015,

2014

Adrian Tate, Amir Kamil, Anshu Dubey, Armin Größlinger, Brad Chamberlain, Brice Goglin, Carter Edwards, Chris J. Newburn, David Padua, Didem Unat, Emmanuel Jeannot, Frank Hannig, Gysi Tobias, Hatem Ltaief, James Sexton, Jesus Labarta, John Shalf, Karl Fuerlinger, Kathryn O’Brien, Leonidas Linardakis, Maciej Besta, Marie-Christine Sawley, Mark Abraham, Mauro Bianco, Miquel Pericàs, Naoya Maruyama, Paul Kelly, Peter Messmer, Robert B. Ross, Romain Cledat, Satoshi Matsuoka, Thomas Schulthess, Torsten Hoefler, Vitus Leung, "Programming Abstractions for Data Locality", 2014 Workshop on Programming Abstractions for Data Locality, April 29, 2014,

The goal of the workshop and this report is to identify common themes and standardize concepts for locality-preserving abstractions for exascale programming models. Current software tools are built on the premise that computing is the most expensive component, we are rapidly moving to an era that computing is cheap and massively parallel while data movement dominates energy and performance costs. In order to respond to exascale systems (the next generation of high performance computing systems), the scientific computing community needs to refactor their applications to align with the emerging data-centric paradigm. Our applications must be evolved to express information about data locality. Unfortunately current programming environments offer few ways to do so. They ignore the incurred cost of communication and simply rely on the hardware cache coherency to virtualize data movement. With the increasing importance of task-level parallelism on future systems, task models have to support constructs that express data locality and affinity. At the system level, communication libraries implicitly assume all the processing elements are equidistant to each other. In order to take advantage of emerging technologies, application developers need a set of programming abstractions to describe data locality for the new computing ecosystem. The new programming paradigm should be more data centric and allow to describe how to decompose and how to layout data in the memory.
Fortunately, there are many emerging concepts such as constructs for tiling, data layout, array views, task and thread affinity, and topology aware communication libraries for managing data locality. There is an opportunity to identify commonalities in strategy to enable us to combine the best of these concepts to develop a comprehen- sive approach to expressing and managing data locality on exascale programming systems. These programming model abstractions can expose crucial information about data locality to the compiler and runtime system to en- able performance-portable code. The research question is to identify the right level of abstraction, which includes techniques that range from template libraries all the way to completely new languages to achieve this goal.

The goal of the workshop and this report is to identify common themes and standardize concepts for locality-preserving abstractions for exascale programming models. Current software tools are built on the premise that computing is the most expensive component, we are rapidly moving to an era that computing is cheap and massively parallel while data movement dominates energy and performance costs. In order to respond to exascale systems (the next generation of high performance computing systems), the scientific computing community needs to refactor their applications to align with the emerging data-centric paradigm. Our applications must be evolved to express information about data locality. Unfortunately current programming environments offer few ways to do so. They ignore the incurred cost of communication and simply rely on the hardware cache coherency to virtualize data movement. With the increasing importance of task-level parallelism on future systems, task models have to support constructs that express data locality and affinity. At the system level, communication libraries implicitly assume all the processing elements are equidistant to each other. In order to take advantage of emerging technologies, application developers need a set of programming abstractions to describe data locality for the new computing ecosystem. The new programming paradigm should be more data centric and allow to describe how to decompose and how to layout data in the memory.

Fortunately, there are many emerging concepts such as constructs for tiling, data layout, array views, task and thread affinity, and topology aware communication libraries for managing data locality. There is an opportunity to identify commonalities in strategy to enable us to combine the best of these concepts to develop a comprehensive approach to expressing and managing data locality on exascale programming systems. These programming model abstractions can expose crucial information about data locality to the compiler and runtime system to enable performance-portable code. The research question is to identify the right level of abstraction, which includes techniques that range from template libraries all the way to completely new languages to achieve this goal.

Anshu Dubey, Ann Almgren, John Bell, Martin Berzins, Steve Brandt, Greg Bryan, Phillip Colella, Daniel Graves, Michael Lijewski, Frank L\ offler, others, "A survey of high level frameworks in block-structured adaptive mesh refinement packages", Journal of Parallel and Distributed Computing, 2014, 74:3217--3227, doi: 10.1016/j.jpdc.2014.07.001

2013

2009

Bronis R de Supinski, Sadaf Alam, David H Bailey, Laura, Chris Daley, Anshu Dubey, Todd Gamblin, Dan, Paul D Hovland, Heike Jagode, Karen Karavanic, Marin, John Mellor-Crummey, Shirley Moore, Boyana, Leonid Oliker, Catherine Olschanowsky, Philip C, Martin Schulz, Sameer Shende, Allan Snavely, Wyatt, Mustafa Tikir, Jeff Vetter, Pat Worley, Nicholas Wright, "Modeling the Office of Science ten year facilities plan: The PERI Architecture Tiger Team", Journal of Physics: Conference Series, 2009, 180:012039, doi: 10.1088/1742-6596/180/1/012039

Dan Graves

2017

Dharshi Devendran, Daniel T. Graves, Hans Johansen,Terry Ligocki, "A Fourth Order Cartesian Grid Embedded Boundary Method for Poisson's Equation", Communications in Applied Mathematics and Computational Science, edited by Silvio Levy, May 12, 2017, 12:51-79, doi: DOI 10.2140/camcos.2017.12.51

2016

Anshu Dubey, Hajime Fujita, Daniel T. Graves, Andrew Chien Devesh Tiwari, "Granularity and the Cost of Error Recovery in Resilient AMR Scientific Applications", SuperComputing 2016, August 10, 2016,

2015

Anshu Dubey, Daniel T. Graves, "A Design Proposal for a Next Generation Scientific Software Framework", EuroPar 2015, July 31, 2015,

D. Devendran, D. T. Graves, H. Johansen, "A higher-order finite-volume discretization method for Poisson's equation in cut cell geometries", submitted to SIAM Journal on Scientific Computing (preprint on arxiv), 2015,

Peter Schwartz, Julie Percelay, Terry J. Ligocki, Hans Johansen, Daniel T. Graves, Dharshi Devendran, Phillip Colella, Eli Ateljevich, "High-accuracy embedded boundary grid generation using the divergence theorem", Communications in Applied Mathematics and Computational Science 10-1 (2015), 83--96. DOI 10.2140/camcos.2015.10.83, March 31, 2015,

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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

M. Adams, P. Colella, D. T. Graves, J.N. Johnson, N.D. Keen, T. J. Ligocki. D. F. Martin. P.W. McCorquodale, D. Modiano. P.O. Schwartz, T.D. Sternberg, B. Van Straalen, "Chombo Software Package for AMR Applications - Design Document", Lawrence Berkeley National Laboratory Technical Report LBNL-6616E, January 9, 2015,

