Research and Publications that make use of PETSc

Nano-simulations

Evaluation of overlapping restricted additive Schwarz preconditioning for parallel solution of very large power flow problems, S. Abhyankar, B. F. Smith, and E. Constantinescu, HiPCNA-PG’13, 2013. BibTeX

PETSc: An Advanced Math and Computing Framework for Rapidly Developing Parallel Smart Grid Applications, S. Abhyankar and B. F. Smith, Proceedings of the IEEE PES General Meeting, 2013. BibTeX

PETSc/TS: A Modern Scalable DAE/ODE Solver Library, Shrirang Abhyankar, Jed Brown, Emil Constantinescu, Debojyoti Ghosh, and Barry F. Smith, ANL, ANL/MCS-P5061-0114, 2014. BibTeX

A graphical extension for the Windows version of the Parallel Finite Element Micromagnetics Package (MagParExt), Tomasz Blachowicz and Bartlomiej Baron, 2008. BibTeX

Field induced vortex dynamics in magnetic Ni nanotriangles, R. Y. Jaafar, A Asenjo, O Chubykalo-Fesenko, M Vazquez, E M Gonzalez, and J L Vicent, Nanotechnology, 19, 2008. BibTeX

Micromagnetic Simulation of Magnetic Particles with Surface Anisotropy, Lin Yuan, Jianjun Jiang, Gang Du, Zhongyou Wang, and Huahui He, Journal of the Magnetics Society of Japan, 32, 50-53, 2008. BibTeX

Magnetic strip patterns induced by focused ion beam irradiation, D. Makarov, S. Tibus, C. T. Rettner, T. Thomson, B. D. Terris, T. Schrefl, and M. Albrecht, J. Appl. Phys., 103, 2008. BibTeX

Patterning of magnetic films by focused ion beam irradiation, S. Tibus, D. Makarov, C. T. Rettner, T. Thomson, B. D. Terris, T. Schrefl, and M. Albrecht, Intermag 2008 paper no. CM-05, submitted to IEEE Trans. Magn., 2008. BibTeX

Micromagnetic simulation of the magnetic dispersion angle and effective damping factor for the single-phase soft magnetic films, Lin Yuan, Jianju Jiang, Yongjiang di, Shaowei Bie, and Huahui He, J. Magn. Magn. Mater., 320, 7, 1393-1397. BibTeX

Micromagnetic simulation and experimental study on microwave permeability of nano-magnetic films, DENG Lian-wen, HUANG Xiao-zhong, ZH0U Ke-sheng, and YANG, Transactions of Nonferrous Metals Society of China, 756-759, 2007. BibTeX

Micromagnetic Simulation of Magnetic Particles with Surface Anisotropy, Lin Yuan, Jianjun Jiang, Gang Du, Zhongyou Wang, and Huahui He, Journal of the Magnetics Society of Japan, 32, 50-53, 2008. BibTeX

Micromagnetic study of magnetization reversal in patterned DyFeCo thin films, Ching-Ming Lee, L. X. Ye, J. M. Lee, and Te-Ho Wu, Phys. Stat. Sol., 204, 12, 4049-4052, 2007. BibTeX

Micromagnetic Simulations of Magnetic Recording Media, Simon Greaves, High Performance Computing on Vector Systems 2007. BibTeX

Magnetic Configurations and Phase Diagrams of sub-100 nm NiFe Nanorings, Nadjib Benatmane, Werner Scholz, and T.W. Clinton, IEEE Trans. Magn., 43, 2884-2886, 2007. BibTeX

A Systematic Approach to Multiphysics Extensions of Finite-Element-Based Micromagnetic Simulations: Nmag., T. Fischbacher, M. Franchin, G. Bordignon, and H. Fangohr, IEEE Trans. Magn. Volume, 43, 2896-2898. BibTeX

The Science of Hysteresis, R. Dittrich, J. Fidler, D. Suess, W. Schol, and H. Forster, T. Schrefl. BibTeX

Handbook of Theoretical and Computational Nanotechnology, J. Fidler, T. Schrefl, and W. Scholz. BibTeX

Handbook of Magnetism and Advanced Magnetic Materials, Thomas Schrefl, Gino Hrkac, Simon Bance, Dieter Suess, Otmar Ertl, and Josef Fidler. BibTeX

Handbook of Magnetic Materials, D. Suess, J. Fidler, and T. Schrefl. BibTeX

Writer Flux Closure and Transition Degradation Mechanism in Perpendicular Recording., J. Fernandez-de-Castro, Xiao Shen, Jianhua Xue, Yuming Zhou, and S. Sharma, IEEE Trans. Magn. Volume, 43, 2175-2177. BibTeX

Effect of write current waveform on magnetization and head field dynamics of perpendicular recording heads, W. Scholz and S. Batra, IEEE Trans. Magn., 42, 2264--2266, 2006. BibTeX

Effect of thermal fluctuation field on the noise performance of a perpendicular recording system, S. Batra, W. Scholz, and T. Roscamp, J. Appl. Phys., 99, 2006. BibTeX

Micromagnetic simulations of the dependence of domain wall width with grain size in systems with cubic and uniaxial anisotropy., F. Johnson, S. Amancherla, G.J. Parker, L.E. Iorio, and P.R. Subramanian, Intermag 2006 Conference. BibTeX

A Micromagnetic Study of the Effect of Spatial Variations in Damping in Perpendicular Recording Heads, A. Kaya, M. Benakli, M.L. Mallary, and J.A. Bain, IEEE Trans. Magn., 42, 2428--2430, 2006. BibTeX

Control of Domain Wall Motion in Permalloy Ring, C. C. Chang, Y. C. Chang, C. M. Lee, C. C. Chen, and J. Wu, IEEE Trans. Magn., 42, 2960--2962, 2006. BibTeX

Micromagnetic modelling of ferromagnetic cones, Richard P. Boardman, Hans Fangohr, Matthew J. Fairman, J. Zimmermann, Simon J. Cox, Alexander A. Zhukov, and Peter A.J. de Groot, J. Magn. Magn. Mater., 312, 234-238, 2007. BibTeX

Computer simulation studies of magnetic nanostructures, Richard Boardman, 2005. BibTeX

MPI Performance Analysis Tools on Blue Gene/L, I-Hsin Chung, Robert E. Walkup, Hui-Fang Wen, and Hao Yu, ACM/IEEE SC 2006 Conference (SC'06), 2006. BibTeX

A Case Study Using Automatic Performance Tuning for Large-Scale Scientific Programs, I.-H. Chung and J.K. Hollingsworth, High Performance Distributed Computing, 2006 15th IEEE International Symposium, 45--56. BibTeX

Multibit MRAM using a pair of memory cells, C. K. Lim, Y. S. Kim, N. Y. Park, and J. Lee, IEEE Trans. Magn., 41, 2670-2672, 2005. BibTeX

Vortex state oscillations in soft magnetic cylindrical dots, K. Yu. Guslienko, W. Scholz, R. W. Chantrell, and V. Novosad, Phys. Rev. B, 71, 2005. BibTeX

Nonlinear Magnetization Dynamics in Thin-Films and Nanoparticles, Massimiliano d'Aquino. BibTeX

Micromagnetic Simulations of Domainstructures in Softmagnetic Thin Films, T. Schrefl, W. Scholz, R. Dittrich, H. Forster, D. Suess, M. Stehno, and J. Fidler. BibTeX

Effect of write current waveform on magnetization and head field dynamics of perpendicular recording heads, W. Scholz and S. Batra, Intermag 2006 Conference, San Diego, CA, paper no. EF-03. BibTeX

Micromagnetic Simulation of Head Field and Write Bubble Dynamics in Perpendicular Recording, W. Scholz and S. Batra, IEEE Trans. Magn., submitted, 2005. BibTeX

Micromagnetic Modeling of Head Field Rise Time for High Data-Rate Recording, W. Scholz and S. Batra, IEEE Trans. Magn., 41, 702-706, 2005. BibTeX

Micromagnetic Analysis of Fast Precessional Switching, M. d'Aquino, W. Scholz, T. Schrefl, C. Serpico, and J. Fidler, J. Magn. Magn. Mater., 290-291, 510-513, 2005. BibTeX

Numerical and analytical study of fast precessional switching, M. d'Aquino, W. Scholz, T. Schrefl, C. Serpico, and J. Fidler, J. Appl. Phys., 95, 7055-7057, 2004. BibTeX

Multiprocessing of the Time Domain Analysis of Thin-Wire Antennas and Scatterers, E. M. Garzon, S. Tabik, I. Garcia, and A. R. Bretones, 12th Euromicro Conference on Parallel, Distributed and Network-Based Processing (PDP'04), 80--, 2004. BibTeX

Analysis of fast precessional switching in magnetic thin films, M. d'Aquino, W. Scholz, T. Schrefl, C. Serpico, and G. Miano, Proceedings of PIERS (Progress In Electromagnetic Research Symposium), 257-260, 2004. BibTeX

Numerical Micromagnetic Simulation of Fe-Pt Nanoparticles with Multiple Easy Axes, W. Scholz, J. Fidler, T. Schrefl, D. Suess, H. Forster, R. Dittrich, and V. Tsiantos, J. Magn. Magn. Mater., 1524-1525, 2004. BibTeX

Micromagnetic simulation studies of ferromagnetic part-spheres, Richard Boardman, Juergen Zimmermann, Hans Fangohr, Alexander Zhukov, and Peter de Groot, Journal of Applied Physics, 2005. BibTeX

High Density Magnetic Random Access Memory Using a Pair of Asymmetrical Cell, C. K. Lim, Y. S. Kim, N. Y. Park, and J. Lee, IEEE Trans. Magn., submitted. BibTeX

Micromagnetic simulation of magnetization reversal in small particles with surface anisotropy, W. Scholz, D. Suess, T. Schrefl, and and J. Fidler, J. Appl. Phys., 95, 6807-6809, 2004. BibTeX

Micromagnetic simulation of the pinning and depinning process in permanent magnets, W. Scholz, T. Schrefl, J. Fidler, T. Matthias, D. Suess, and V. Tsiantos, IEEE Trans. Magn., 39, 2920-2922, 2003. BibTeX

Transition from single-domain to vortex state in soft magnetic cylindrical nanodots, W. Scholz, K. Y. Guslienko, V. Novosad, D. Suess, T. Schrefl, R. W. Chantrell, and J. Fidler, J. Magn. Magn. Mater., 266, 155-163, 2003. BibTeX

Scalable Parallel Micromagnetic Solvers for Magnetic Nanostructures, W. Scholz, J. Fidler, T. Schrefl, D. Suess, R. Dittrich, H. Forster, and V. Tsiantos, Comp. Mat. Sci, 28, 366--383, 2003. BibTeX

Scalable Parallel Micromagnetic Solvers for Magnetic Nanostructures, W. Scholz, 2003. BibTeX

Implementation of a high performance parallel finite element micromagnetics package, W. Scholz, D. Suess, R. Dittrich, T. Schrefl, V. Tsiantos, H. Forster, and J. Fidler, J. Magn. Magn. Mater., 2004. BibTeX


Numerical Treatment of Multiphase Flows in Porous Media, Lecture Notes in Physics, vol. 552, W. Zhang and I. Gladwell, 2000. BibTeX

Combined Atomistic and Mesoscale simulation of grain growth in nanocrystalline thin films, A. J. Haslan, D. Moldovan, S. R. Phillpot, and V. Yamakov, Phil. Mag. A, 2003. BibTeX

Mesoscopic simulation of two dimensional grain growth with anisotropic grain-boundary properties, A. J. Haslan, D. Moldovan, S. R. Phillpot, and H. Gleiter, Computational Materials Science, 23, 15--32, 2001. BibTeX

Role of grain rotation in grain growth by mesoscale simulation, D. Moldovan, S. R. Phillpot, and A. J. Haslan, Phil. Mag. A, 82, 1271--1297, 2002. BibTeX


Bidimensional Study of the Maxwell-Bloch Model in a Nonlinear Crystal, Olivier Saut, SIAM Journal on Scientific Computing, submitted, 2004. BibTeX

Biology -- Medical

Parallel implementation of the accelerated BEM approach for EMSI of the human brain, Y. Ataseven, Z. Akaliota n-Acar, C. E. Acar, and N. G. Gen\ccer, Medical and Biological Engineering and Computing, doi 10.1007/s11517-008-0316-0, 2008. BibTeX

Finite-element simulation of cooling of realistic 3-D human head and neck, B. H. Dennis, R. C. Eberhart, G. S. Dulikravich, and S.W. Radons, J Biomech Eng, 125, 6, 832-840, 2003. BibTeX

A parallel reduced-space sequential-quadratic programming algorithm for frequency-domain small animal optical tomography, Gu, X., Kim, H.K., Masciotti, J., and Hielscher, A.H., 717406. BibTeX

Using domain decomposition techniques for the calculation of low-frequency electric current densities in high-resolution 3D human anatomy models, Barchanski, A., Clemens, M., De Gersem, H., Steiner, T., and Weiland, T., COMPEL: The International Journal for Computation and Mathematics in Electrical and Electronic Engineering, 24, 2, 458--467, 2005. BibTeX

Computation of currents induced by ELF electric fields in anisotropic human tissues using the Finite Integration Technique, V. C. Motrescu and U. van Rienen, Advances in Radio Science, 3, 227--231, 2005. BibTeX

Computation of electrostatic fields in anisotropic human tissues using the Finite Integration Technique (FIT), V. C. Motrescu and U. van Rienen, Advances in Radio Science, 2, 309--313, 2004. BibTeX

Computational arterial flow modeling using a parallel Navier-Stokes solver, Enzo A. Dari, Mariano I. Cantero, and Raul A. Feijoo, ECCOMAS2000, 2000. BibTeX

Parallel Simulation Engines for Whole-Cell Models, Markus Schwehm, Nils Gehlenborg, Hendrik Post, Amelie Stein, and Kirstin Weber, University of Tubingen, ZBIT - Zentrum fur Bioinformatik Tubingen, Poster at Second International Conference on Systems Biology (ICSB) 2001, 2001. BibTeX

Two-level Newton and hybrid Schwarz preconditioners for fluid-structure interaction, Barker, A.T. and Cai, X.C., SIAM Journal on Scientific Computing, 32, 4, 2395--2417, 2010. BibTeX

Scalable parallel methods for monolithic coupling in fluid-structure interaction with application to blood flow modeling, Barker, A.T. and Cai, X.C., Journal of Computational Physics, 229, 3, 642--659, 2010. BibTeX

NKS for fully coupled fluid-structure interaction with application, Barker, A.T. and Cai, X.C., Domain Decomposition Methods in Science and Engineering XVIII, 275--282, 2009. BibTeX


Treating fractures of the hip and spine is a major medical cost. Understanding bone mechanical properties and how they may lead to fractures is thus an important medical research activity. PETSc and Prometheus have been used for extremely large scale finite element simulation of the solid mechanics of a portion of a human spine by a team of doctors and computational scientists. This computation was a winner of a Gordon Bell Special Prize at SC2004 and ran scalably with over 4000 processors.

A scalable multi-level preconditioner for matrix-free \mu-finite element analysis of human bone structures, Arbenz, P., van Lenthe, G.H., Mennel, U., M\üller, R., and Sala, M., International Journal for Numerical Methods in Engineering, 73, 7, 927--947, 2008. BibTeX

Ultrascalable implicit finite element analyses in solid mechanics with over a half a billion degrees of freedom, Adams, M. F., Bayraktar, H.H., Keaveny, T.M., and Papadopoulos, P., ACM/IEEE Proceedings of SC2004: High Performance Networking and Computing, Gordon Bell Award, 2004. BibTeX

Applications of Algebraic Multigrid to Large-Scale Finite Element Analysis of Whole Bone Micro-Mechanics on the IBM SP, Adams, M. F., Bayraktar, H.H., Keaveny, T.M., and Papadopoulos, P., ACM/IEEE Proceedings of SC2003: High Performance Networking and Computing, 2003. BibTeX

Parallel Multiscale Gauss-Newton-Krylov Methods For Inverse Wave Propagation, Volkan Akcelik, George Biros, and Omar Ghattas, Procceedings of SC2002, Winner of SC2002 Best Paper. A parallel algorithm for inverse problems governed by time-dependent PDEs, and scalability results for an inverse wave propagation problem of determining the material field of an acoustic medium. Using the algorithm, they solved a synthetic inverse wave propagation problem though a pelvic bone geometry involving 2.1 million inversion parameters in 3 hours on 256 processors., 2002. BibTeX


Arrhythmias are disorders of the regular rhythmic beating of the heart; they are the cause of the majority of sudden cardiac deaths. The heart beat is controlled by electrical signals moving through the heart. PETSc has been used by several research groups to simulate the electronic behavior of the heart in an attempt to more fully understand the developments of arrhthmias.

A Parallel Dynamic-Mesh Lagrangian Method for Simulation of Flows with Dynamic Interfaces, J. Antaki, G. Belloch, O. Ghattas, I. Malcevic, G. Miller, and N. Walkington, Procceedings of SC2000, Blood flow modeling at the microscale including effects on individual blood cells, for designing heart assist pumps, etc., 2000. BibTeX

Complex Systems in Biomedicine, P. Colli Franzone, L. F. Pavarino, and G. Savare, 2006. BibTeX

Determining recovery times from transmembrane action potentials and unipolar electrograms in normal heart tissue, P. Colli Franzone, L. F. Pavarino, S. Scacchi, and B. Taccardi, FIMH07, 139--149, 2007. BibTeX

Framework for Modular, Flexible and Efficient Solving the Cardiac Bidomain Equations Using PETSc, Seemann, G., Sachse, FB, Karl, M., Weiss, DL, Heuveline, V., and D\össel, O., Progress in Industrial Mathematics at ECMI 2008, 363--369, 2010. BibTeX

Monodomain Simulations of Excitation and Recovery in Cardiac Blocks with Intramural Heterogeneity, Luca F. Pavarino, Piero Colli Franzone, and Bruno Taccardi, Functional Imaging and modeling of the Heart (FIMH05), 267--277, 2005. BibTeX

On the order of accuracy of the immersed boundary method: Higher order convergence rates for sufficiently smooth problems, Boyce E. Griffith and Charles S. Peskin, Journal of Computational Physics, 208, 75--105, 2005. BibTeX

An adaptive, formally second order accurate version of the immersed boundary method, Griffith, B.E., Hornung, R.D., McQueen, D.M., and Peskin, C.S., Journal of Computational Physics, 223, 1, 10--49, 2007. BibTeX

Simulating the blood-muscle-valve mechanics of the heart by an adaptive and parallel version of the immersed boundary method, Boyce Griffith, 2005. BibTeX

Parallel Algorithms and Software for Time-Dependent System of Nonlinear Partial Differential Equations with an Application in Computational Biology, Maria S. Murillo, 2002. BibTeX

Parallel multigrid preconditioner for the cardiac bidomain model, Rodrigo Weber Dos Santos, G. Plank, and S. Bauer, IEEE Trans. Biomed. Eng, 51, 1960--1968, 2004. BibTeX

Computational Tools for Modeling Electrical Activity in Cardiac Tissue, E. J. Vigmond, M. Hughes, and G. Plank, L.J. Leon, J. Electrocardiol., 36, 69--74, 2003. BibTeX

Preconditioning Techniques for the Bidomain Equations, Rodrigo Weber Dos Santos, G. Plank, S. Bauer, and and E.J. Vigmond, Proceedings of the 15th International Conference on Domain Decomposition Methods, 571--580, 2003. BibTeX

A parallel solver for reaction-diffusion systems in computational electrocardiology, P. Colli Franzone and L. F. Pavarino, Mathematical Models and Methods in Applied Sciences, 14, 6, 883--912, 2004. BibTeX

Simulating patterns of excitation, repolarization and action potential durationwith cardiac Bidomain and Monodomain models, P. Colli Franzone, L. F. Pavarino, and B. Taccardi, Mathematical Biosciences, 197, 1, 35--66, 2005. BibTeX

Effects of transmural electrical heterogeneities and electrotonic interactions on the dispersion of cardiac repolarization and action potential duration: a simulation study, P. Colli Franzone, L. F. Pavarino, and B. Taccardi, Mathematical Biosciences, 204, 1, 132--165, 2006. BibTeX

MODELING ANISOTROPIC AND HETEROGENEOUS CARDIAC MODELS: PARALLEL SIMULATIONS, P. Colli-Franzone, L.F. Pavarino, and B. Taccardi, MEDICON and HEALTH TELEMATICS 2004, Health in the Information Society, X Mediterranean Conference on Medical and Biological Engineering, 2004. BibTeX

Parallel Solution of Cardiac Reaction-Diffusion Models, Luca F. Pavarino and Piero Colli Franzone, Proceedings of the 15th International Conference on Domain Decomposition Methods, 669--776, 2003. BibTeX

A fully implicit parallel algorithm for simulating the non-linear electrical activity of the heart, Maria Murillo and Xiao-Chuan Cai, Numerical Linear Algebra with Applications, 11, 261 - 277, 2004. BibTeX

Monitoring and Migration of a PETSc-based Parallel Application for Medical Imaging in a Grid computing PSE, Murli, A., Boccia, V., Carracciuolo, L., D’Amore, L., Laccetti, G., and Lapegna, M., Grid-Based Problem Solving Environments, 421--432, 2007. BibTeX

Towards a parallel component for imaging in PETSc programming environment: a case study in 3-D echocardiography, Carracciuolo, L., D'Amore, L., and Murli, A., Parallel Comput., 32, 67--83, 2006. BibTeX

Integration of emerging computer technologies for an efficient image sequences analysis, L. D'Amore, D. Casaburi, A. Galletti, L. Marcellino, and A. Murli, Integrated Computer-Aided Engineering , 18, 4, 365 - 378, 2011. BibTeX

Fast Implicit Simulation of Oscillatory Flow in Human Abdominal Bifurcation using a Schur Complement Preconditioner, K. Burckhardt, D. Szczerba, J. Brown, K. Muralidhar, and and G. Székely, Euro-Par 2009 Parallel Processing, H. Sips, D. Epema, and and H.-X. Lin, 747-759, 2009. BibTeX


A deformable digital brain atlas system according to Talairach and Tournoux, Ganser, K.A., Dickhaus, H., Metzner, R., and Wirtz, C.R., Medical Image Analysis, 8, 1, 3--22, 2004. BibTeX

TACC supercomputer performs laser cancer surgery on canine, In April, the Lonestar supercomputer at the Texas Advanced Computing Center in Austin performed laser surgery on a dog in Houston without the intervention of a surgeon. The treatment was developed collaboratively by computational experts from the Institute for Computational Engineering and Sciences (ICES) at UT-Austin, leading technologists from the M.D. Anderson Cancer Center in Houston, and cyberinfrastructure specialists and systems from TACC. Using precise lasers, state-of-the-art thermal imaging technology, and advanced computational methods, dynamic, data-driven treatments are being pursued as a minimally invasive alternative to the standard treatment of cancer.. BibTeX

Nanoshell-Mediated Laser Surgery Simulation for Prostate Cancer Treatment, Yusheng Feng, David Fuentes, Andrea Hawkins, Jon Bass, Marissa Nichole Rylander, Andrew Elliott, Anil Shetty, R. Jason Stafford, and J. Tinsley Oden, Engineering with Computers, Special issue on Computational Bioengineering, 2008. BibTeX

Computational Infrastructure for the Real-Time Patient-Specific Treatment of Cancer, K. R. Diller, J. T. Oden, C. Bajaj, J. C. Browne, J. Hazle, I. Babu{\vs}ka, J. Bass, L. Bidaut, L. Demkowicz, A. Elliott, Y. Feng, D. Fuentes, S. Goswami, A. Hawkins, S. Khoshnevis, B. Kwon, S. Prudhomme, and R. J. Stafford, University of Texas at Austin, 2008. BibTeX

Evaluation of the Adjoint Equation Based Algorithm for Elasticity Imaging, A.A. Oberai, N.H. Gokhale, M.M. Doyley, and J.C.Bamber, Physics in Medicine and Biology, 49, 2955--2947, 2004. BibTeX

A Dynamic Data Driven Grid System for Intra-Operative Image Guided Neurosurgery, A. Majumdar, A. Birnbaum, D. Choi, A. Trivedi, S. K. Warfield, K. Baldridge, and P. Krysl, ICCS 2005, V.S. Sunderam et al., 672--679, 2005. BibTeX

A parallel implementation of non-rigid registration using a volumetric biomechanical model, Sermesant, M., Clatz, O., Li, Z., Lanteri, S., Delingette, H., and Ayache, H., 2003. BibTeX

A Novel Nonrigid Registration Algorithm And Applications, J. Rexilius, S.K. Warfield, C.R.G. Guttmann, X. Wei, R. Benson, L. Wolfson, M. Shenton, H. Handels, and R. Kikinis, 2003. BibTeX

Capturing intraoperative deformations: research experience at Brigham and Women's hospital, Simon K. Warfield, Steven J. Haker, Ion-Florin Talos, Corey A. Kemper, Neil Weisenfeld, Andrea U.J. Mewes, Daniel Goldberg-Zimring, Kelly H. Zou, Carl-Fredrik Westin, William M. Wells, Clare M.C. Tempany, Alexandra Golby, Peter M. Black, Ferenc A. Jolesz, and Ron Kikinis, Medical Image Analysis, 2005. BibTeX

Real-Time Registration of Volumetic Brain MRI by Biomechanical Simulation of Deformation during Image Guided Neurosurgery, Simon K. Warfield, Florin Talos, Alida Tei, Arya Nabavi, Matthieu Ferrant, Peter McL. Black, Ferenc A. Jolesz, and Ron Kikinis, Computing and Visualization in Science, 2002. BibTeX

Registration of 3D Intraoperative MR Images of the Brain using a Finite Element Biomechanical Model, Matthieu Ferrant, Arya Nabavi, Benoit Macq, Ferenc A. Jolesz, Ron Kikinis, and Simon K. Warfield, IEEE Transactions on Medical Imaging, 2001. BibTeX

Real-Time Biomechanical Simulation of Volumetric Brain Deformation for Image Guided Neurosurgery, Simon K. Warfield, Matthieu Ferrant, Xavier Gallez, Arya Nabavi, Ferenc A. Jolesz, and Ron Kikinis, Proceedings of SC2000, 2000. BibTeX

Parallelized Bayesian inversion for three-dimensional dental X-ray imaging, V. Kolehmainen, A. Vanne, S. Siltanen, S. Jarvenpaa, J.P. Kaipio, M. Lassas, and M. Kalke, IEEE Transactions on Medical Imaging, 25, 2, 218--228, 2006. BibTeX

Fusion

Comparison of particle trajectories and collision operators for collisional transport in nonaxisymmetric plasmas, M. Landreman, H. M. Smith, A. Mollen, and P. Helander, Physics of Plasmas, 21, 2014. BibTeX

Radially global delta-f computation of neoclassical phenomena in a tokamak pedestal, M. Landreman, F. I Parra, P. J. Catto, D. Ernst, and I. Pusztai, Plasma Physics and Controlled Fusion, 56, 2014. BibTeX

First Results from Core-Edge Parallel Composition in the FACETS Project, J. Cary, J. Candy, R. Cohen, S. Krasheninnikov, D. McCune, D. Estep, J. Larson, A. Malony, A. Pankin, P. Worley, J. Carlsson, A. Hakim, P. Hamill, S. Kruger, M. Miah, S. Muzsala, A. Pletzer, S. Shasharina, D. Wade-Stein, N. Wang, S. Balay, L. McInnes, H. Zhang, T. Casper, L. Diachin, T. Epperly, T. Rognlien, M. Fahey, J. Cobb, A. Morris, S. Shende, G. Hammett, K. Indireshkumar, D. Stotler, and A. Pigarov, J. Phys.: Conf. Ser., c125, 012040, 2008. BibTeX

Concurrent, Parallel, Multiphysics Coupling in the FACETS Project, J. Cary, J. Candy, J. Cobb, R. H. Cohen, T. Epperly, D. Estep, S. Krasheninnikov, A. Malony, D. McCune, L. McInnes, A. Pankin, S. Balay, J. Carlsson, M. R. Fahey, R. Groebner, A. Hakim, S. Kruger, M. Miah, A. Pletzer, S. Shasharina, S. Vadlamani, D. Wade-Stein, T. Rognlien, A. Morris, S. Shende, G. W. Hammett, K. Indireshkumar, A. Pigarov, and H. Zhang, J. Phys.: Conf. Ser., 180, 012056, 2009. BibTeX

Coupled Whole Device Simulations of Plasma Transport in Tokamaks with the FACETS Code, A. Hakim, J. Cary, J. Candy, J. Cobb, R. Cohen, T. Epperly, D. Estep, S. Krasheninnikov, A. Malony, D McCune, L.C. McInnes, A. Pankin, S. Balay J. Carlsson, M. Fahey, R. Groebner, S. Kruger, M. Miah, A. Pletzer, S. Shasharina, S. Vadlamani, D. Wade-Stein, T. Rognlein, A. Morris, S. Shende, G. Hammett, K. Indareshkumar, A. Pigarov, and H. Zhang, Proceedings of SciDAC 2010 Conference, 2010. BibTeX

Concurrent, Parallel, Coupled Core-Edge Simulations of Pedestal Formation Using the FACETS Framework, J. Cary, A. Hakim, A. Pletzer, M. Miah, S. Kruger, S. Shasharina, S. Vadlamani, J. Carlsson, A. Pankin, T. Rognlien, R. Cohen, D. McCune, K. Indireshkumar, A. Pigarov, L.C. McInnes, and H. Zhang, Proceedings of the 23rd annual IAEA Fusion Energy Conference (FEC 2010), Daejon, Republic of Korea, 2010. BibTeX

FACETS: A Framework for Parallel Coupling of Fusion Components, J. Cary, A. Hakim, M. Miah, S. Kruger, A. Pletzer, S. Shasharina, S. Vadlamani, A. Pankin, R. Cohen, T. Epperly, T. Rognlien, R. Groebner, S. Balay, L. McInnes, and H. Zhang, Proceedings of Euromicro PDP 2010 (The 18th Euromicro International Conference on Parallel, Distributed and Network-Based Computing), Pisa, Italy, 2010. BibTeX

The hypersecant Jacobian approximation for quasi-Newton solves of sparse nonlinear systems, Johan Carlsson, John R. Cary, arXiv, http://arxiv.org/abs/0905.1054, 2009. BibTeX