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,

2014

Dharshi Devendran, Daniel T. Graves, Hans Johansen, "A Hybrid Multigrid Algorithm for Poisson's equation using an Adaptive, Fourth Order Treatment of Cut Cells", LBNL Report Number: LBNL-1004329, November 11, 2014,

Gunther H. Weber, Hans Johansen, Daniel T. Graves, Terry J. Ligocki, "Simulating Urban Environments for Energy Analysis", Proceedings Visualization in Environmental Sciences (EnvirVis), 2014, LBNL 6652E,

Anshu Dubey, Ann Almgren, John Bell, Martin Berzins, Steve Brandt, Greg Bryan, Phillip Colella, Daniel Graves, Michael Lijewski, Frank L\ offler, others, "A survey of high level frameworks in block-structured adaptive mesh refinement packages", Journal of Parallel and Distributed Computing, 2014, 74:3217--3227, doi: 10.1016/j.jpdc.2014.07.001

2013

Daniel T. Graves, Phillip Colella, David Modiano, Jeffrey Johnson, Bjorn Sjogreen, Xinfeng Gao, "A Cartesian Grid Embedded Boundary Method for the Compressible Navier Stokes Equations", Communications in Applied Mathematics and Computational Science, December 23, 2013,

In this paper, we present an unsplit method for the time-dependent
  compressible Navier-Stokes equations in two and three dimensions.
  We use a a conservative, second-order Godunov algorithm.
  We use a Cartesian grid, embedded boundary method to resolve complex
  boundaries.  We solve for viscous and conductive terms with a
  second-order semi-implicit algorithm.  We demonstrate second-order
  accuracy in solutions of smooth problems in smooth geometries and
  demonstrate robust behavior for strongly discontinuous initial
  conditions in complex geometries.

S.L. Cornford, D.F. Martin, D.T. Graves, D.F. Ranken, A.M. Le Brocq, R.M. Gladstone, A.J. Payne, E.G. Ng, W.H. Lipscomb, "Adaptive mesh, finite volume modeling of marine ice sheets", Journal of Computational Physics, 232(1):529-549, 2013,

2012

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.

2011

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. Van Straalen, P. Colella, D. T. Graves, N. Keen, "Petascale Block-Structured AMR Applications Without Distributed Meta-data", Euro-Par 2011 Parallel Processing - 17th International Conference, Euro-Par 2011, August 29 - September 2, 2011, Proceedings, Part II. Lecture Notes in Computer Science 6853 Springer 2011, ISBN 978-3-642-23396-8, Bordeaux, France, 2011,

2010

E. Ateljevich, P. Colella, D.T. Graves, T.J. Ligocki, J. Percelay, P.O. Schwartz, Q. Shu, "CFD Modeling in the San Francisco Bay and Delta", 2009 Proceedings of the Fourth SIAM Conference on Mathematics for Industry (MI09), pp. 99-107, 2010,

R.K. Crockett, P. Colella, and D.T. Graves, "A Cartesian Grid Embedded Boundary Method for Solving the Poisson and Heat Equations with Discontinuous Coefficients in Three Dimensions", Journal of Computational Physics , 230(7):2451-2469, 2010,

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,

2008

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,

Martin, D.F., Colella, P., and Graves, D.T., "A Cell-Centered Adaptive Projection Method for the Incompressible Navier-Stokes Equations in Three Dimensions", Journal of Computational Physics Vol 227 (2008) pp. 1863-1886., 2008, LBNL 62025,

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,

2006

Colella, P., Graves, D.T., Keen, B.J., Modiano, D., "A Cartesian Grid Embedded Boundary Method for Hyperbolic Conservation Laws", Journal of Computational Physics. Vol. 211 (2006), pp. 347-366., 2006, LBNL 56420,

2005

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,

2002

Colella, P., Graves, D.T., Greenough, J.A., "A Second-Order Method for Interface Recontruction in Orthogonal Coordinate Systems", January 2002, LBNL 45244,

1999

Colella, P., Graves, D.T., Modiano, D., Puckett, E.G., Sussman, M., "An Embedded Boundary / Volume of Fluid Method for Free Surface Flows in Irregular Geometries", ASME Paper FEDSM99-7108, in Proceedings of the 3rd ASME/JSME Joint Fluids Engineering Conference, 18-23 July, San Francisco, CA, 1999,

1996

An Approximate Projection Method Suitable for the Modeling of Rapidly Rotating Flows, Graves, D.T., 1996,

Hans Johansen

2017

Nishant Nangia, Hans Johansen, Neelesh A. Patankar, Amneet Pal Singh Bhalla, "A moving control volume approach to computing hydrodynamic forces and torques on immersed bodies", Journal of Computational Physics, June 29, 2017, doi: 10.1016/j.jcp.2017.06.047

Bryce Adelstein Lelbach, Hans Johansen, Samuel Williams, "Solving Large Quantities of Small Matrix Problems on Cache-Coherent Many-Core SIMD Architectures", Parallel and Distributed Scientific and Engineering Computing (PDSEC), June 2017,

Dharshi Devendran, Daniel T. Graves, Hans Johansen,Terry Ligocki, "A Fourth Order Cartesian Grid Embedded Boundary Method for Poisson's Equation", Communications in Applied Mathematics and Computational Science, edited by Silvio Levy, May 12, 2017, 12:51-79, doi: DOI 10.2140/camcos.2017.12.51

2016

Bin Dong, Suren Byna, Kesheng Wu, Prabhat, Hans Johansen, Jeffrey N. Johnson, and Noel Keen, "Data Elevator: Low-contention Data Movement in Hierarchical Storage System", The 23rd annual IEEE International Conference on High Performance Computing, Data, and Analytics (HiPC) (Acceptance rate: 25%), December 19, 2016,

Jared O. Ferguson, Christiane Jablonowski, Hans Johansen, Peter McCorquodale, Phillip Colella, Paul A. Ullrich, "Analyzing the adaptive mesh refinement (AMR) characteristics of a high-order 2D cubed-sphere shallow-water model", Mon. Wea. Rev., November 9, 2016, 144:4641–4666, doi: 10.1175/MWR-D-16-0197.1

Dharshi Devendran, Suren Byna, Bin Dong, Brian van Straalen, Hans Johansen, Noel Keen, and Nagiza Samatova,, "Collective I/O Optimizations for Adaptive Mesh Refinement Data Writes on Lustre File System", Cray User Group (CUG) 2016, May 10, 2016,