Performance enhancements to ELMFIRE gyrokinetic code leading to new ranges of application, F. Ogando, A. Signell, J.A. Heikkinen, M. Aspnäs, S. Henriksson, S.J. Janhunen, and T.P. Kiviniemi, 33rd EPS Conference on Plasma Phys., European fusion code, 2006. BibTeX

Intermediate nonlinear evolution of the Parker instability: Formation of convection-induced discontinuities and absence of finite-time singularities, P. Zhu, A. Bhattacharjee, and K. Germaschewski, Phys. Rev. Lett., 96, 065001, doi:10.1103/PhysRevLett.96.065001, 2006. BibTeX

Solution of Reduced Resistive Magnetohydrodynamics using Implicit Adaptive Mesh Refinement, B. Philip, M. Pernice, and L.Chacon, Proceedings of the 16th International Conference on Domain Decomposition methods, 2005. BibTeX

Solution of Equilibrium Radiation Diffusion Problems using Adaptive Mesh Refinement, M. Pernice and B. Philip, SIAM J. of Sci. Comput., 2005. BibTeX

The SEL macroscopic modeling code, A. H. Glasser and X. Z. Tang, Computer Physics Communications, 164, 237--243, 2004. BibTeX

A finite element mesh in a tokamak edge geometry, Y. Nishimura and Z.Lin, Contributions to Plasma Physics, 22, 2006. BibTeX

A finite element Poisson solver for gyrokinetic particle simulations in a global field aligned mesh, Y. Nishimura, Z.Lin, J.Lewandowski, and S.Ethier, J. Comput. Phys., 214, 657, 2006. BibTeX

Global gyrokinetic Particle-in-cell Simulations with Trapped Electrons, J.L.V Lewandowski, Y.Nishimura, W.W.Lee, Z.Lin, and S. Ethier, Sherwood Fusion Theory Conference, Missoula, MT, 2004. BibTeX

Electromagnetic gyrokinetic simulation with a fluid-kinetic hybrid electron model, Y. Nishimura, Z.Lin, L.Chen, J.Lewandowski, S.Ethier, and W. Wang, Sherwood Fusion Theory Conference, Missoula, MT, 2004. BibTeX

Numerical studies of a steady state axisymmetric co-axial helicity injection plasma, X. Z.~Tang and A.~H.~Boozer, Physics of Plasmas, 11, 171--185, 2004. BibTeX

Inclusion of electromagnetic effects into gyrokinetic particle simulations, Y. Nishimura, Z.Lin, L.Chen, and W. Wang, American Physical Society 45th Annual Meeting Division of Plasma Physics, Albuquerque, New Mexico, October 2003, 2003. BibTeX

Resistive Magnetohydrodynamics Simulation of Fusion Plasmas, X. Z. Tang, G. Y. Fu, S. C. Jardin, L. L. Lowe, W. Park, and H. R. Strauss, Princeton Plasma Physics Laboratory, PPPL-3532, Presented at 10th Society for Industrial and Applied Mathematics (SIAM) Conference on Parallel Processing for Scientific Computing, Portsmouth, Virginia, March 12-14, 2001., 2001. BibTeX

Geosciences

Influences of surface processes on fold growth during 3-D detachment folding}, Collignon, M., Kaus, B., May, D.A., and Fernandez, N., Geochem Geophy Geosy, 2014. BibTeX

Fold interaction and wavelength selection in 3D models of multilayer detachment folding}, Fernández, N. and Kaus, B., Tectonophysics, 2014. BibTeX

Constraining effective rheology through parallel joint geodynamic inversion}, Baumann T, Kaus B.J.P., and Popov A., Tectonophysics, 2014. BibTeX

Quantifying the impact of mechanical layering and underthrusting on the dynamics of the modern India-Asia collisional system with 3-D numerical models}, Lechmann S.M., Schmalholz S.M., Hetenyi G., May D.A., and Kaus B.J.P., Journal of Geophysical Research - Solid Earth, 2014. BibTeX

Analytical and numerical investigation of 3D multilayer detachment, Fernandez N. and Kaus B.J.P., 2014. BibTeX

Comparing thin-sheet models with 3D multilayer models for continental collision}, Lechmann S.M., May D.A., Kaus B.J.P., and Schmalholz S.M., Geophysical Journal International, 2011. BibTeX

Effective toughness of heterogeneous media, Hossein, M.Z., Hsueh, C.-J., Bourdin, B., and Bhattacharya, K., J. Mech. Phys. Solids, 71, 320--348, 2014. BibTeX

On the asymptotic derivation of Winkler-type energies from 3D elasticity, León Baldelli, A.A. and Bourdin, B., Submitted., 2014. BibTeX

A Variational Model For Fracture And Delamination Of Thin Films, Leòn-Baldelli, A. A., Babadjian, J.-F., Bourdin, B., Henao, D., and Maurini, C., J. Mech. Phys. Solids, 70, 15-32, 2014. BibTeX

Validation simulations for the variational approach to fracture, Mesgarnejad, A., Bourdin, B., and Khonsari, M. M., Comp. Methods Appl. Mech. Engng., Submitted, 2014. BibTeX

A Variational Approach To The Modeling And Numerical Simulation Of Hydraulic Fracturing Under In-Situ Stresses, Bourdin, B., Chukwudozie, C., and Yoshioka, K., Proceedings of the 38th Workshop on Geothermal Reservoir Engineering Stanford University, Stanford, CA, 2013. BibTeX

Crack patterns obtained by unidirectional drying of a colloidal suspension in a capillary tube: experiments and numerical simulations using a two-dimensional variational approach, Maurini, C., Bourdin, B., Gauthier, G., and Lazarus, V., Int. J. Fracture, 184, 1-2, 75-91, 2013. BibTeX

A variational approach to the fracture of brittle thin films under out of plane loading, Mesgarnejad, A., Bourdin, B., and Khonsari, M.M., J. Mech. Phys Solids, 61, 11, 2360--2379, 2013. BibTeX

A Variational Approach to the Numerical Simulation of Hydraulic Fracturing, Bourdin, B., Chukwudozie, C., and Yoshioka, K., Proceedings of the 2012 SPE Annual Technical Conference and Exhibition, 2012. BibTeX

Numerical simulation of water resources problems: Models, methods, and trends, Cass T. Miller, Clint N. Dawson, Matthew W. Farthing, Thomas Y. Hou, Jingfang Huang, Christopher E. Kees, C.T. Kelley, and Hans Petter Langtangen, Advances in Water Resources, 51, 0, 405--437, 35th Year Anniversary Issue, 2013. BibTeX

A finite element sea ice model of the Canadian Arctic Archipelago, Terwisscha van Scheltinga, ArjenD., Myers, PaulG., and Pietrzak, JulieD., Ocean Dynamics, 60, 6, 1539-1558, 2010. BibTeX

Towards preconditioned nonlinear conjugate gradients for generic geophysical inversions, M. De Stefano, F. Golfré Andreasi, and A. Secchi. BibTeX

Kinematic interpretation of the 3D shapes of metamorphic core complexes, L. Le Pourhiet, B. Huet, D. A. May, L. Labrousse, and L. Jolivet, Geochem. Geophys. Geosyst., 13, Q09002, 2012. BibTeX

Comparing thin-sheet models with 3-D multilayer models for continental collision, S. M. Lechmann, D. A. May, B. J. P. Kaus, and S. M. Schmalholz, Geophysical Journal International, 187, 2011. BibTeX

Multiple-domain, simultaneous joint inversion of geophysical data with application to subsalt imaging, Michele De Stefano, Federico Golfré Andreasi, Simone Re, Massimo Virgilio, and Fred F. Snyder, Geophysics, 76, 3, R69-R80, 2011. BibTeX

Simultaneous joint inversion for susceptibility and velocity, Michele De Stefano, SEG Technical Program Expanded Abstracts, 30, 1, 806-810, 2011. BibTeX

Optimal, scalable forward models for computing gravity anomalies, Dave A. May and Matthew G. Knepley, Geophysical Journal International, 187, 1, 161--177, http://arxiv.org/abs/1107.5951, 2011. BibTeX

Numerical Simulation of Reservoir Stimulation - A Variational Approach, Blaise Bourdin, Matthew G. Knepley, and C. Maurini, Proceedings of the 37th Stanford Geothermal Workshop, http://www.geothermal-energy.org/pdf/IGAstandard/SGW/2011/bourdin.pdf, 2010. BibTeX

Secondary Thermal Cracks in EGS: a Variational Approach, Blaise Bourdin, Matthew G. Knepley, and C. Maurini, Proceedings of the 34th Annual Meeting of the Geothermal Resources Council, https://www.math.lsu.edu/ bourdin/Biography_assets/Bourdin-Knepley-Maurini-2010.pdf, 2010. BibTeX

Full 3D tomography for the crustal structure of the Los Angeles region, Chen, P., Zhao, L., and Jordan, T.H., Bulletin of the Seismological Society of America, 97, 4, 1094, 2007. BibTeX

Efficient Nonlinear Solvers for Nodal High-Order Finite Elements in 3D, Brown, Jed, Journal of Scientific Computing, 45, 48-63, 2010. BibTeX

Computational methods for ice flow simulation, Jed Brown, 2011. BibTeX

Achieving textbook multigrid efficiency for hydrostatic ice flow, Jed Brown, Barry F. Smith, and Aron Ahmadia, SIAM Journal on Scientific Computing, 35, 2, 359--375, Also preprint ANL/MCS-P743-1298, 2013. BibTeX

Low-rank quasi-Newton updates for robust Jacobian lagging in Newton-type methods, Jed Brown and Peter Brune, International Conference on Mathematics and Computational Methods Applied to Nuclear Science and Engineering, 2554--2565, 2013. BibTeX

Block Preconditioners and Advanced Software for Multiphysics Problems in Solid Earth Geodynamics, Marc Spiegelman, presentation at the 2010 SIAM Conference on Parallel Processing for Scientific Computing, 2010. BibTeX

Large scale simulation of wave propagation in soils interacting with structures using FEM and SBFEM, Marco Schauer, Sabine Langer, Jose E. Roman, and Enrique S. Quintana-Ort\'\i, Journal of Computational Acoustics, 19, 1, 75--93, 2011. BibTeX

Achieving textbook multigrid efficiency for hydrostatic ice sheet flow, J. Brown, B. Smith, and A. Ahmadia, submitted to SIAM Journal on Scientific Computing, 2012. BibTeX

Melting and channelized magmatic flow in chemically heterogeneous, upwelling mantle, S. Weatherley and R.F. Katz, Geochem.\ Geophys.\ Geosys., 13, 1, Q0AC18, 2012. BibTeX

Consequences of mantle heterogeneity for melt extraction at mid-ocean ridges, R.F. Katz and S. Weatherley, Earth\ Planet.\ Sci.\ Lett., 335-336, 226-237, 2012. BibTeX

Porosity-driven convection and asymmetry beneath mid-ocean ridges, R.F. Katz, Geochem.\ Geophys.\ Geosys., 10, Q0AC07, 2010. BibTeX

Melting above the anhydrous solidus controls the location of volcanic arcs, P.C. England and R.F. Katz, Nature, 467, 700--703, 2010. BibTeX

Plate-Driven Mantle Dynamics and Global Patterns of Mid-Ocean Ridge Bathymetry, S. Weatherley and R.F. Katz, Geochem.\ Geophys.\ Geosys., 11, 10, 2010. BibTeX

The stability of ice-sheet grounding lines, R.F. Katz and M.G. Worster, Proc. Roy.~Soc.~A, 466, 1597--1620, 2010. BibTeX

Stress balances of ice streams in a vertically integrated, higher-order formulation, Kyrke-Smith, T.M., Katz, R.F., and Fowler, A.C., Journal of Glaciology, 59, 215, 449--466, 2013. BibTeX

Consequences of viscous anisotropy in a deforming, two-phase aggregate: 1. Governing equations and linearised analysis, Takei Y. and R.F. Katz, J.\ Fluid\ Mech., 734, 424-455, 2013. BibTeX

Consequences of viscous anisotropy in a deforming, two-phase aggregate: 2. Numerical solutions of the full equations, Katz R.F. and Y. Takei, J.\ Fluid\ Mech., 734, 456-485, 2013. BibTeX

Subglacial hydrology and the formation of ice streams, Kyrke-Smith, T.M., R.F. Katz, and A.C. Fowler, Proc.\ Roy.\ Soc.\ A, 470, 2161, 2014. BibTeX

Shallow shelf approximation as a ``sliding law'' in a thermomechanically coupled ice sheet model, Bueler, E. and Brown, J., Journal of Geophysical Research-Earth Surface, 114, F3, F03008, 2009. BibTeX

Exact solutions to the thermomechanically coupled shallow ice approximation: effective tools for verification, Bueler, E., Brown, J., and Lingle, C., J. Glaciol, 53, 499--516, 2007. BibTeX

Fast computation of a viscoelastic deformable Earth model for ice-sheet simulations, Bueler, E., Lingle, C.S., and Brown, J., Ann. Glaciol, 46, 97--105, 2007. BibTeX

Exact solutions and numerical verification for isothermal ice sheets, E. Bueler, C. S. Lingle, J. A. Kallen-Brown, D. N. Covey, and L. N. Bowman, J. Glaciol., 51, 173, 291--306, 2005. BibTeX

Programming on Numerical Simulation of Tsunami with PETSc and FEPG, Chao-fan, Z. and Yao-lin, S., Earthquake, 2008. BibTeX

A Domain Decomposition Approach to Implementing Fault Slip in Finite-Element Models of Quasi-static and Dynamic Crustal Deformation, Brad T. Aagaard, Matthew G. Knepley, and Charles A. Williams, Journal of Geophysical Research: Solid Earth, 118, 6, 3059--3079, http://dx.doi.org/10.1002/jgrb.50217, 2013. BibTeX

PyLith: A Finite-Element Code for Modeling Quasi-Static and Dynamic Crustal Deformation, Charles A. Williams, Brad Aagaard, and Matthew G. Knepley, Eos Transactions of the AGU, Fall Meeting Supplemental, Abstract DI14A-08, 2011. BibTeX

Acceleration of low order finite element computation with GPUs (Invited), Matthew G. Knepley, Eos Transactions of the AGU, Fall Meeting Supplemental, Abstract IN44A-01, 2010. BibTeX

CitcomSX: Robust preconditioning in CitcomS via PETSc, Dave A. May, Matthew G. Knepley, and Michael Gurnis, Eos Transactions of the AGU, Fall Meeting Supplemental, Abstract P31A-A1241, 2009. BibTeX

The Coming Role of GPU in Computational Geodynamics, David A. Yuen, Matthew G. Knepley, Gordon Erlebacher, and Grady B. Wright, Eos Transactions of the AGU, Fall Meeting Supplemental, Abstract DI22A-05, 2009. BibTeX

PyLith: A Finite-Element Code for Modeling Quasi-Static and Dynamic Crustal Deformation, Brad Aagaard, Charles A. Williams, and Matthew G. Knepley, Eos Transactions of the AGU, Fall Meeting Supplemental, Abstract T41A-1925, 2007. BibTeX