Xiaocheng Zou, David Boyuka, Dhara Desai, Martin, Suren Byna, Kesheng Wu, Kushal, Bin Dong, Wenzhao Zhang, Houjun Tang Dharshi Devendran, David Trebotich, Scott, Hans Johansen, Nagiza Samatova, "AMR-aware In Situ Indexing and Scalable Querying", The 24th High Performance Computing Symposium (HPC, January 1, 2016,

2015

P. McCorquodale, P.A. Ullrich, H. Johansen, P. Colella, "An adaptive multiblock high-order finite-volume method for solving the shallow-water equations on the sphere", Comm. App. Math. and Comp. Sci., 2015, 10:121-162, doi: 10.2140/camcos.2015.10.121

Xiaocheng Zou, Kesheng Wu, David A. Boyuka, Daniel F. Martin, Suren Byna, Houjun, Kushal Bansal, Terry J. Ligocki, Hans Johansen, and Nagiza F. Samatova, "Parallel In Situ Detection of Connected Components Adaptive Mesh Refinement Data", Proceedings of the Cluster, Cloud and Grid Computing (CCGrid) 2015, 2015,

D. Devendran, D. T. Graves, H. Johansen, "A higher-order finite-volume discretization method for Poisson's equation in cut cell geometries", submitted to SIAM Journal on Scientific Computing (preprint on arxiv), 2015,

Peter Schwartz, Julie Percelay, Terry J. Ligocki, Hans Johansen, Daniel T. Graves, Dharshi Devendran, Phillip Colella, Eli Ateljevich, "High-accuracy embedded boundary grid generation using the divergence theorem", Communications in Applied Mathematics and Computational Science 10-1 (2015), 83--96. DOI 10.2140/camcos.2015.10.83, March 31, 2015,

2014

J. Ferguson, C. Jablonowski, H. Johansen, R. English, P. McCorquodale, P. Colella, J. Benedict, W. Collins, J. Johnson, P. Ullrich, "Assessing Grid Refinement Strategies in the Chombo Adaptive Mesh Refinement Model", AGU Fall Meeting, San Francisco, CA, December 15, 2014,

Dharshi Devendran, Daniel T. Graves, Hans Johansen, "A Hybrid Multigrid Algorithm for Poisson's equation using an Adaptive, Fourth Order Treatment of Cut Cells", LBNL Report Number: LBNL-1004329, November 11, 2014,

Gunther H. Weber, Hans Johansen, Daniel T. Graves, Terry J. Ligocki, "Simulating Urban Environments for Energy Analysis", Proceedings Visualization in Environmental Sciences (EnvirVis), 2014, LBNL 6652E,

2010

Q. Zhang, H. Johansen and P. Colella, "A Fourth-Order Accurate Finite-Volume Method with Structured Adaptive Mesh Refinement for Solving the Advection-Diffusion Equation", SIAM Journal on Scientific Computing, Vol. 34, No. 2. (2012), B179, doi:10.1137/110820105, 2010,

2001

McCorquodale, P., Colella, P., Johansen, H., "A Cartesian Grid Embedded Boundary Method for the Heat Equation on Irregular Domains", J. Comput. Phys. Vol.173 (2001), pp. 620-635, 2001,

1998

Johansen, H., Colella, P., "A Cartesian Grid Embedded Boundary Method for Poisson's Equation on Irregular Domains", J. Comput. Physics, Vol.147, No.1, pp. 60-85, November 1998,

1997

Cartesian Grid Embedded Boundary Finite Difference Methods for Elliptic and Parabolic Partial Differential Equations on Irregular Domains, Johansen, H., 1997,

Terry J. Ligocki

2017

Dharshi Devendran, Daniel T. Graves, Hans Johansen,Terry Ligocki, "A Fourth Order Cartesian Grid Embedded Boundary Method for Poisson's Equation", Communications in Applied Mathematics and Computational Science, edited by Silvio Levy, May 12, 2017, 12:51-79, doi: DOI 10.2140/camcos.2017.12.51

2015

Xiaocheng Zou, Kesheng Wu, David A. Boyuka, Daniel F. Martin, Suren Byna, Houjun, Kushal Bansal, Terry J. Ligocki, Hans Johansen, and Nagiza F. Samatova, "Parallel In Situ Detection of Connected Components Adaptive Mesh Refinement Data", Proceedings of the Cluster, Cloud and Grid Computing (CCGrid) 2015, 2015,

Peter Schwartz, Julie Percelay, Terry J. Ligocki, Hans Johansen, Daniel T. Graves, Dharshi Devendran, Phillip Colella, Eli Ateljevich, "High-accuracy embedded boundary grid generation using the divergence theorem", Communications in Applied Mathematics and Computational Science 10-1 (2015), 83--96. DOI 10.2140/camcos.2015.10.83, March 31, 2015,

M. Adams, P. Colella, D. T. Graves, J.N. Johnson, N.D. Keen, T. J. Ligocki. D. F. Martin. P.W. McCorquodale, D. Modiano. P.O. Schwartz, T.D. Sternberg, B. Van Straalen, "Chombo Software Package for AMR Applications - Design Document", Lawrence Berkeley National Laboratory Technical Report LBNL-6616E, January 9, 2015,

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,

2014

Yu Jung Lo, Samuel Williams, Brian Van Straalen, Terry J. Ligocki, Matthew J. Cordery, Leonid Oliker, Mary W. Hall, "Roofline Model Toolkit: A Practical Tool for Architectural and Program Analysis", Performance Modeling, Benchmarking and Simulation of High Performance Computer Systems (PMBS), November 2014, doi: 10.1007/978-3-319-17248-4_7

Gunther H. Weber, Hans Johansen, Daniel T. Graves, Terry J. Ligocki, "Simulating Urban Environments for Energy Analysis", Proceedings Visualization in Environmental Sciences (EnvirVis), 2014, LBNL 6652E,

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

2012

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.