PyLith: A Finite-Element Code for Modeling Quasi-Static and Dynamic Crustal Deformation, Charles A. Williams, Brad Aagaard, and Matthew G. Knepley, Eos Transactions of the AGU, Fall Meeting Supplemental, Abstract T21B-1798, 2007. BibTeX

Development of software for studying earthquakes across multiple spatial and temporal scales by coupling quasi-static and dynamic simulations, Charles A. Williams, Brad Aagaard, and Matthew G. Knepley, Eos Transactions of the AGU, Fall Meeting Supplemental, Abstract S53A-1072, 2005. BibTeX

Modeling of Multiple Earthquake Cycles in Southern California Using the SCEC Community Fault Model, Charles A. Williams, Carl Gable, Bradford H. Hager, Brendan Meade, Brad Aagaard, and Matthew G. Knepley, Proceedings of Geosciences '08, 2008. BibTeX

Two New Approaches in Solving the Nonlinear Shallow Water Equations for Tsunamis, C. Zhang, M. G. Knepley, D. A. Yuen, and Y. Shi, ANL, ANL/MCS-P1459-0907, 2007. BibTeX

Magma dynamics with the enthalpy method: Benchmark solutions and magmatic focusing at mid-ocean ridges, Richard F. Katz, J. Petrology, 49, 2099--2121, 2008. BibTeX

On preconditioning for a parallel solution of the Richards equation, Michael Herbst, Swen Gottschalk, Martin Reissel, Horst Hardelauf, Roy Kasteel, Matthieu Javaux, Jan Vanderborght, and Harry Vereeckena, Computers and Geosciences, 34, 1958--1963, 2008. BibTeX

Preconditioned iterative methods for Stokes flow problems arising in computational geodynamics, Dave A. May and Louis Moresi, Physics of the Earth and Planetary Interiors, 171, 1-4, 33--47, Recent Advances in Computational Geodynamics: Theory, Numerics and Applications, 2008. BibTeX

Simulation of directional solidification, thermochemical convection, and chimney formation in a Hele-Shaw cell, R.F. Katz and M.G. Worster, J. Comp. Phys., 227, 9823-9840, 2008. BibTeX

Full waveform inversion for seismic velocity and anelastic losses in heterogeneous structures, A. Askan, V. Akcelik, J. Bielak, and O. Ghattas, Bulletin of Seismological Society of America, 97, 1990--2008, 2007. BibTeX

The dynamics of melt and shear localization in partially molten aggregates, Richard F. Katz, Marc Spiegelman, and Benjamin Holtzman, Nature, 442, 676--679, 2006. BibTeX

Parallel Preconditioning for Sedimentary Basin Simulations, Roland Masson, Philippe Quandalle, Stephane Requena, and Robert Scheichl, Large-Scale Scientific Computing: 4th International Conference, LSSC 2003, Sozopol, Bulgaria, June 4-8, 2003, 2003. BibTeX

PFLOTRAN: Massively Parallel 3-D Simulator for CO2 Sequestration in Geologic Media, Chuan Lu and Peter C. Lichtner, Fourth Annual Conference on Carbon Capture and Sequestration DOE/NETL, 2005. BibTeX

Decoupling and Block Preconditioning for Sedimentary Basin Simulations, R. Scheichl, R. Masson, and J. Wendebourg, Computational Geosciences, 7, 295--318, 2003. BibTeX

Versatile multilevel Schwarz preconditioners for multiphase flow, C. E. Kees, C.T. Miller, E.W. Jenkins, and C.T. Kelley, Computational Geosciences, 7, 91--114, 2003. BibTeX

Improving depth imaging by automated model updating, JN Buur and T Kuehnel, The Leading Edge, 22, 310-318, 2003. BibTeX


Simulation of the earth's mantle and crust is valuable to understanding earthquakes, volcanos, etc. PETSc has been used for a variety of these simulations.

Mantle convection modeling with viscoelastic/brittle lithosphere: Numerical and computational methodology, B. Appelbe, D. May, S. Quenette, S. Tang, F. Wang, and L. Moresi, Lecture Notes in Computer Science, volume 2659, part of the ICCS Conference Proceedings, 2003. BibTeX

Parallelization of a 3D Seismic Migration Code with PETSc, Guillaume Dumont and Michel Kern, Proceedings of the Ninth SIAM Conference on Parallel Processing for Scientific Computing, 1999. BibTeX

               

Figures from the work of Richard Katz

The deep roots of volcanoes: models of magma dynamics with applications to subduction zones, R.F. Katz, 2005. BibTeX

Developing a Geodynamics Simulator with PETSc, Knepley, Matthew G., Katz, Richard F., and Smith, Barry, Numerical Solution of Partial Differential Equations on Parallel Computers, Bruaset, Are Magnus and Tveito, Aslak, 413-438, 10.1007/3-540-31619-1\_12, 2006. BibTeX

Ridge migration, asthenospheric flow and the origin of magmatic segmentation in the global mid-ocean ridge system, Richard F. Katz, Marc Spiegelman, and S.M. Carbotte, Geophys.\ Res.\ Letts., 31, L15605, 2004. BibTeX

Numerical simulation of geodynamic processes with the Portable Extensible Toolkit for Scientific Computation, Richard F. Katz, Matthew G. Knepley, Barry Smith, Marc Spiegelman, and Ethan Coon, Phys. Earth Planet. In., 163, 52--68, 2007. BibTeX

Development of a package for modeling stress in the lithosphere, Williams, CA, Eos Trans. AGU, 87, 36, 2006. BibTeX

Lithosphere tearing at STEP faults: response to edges of subduction zones, R. Govers and M.J.R. Wortel, Earth and Planetary Science Letters, 236/1-2, 505-523, 2005. BibTeX

Towards Rapid Geoscience Model Development - The Snark Project, B. Appelbe, D. May, S. Quenette, S. Tang, F. Wang, and L. Moresi, Proceedings of 3rd ACES (APEC Cooperation for Earthquake Simulation) Workshop, 2002. BibTeX

Snark - A Reusable Framwork for Geoscience Computational Models, Bill Appelbe, David May, Louis Moresi, Steve Quenette, Siew-Chiang Tan, and Feng Wang, Submitted to Pure and Applied Geosciences. BibTeX

High Resolution Forward and Inverse Earthquake Modeling on Terascale Computers, Volkan Akcelik, Jacobo Bielak, George Biros, Ioannis Epanomeritakis, Antonio Fernandez, Omar Ghattas, Eui Joong Kim, David O'Hallaron, and Tiankai Tu, Proceedings of SC2003, A winner of the Gordon Bell Prize for special achievement at SC2003, 2003. BibTeX

Simultaneous Joint Inversion of Refraction Tomography and Magnetic Data, Michele De Stefano, PIERS Proceedings, 491--495, 2012. BibTeX


A computational framework for simulation of biogeochemical tracers in the ocean, Khatiwala, S., Glob. Biogeochem. Cycles, 21, 2007. BibTeX

A finite-element Ocean Model: Principles and Evaluation, Sergey Danilov, Gennady Kivman and Jens Schroeter, Ocean Modelling, 6(2), 125-150, 2004. BibTeX

Evaluation of an eddy-permitting finite-element ocean model in the North Atlantic, S. Danilov, G. Kivman, and J. Schroter, Ocean Modelling, 2004. BibTeX

Data Assimilation with the Ensemble Kalman Filter and the SEIK Filter applied to a Finite Element Model of the North Atlantic, L. Nerger, S. Danilov, G. Kivman, W. Hiller, and J. Schroter, Journal of marine systems, 2004. BibTeX

A self-adaptive finite element model of the atmosphere, Rakowsky, N., Frickenhaus, S., Hiller, W., L\äuter, M., Handorf, D., Dethloff, K., Zwieflhofer, W., and Kreitz, N., World Scientific Pub Co, 2003. BibTeX

GrossrAumige Zirkulationsstrukturen in einem nichtlinearen adaptiven AtmosphArenmodell, M. Lauter, Berichte zur Polar- und Meeresforschung, 2004. BibTeX

Unsteady analytical solutions of the spherical shallow water equations, M. Lauter, D. Handorf, and K. Dethloff, Journal of computational physics, 2004. BibTeX

GrossAumige Zirkulationsstrukturen in einem nichtlinearen adaptiven AtmosphArenmodell, M. Lauter, UniversitAt Potsdam, 134 P., UniversitAt Potsdam, 2004. BibTeX

FoSSI : The Family of Simplified Solver Interfaces for the rapid development of parallel numerical atmosphere and ocean models, S. Frickenhaus, W. Hiller, and M. Best, Ocean Modelling, 10, 185--191, 2005. BibTeX

A Newton-CG method for large-scale three-dimensional elastic full-waveform seismic inversion, I Epanomeritakis, V Ak\ccelik, O Ghattas, and J Bielak, Inverse Problems, 24, 3, 034015 (26pp), 2008. BibTeX

Environmental -- Subsurface Flow


Modeling surface flow of water is valuable for both flood control and agricultural and environmental reasons. For example, regenerating the Florida Everglades requires extensive understanding of the surface water characteristics over thousands of square miles. PETSc has been used for a variety of these simulations.

Modeling subsurface reactive flows using leadership-class computing, Mills, R.T., Hammond, G.E., Lichtner, P.C., Sripathi, V., Mahinthakumar, G.K., and Smith, B.F., Journal of Physics: Conference Series, 180, 012062, 2009. BibTeX

Simulating subsurface flow and transport on ultrascale computers using PFLOTRAN, Mills, R.T., Lu, C., Lichtner, P.C., and Hammond, G.E., IOP Publishing, 2007. BibTeX

Modeling subsurface reactive flows using leadership-class computing, Mills, R.T., Hammond, G.E., Lichtner, P.C., Sripathi, V., Mahinthakmuar, G., and Smith, B., Journal of Physics: Conference Series, 102062, 2009. BibTeX

STOMP (Subsurface Transport Over Multiple Phases) webpage. BibTeX

Methods and Experiences For Parallelizing Flood Models, L. Hluchy, V.D. Tran, D.Froehlich, and W.Castaings, Recent Advances in Parallel Virtual Machine and Message Passing Interface: 10th European PVM/MPI User's Group Meeting, Springer Lecture Notes in Computer Science, Volume 2840, 2003. BibTeX

Flood Modeling System and Its Parallelization, L. Hluchy, V.D. Tran, J. Astalos, M. Dobrucky, G. T. Nguyen, and D.Froehlich, Proceedings of the International Conference on Parallel Computing in Electrical Engineering, 2002. BibTeX

High-Performance Simulation of Surface-Subsurface Coupled Flow and Reactive Transport at Watershed Scale, J. P. Gwo and G. T. Yeh, The International Conference on Computational Methods, 2004. BibTeX

An efficient parallel method for large-scale groundwater flow equation based on PETSc, Cheng, T., Ji, X., and Wang, Q., IEEE. BibTeX

The South Florida Regional Simulation Model and Hydrologic Simulation Engine, Simulates overland, groundwater and canal flows for south Florida. Uses PETSc for its linear solves. BibTeX


Dynamic data driven inversion for terascale simulations: real-time indentification of airborne contaminants, Volkan Ak\c celik, George Biros, Andrei Dr{\ua}g{\ua}nescu, Omar Ghattas, Judith C. Hill, and Gart~G. van Bloemen Waanders, Proceedings of SC2005, 2005. BibTeX

Comparison of Two Local Refinement Methods for Large Scale Air Pollution Simulations, Anton Antonov, Krassimir Georgiev, Emilia Komsalova, and Zahari Zlatev, Large-Scale Scientific Computing: 4th International Conference, LSSC 2003, 2003. BibTeX

Object-Oriented Framework for Large Scale Air Pollution Modeling, Anton Antonov, Large-Scale Scientific Computing : Third International Conference, LSSC 2001, Sozopol, Bulgaria, Springer Lecture Notes in Computer Science, Volume 2179, 2001. BibTeX


Mineralogical heterogeneity in fractured, porous media and its representation in reactive transport models, William E. Glassley, Ardyth M. Simmons, and James R. Kercher, Applied Geochemistry, 17, 699--708, 2000. BibTeX

The impact of climate change on vadose zone pore waters and its implication for long-term monitoring, William E. Glassley, John J. Nitao, Charles W. Grant, James W. Johnson, Carl I. Steefel, and James R. Kercher, Computers and Geosciences, 29, 399-411, 2003. BibTeX

Reactive transport modeling: An essential tool and a new research approach for the Earth sciences, Carl I. Steefel, Donald J. DePaolo, and Peter C. Lichtner, Earth and Planetary Science Letters, 2005. BibTeX


Sample strong scaling for the LANL PFLOTRAN flow and geochemical transport suite. (Courtesy of Richard Mills, ORNL)

Hierarchical parallelisation for the solution of stochastic finite element equations, A. Keese and H. G. Matthies, Computers and Structures, 83, 1033--1047, 2005. BibTeX

Numerical Modeling of NAPL Source Zone Treatment, Hammond, G.E., A.J. Valocchi and P.C. Lichtner, Poster at American Geophysical Union Fall 2002 Meeting, San Francisco, CA., 2002. BibTeX

Innovative Methods for Solving Multicomponent Biogeochemical Groundwater Transport on Supercomputers, Glenn E. Hammond, 2003. BibTeX

Parallel Least-Squares Finite Element Method for Large Eddy Simulation of Large Scale Environmental Flows and Transport Processes, EPA funded work to simulate turbulent dispersion of toxic chemicals around buildings and in Green Bay. Used PETSc for its linear solvers, 1999. BibTeX

Modeling Multicomponent Reactive Transport on Parallel Computers Using Jacobian-Free Newton Krylov with Operator-Split Preconditioners, Glenn E. Hammond, Albert J. Valocchi, and Peter C. Lichtner, Proceedings of the XIV International Conference on Computational Methods in Water Resources, Delft, The Netherlands., 2002. BibTeX

Software for modeling multicomponent, multidimensional reactive transport, C. I. Steefel, Lawrence Livermore National Laboratory, UCRL-MA-143182, 2001. BibTeX

A coupled model for transport of multiple chemical-species and kinetic precipitation dissolution reactions with application to reactive flow in single-phase hydrothermal systems, C. I. Steefel and A. C. Lasaga, Americal Journal of Science, 294, 5, 529-592, 1994. BibTeX

OS3D/GIMRT, Software for Multicomponent-Multidimensional reactive transport: User's manual and programmer's guide, C. I. Steefel and S. B. Yabusaki, Pacific Northwest National Laboratory, PNNL-11166, 1996. BibTeX

Application of Jacobian-free Newton-Krylov with physics-based preconditioning to biogeochemical transport, G. E. Hammond, A.J. Valocchi, and P.C. Lichtner, Advances in Water Resources, 28, 359--376, 2005. BibTeX

A Markov random field model of contamination source identification in porous media flow, J Wang and N Zabaras, Int. J. Heat and Mass Transfer, 2005. BibTeX

Lecture Notes in Computer Science, Jong G. Kim and Hyoung W. Park, 2004. BibTeX

Parallel Implementation of Finite Element Groundwater Flow Model, Kim, J. G. and Kim, J., AGU Spring Meeting Abstracts, 32-+, 2001. BibTeX

CASE STUDY: A MODEL TO SIMULATE REGIONAL FLOW IN SOUTH FLORIDA, A. M. Wasantha Lal, Randy Van Zee, and Mark Belnap, Journal of Hydraulic Engineering, 131, 4, 247--258, 2005. BibTeX

A parallel RMA2 model for simulating large-scale free surface flows, Prasada Rao, Environmental Modelling and Software, 47--53, 2005. BibTeX

An Efficient Scalable Finite Element Model for Simulating Large Scale Hydrodynamic Flows, Prasada Rao, Proceedings of the American Society of Civil Engineers 16th Engineering Mechanics Conference, 2003. BibTeX

Modeling Thermal-Hydrological-Chemical (THC) Coupled Processes with Applications to Underground Nuclear Tests at the Nevada Test Site; A Grand Challenge Supercomputing Problem, Peter C. Lichtner and Andrew Wolfsberg, MPU Workshop: Conceptual Model Development for Subsurface Reactive Transport Modeling of Inorganic Contaminants, Radionuclides and Nutrients, Also Los Alamos National Laboratory report: LA-UR-04-1826, 2004. BibTeX


Parallel Compositional Reservior Simulation on Clusters of PCs, Jason Abate, Peng Wang, and Kamy Sepehrnoori, Int. J. High Performance Computing Applications, 15, 1, 13--21, 2001. BibTeX

Preconditioned Newton Methods for Simulation of Reservoirs with Surface Facilities, Thomas James Byer, 2000. BibTeX

Experience with Parallel Computing for Reservoir and Geomechanics Simulation on a Win32 Cluster, Peter J. Puchyr, Proceedings of the Canadian International Petroleum Conference, Paper number CIPC2006-207, 2006. BibTeX

A Fully Implicit Parallel EOS Compositional Simulator for Large Scale Reservoir Simulation, P. Wang, S. Balay, K. Seperhrnoori, J. Wheeler, J. Abate, B. Smith, and G. A. Pope, Proceedings of the 1999 Society of Petroleum Engineers 15th Reservoir Simulation Symposium, also available as Argonne preprint ANL/MCS-P743-1298, 1998. BibTeX

CFD

Simulations of Zigzag Maneuvers for a Container Ship with Direct Moving Rudder and Propeller, A. Mofidi and P. M. Carrica, Computers and Fluids, 191--203, 2014. BibTeX

Fluid-Structure Interaction for an Elastic Structure Interacting with Free Surface in a Rolling Tank, K. Paik and P. M. Carrica, Ocean Engineering, 201--212, 2014. BibTeX

Bubble size distribution prediction for large-scale ship flows: Model evaluation and numerical issues, A. M. Castro and P. M. Carrica, International Journal of Multiphase Flow 57, 131--150, 2013. BibTeX

Turn and Zigzag Maneuvers of a Surface Combatant Using a URANS Approach with Dynamic Overset Grids, P. M. Carrica, F. Ismail, M. Hyman, S. Bhushan, and F. Stern, Journal of Marine Science and Technology, 166--181, 2013. BibTeX

Eulerian polydispersed modeling of bubbly flows around ships with application to Athena R/V,, A. M. Castro and P. M. Carrica, International Shipbuilding Progress, 403--433, 2013. BibTeX

Overset simulations of a Submarine in Towed, Self-Propelled and Maneuvering Conditions, N. Chase, T. Michael, and P. M. Carrica, International Shipbuilding Progress, 171--205, 2013. BibTeX

CFD Simulation and Validation of Added Resistance of KVLCC2 with Fixed and Free Surge Conditions in Short and Long Head Waves, H. Sadat-Hosseini, P. -C. Wu, P. M. Carrica, H. Kim, Y. Toda, and F. Stern., Ocean Engineering, 59, 240--273, 2013. BibTeX

CFD Simulations of a Submarine Propeller and Application to Self-Propulsion of a Submarine, N. Chase and P. M. Carrica, Ocean Engineering, 68--80, 2013. BibTeX

CFD Analysis of Broaching for a Model Surface Combatant with Explicit Simulation of Moving Rudders and Rotating Propellers, P. M. Carrica, H. Sadat-Hosseini, and F. Stern, Computers and Fluids 53, 117--132, 2012. BibTeX

"URANS Simulations of Static and Dynamic Maneuvering for Surface Combatant-Part 1: Verification and Validation for Forces, Moment, and Hydrodynamic Derivatives, N. Sakamoto, P. M. Carrica, and F. Stern, 422--445, 2012. BibTeX

URANS Simulations of Static and Dynamic Maneuvering for Surface Combatant-Part 2: Analysis and Validation of Local Flow Characteristics, N. Sakamoto, P. M. Carrica, and F. Stern, Journal of Marine Science and Technology, 446--468, 2012. BibTeX

Dynamic Overset CFD Simulations of Wind Turbine Aerodynamics, Y. Li, T. Xing, K. Paik, and P. M. Carrica, Renewable Energy, 285--298, 2012. BibTeX

A Method to Compute Ship Exhaust Plumes with Waves and Wind, J. Huang, P. M. Carrica, and F. Stern, International Journal for Numerical Methods in Fluids, 160--180, 2012. BibTeX

A geometry-based level set method for curvilinear overset grids with application to ship hydrodynamics, J. Huang, P. M. Carrica, and F. Stern, International Journal for Numerical Methods in Fluids, 494--521, 2012. BibTeX

Computations of self-propulsion free to sink and trim and of motions in head waves of the KRISO Container Ship (KCS) model, P. M. Carrica, H. Fu, and F. Stern, Applied Ocean Research, 309--320, 2011. BibTeX

Scalability and Validation Study for Large Scale Surface Combatant Computations Using CFDShip-Iowa, S. Bhushan, P. M. Carrica, J. Yang, and F. Stern, International Journal of High Performance Computing Applications, 466--487, 2011. BibTeX

Full scale self-propulsion computations using discretized propeller for the KRISO container ship KCS, A. M. Castro, P. M. Carrica, and F. Stern, Computers and Fluids, 35--47, 2011. BibTeX

Multi-fidelity Optimization of a High-speed Foil-assisted Semi-planing Catamaran for Low Wake, M. Kandasamy, S. K. Ooi, P. M. Carrica, F. Stern, E. F. Campana, D. Peri, P. Osborne, J. Cote, N. Macdonald, and N. de Waal, Journal of Marine Science and Technology, 143--156, 2011. BibTeX

CFD Validation Studies for a High-speed Foil-assisted Semi-planing Catamaran, M. Kandasamy, S. K. Ooi, P. M. Carrica, F. Stern, E. F. Campana, D. Peri, P. Osborne, J. Cote, N. Macdonald, and N. de Waal, Journal of Marine Science and Technology, 157--167, 2011. BibTeX

"CFD System-Based and EFD Study of Ship Dynamic Instability Events: Surf Riding, Periodic Motion and Broaching, H. Sadat-Hosseini, P. M. Carrica, F. Stern, N. Umeda, H. Hashimoto, S. Yamamura, and A. Mastuda, Ocean Engineering, 88--110, 2011. BibTeX

Development and Validation of Harmonic Wave Group Single-Run Procedure for RAO with Comparison to Regular Wave and Transient Wave Group Procedures Using URANS, M. Mosaviraad, P. M. Carrica, and F. Stern, Ocean Engineering, 653--666, 2010. BibTeX

Large-Scale DES Computations of the Forward Speed Diffraction and Pitch and Heave Problems for a Surface Combatant, P. M. Carrica, J. Huang, R. Noack, D. Kaushik, B. Smith, and F. Stern, Computers and Fluids, 1095--1111, 2010. BibTeX

Self-Propulsion Computations Using Speed Controller and Discretized Propeller with Dynamic Overset Grids, P. M. Carrica, A. M. Castro, and F. Stern, Journal of Marine Science and Technology, 316--330, 2010. BibTeX

Evaluation of Linear and Non-Linear Convection Schemes on Multidimensional Non-Orthogonal Grids with Applications to KVLCC2 Tanker, F. Ismail, P. M. Carrica, T. Xing, and F. Stern, International Journal of Numerical Methods in Fluids, 850--886, 2010. BibTeX

Integral Force/Moment Waterjet Model for CFD Simulations, M. Kandasamy, S. K. Ooi, P. M. Carrica, and F. Stern, Journal of Fluids Engineering, 101103, 2010. BibTeX

Modeling hypersonic entry with the fully-implicit Navier--Stokes (FIN-S) stabilized finite element flow solver, Kirk, Benjamin S, Stogner, Roy H, Bauman, Paul T, and Oliver, Todd A, Computers & Fluids, 92, 0, 281--292, 2014. BibTeX

Computational simulations of 3D large-scale time-dependent viscoelastic flows in high performance computing environment, L. Carracciuolo, D. Casaburi, L. D’Amore, G. D’Avino, P.L. Maffettone, and A. Murli, Journal of Non-Newtonian Fluid Mechanics , 166, 23--24, 1382--1395, 2011. BibTeX

Towards multi-phase flow simulations in the PDE framework Peano, Bungartz, Hans-Joachim, Gatzhammer, Bernhard, Lieb, Michael, Mehl, Miriam, and Neckel, Tobias, Computational Mechanics, 48, 3, 365-376, 2011. BibTeX

{On CFL Evolution Strategies for Implicit Upwind Methods in Linearized Euler Equations}, H. M. Bücker, B. Pollul, and A. Rasch, International Journal for Numerical Methods in Fluids, 59, 1, 1--18, 2009. BibTeX

Parallel unstructured three-dimensional turbulent flow analyses using efficiently preconditioned newton-krylov solver, Bonfiglioli, A, Campobasso, M S, and Carpentieri, B, 2010. BibTeX

RANS simulations of a junction flow, Paciorri, Renato, Bonfiglioli, Aldo, Di Mascio, Andrea, and Favini, Bernardo, International Journal of Computational Fluid Dynamics, 19, 2, 179-189, 2005. BibTeX

Performance Analysis of Parallel Algebraic Preconditioners for Solving the RANS Equations Using Fluctuation Splitting Schemes, Bonfiglioli, A., Carpentieri, B., and Sosonkina, M., Numerical Mathematics and Advanced Applications, Kunisch, Karl, Of, Günther, and Steinbach, Olaf, 151-158, 2008. BibTeX

EulFS: A Parallel CFD Code for the Simulation of Euler and Navier-Stokes Problems on Unstructured Grids, Bonfiglioli, Aldo, Carpentieri, Bruno, and Sosonkina, Masha, Applied Parallel Computing. State of the Art in Scientific Computing, Kågström, Bo, Elmroth, Erik, Dongarra, Jack, and Wasniewski, Jerzy, 676-685, 2007. BibTeX

Automated FEM Discretizations for the Stokes Equation, Andy R. Terrel, L. Ridgway Scott, Matthew G. Knepley, and Robert C. Kirby, BIT, 48, 2, 2008. BibTeX

A methodology for the development of discrete adjoint solvers using automatic differentiation tools, A. C. Marta, C. A. Mader, J. R. R. A. Martins, E. Van der Weide, and J. J. Alonso, Computational Fluid Dyanmics, 21, 307--327, 2007. BibTeX

Variational Space-time (Dis)continuous Galerkin Method for Linear Free Surface Waves, V.R. Ambati, J.J.W. van der Vegt, and O. Bokhove, University of Twente, the Netherlands, 2008. BibTeX

Towards Numerical Simulation of Flapping Foils on Fixed Cartesian Grids, M. Bozkurttas, H. Dong, V. Seshadri, and R. Mittal, 43rd AIAA Aerospace Sciences Meeting and Exhibit, 2005. BibTeX

A MULTILEVEL FINITE VOLUME METHOD WITH MULTISCALE-BASED GRID ADAPTATION FOR STEADY COMPRESSIBLE FLOWS, S. Muller and Y. Stiriba, European Conference on Computational Fluid Dynamics: ECCOMAS CFD 2006, 2006. BibTeX

Parallel three-dimensional simulation of the injection molding process, B. J. Araújo, J. C. F. Teixeira, A. M. Cunha, and C. P. T. Groth, International Journal for Numerical Methods in Fluids, 2008. BibTeX

a parallel coupled algorithm for collocated grids and its application to Large Eddy Simulation of a turbulent wake, A. Cubero, 2008. BibTeX

A Compact Momentum Interpolation Method for unsteady flows and relaxation, A. Cubero and N. Fueyo, Numerical Heat Transfer, part B-Fundamentals, 56, 6, 507--529, 2007. BibTeX

Preconditioning based on a partially implicit implementation of Momentum Interpolation for coupled solvers, A. Cubero and N. Fueyo, Fluid Mechanics Group of the University of Zaragoza (Spain), 2007. BibTeX

Robust Mesh Deformation using the Linear Elasticity Equations, Richard Dwight, Computational Fluid Dynamics 2006, H. Deconinck and E. Dick, 2006. BibTeX

Effect of Various Approximations of the Discrete Adjoint on Gradient-Based Optimization, Richard Dwight and Joel Brezillon, Proceedings of the 44th AIAA Aerospace Sciences Meeting and Exhibit, Reno NV. AIAA-2006-0690, 2006. BibTeX

Efficiency Improvements of RANS-Based Analysis and Optimization using Implicit and Adjoint Methods on Unstructured Grids, Richard Dwight, 2006. BibTeX

An adaptive Lagrange-Galerkin shallow-water model on the sphere, M. Lauter, D. Handorf, K. Dethloff, S. Frickenhaus, N. Rakowsky, and W. Hiller, Workshop Proceedings Current Development in Shallow Water Models on the Sphere March, 10-14, 2003, Munich University of Technology, German, 2003. BibTeX

The Embedded Boundary Integral Method (EBI) for the Incompressible Navier-Stokes equations, George Biros, Lexing Ying, and Denis Zorin, IABEM 2002, International Association for Boundary Element Methods, UT Austin, 2002. BibTeX

Benchmarking of a 3D, unstructured, finite volume code for incompressible Navier-Stokes equation on a cluster of distributed-memory computers, S.A. Mohsen Karimian and Anthony G. Straatman, Proceedings of the 19th International Symposium on High Performance Computing Systems and Applications, 11--16, 2005. BibTeX

Multidimensional Residual Distribution Schemes for the Pseudo-Compressible Euler and Navier-Stokes equations on Unstructured Meshes, A. Bonglioli, Universita della Basilicata via della Tecnica 3, 1996. BibTeX

A new fully coupled method for computing turbulent flows, G. B. Deng, J. Piquet, X. Vasseur, and M. Visonneau", Computers and Fluids, 30, 445--472, 2001. BibTeX

Multilevel Preconditioning for Parallel CFD, Matthew G. Knepley, Vivek Sarin, and Ahmed H. Sameh, International Conference On Preconditioning Techniques For Large Sparse Matrix Problems In Industrial Applications, 1999. BibTeX

Fast Elliptic Solver for Incompressible Navier Stokes Flow and Heat Transfer Problems on the Grid, M. Garbey, B. Hadri, and W. Shyy., Aerospace Sciences Meeting and Exhibit, Paper No. 2005-1386, 2005. BibTeX

An unsteady single-phase level set method for viscous free surface flows, Carrica, PM, Wilson, RV, and Stern, F., International Journal for Numerical Methods in Fluids, 53, 2, 229--256, 2007. BibTeX

A Multidimensional Two-Phase Flow Model for the Total Dissolved Gas Downstream of Spillways, M. S. Politano, P. M. Carrica, C. Turan, and L. Weber, Journal of Hydraulic Research, accepted for publication, 2004. BibTeX