2011

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,

M. Christen, N. Keen, T. Ligocki, L. Oliker, J. Shalf, B. van Straalen, S. Williams, "Automatic Thread-Level Parallelization in the Chombo AMR Library", LBNL Technical Report, 2011, LBNL 5109E,

2010

E. Ateljevich, P. Colella, D.T. Graves, T.J. Ligocki, J. Percelay, P.O. Schwartz, Q. Shu, "CFD Modeling in the San Francisco Bay and Delta", 2009 Proceedings of the Fourth SIAM Conference on Mathematics for Industry (MI09), pp. 99-107, 2010,

2009

B.V. Straalen, J. Shalf, T. Ligocki, N. Keen, and W. Yang, "Scalability Challenges for Massively Parallel AMR Application", 23rd IEEE International Symposium on Parallel and Distributed Processing, 2009., 2009,

Brian van Straalen, Shalf, J. Ligocki, Keen, Woo-Sun Yang, "Scalability challenges for massively parallel AMR applications", IPDPS, 2009, 1-12,

2008

G.H. Weber, V. Beckner, H. Childs, T. Ligocki, M. Miller, B. van Straalen, E.W. Bethel, "Visualization of Scalar Adaptive Mesh Refinement Data", Numerical Modeling of Space Plasma Flows: Astronum-2007 (Astronomical Society of the Pacific Conference Series), April 2008, 385:309-320, LBNL 220E,

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,

T.J. Ligocki, P.O. Schwartz, J. Percelay, P. Colella, "Embedded Boundary Grid Generation using the Divergence Theorem, Implicit Functions, and Constructive Solid Geometry", 2008 J. Phys.: Conf. Ser. 125 012080, 2008,

2007

Phillip Colella, John Bell, Noel Keen, Terry Ligocki, Michael Lijewski, Brian van Straalen, "Performance and Scaling of Locally-Structured Grid Methods for Partial Differential Equations", presented at SciDAC 2007 Annual Meeting, 2007,

2006

Schwartz, P., Barad, M., Colella, P., Ligocki, T.J., "A Cartesian Grid Embedded Boundary Method for the Heat Equation and Poisson's Equation in Three Dimensions", Journal of Computational Physics. Vol. 211 (2006), pp. 531-550., 2006, LBNL 56607,

2001

Gunther H. Weber, Oliver Kreylos, Terry J. Ligocki, Jonh Shalf, Hans Hagen, Bernd Hamann, Ken I. Joy, Kwan-Liu Ma, High-quality Volume Rendering of Adaptive Mesh Refinement Data, VMV, Pages: 121-128 2001,

Daniel F. Martin

2017

Esmond Ng, Katherine J. Evans, Peter Caldwell, Forrest M. Hoffman, Charles Jackson, Kerstin Van Dam, Ruby Leung, Daniel F. Martin, George Ostrouchov, Raymond Tuminaro, Paul Ullrich, Stefan Wild, Samuel Williams, "Advances in Cross-Cutting Ideas for Computational Climate Science (AXICCS)", January 2017, doi: 10.2172/1341564

2016

S.L. Cornford, D.F.Martin, V. Lee, A.J. Payne, E.G. Ng, "Adaptive mesh refinement versus subgrid friction interpolation in simulations of Antarctic ice dynamics", Annals of Glaciology, September 2016, 57 (73), doi: 10.1017/aog.2016.13

Xylar S. Asay-Davis, Stephen L. Cornford, Gaël Durand, Benjamin K. Galton-Fenzi, Rupert M. Gladstone, G. Hilmar Gudmundsson, Tore Hattermann, David M. Holland, Denise Holland, Paul R. Holland, Daniel F. Martin, Pierre Mathiot, Frank Pattyn, Hélène Seroussi, "Experimental design for three interrelated marine ice sheet and ocean model intercomparison projects: MISMIP v. 3 (MISMIP +), ISOMIP v. 2 (ISOMIP +) and MISOMIP v. 1 (MISOMIP1)", Geoscientific Model Development, July 2016, 9(7), doi: doi:10.5194/gmd-9-2471-2016

Xiaocheng Zou, David Boyuka, Dhara Desai, Martin, Suren Byna, Kesheng Wu, Kushal, Bin Dong, Wenzhao Zhang, Houjun Tang Dharshi Devendran, David Trebotich, Scott, Hans Johansen, Nagiza Samatova, "AMR-aware In Situ Indexing and Scalable Querying", The 24th High Performance Computing Symposium (HPC, January 1, 2016,

2015

S. L. Cornford, D. F. Martin, A. J. Payne, E. G. Ng, A. M. Le Brocq, R. M. Gladstone, T. L. Edwards, S. R. Shannon, C. Agosta, M. R. van den Broeke, H. H. Hellmer, G. Krinner, S. R. M. Ligtenberg, R. Timmermann, D. G. Vaughan, "Century-scale simulations of the response of the West Antarctic Ice Sheet to a warming climate", The Cryosphere, August 18, 2015, doi: 10.5194/tc-9-1579-2015, 2015

Xiaocheng Zou, Kesheng Wu, David A. Boyuka, Daniel F. Martin, Suren Byna, Houjun, Kushal Bansal, Terry J. Ligocki, Hans Johansen, and Nagiza F. Samatova, "Parallel In Situ Detection of Connected Components Adaptive Mesh Refinement Data", Proceedings of the Cluster, Cloud and Grid Computing (CCGrid) 2015, 2015,

Daniel Martin, Xylar Asay-Davis, Stephen Cornford, Stephen Price, Esmond Ng, William Collins, A Tale of Two Forcings: Present-Day Coupled Antarctic Ice-sheet/Southern Ocean dynamics using the POPSICLES model., European Geosciences Union General Assembly 2015, April 16, 2015,

Daniel Martin, Peter O. Schwartz, Esmond G. Ng, Improving Grounding Line Discretization using an Embedded-Boundary Approach in BISICLES, 2015 SIAM Conference on Computational Science and Engineering, March 14, 2015,

Daniel F. Martin, Response of the Antarctic Ice Sheet to Ocean Forcing using the POPSICLES Coupled Ice sheet-ocean model, Joint Land Ice Working Group/Polar Climate Working Group Meeting, Boulder, CO, February 3, 2015,

M. Adams, P. Colella, D. T. Graves, J.N. Johnson, N.D. Keen, T. J. Ligocki. D. F. Martin. P.W. McCorquodale, D. Modiano. P.O. Schwartz, T.D. Sternberg, B. Van Straalen, "Chombo Software Package for AMR Applications - Design Document", Lawrence Berkeley National Laboratory Technical Report LBNL-6616E, January 9, 2015,

2014

E.G. Ng, D.F. Martin, X. S. Asay-Davis , S.F. Price , W.D. Collins, "High-resolution coupled ice sheet-ocean modeling using the POPSICLES model", American Geophysical Union Fall Meeting, December 17, 2014,

D.F. Martin, X.S.Asay-Davis, S.F. Price, S.L. Cornford, M. Maltrud, E.G. Ng, W.D. Collins, "Response of the Antarctic ice sheet to ocean forcing using the POPSICLES coupled ice sheet-ocean model", AmericanGeophysical Union Fall Meeting, December 17, 2014,

Daniel Martin, Xylar Asay-Davis, Stephen Price, Stephen Cornford, Esmond Ng, William Collins, Response of the Antarctic ice sheet to ocean forcing using the POPSICLES coupled ice sheet - ocean model, Twenty-first Annual WAIS Workshop, September 25, 2014,

2013

S.L. Cornford, D.F. Martin, D.T. Graves, D.F. Ranken, A.M. Le Brocq, R.M. Gladstone, A.J. Payne, E.G. Ng, W.H. Lipscomb, "Adaptive mesh, finite volume modeling of marine ice sheets", Journal of Computational Physics, 232(1):529-549, 2013,

2012

P.S. Li, D.F. Martin, R.I. Klein, and C.F. McKee, "A Stable, Accurate Methodology for High Mach Number, Strong Magnetic Field MHD Turbulence with Adaptive Mesh Refinement: Resolution and Refinement Studies", The Astrophysical Journal Supplement Series, 2012,

2011

F. Miniati and D.F. Martin, "Constrained-transport Magnetohydrodynamics with Adaptive Mesh Refinement in CHARM", The Astrophysical Journal Supplement Series, 195(1):5, 2011,

Deines E., Weber, G.H., Garth, C., Van Straalen, B. Borovikov, S., Martin, D.F., and Joy, K.I., "On the computation of integral curves in adaptive mesh refinement vector fields", Proceedings of Dagstuhl Seminar on Scientific Visualization 2009, Schloss Dagstuhl, 2011, 2:73-91, LBNL 4972E,

  • Download File: 7.pdf (pdf: 799 KB)

P. Colella, M.R. Dorr, J.A.F. Hittinger, and D.F. Martin, "High-Order Finite-Volume Methods in Mapped Coordinates", Journal of Computational Physics, 230(8):2952-2976 (2011), 2011,

2010

R.H. Cohen, J. Compton, M. Dorr, J. Hittinger, W.M Nevins, T.D. Rognlien, Z.Q. Xu, P. Colella, and D. Martin, "Testing and Plans for the COGENT edge kinetic code", (abstract) submitted to Sherwood 2010, 2010,

G. H. Weber, S. Ahern, E.W. Bethel, S. Borovikov, H.R. Childs, E. Deines, C. Garth, H. Hagen, B. Hamann, K.I. Joy, D. Martin, J. Meredith, Prabhat, D. Pugmire, O. Rübel, B. Van Straalen and K. Wu, "Recent Advances in VisIt: AMR Streamlines and Query-Driven Visualization", Numerical Modeling of Space Plasma Flows: Astronum-2009 (Astronomical Society of the Pacific Conference Series, 3185E, 2010, 429:329-334,

Prateek Sharma, Phillip Colella, and Daniel F. Martin, "Numerical Implementation of Streaming Down the Gradient: Application to Fluid Modeling of Cosmic Rays", SIAM Journal on Scientific Computing , Vol 32(6), 3564-3583, 2010,

2009

P. Colella, M. Dorr, J. Hittinger, D.F. Martin, and P. McCorquodale, "High-Order Finite-Volume Adaptive Methods on Locally Rectangular Grids", 2009 J. Phys.: Conf. Ser. 180 012010, 2009,

P. Colella, M. Dorr, J. Hittinger, P.W. McCorquodale, and D.F. Martin, "High-Order Finite-Volume Methods on Locally-Structured Grids", Numerical Modeling of Space Plasma Flows: Astronum 2008 -- Proceedings of the 3rd International Conference, June 8-13, 2008, St John, U.S. Virgin Islands, 2009, pp. 207-216, 2009,

2008

Martin, D.F., Colella, P., and Graves, D.T., "A Cell-Centered Adaptive Projection Method for the Incompressible Navier-Stokes Equations in Three Dimensions", Journal of Computational Physics Vol 227 (2008) pp. 1863-1886., 2008, LBNL 62025,

2006

Martin, D.F., Colella, P.. and Keen, N., A. Deane, G. Brenner, A. Ecer, D. Emerson, J. McDonough, J. Periaux, N. Satofuka, & D. Tromeur-Dervout (Eds.), "An Incompressible Navier-Stokes with Particles Algorithm and Parallel Implementation", Parallel Computational Fluid Dynamics: Theory and Applications, Proceedings of the 2005 International Conference on Parallel Computational Fluid Dynamics, May 24-27, College Park, MD, USA, Elsevier (2006), p. 461-468., 2006, LBNL 58787,

2005

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,

Martin, D.F., Colella, P., Anghel, M., Alexander, F., "Adaptive Mesh Refinement for Multiscale Nonequilibrium Physics", Computing in Science and Engineering Vol.7 N.3 (2005), pp. 24-31, 2005,

2004

Samtaney, R., Colella, P., Jardin, S.C., Martin, D.F., "3D Adaptive Mesh Refinement Simulations of Pellet Injection in Tokamaks", Computer Physics Communications Vol.164 (2004), pp. 220-228, 2004,

2000

Martin D., Colella, P., "A Cell-Centered Adaptive Projection Method for the Incompressible Euler Equations", J. Comput. Phys. Vol.163 (2000), pp. 271-312, 2000,

1998

An Adaptive Cell-Centered Projection Method for the Incompressible Euler Equations, Martin, D.F., 1998,

1996

Martin, D.F., Cartwright, K.L., "Solving Poisson's Equation using Adaptive Mesh Refinement", U.C. Berkeley Electronics Research Laboratory report No. UCB/ERL M96/66, October 19, 1996,

Peter McCorquodale

2016

Jared O. Ferguson, Christiane Jablonowski, Hans Johansen, Peter McCorquodale, Phillip Colella, Paul A. Ullrich, "Analyzing the adaptive mesh refinement (AMR) characteristics of a high-order 2D cubed-sphere shallow-water model", Mon. Wea. Rev., November 9, 2016, 144:4641–4666, doi: 10.1175/MWR-D-16-0197.1

2015

Stephen M. Guzik, Xinfeng Gao, Landon D. Owen, Peter McCorquodale, Phillip Colella, "A freestream-preserving fourth-order finite-volume method in mapped coordinates with adaptive-mesh refinement", Computers & Fluids, December 21, 2015, 123:202–217, doi: 10.1016/j.compfluid.2015.10.001

P. McCorquodale, P.A. Ullrich, H. Johansen, P. Colella, "An adaptive multiblock high-order finite-volume method for solving the shallow-water equations on the sphere", Comm. App. Math. and Comp. Sci., 2015, 10:121-162, doi: 10.2140/camcos.2015.10.121

P. McCorquodale, M.R. Dorr, J.A.F. Hittinger, P. Colella, "High-order finite-volume methods for hyperbolic conservation laws on mapped multiblock grids", J. Comput. Phys., May 1, 2015, 288:181-195, doi: 10.1016/j.jcp.2015.01.006