Unsteady RANS Method for Ship Motions with Application to Roll for a Surface Combatant, R. V. Wilson, P. M. Carrica, and F. Stern, Computers and Fluids, in press, 2004. BibTeX

Unsteady RANS Simulation of the Ship Forward Speed Diffraction Problem, P. M. Carrica, R. V. Wilson, and F. Stern, Computers and Fluids, accepted for publication, 2005. BibTeX

Large-Scale DES Computations of the Forward Speed Diffraction and Pitch and Heave Problems for a Surface Combatant, P. M. Carrica, J. Huang, R. Noack, D. Kaushik, B. Smith, and F. Stern, Computers and Fluids, 39, 7, 1095--1111, 2010. BibTeX

Toward Large-Scale Computations of Ship Motions with Dynamic Overset Curvilinear Grids, P. M. Carrica, J. Huang, R. Noack, D. Kaushik, B. Smith, and F. Stern, Proceedings of the 27th Symposium on Naval Hydrodynamics, Seoul, Korea, 2008. BibTeX

Application of Algebraic Multigrid Methods to the Solution of Stratified Flows About Submerged Bodies, M. T. Jozkowski, 2005. BibTeX

Detached-Eddy Simulation of High Reynolds Number Beveled-Trailing-Edge Flows and Wakes, E. G. Paterson and L. J. Peltier, ASME Journal of Fluids Engineering, In press, 2005. BibTeX

Computational Study of the Wake and Contaminant Transport of a Walking Human, B. A. Edge, E. G. Paterson, and G. Settles, ASME Journal of Fluids Engineering, In press, 2005. BibTeX

Computation of Maneuvering Coefficients for Non-Body-of-Revolution Submarines Using Unsteady RANS CFD, B. Racine and E. G. Paterson, 35th AIAA Fluid Dynamics Conference and Exhibit, 2005. BibTeX

Prediction of Forces and Moments on a Sonobuoy Configuration Using Overset Grids and DES, B. A. Edge, M. F. Trujillo, E. G. Paterson, and L. J. Peltier, 7th Overset Composite Grid and Solution Technology Symposium, 2004. BibTeX

Localized turbulence simulation for naval hydrodynamics: issues in using overset refinement grids and detached-eddy simulation, E. G. Paterson and L. J. Peltier, 7th Overset Composite Grid and Solution Technology Symposium, 2004. BibTeX

Experimental and Computational Study of Cavitation Inception on Co-Flow Nozzles, R. Meyer, F. J. Zajackowski, and W. A. Straka,and E. G. Paterson, 25th Symposium on Naval Hydrodynamics, 2004. BibTeX

A Physics-Based Simulation Methodology for Predicting Trailing-Edge Singing, E. G. Paterson, J. E. Poremba, L. J. Peltier, and S. A. Hambric, 25th Symposium on Naval Hydrodynamics, 2004. BibTeX

Detached-Eddy Simulation of High Reynolds Number Trailing-Edge Flows and Wakes, E. G. Paterson and L. J. Peltier, Symposium on LES Advancements and Applications, ASME FED Summer Meeting, 2004. BibTeX

Simulation of Steady Circulation Control for the General Aviation Circulation Control Wing, W. J. Baker, E. G., and Paterson, NASA/ONR Workshop on Circulation Control, 2004. BibTeX

RANS and Detached-Eddy Simulation of the NCCR airfoil, E. G. Paterson and W. J. Baker, NASA/ONR Workshop on Circulation Control, 2004. BibTeX

Simulation of Steady and Pulsed Circulation Controlfor Marine-Vehicle Control Surfaces, E. G. Paterson and W. J. Baker, 42nd AIAA Aerospace Sciences Meeting, 2004. BibTeX

CFD Modelling of the Flow Around the Ahmed Vehicle Model, G. Frank and J. D'Elia, Proceedings of the 2nd Conference on Advances and Applications of GiD, 2004. BibTeX

Science and Supercomputing at CINECA, A.Bonfiglioli, 2001. BibTeX

Computing high-Reynolds number vortical flows: a highly accurate method with a fully meshless formulation, L. A. Barba, International Conference on Parallel CFD, Grand Canary, May 2004, Submitted, 2004. BibTeX

Computation of Viscous Vortices with Fully Meshless Method, L. A. Barba and A. Leonard, Proceedings of ICTAM meeting in Warsaw, August 2004, Submitted, 2004. BibTeX

Experimental Validation of 3-D Lagrangian VOF Model: Bubble Shape and Rise Velocity, B. G. M. Van Wachem and J. C. Schouten, AIChE, 12, 2002. BibTeX

Precondizionatori paralleli per la fluidodinamica computazionale, P. Leggiero, A. Bonfiglioli, P. Amodio, and F. Mazzi, Dipartimento Interuniversitario di Matematica Universiti degli Studi-Politecnico di Bari Italy, 25/02, 2002. BibTeX

Higher Order Time Integration Methods for Two-Phase Flow, C. E. Kees and C. T. Miller, Advances in Water Resources, 25, 2, 159-177., 2002. BibTeX

Multilevel Parallel High Order Schemes for Invisid Flow Computations on 3D Unstructured Meshes, I. Lepot, F. Meers, and J.A. Essers, ECCOMAS Computational Fluid Dynamics Conference 2001, 2001. BibTeX

Parallel Building Blocks for Finite Element Simulations: Application to Solid-Liquid Mixture Flows, Matthew Knepley and Denis Vanderstraeten, Proceedings of Parallel CFD'97, 281--287, 1998. BibTeX

Parallel Implicit PDE Computations: Algorithms and Software, William D. Gropp, David E. Keyes, Lois Curfman McInnes, and M. D. Tidriri, Proceedings of Parallel CFD'97, 333-344, 1998. BibTeX

Parallel Simulation of Particulate Flows, Matthew Knepley, Ahmed H. Sameh, and Vivek Sarin, Solving Irregularly Structured Problems in Parallel, 226--237, 1998. BibTeX

Globalized Newton-Krylov-Schwarz Algorithms and Software for Parallel Implicit CFD, William D. Gropp, David E. Keyes, Lois Curfman McInnes, and M. D. Tidriri, Int. J. High Performance Computing Applications, 14, 102-136, 2000. BibTeX

Achieving High Sustained Performance in an Unstructured Mesh CFD Application, W. K. Anderson, W. D. Gropp, D. K. Kaushik, D. E. Keyes, and B. F. Smith, ACM/IEEE Proc. of SC 99: High Performance Networking and Computing, Winner of Gordon Bell Special Prize at SC 99, 1999. BibTeX

High Performance Parallel Implicit CFD, W. D. Gropp, D. K. Kaushik, D. E. Keyes, and B. F. Smith, Journal of Parallel Computing, 27, 337-362, 2001. BibTeX

Finite Difference lattice Boltzmann model for Liquid Vapour Systems, Artur Cristea and Victor Sofonea, Proceedings of the Romanian Academy, Series A: Mathematics, Physics, Technical Sciences, Information Sciences, 3, 3, 2002. BibTeX

Two component lattice Boltzmann model with flux limiter techniques, Artur Cristea and Victor Sofonea, Proceedings of the Romanian Academy, Series A: Mathematics, Physics, Technical Sciences, Information Sciences, 4, 1, 59--64, 2003. BibTeX

Two component lattice Boltzmann model with flux limiters, Artur Cristea and Victor Sofonea, Central European Journal of Physics, 2, 2, 382--396, 2004. BibTeX

Finite-difference lattice Boltzmann model with flux limiters for liquid-vapor systems, Victor Sofonea, Antonio Lamura, Giuseppe Gonnella, and Artur Cristea, Physical Review E, 70, 4, 046702-1 / 046702-9, 2004. BibTeX

Latency, Bandwidth, and Concurrent Issue Limitations in High-Performance CFD, W. D. Gropp, D. K. Kaushik, D. E. Keyes, and B. F. Smith, Proceedings of the First MIT Conference on Computational Fluid and Solid Mechanics, 2001. BibTeX

Understanding the Parallel Scalability of An Implicit Unstructured Mesh CFD Code, W. D. Gropp, D. K. Kaushik, D. E. Keyes, and B. F. Smith, Proceedings of the 7th International Conference on High Performance Computing (HiPC '2000), 395--404, 2000. BibTeX

Performance Modeling and Tuning of an Unstructured Mesh CFD Application, W. D. Gropp, D. K. Kaushik, D. E. Keyes, and B. F. Smith, Proceedings of SC2000, 2000. BibTeX

Design of Large Scale Parallel Simulations, Matthew Knepley, Ahmed H. Sameh, and Vivek Sarin, Proceedings of Parallel CFD'99, 1999. BibTeX

Towards Realistic Performance Bounds for Implicit CFD codes, W. D. Gropp, D. K. Kaushik, D. E. Keyes, and B. F. Smith, Proceedings of Parallel CFD'99, 1999. BibTeX

On the Interaction of Architecture and Algorithm in the Domain-Based Parallelization of an Unstructured Grid Incompressible Flow Code, D. K. Kaushik, D. E. Keyes, and B. F. Smith, Proceedings of the 10th International Conference on Domain Decomposition Methods, J. Mandel et al., 311--319, 1997. BibTeX

Newton-Krylov-Schwarz Methods for Aerodynamic Problems: Compressible and Incompressible Flows on Unstructured Grids, D. K. Kaushik, D. E. Keyes, and B. F. Smith, Proceedings of the 11th International Conference on Domain Decomposition Methods, 1999. BibTeX

Perspectives for CFD on Petaflops Systems, D. E. Keyes, D. K. Kaushik, and B. F. Smith, CFD Review 1998, M. Hafez and K. Oshima, 1079--1096, 1998. BibTeX

Parallel Simulation of Compressible Flow Using Automatic Differentiation and PETSc, P. D. Hovland and L. C. McInnes, Parallel Computing, special issue of Parallel Computing on ``Parallel Computing in Aerospace'', 2000. BibTeX

Fast Multipole Method for particle interactions: an open source parallel library component, Felipe A. Cruz, Lorena A. Barba, and Matthew G. Knepley, Proceedings of ParCFD2008, Tromeur-Dervout et. al., 2008. BibTeX

A parallel nonlinear additive Schwarz preconditioned inexact Newton algorithm for incompressible Navier-Stokes equations, F.-N. Hwang and X.-C. Cai, J. Comput. Phys., 204, 666--691, 2005. BibTeX

Emergence and evolution of tripole vortices from net-circulation initial conditions, Lorena A Barba and Anthony Leonard, Phys. Fluids, 19, 017101, 2007. BibTeX

Non-shielded multipolar vortices at high Reynolds number, Lorena A Barba, Phys. Rev. E, 73, 065303, 2006. BibTeX

Multi-material incompressible flow simulation using the moment-of-fluid method, Schofield, S.P., Christon, M.A., Dyadechko, V., Garimella, R.V., Lowrie, R.B., and Swartz, B.K., International Journal for Numerical Methods in Fluids, 63, 8, 931--952, 2010. BibTeX

Wave propagation and the Helmholtz equation

article{DeGersem99, author = {Ji Wng and Yu Wang and Wen-ke Hu and Jian-ke Du}, title = {The high performance of finite element analysis and applications of surface acoustic waves in finite elastic solids}, }

On the convergence of shifted Laplace preconditioner combined with multilevel deflation, Sheikh, A. H., Lahaye, D., and Vuik, C., Numerical Linear Algebra with Applications, 20, 4, 645--662, 2013. BibTeX

A parallel computing approach for solving the Helmholtz equation in 3D domains: Application to the study of acoustic behaviour of silencers, J.M., Alonso, G. Garcia, V. Hernandez, F.D. Denia, and F.J. Fuenmayor, Eurppean Congress on Computational Methods in Applied Sciences and Engineering (ECCOMAS), 2004. BibTeX

Comparison of Quasi Minimal Residual and Bi-Conjugate Gradient Iterative Methods to Solve Complex Symmetric Systems Arising from Time-Harmonic Simulations, H. De Gersem, Domenico Lahaye, S. Vandewalle, and K. Hameyer, COMPEL, 18, 3, 298--310, 1999. BibTeX

Schwarz Methods for Helmholtz's Equation, Olof B. Widlund, Mathematical and Numerical Aspects of Wave Propagation, John A. DeSanto, 620--622, Proceedings of the Fourth International Conference on Mathematical and Numerical Aspects of Wave Propagation, Golden, Colorado, June 1--5, 1998. BibTeX

Overlapping Schwarz Methods for Maxwell's Equations in Conductive Media, Andrea Toselli, Mathematical and Numerical Aspects of Wave Propagation, John A. DeSanto, 540--542, Proceedings of the Fourth International Conference on Mathematical and Numerical Aspects of Wave Propagation, Golden, Colorado, June 1--5, 1998. BibTeX

Parallel Solution of Helmholtz Problems using Additive Schwarz Methods, L. C. McInnes, R. Susan-Resiga, H. M. Atassi, and D. E. Keyes, Mathematical and Numerical Aspects of Wave Propagation, John A. DeSanto, 623--625, Proceedings of the Fourth International Conference on Mathematical and Numerical Aspects of Wave Propagation, Golden, Colorado, June 1--5, 1998. BibTeX

Additive Schwarz Methods with Nonreflecting Boundary Conditions for the Parallel Computation of Helmholtz Problems, L. C. McInnes, R. Susan-Resiga, D. E. Keyes, and H. M. Atassi, Proceedings of the 10th Intl. Conf. on Domain Decomposition Methods, J. Mandel et al., 349--357, 1998. BibTeX

Overlapping Schwarz Algorithms for Solving Helmholtz's Equation, X.-C. Cai, M. A. Casarin, Jr., F. W. Elliott, Jr., and O. B. Widlund, Proceedings of the 10th Intl. Conf. on Domain Decomposition Methods, J. Mandel et al., 437-445, 1998. BibTeX

Parallel Computing Using Schwarz Domain Decomposition Method for Aeroacoustic Problems, R. Susan-Resiga and H. M. Atassi, Proceedings of the 4th AIAA/CEAS Aeroacoustics Conference, 86-96, AIAA paper 98-2218, 1998. BibTeX

Parallel Computation of Harmonic Waves using Domain Decomposition, Part I: General Formulation, H. M. Atassi and R. Susan-Resiga, Proceedings of the ASME Noise Control and Acoustics Division, 375-379, NCA-25, 1998. BibTeX

Parallel Computation of Harmonic Waves using Domain Decomposition, Part II: Numerical Implementation and Applications, R. Susan-Resiga and H. M. Atassi, Proceedings of the ASME Noise Control and Acoustics Division, 381 -388, NCA-25, 1998. BibTeX

Overlapping Schwarz methods for solving Helmholtz's Equation, Xiao-Chuan Cai, Mario A. Casarin, Frank W. Elliott, Jr., and Olof B. Widlund, Domain Decomposition Methods 10, 437--445, 1998. BibTeX

PetClaw: A Scalable Parallel Nonlinear Wave Propagation Solver for Python, Amal Alghamdi, Aron Ahmadia, David I. Ketcheson, Matthew G. Knepley, Kyle T. Mandli, and Lisandro Dalcin, Proceedings of SpringSim 2011, 2011. BibTeX