M. Adams, P. Colella, D. T. Graves, J.N. Johnson, N.D. Keen, T. J. Ligocki. D. F. Martin. P.W. McCorquodale, D. Modiano. P.O. Schwartz, T.D. Sternberg, B. Van Straalen, "Chombo Software Package for AMR Applications - Design Document", Lawrence Berkeley National Laboratory Technical Report LBNL-6616E, January 9, 2015,

2014

J. Ferguson, C. Jablonowski, H. Johansen, R. English, P. McCorquodale, P. Colella, J. Benedict, W. Collins, J. Johnson, P. Ullrich, "Assessing Grid Refinement Strategies in the Chombo Adaptive Mesh Refinement Model", AGU Fall Meeting, San Francisco, CA, December 15, 2014,

2012

S. Guzik, P. McCorquodale, P. Colella, "A Freestream-Preserving High-Order Finite-Volume Method for Mapped Grids with Adaptive-Mesh Refinement", 50th AIAA Aerospace Sciences Meeting Nashville, TN, 2012,

2011

P. McCorquodale and P. Colella, "A High-Order Finite-Volume Method for Conservation Laws on Locally Refined Grids", Communications in Applied Mathematics and Computational Science, Vol. 6 (2011), No. 1, 1-25, 2011,

2009

P. Colella, M. Dorr, J. Hittinger, D.F. Martin, and P. McCorquodale, "High-Order Finite-Volume Adaptive Methods on Locally Rectangular Grids", 2009 J. Phys.: Conf. Ser. 180 012010, 2009,

P. Colella, M. Dorr, J. Hittinger, P.W. McCorquodale, and D.F. Martin, "High-Order Finite-Volume Methods on Locally-Structured Grids", Numerical Modeling of Space Plasma Flows: Astronum 2008 -- Proceedings of the 3rd International Conference, June 8-13, 2008, St John, U.S. Virgin Islands, 2009, pp. 207-216, 2009,

2007

McCorquodale, P., Colella, P., Balls, G.T., and Baden, S.B., "A Local Corrections Algorithm for Solving Poisson's Equation in Three Dimensions", Communications in Applied Mathematics and Computational Science Vol. 2, No. 1 (2007), pp. 57-81., 2007,

2005

McCorquodale, P., Colella, P., Balls, G., Baden, S.B., "A Scalable Parallel Poisson Solver with Infinite-Domain Boundary Conditions", Proceedings of the 7th Workshop on High Performance Scientific and Engineering Computing, Oslo, Norway, June 2005,

Ryne, R., Abell, D., Adelmann, A., Admundson, J., Bohn, C., Cary, J., Colella, P., Dechow, D., Decyk, V., Dragt, A., Gerber, R., Habib, S., Higdon, D., Katsouleas, T., Ta, K.L., McCorquodale, P., Mihalcea, D., Mitchell, C., Mori, W., Mottershead, C.T., Neri, F., Pogorelov, I., Quiang, J., Samulyak, R., Serafini, D., Shalf, J., Siegerist, C., Spentzouris, P., Stoltz, P., Terzic, B., Venturini, M., Walstrom, P., "SciDAC Advances and Applications in Computational Beam Dynamics", June 2005, LBNL 58243,

2004

McCorquodale, P., Colella, P., Grote, D., Vay, J.L., "A Node-Centered Local Refinement Algorithm for Poisson's Equation in Complex Geometries", J. Comput. Phys. Vol.201 (2004), pp. 34-60, 2004,

Vay, J.L., Colella, P., Friedman, A., Grote, D.P., McCorquodale, P., Serafini, D.B., "Implementations of Mesh Refinement Schemes for Particle-in-Cell Plasma Simulations", Computer Physics Communications Vol.164 (2004), pp. 297-305, 2004,

Vay, J.L., Colella, P., Kwan, J.W., McCorquodale, P., Serafini, D.B., Friedman, A., Grote, D.P., Westenskow, G., Adam, J.C., "Application of Adaptive Mesh Refinement to Particle-in-Cell Simulations of Plasmas and Beams", Physics of Plasmas Vol.11 (2004), pp. 2928-2934, 2004,

2002

Vay, J.L., Colella, P., McCorquodale, P., Van Straalen, B., Friedman, A., Grote, D.P., "Mesh Refinement for Particle-in-Cell Plasma Simulations: Applications to and Benefits for Heavy Ion Fusion", Laser and Particle Beams. Vol.20 N.4 (2002), pp. 569-575, 2002,

2001

McCorquodale, P., Colella, P., Johansen, H., "A Cartesian Grid Embedded Boundary Method for the Heat Equation on Irregular Domains", J. Comput. Phys. Vol.173 (2001), pp. 620-635, 2001,

Andrew Myers

2016

Mark R. Krumholz, Andrew T. Myers, Richard I. Klein, Christopher F. McKee,, "What Physics Determines the Peak of the IMF? Insights from the Structure of Cores in Radiation-Magnetohydrodynamic Simulations", accepted by MNRAS, May 19, 2016,

Andrew Myers, Phillip Colella, Brian Van Straalen, "A 4th-Order Particle-in-Cell Method with Phase-Space Remapping for the Vlasov-Poisson Equation", submitted to SISC, February 1, 2016,

Andrew Myers, Phillip Colella, Brian Van Straalen, "The Convergence of Particle-in-Cell Schemes for Cosmological Dark Matter Simulations", The Astrophysical Journal, Volume 816, Issue 2, article id. 56, 2016,

2015

Andrew Myers, Christopher McKee, Pak Shing Li, "The CH+ abundance in turbulent, diffuse molecular clouds", Monthly Notices of the Royal Astronomical Society, Volume 453, Issue 3, p.2747-2758, November 1, 2015,

2014

Andrew Myers, Richard Klein, Mark Krumholz, Christopher McKee, "Star cluster formation in turbulent, magnetized dense clumps with radiative and outflow feedback", Monthly Notices of the Royal Astronomical Society, Volume 439, Issue 4, p.3420-3438, April 1, 2014,

2013

Andrew Myers, Christopher McKee, Andrew Cunningham, Richard Klein, Mark Krumholz, "The Fragmentation of Magnetized, Massive Star-forming Cores with Radiative Feedback", The Astrophysical Journal, Volume 766, Issue 2, article id. 97, April 1, 2013,

2012

Pak Shing Li, Andrew Myers, Christopher McKee, "Ambipolar Diffusion Heating in Turbulent Systems", The Astrophysical Journal, Volume 760, Issue 1, article id. 33, November 1, 2012,

2011

Andrew Myers, Mark Krumholz, Richard Klein, Christopher McKee, "Metallicity and the Universality of the Initial Mass Function", The Astrophysical Journal, Volume 735, Issue 1, article id. 49, 2011,