PyClaw: Accessible, Extensible, Scalable Tools for Wave Propagation Problems, David I. Ketcheson, Kyle T. Mandli, Aron J. Ahmadia, Amal Alghamdi, Manuel Quezada de Luna, Matteo Parsani, Matthew G. Knepley, and Matthew Emmett, SIAM Journal on Scientific Computing, 34, 4, C210--C231, http://arxiv.org/abs/1111.6583, 2012. BibTeX

Optimization

Parallel Fully Coupled Lagrange-Newton-Krylov-Schwarz Algorithms and Software for Optimization Problems Constrained by Partial Differential Equations, Ernesto Prudencio, 2005. BibTeX

Parallel multilevel restricted Schwarz preconditioners with pollution removing for PDE-constrained optimization, Ernesto Prudencio and X. C. Cai, SIAM J. Sci. Comp., Submitted with revisions. BibTeX

Parallel full space SQP Lagrange-Newton-Krylov-Schwarz algorithms for PDE-constrained Optimization Problems, Ernesto Prudencio, R. Byrd, and X. C. Cai, SIAM J. Sci. Comp., 27, 1305--1328, 2006. BibTeX

Domain decomposition methods for PDE-constrained optimization problems, Ernesto Prudencio, R. Byrd, and X. C. Cai, VECPAR 2004, M. Dayde, J. Dongarra, V. Hernandex, and J. Palma, 569--582, 2004. BibTeX

Three-dimensional anisotropic mesh adaptation for phase change problems, Youssef Belhamadia, Andre Fortin, and Eric Chamberland, Journal of Computational Physics, 201, 753-770, 2004. BibTeX

A Lagrange-Newton-Krylov-Schur Method for PDE Constrained Optimization, George Biros and Omar Ghattas, SIAG-Opt Views and News, 11, 2, 2000. BibTeX

A case study in the performance and scalability of optimization algorithms, Steve Benson, Lois Curfman McInnes, and Jorge Moré;, ACM Transactions on Mathematical Software, 27, 3, 361--376, 2001. BibTeX

Parallel preconditioners for KKT systems arising in optimal control of viscous incompressible flows, George Biros and Omar Ghattas, Proceedings of Parallel CFD '99, Williamsburg, Virginia, USA, May 23-26, 1999, 1999. BibTeX

Using Automatic Differentiation for Second-order Matrix-free Methods in PDE-constrained Optimization, P. D. Hovland, D. E. Keyes, L. C. McInnes, and W. Samyono, Automatic Differentiation of Algorithms: From Simulation to Optimization, George Corliss, Christèle Faure, Andreas Griewank, Laurent Hascoët, and Uwe Naumann, 2002. BibTeX

Parallel Lagrange-Newton-Krylov-Schur Methods for PDE-Constrained Optimization. Part I: The Krylov-Schur Solver, George Biros and Omar Ghattas, Laboratory for Mechanics, Algorithms, and Computing, Carnegie Mellon University, 2001. BibTeX

Parallel Lagrange-Newton-Krylov-Schur Methods for PDE-Constrained Optimization. Part II: The Lagrange-Newton Solver, and its Application to Optimal Control of Steady Viscous Flows, George Biros and Omar Ghattas, Laboratory for Mechanics, Algorithms, and Computing, Carnegie Mellon University, 2001. BibTeX

Fast Algorithms

A New Parallel Kernel-independent Fast Multipole Method, Lexing Ying, G. Biros, D. Zorin, and H. Langston, Proceedings of the ACM/IEEE conference on Supercomputing 2003, Winner of the Best Student Paper at SC2003, 2003. BibTeX

PetRBF -- A parallel O(N) algorithm for radial basis function interpolation, Rio Yokota, L A Barba, and Matthew G Knepley, Computer Methods in Applied Mechanics and Engineering, 199, 25-28, 1793--1804, http://arxiv.org/abs/0909.5413v1, 2010. BibTeX

PetFMM -- A dynamically load-balancing parallel fast multipole library, Felipe A Cruz, Matthew G Knepley, and L A Barba, International Journal of Numerical Methods in Engineering, 85, 4, 403--428, http://arxiv.org/abs/0905.2637, 2010. BibTeX

Other Application Areas

IDEA -- An API for Parallel Computing with Large Spatial Datasets, Yan, Baoqiang and Rhodes, Philip J., Proceedings of the 2011 International Conference on Parallel Processing, 355--364, 2011. BibTeX

Cu(ii)-porphyrin molecular dynamics as seen in a novel EPR/Stochastic Liouville equation study, Hakansson, Par, Nguyen, ThaoNguyen, Nair, Prasanth B., Edge, Ruth, and Stulz, Eugen, Phys. Chem. Chem. Phys., 15, 10930-10941, 2013. BibTeX

Implicit numerical schemes for the stochastic Liouville equation in Langevin form, Hakansson, Par and Nair, Prasanth B., Phys. Chem. Chem. Phys., 13, 9578-9589, 2011. BibTeX

A Differential Variational Inequality Approach for the Simulation of Heterogeneous Materials, Lei Wang, Jungho Lee, Mihai Anitescu, Anter El Azab, Lois Curfman McInnes, Todd Munson, and Barry Smith, Proceedings of SciDAC 2011 Conference, 2011. BibTeX

A time-discrete model for dynamic fracture based on crack regularization, Blaise Bourdin, Christopher Larsen, and Casey Richardson, International Journal of Fracture, 168, 133--143, 2011. BibTeX

The Variational Approach to Fracture, Blaise Bourdin, Gilles Francfort, and Jean-Jacques Marigo, Springer, 2008. BibTeX

The Variational Approach to Fracture, Blaise Bourdin, Gilles Francfort, and Jean-Jacques Marigo, J. Elasticity, 91, 1--148, 2008. BibTeX

Spectrum of the non-abelian phase in Kitaev's honeycomb lattice model, Lahtinen, V., Kells, G., Carollo, A., Stitt, T., Vala, J., and Pachos, J.K., Annals of Physics, 323, 9, 2286--2310, 2008. BibTeX

Discriminative language modeling with conditional random fields and the perceptron algorithm, Roark, B., Saraclar, M., Collins, M., and Johnson, M., Proceedings of the 42nd Annual Meeting on Association for Computational Linguistics, 47, 2004. BibTeX

Discriminative n-gram language modeling, Roark, B., Saraclar, M., and Collins, M., Computer Speech & Language, 21, 2, 373--392, 2007. BibTeX

Parallel performance of the PETSc Krylov methods applied to linear systems of 3D nanodevice simulators, Garcia-Rivera, A., Valin, R., Seoane, N., Garcia-Loureiro, A., and Aldegunde, M., IEEE. BibTeX

A parallel artificial neural network implementation, Wesley-Smith, I., 2006. BibTeX

Parallel Newton-Krylov-Schwarz algorithms for the three-dimensional Poisson-Boltzmann equation in numerical simulation of colloidal particle interactions, F.-N. Hwang, S.-R. Cai, Y.-L. Shao, and J.-S. Wu, Computer Physics Communications, 1529--1537, 2010. BibTeX

Parallel pseudo-transient Newton-Krylov-Schwarz continuation algorithms for bifurcation analysis of incompressible sudden expansion flows, C.-Y. Huang and F.-N. Hwang, Applied Numerical Mathematics, 60, 738--751, 2010. BibTeX

A parallel additive Schwarz preconditioned Jacobi-Davidson algorithm for polynomial eigenvalue problems in quantum dot simulation, F.-N. Hwang, Z.-H. Wei, T.-M. Huang, and W. Wang, Journal of Computational Physics, 229, 2932--2947, 2010. BibTeX

A Parallel Scalable PETSc-Based Jacobi-Davidson Polynomial Eigensolver with Application in Quantum Dot Simulation, Wei, Z.H., Hwang, F.N., Huang, T.M., and Wang, W., Domain Decomposition Methods in Science and Engineering XIX, 157--164, 2011. BibTeX

Sequential and parallel resolution of the two-group transient neutron diffusion equation using second-degree iterative methods, Flores-Sánchez, O., Vidal, V., Garc\'\ia, V., and Flores-S\'anchez, P., High Performance Computing for Computational Science-VECPAR 2006, 426--438, 2007. BibTeX

Enabling High Fidelity Neutron Transport Simulations on Petascale Architectures, Dinesh Kaushik, Michael Smith, Allan Wollaber, Barry Smith, Andrew Siegel, and Won Sik Yang, ACM/IEEE Proceedings of SC2009: High Performance Networking and Computing, SC'09 Gordon Bell Prize Finalist, 2009. BibTeX

An Efficient Algorithm for Classical Density Functional Theory in Three Dimensions: Ionic Solutions, Matthew G. Knepley, Dmitry A. Karpeev, Seth Davidovits, Robert S. Eisenberg, and Dirk Gillespie, Journal of Physical Chemistry, 132, 12, 124101--124111, http://arxiv.org/abs/0910.1531, 2010. BibTeX

Energetics of Calcium Selectivity: A Three-Dimensional Classical Density Functional Theory Approach, Knepley, M. G., Karpeev, D.~A., Eisenberg, R.~S., and Gillespie, D., Biophysical Journal, 96, 661, 2009. BibTeX

PARALLEL FINITE ELEMENT METHOD FOR COUPLED CHLORIDE MOISTURE DIFFUSION IN CONCRETE, SUWITO AND XIAO-CHUAN CAI AND YUNPING XI, INTERNATIONAL JOURNAL OF NUMERICAL ANALYSIS AND MODELING, 3, 4, 2006. BibTeX

High Performance Simulations of Electrokinetic Flow and Transport in Microfluidic Chips, Pablo A. Klera, Lisandro D. Dalcin, Fabio A. Guarnieria, and Mario A. Stortia, 2008. BibTeX

Parallel Computation of 3-D Soil-Structure Interaction in Time Domain with a Coupled FEM/SBFEM Approach, Schauer, Marco, Roman, Jose, Quintana-Ortí, Enrique, and Langer, Sabine, Journal of Scientific Computing, 1-22, 10.1007/s10915-011-9551-x. BibTeX

Parallel Finite Element Computations for Soil-Foundation-Structure Interaction Problems Report, Boris Jeremic and Guanzhou Jie, UCD CompGeoMech 02--2007, 2007. BibTeX

Fast 3D frequency-dependent Radiative Transfer for Magneto-Hydrodynamics, Rolf Kuiper, Max-Planck-Institute for Astronomy, 2008. BibTeX

Fast reactor core simulations using the UNIC code, M. A. Smith, C. Rabiti, D. Kaushik, B. Smith, W. S. Yang, and G. Palmiotti, Proceedings of the International Conference on the Physics of Reactors, Nuclear Power: A Sustainable Resource, 2008. BibTeX

UNIC: Ultimate Neutronic Investigation Code, G. Palmiotti, M. A. Smith, C. Rabiti, M. Leclere, D. Kaushik, A. Siegel, B. Smith, and E. E. Lewis, Joint International Topical Meeting on Mathematics and Computation and Supercomputing in Nuclear Applications, 2007. BibTeX

PNFE Component of the UNIC Code, M. A. Smith, G. Palmiotti, C. Rabiti, D. Kaushik, A. Siegel, B. Smith, and E. E. Lewis, Joint International Topical Meeting on Mathematics and Computation and Supercomputing in Nuclear Applications, 2007. BibTeX

Object-oriented programming for fast-and-easy development of parallel applications in forming processes simulation, H. Digonnet and T. Coupez, Proceedings of the Second MIT Conference on Computational Fluid and Solid Mechanics, 2003. BibTeX

Calcul parallele en mise en forme des materiaux, H. Digonnet and T. Coupez, XVIeme Congres Francais de Mecanique, 2003. BibTeX

Parallel computation for solving efficiently viscoelastic fluid flow problems, H. Digonnet, L. Silva, and T. Coupez, Proceedings of ECCOMAS 2004, 2004. BibTeX

Parallel computation applied to 3D FE simulation of polymer injection molding, H. Digonnet, L. Silva, and T. Coupez, Proceedings of WCCM VI, 2004. BibTeX

Calcul parallele appliqu aux coulements de fluides complexe, H. Digonnet, O. Basset, T. Coupez, and L. Silva, Proceedings of Eme Congres Francais de Mecanique, 2005. BibTeX

Sparse Triangular Solves for ILU Revisited: Data Layout Crucial to Better Performance, B. Smith and H. Zhang, International Journal of High Performance Computing Applications, 25, 4, 386--391, 2011. BibTeX

SIPs: Shift-and-Invert Parallel Spectral Transformations, H. Zhang, B. Smith, M. Sternberg, and P. Zapol, TOMS, 2, 2007. BibTeX

The detachment of a viscous drop in a viscous solution in the presence of a soluble surfactant, Fang Jin, Nivedita R. Gupta, and Kathleen J. Stebe, Phys. Fluids, 18, 2006. BibTeX

Phase Field Simulations of Liquid-Liquid Demixing During Immersion Precipitation of Polymeric Membranes in 2D and 3D, Bo Zhou and Adam Powell, J. Membrane Sci., 268, 2, 150--164, 2006. BibTeX

Flame Acceleration Distance in Obstacle-Laden Tubes, Anke Veser, Wolfgang Breitung, Sergey Dorofeev, and Alexander Efimenko, Proceedings of the NINTH INTERNATIONAL CONFERENCE ON NUMERICAL COMBUSTION, 2002. BibTeX

Discrete Willmore Flow, Alexander I. Bobenko and Peter Schrader, Eurographics Symposium on Geometry Processing, M. Desbrun and H. Pottmann, 2005. BibTeX

A numerical method for inverse design based on the inverse Euler equations, A. Scascighini, A. Troxler, and R. Jeltsch, International Journal for Numerical Methods in Fluids, 41, 339--355, 2003. BibTeX

A Numerical Method for the Design of Internal Flow Configurations Based on the Inverse Euler Equations, ANDREA SCASCIGHINI, 2001. BibTeX

A fast, higher-order solver for scattering by penetrable bodies in three dimensions, E. McKay Hyde and Oscar P. Bruno, Journal of Computational Physics, 202, 236--261, 2005. BibTeX

PARALLEL SOLUTION OF HIGH ORDER FINITE DIFFERENCE SCHEMES FOR PRICING MULTI-DIMENSIONAL AMERICAN OPTIONS, Matthew F Dixon, 2002. BibTeX

Fast Parallel PageRank: A Linear System Approach, David Gleich, Leonid Zhukov, and Pavel Berkhin, Stanford University, 2004. BibTeX

A DIAL-AN-OPERATOR APPROACH TO SIMULATION OF IMPURITY DIFFUSION IN SEMICONDUCTORS, Daniel W. Yergeau, 1999. BibTeX

KULL: LLNL's ASCI Inertial Confinement Fusion Simulation Code, J.A. Rathkopf, D.S. Miller, J.M. Owen, L.M. Stuart, M.R. Zika, P.G. Eltgroth, N.K. Madsen, K.P. McCandless, P.F. Nowak, M.K. Nemanic, N.A. Gentile, N.D. Keen, and T.S. Palmer, Physor 2000 American Nuclear Society Topical Meeting on Advances in Reactor Physics and Mathematics and Computation into the Next Millennium, 2000. BibTeX

An Implicit Fluctuation Splitting Scheme for Turbomachinery Flows, A. Bonfiglioli, P. De Palma, G. Pascazio, and M. Napolitano, Journal of Turbomachinery, 127, 395-401, 2005. BibTeX