Peter O. Schwartz

2015

M. Dorf, M. Dorr, J. Hittinger, T. Rognlien, P. Colella, P. Schwartz,R. Cohen, W. Lee, "Modeling Edge Plasma with the Continuum Kinetic Code COGENT", 2015,

Peter Schwartz, Julie Percelay, Terry J. Ligocki, Hans Johansen, Daniel T. Graves, Dharshi Devendran, Phillip Colella, Eli Ateljevich, "High-accuracy embedded boundary grid generation using the divergence theorem", Communications in Applied Mathematics and Computational Science 10-1 (2015), 83--96. DOI 10.2140/camcos.2015.10.83, March 31, 2015,

Daniel Martin, Peter O. Schwartz, Esmond G. Ng, Improving Grounding Line Discretization using an Embedded-Boundary Approach in BISICLES, 2015 SIAM Conference on Computational Science and Engineering, March 14, 2015,

M. Adams, P. Colella, D. T. Graves, J.N. Johnson, N.D. Keen, T. J. Ligocki. D. F. Martin. P.W. McCorquodale, D. Modiano. P.O. Schwartz, T.D. Sternberg, B. Van Straalen, "Chombo Software Package for AMR Applications - Design Document", Lawrence Berkeley National Laboratory Technical Report LBNL-6616E, January 9, 2015,

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,

2014

R.H. Cohen,M Dorf, M. Dorr, D.D. Ryutov, P.Schwartz, Plans for Extending COGENT to Model Snowflake Divertors, APS-DPP Meeting, New Orleans LA, October 27, 2014,

R.H. Cohen, M. Dorf, M. Dorr, D.D. Ryutov, P.Schwartz, "Plans for Extending COGENT to Model Snowflake Divertors", ESL Team Meeting, GA, September 30, 2014,

2010

E. Ateljevich, P. Colella, D.T. Graves, T.J. Ligocki, J. Percelay, P.O. Schwartz, Q. Shu, "CFD Modeling in the San Francisco Bay and Delta", 2009 Proceedings of the Fourth SIAM Conference on Mathematics for Industry (MI09), pp. 99-107, 2010,

Schwartz, P., and Colella P., "A Second-Order Accurate Method for Solving the Signed Distance Function Equation", Communications in Applied Mathematics and Computational Science, Vol. 5 (2010), No. 1, 81-97, 2010,

2008

T.J. Ligocki, P.O. Schwartz, J. Percelay, P. Colella, "Embedded Boundary Grid Generation using the Divergence Theorem, Implicit Functions, and Constructive Solid Geometry", 2008 J. Phys.: Conf. Ser. 125 012080, 2008,

2006

Schwartz, P., Barad, M., Colella, P., Ligocki, T.J., "A Cartesian Grid Embedded Boundary Method for the Heat Equation and Poisson's Equation in Three Dimensions", Journal of Computational Physics. Vol. 211 (2006), pp. 531-550., 2006, LBNL 56607,

2005

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,

Schwartz, P., Adalsteinsson, D., Colella, P., Arkin, A.P., Onsum, M., "A Tightly Coupled Particle-Fluid Model for DNA-laden Flows in Complex Microscale Geometries", Proc. Nat. Acad. Sci. Vol. 102 (2005), pp. 11151-11156, 2005,

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,

David Trebotich

2017

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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

2015

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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

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,

2014

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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

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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

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

2013

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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,

2012

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,

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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,

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.

2011

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,

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,

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

2010

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,

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,

2009

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,

2008

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,

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. 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,

2007

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 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,

2006

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

2005

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,

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,

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,

2001

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

1999

Colella, P., Trebotich, D., "Numerical Simulation of Incompressible Viscous flow in Deforming Domains", Proceedings of the National Academy of Sciences of the United States of America Vol.96, (1999), pp. 5378-5381, 1999,

1998

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

Brian Van Straalen

2017

Protonu Basu, Samuel Williams, Brian Van Straalen, Leonid Oliker, Phillip Colella, Mary Hall, "Compiler-Based Code Generation and Autotuning for Geometric Multigrid on GPU-Accelerated Supercomputers", Parallel Computing (PARCO), April 2017, doi: 10.1016/j.parco.2017.04.002

2016

Dharshi Devendran, Suren Byna, Bin Dong, Brian van Straalen, Hans Johansen, Noel Keen, and Nagiza Samatova,, "Collective I/O Optimizations for Adaptive Mesh Refinement Data Writes on Lustre File System", Cray User Group (CUG) 2016, May 10, 2016,

Samuel Williams, Mark Adams, Brian Van Straalen, Performance Portability in Hybrid and Heterogeneous Multigrid Solvers, Copper Moutain, March 2016,

Andrew Myers, Phillip Colella, Brian Van Straalen, "A 4th-Order Particle-in-Cell Method with Phase-Space Remapping for the Vlasov-Poisson Equation", submitted to SISC, February 1, 2016,

Andrew Myers, Phillip Colella, Brian Van Straalen, "The Convergence of Particle-in-Cell Schemes for Cosmological Dark Matter Simulations", The Astrophysical Journal, Volume 816, Issue 2, article id. 56, 2016,

2015

Protonu Basu, Samuel Williams, Brian Van Straalen, Mary Hall, Leonid Oliker, Phillip Colella, "Compiler-Directed Transformation for Higher-Order Stencils", International Parallel and Distributed Processing Symposium (IPDPS), May 2015,

M. Adams, P. Colella, D. T. Graves, J.N. Johnson, N.D. Keen, T. J. Ligocki. D. F. Martin. P.W. McCorquodale, D. Modiano. P.O. Schwartz, T.D. Sternberg, B. Van Straalen, "Chombo Software Package for AMR Applications - Design Document", Lawrence Berkeley National Laboratory Technical Report LBNL-6616E, January 9, 2015,

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,

A Chien, P Balaji, P Beckman, N Dun, A Fang, H Fujita, K Iskra, Z Rubenstein, Z Zheng, R Schreiber, others, "Versioned Distributed Arrays for Resilience in Scientific Applications: Global View Resilience", Journal of Computational Science, 2015,

2014

Yu Jung Lo, Samuel Williams, Brian Van Straalen, Terry J. Ligocki, Matthew J. Cordery, Leonid Oliker, Mary W. Hall, "Roofline Model Toolkit: A Practical Tool for Architectural and Program Analysis", Performance Modeling, Benchmarking and Simulation of High Performance Computer Systems (PMBS), November 2014, doi: 10.1007/978-3-319-17248-4_7

Protonu Basu, Samuel Williams, Brian Van Straalen, Leonid Oliker, Mary Hall, "Converting Stencils to Accumulations for Communication-Avoiding Optimization in Geometric Multigrid", Workshop on Stencil Computations (WOSC), October 2014,

Mark F. Adams, Jed Brown, John Shalf, Brian Van Straalen, Erich Strohmaier, Samuel Williams, "HPGMG 1.0: A Benchmark for Ranking High Performance Computing Systems", LBNL Technical Report, 2014, LBNL 6630E,

Anshu Dubey, Ann Almgren, John Bell, Martin Berzins, Steve Brandt, Greg Bryan, Phillip Colella, Daniel Graves, Michael Lijewski, Frank L\ offler, others, "A survey of high level frameworks in block-structured adaptive mesh refinement packages", Journal of Parallel and Distributed Computing, 2014, 74:3217--3227, doi: 10.1016/j.jpdc.2014.07.001

Samuel Williams, Mike Lijewski, Ann Almgren, Brian Van Straalen, Erin Carson, Nicholas Knight, James Demmel, "s-step Krylov subspace methods as bottom solvers for geometric multigrid", Parallel and Distributed Processing Symposium, 2014 IEEE 28th International, January 2014, 1149--1158, doi: 10.1109/IPDPS.2014.119

2013

Protonu Basu, Anand Venkat, Mary Hall, Samuel Williams, Brian Van Straalen, Leonid Oliker, "Compiler generation and autotuning of communication-avoiding operators for geometric multigrid", 20th International Conference on High Performance Computing (HiPC), December 2013, 452--461,

P. Basu, A. Venkat, M. Hall, S. Williams, B. Van Straalen, L. Oliker, "Compiler Generation and Autotuning of Communication-Avoiding Operators for Geometric Multigrid", Workshop on Stencil Computations (WOSC), 2013,

Christopher D. Krieger, Michelle Mills Strout, Catherine Olschanowsky, Andrew Stone, Stephen Guzik, Xinfeng Gao, Carlo Bertolli, Paul H.J. Kelly, Gihan Mudalige, Brian Van Straalen, Sam Williams, "Loop chaining: A programming abstraction for balancing locality and parallelism", Parallel and Distributed Processing Symposium Workshops & PhD Forum (IPDPSW), 2013 IEEE 27th International, May 2013, 375--384, doi: 10.1109/IPDPSW.2013.68

2012

Samuel Williams, Dhiraj D. Kalamkar, Amik Singh, Anand M. Deshpande, Brian Van Straalen, Mikhail Smelyanskiy,
Ann Almgren, Pradeep Dubey, John Shalf, Leonid Oliker,
"Implementation and Optimization of miniGMG - a Compact Geometric Multigrid Benchmark", December 2012, LBNL 6676E,

S. Williams, D. Kalamkar, A. Singh, A. Deshpande, B. Van Straalen, M. Smelyanskiy, A. Almgren, P. Dubey, J. Shalf, L. Oliker, "Optimization of Geometric Multigrid for Emerging Multi- and Manycore Processors", Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis (SC), November 2012, doi: 10.1109/SC.2012.85

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.

A Mignone, C Zanni, P Tzeferacos, B van Straalen, P Colella, G Bodo, The PLUTO code for adaptive mesh computations in astrophysical fluid dynamics, The Astrophysical Journal Supplement Series, Pages: 7 2012,

2011

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,

Deines E., Weber, G.H., Garth, C., Van Straalen, B. Borovikov, S., Martin, D.F., and Joy, K.I., "On the computation of integral curves in adaptive mesh refinement vector fields", Proceedings of Dagstuhl Seminar on Scientific Visualization 2009, Schloss Dagstuhl, 2011, 2:73-91, LBNL 4972E,

  • Download File: 7.pdf (pdf: 799 KB)

M. Christen, N. Keen, T. Ligocki, L. Oliker, J. Shalf, B. van Straalen, S. Williams, "Automatic Thread-Level Parallelization in the Chombo AMR Library", LBNL Technical Report, 2011, LBNL 5109E,

B. Van Straalen, P. Colella, D. T. Graves, N. Keen, "Petascale Block-Structured AMR Applications Without Distributed Meta-data", Euro-Par 2011 Parallel Processing - 17th International Conference, Euro-Par 2011, August 29 - September 2, 2011, Proceedings, Part II. Lecture Notes in Computer Science 6853 Springer 2011, ISBN 978-3-642-23396-8, Bordeaux, France, 2011,

2010

G. H. Weber, S. Ahern, E.W. Bethel, S. Borovikov, H.R. Childs, E. Deines, C. Garth, H. Hagen, B. Hamann, K.I. Joy, D. Martin, J. Meredith, Prabhat, D. Pugmire, O. Rübel, B. Van Straalen and K. Wu, "Recent Advances in VisIt: AMR Streamlines and Query-Driven Visualization", Numerical Modeling of Space Plasma Flows: Astronum-2009 (Astronomical Society of the Pacific Conference Series, 3185E, 2010, 429:329-334,

2009

B.V. Straalen, J. Shalf, T. Ligocki, N. Keen, and W. Yang, "Scalability Challenges for Massively Parallel AMR Application", 23rd IEEE International Symposium on Parallel and Distributed Processing, 2009., 2009,

Brian van Straalen, Shalf, J. Ligocki, Keen, Woo-Sun Yang, "Scalability challenges for massively parallel AMR applications", IPDPS, 2009, 1-12,

2008

G.H. Weber, V. Beckner, H. Childs, T. Ligocki, M. Miller, B. van Straalen, E.W. Bethel, "Visualization of Scalar Adaptive Mesh Refinement Data", Numerical Modeling of Space Plasma Flows: Astronum-2007 (Astronomical Society of the Pacific Conference Series), April 2008, 385:309-320, LBNL 220E,

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,

2007

Phillip Colella, John Bell, Noel Keen, Terry Ligocki, Michael Lijewski, Brian van Straalen, "Performance and Scaling of Locally-Structured Grid Methods for Partial Differential Equations", presented at SciDAC 2007 Annual Meeting, 2007,

2002

Vay, J.L., Colella, P., McCorquodale, P., Van Straalen, B., Friedman, A., Grote, D.P., "Mesh Refinement for Particle-in-Cell Plasma Simulations: Applications to and Benefits for Heavy Ion Fusion", Laser and Particle Beams. Vol.20 N.4 (2002), pp. 569-575, 2002,

1998

Kevin Long, Brian Van Straalen, "PDESolve: an object-oriented PDE analysis environment", Object Oriented Methods for Interoperable Scientific and Engineering Computing: Proceedings of the 1998 SIAM Workshop, 1998, 99:225,