High Performance Algorithms for Scalable Spin-Qubit Circuits with Quantum Dots, John Fettig, Nahil Sobh, Dmitriy V. Melnikov, and Jean-Pierre Leburton, Proceedings of the 5th International Conference on Linux Clusters, 2005. BibTeX

Spin configurations in circular and rectangular vertical quantum dots in a magnetic field: Three-dimensional self-consistent simulation, Dmitriy V. Melnikov, Philippe Matagne, Jean-Pierre Leburton, D.G. Austing, G. Yu, S. Tarucha, John Fettig, and Nahil Sobh, Arxiv preprint cond-mat/0506585, 2005. BibTeX

PARALLEL THERMAL RADIATION TRANSPORT IN TWO DIMENSIONS, Richard P. Smedley-Stevenson, 18th International Conference on Transport Theory (18 ICTT), 2003. BibTeX

Comparison Between Non-Equilibrium Green's Function and Monte Carlo Simulations for Transport in a Silicon Quantum Wire Structure, D. Guan, A. Godoy, U. Ravaioli, and F. Gamiz, Journal of Computational Electronics, 2, 335--339, 2003. BibTeX

One-level Newton-Krylov-Schwarz algorithm for unsteady nonlinear radiation diffusion problem, S. Ovtchinnikov and X.-C. Cai, Numer. Lin. Alg. Applics, 11, 867--881, 2004. BibTeX

Floating Solids: Combining Phase Field and Fluid-Structure Interactions, Adam Powell and David Dussault, Appl. Numer. Anal. Comp. Math., 2, 1, 157--166, 2005. BibTeX

Accuracy analysis of the thrust force in 2D-3D finite element models, G. Deliége, F. Henrotte, and K. Hameyer, International Journal for Computation and Mathematics in Electrical and Electronic Engineering (COMPEL), 2005. BibTeX

Finite element modelling of ion convection by electrostatic forces, G. Deliége, F. Henrotte, W. Deprez, and K. Hameyer, IEE Proceedings Science, Measurement and Technology, 151, 6, 2004. BibTeX

Algebraic Multigrid Techniques for Strongly Indefinite Linear Systems from Direct Frequency Response Analysis in Solid Mechanics, Adams M.F., Computional Mechanics, 39, 4, 497-507, 2007. BibTeX

Computational Modeling of Ion Beam-Neutralizer Interactions in Two and Three Dimensions, A. Wheelock and D. Cooke, 40th AIAA/ASME/SAE/ASEE Joint Propulsion Conference and Exhibit, 2004. BibTeX

Parallelizing Pre-rendering Computations on a Net Juggler PC Cluster, Jeremie Allard, Valerie Gouranton, Emmanuel Melin, and Bruno Raffin, Immersive Projection Technology Symposium, 2002. BibTeX

Hybrid and concurrent algorithms for nonlinear magnetic field problems, D Ioan, G Ciuprina, and C Ciobotaru, IEEE Transactions on Magnetics, 2000. BibTeX

Development and Performance Analysis of a Parallel Finite Element Application Implemented in an Object-Oriented Programming Framework, Brian J. Henz and Dale R. Shires, PDPTA 2003, 1286-1292, Resin Transfer Modeling, 2003. BibTeX

Least-Squares Finite Element Methods for Electromagnetic Applications, Rickard Bergstrom, Chalmers, 2000-05, 2000. BibTeX

A Moving Overset Grid Method for Interface Dynamics Applied to Non-Newtonian Hele Shaw Flow, Petri Fast and Michael J. Shelley, Journal of Computational Physics, 195, 117-142, 2004. BibTeX

Efficient Training of Conditional Random Fields, Hanna Wallach, 2002. BibTeX

Stability of explicit-implicit hybrid time-stepping schemes for Maxwells equations, T Rylander and A Bondeson, Journal of Computational Physics, 179, 426-438, 2002. BibTeX

Comparison of two implementations of AMG-preconditioned CG considering an electrostatic problem, Uwe Fabricius, Friedrich Alexander Universitat Erlangen Nurnberg Germany, 04-1, 2004. BibTeX

Lecture Notes in Computer Science, Natalia Seoane and A.J.Garca-Loureiro, 2004. BibTeX

Simulation of Sandia Flame D Using Velocity-Scalar Filtered Density Function, M. B. Nik, S. L. Yilmaz, P. Givi, M. R. H. Sheikhi, and S. B. Pope, AIAA Journal, 48, 7, 1513--1522, 2010. BibTeX

Grid Resolution Effects on VSFMDF/LES, Mehdi B. Nik, Server L. Yilmaz, Mohammad Reza H. Sheikhi, and Peyman Givi, Flow, Turbulence and Combustion, 2010. BibTeX

Towards faster solution of large power flow problems, Idema, Reijer, Papaefthymiou, Georgios, Lahaye, Domenico, Vuik, Cornelis, and van der Sluis, Lou, Power Systems, IEEE Transactions on, 28, 4, 4918--4925, 2013. BibTeX

Scalable Newton-Krylov Solver for Very Large Power Flow Problems, Idema, R., Lahaye, D.J.P., Vuik, C., and Van der Sluis, L., Power Systems, IEEE Transactions on, 27, 1, 390-396, 2012. BibTeX

Computational Methods in Power System Analysis, Idema, Reijer and Lahaye, Domenico JP, Springer, 2014. BibTeX

Development of an implicitly coupled electromechanical and electromagnetic transients simulator for power systems, Shrirang Abhyankar, 2011. BibTeX

Using PETSc to Develop Scalable Applications for Next-Generation Power Grid, Shrirang Abhyankar, Barry Smith, Hong Zhang, and A. Flueck, Proceedings of the 1st International Workshop on High Performance Computing, Networking and Analytics for the Power Grid, 2011. BibTeX

Development of a parallel three-phase transient stability simulator for power systems, Shrirang Abhyankar, Alexander Flueck, Xu Zhang, and H. Flueck, Proceedings of the 1st International Workshop on High Performance Computing, Networking and Analytics for the Power Grid, 2011. BibTeX

An implicitly-coupled solution approach for combined electromechanical and electromagnetic transients simulation, Shrirang Abhyankar and A. Flueck, Proceedings of the IEEE PES General Meeting, 2012. BibTeX

Scalable Newton-Krylov solver for very large Power Flow problems, Reijer Idema, Domenico Lahaye, Cornelis Vuik, and Lou van der Sluis, IEEE Transactions on Power Systems, 27, 390-396, 2012. BibTeX


Material failure, for example, cracking of steel beams resulting in bridge collapse and corrosion, is a little understood phenomena. Thus simulations are important for prediction and prevention. PETSc has been used in a variety of studies of material failure.

Modulized Coupled Simulation of Localized Pit Initiation in Stainless Steel, Yuan He, Joshua Gray, Richard Braatz, and Richard Alkire, American Institute of Chemical Engineers 2004 Annual Meeting, 2004. BibTeX

Algorithms and Computing Architectures for Solving Differential-Algebraic Equation Systems Typically Encountered in Models of Corrosion Pit Initiation, J. Gray, and C. Homescu, L. Petzold, and Richard Alkire, Abstracts of the Electrochemical Society 204th meeting, 2003. BibTeX

A multiscale modeling approach to crack initiation in metallic polycrystals, Erin Lesulauro, Anthony R. Ingraffea, Gerd Heber, and Paul A. Wawrzynek, 44th AIAA/ASME/ASCE/AHS/ASC Structures, Structural Dynamics, and Materials Conference, 2003. BibTeX

Fracture Mechanics on the Intel Itanium Architecture, Gerd Heber, Andrew J. Dolgert, Maxirn Alt, Karen A. Mazurkiewicz, and Lynd Stringer, Intel Corporation, 2001. BibTeX

Modeling of 3D Metallic Polycrystals and Simulation of Crack Initiation, E. Iesulauro, G. Heber, P. A. Wawrzynek, and A. R. Ingraffea, International Conference ON Computational Engineering and Sciences, 2002. BibTeX

Parallel FEM Simulation of Crack Propagation, Bruce Carter, Chuin-Shan Chen, L. Paul Chew, Nikos Chrisochoides, Guang R. Gao, Gerd Heber, Antony R. Ingraffea, Roland Krause, Chris Myers, Demian Nave, Keshav Pingali, Paul Stodghill, Stephen Vavasis, and Paul A. Wawrzynek, Proceedings of Irregular 2000, 2000. BibTeX

Use of Polycrystal Plasticity Theory in Assessing Material Performance, A. J. Beaudoin, Simulation of materials processing: Theory, methods, and applications - Proceedings of the Sixth International Conference, NUMIFORM'98, J. Huétink and F. P. T. Baaijens, 1998. BibTeX


RF3P-A New Parallel Driven Frequency Electromagnetic Solver, JF DeFord and BL Held, Simulation Technology and Applied Research, Discusses their parallel commercial solver that uses PETSc, 2002. BibTeX

Modelling and Finite Element Simulation of Non-Linear and Anisotropic Quasi-Static Electromagnetic Systems, Hans Vande Sande, 2003. BibTeX

Reducing the Computation Time of Non-Linear Problems by an Adaptive Linear System Tolerance, H. Vande Sande, W. Deprez, J. De Coster, F. Henrotte, and K. Hameyer, IEEE Transactions on Magnetics, 40, 1306--1309, 2004. BibTeX

Optimal constraint projection for hyperbolic evolution systems, Michael Holst, Lee Lindblom, Robert Owen, Harald P. Pfeiffer, Mark A. Scheel, and Lawrence E. Kidder, Phys. Rev. D, 70, 084017, 2004. BibTeX

Extended Lifetime in Computational Evolution of Isolated Black Holes, Matthew Anderson and Richard A. Matzner, Foundations of Physics, 35, 1572--9516, 2005. BibTeX

Excision boundary conditions for black hole initial data, Cook, Gregory B. and Pfeiffer, Harald P., Phys. Rev. D, 70, 104016--24, 2004. BibTeX

Initial data for Einstein's equations with superposed gravitational waves, Harald P. Pfeiffer, Lawrence E. Kidder, Mark A. Scheel, and Deirdre Shoemaker, Phys. Rev. D, 71, 024020, 2005. BibTeX

A multidomain spectral method for solving elliptic equations, Pfeiffer, Harald P., Kidder, Lawrence E., Scheel, Mark A., and Teukolsky, Saul A., CPC, 152, 253--273, Solves nonlinear coupled 3-D elliptic equations that arise in general relativity. For a related online version, see arXiv:gr-qc/0202096, 2003. BibTeX

Comparing initial-data sets for binary black hole, Pfeiffer, Harald P., Cook, Gregory B., and Teukolsky, Saul A., PRD, 66, 024047, for a related online version, seearXiv:gr-qc/0203085, 2002. BibTeX

Initial Data for Black Hole Evolutions, Pfeiffer, Harald P., 2003. BibTeX

A fast apparent horizon algorithm, Erik Schnetter, Arxiv preprint gr-qc/0206003, 2002. BibTeX

Finding apparent horizons and other 2-surfaces of constant expansion, Erik Schnetter, Class. Quantum Grav., 20, 4719-4737, 2003. BibTeX

Algebraic multigrid methods for constrained linear systems with applications to contact problems in solid mechanics, Adams, M. F., Numerical Linear Algebra with Applications, 11, 2-3, 141-153, 2004. BibTeX

Solving Nonlinear Magnetic Problems Using Newton Trust Region Methods, H. Vande Sande, H. De Gersem, F. Henrotte, and K. Hameyer, IEEE TRANSACTIONS ON MAGNETICS, 39, 1709--1712, 2003. BibTeX

Parallelization and Integration of a Large Scale Hydrocarbon Pool Fire in the Uintah PSE, Rajesh Rawat, Jennifer P. Spinti, Wing Yee, and Philip J. Smith, In Proceedings of Ninth Internation Conference on Numerical Combustion - ICNC 2002, 49-55, Extended abstract, 2002. BibTeX

An Inherently-Parallel Method for Solving Discretized Diffusion Equations, Bradley R. Eccleston and Todd S. Palmer, Department of Nuclear Engineering, Oregon State University, Funded under the ASCI Level III: Computational Transport Issues for Large-Scale Parallel Simulations, 1999. BibTeX

A scalable modular convex solver for regularized risk minimization, Teo, C.H., Smola, A., Vishwanathan, SVN, and Le, Q.V., Proceedings of the 13th ACM SIGKDD international conference on Knowledge discovery and data mining, 727--736, 2007. BibTeX

A comparison of algorithms for maximum entropy Parameter estimation, Robert Malouf, In Proceedings of the Sixth Conference on Natural Language Learning (CoNLL-2002), 49-55, 2002. BibTeX

Computing the Lambda Modes of a Nuclear Reactor with SLEPc and PETSc, V. Hernandex, J. E. Roman, and V. Vidal, Submitted to CMMSE. BibTeX

Solving finite difference schemes arising in trivariate option pricing, Manfred Gilli, Evis Kellezi, and Giorgio Pauletto, Journal of Economic Dynamics and Control, 26, 1499-1515, 2002. BibTeX

Comparison of three algorithms for nonlinear metal cutting problems, C.J.Palansuriya, C-H.Lai, C.S.Ierotheou, K.A.Pericleous, and D.E.Keyes, Proceedings of the 11th International Conference on Domain Decomposition Methods, C.-H. Lai et al., 1999. BibTeX

Multi-Model Multi-Domain Computational Methods in Aerodynamics and Acoustics Web Page, David E. Keyes, Old Dominion University. BibTeX

Parallelization of Thermal Recovery Simulation Based on PETSc, Liu, L., Xue, W., Shu, J., and Ma, L., IEEE, 2010. BibTeX

New Generation Framework for Petroleum, Reservoir Simulation, University of Texas at Austin and Argonne National Laboratory. BibTeX

Adapting EMAP3D to parallel processing, V. Thiagarajan, K. Milfeld, and KT. Milfeld, IEEE TRANSACTIONS ON MAGNETICS , 37, 143--146, 2001. BibTeX

Parallel computation for electronic waves in quantum corrals, HK Harbury and W Porod, VLSI Design, 6, 47--51, 1998. BibTeX

Mixed Finite Element Beam Propagation Method, Mark Bludszuweit, Journal of Lightwave Technology, 16, 7, 1336--42, 1998. BibTeX

J. L. Friedman and N. Stergioulas, Astrophysics Journal, 492, 301, 1998. BibTeX

S. M. Morsink, N. Stergioulas, and S. Blattnig, Astrophysics Journal, 510, 854, 1999. BibTeX

Ph. D. thesis, N. Stergioulas, University of Wisconsin-Milwaukee, 1996. BibTeX

Solutions of TEAM Problem #13 Using Integral Equations in a Sequential and Parallel Computing Environment, L. Kettunen, K. Forsman, D. Levine, and W. Gropp, Proceedings of the Miami TEAM Workshop, 1993. BibTeX

Solutions of TEAM Problems 13 and 20 Using a Volume Integral Formulation, L. Kettunen, K. Forsman, D. Levine, and W. Gropp, Proceedings of Aix-les-Bains TEAM Workshop, 1994. BibTeX

Computational Electromagnetics and Parallel Dense Matrix Computations, L. Kettunen, K. Forsman, D. Levine, and W. Gropp, Proceedings of the SIAM Parallel Processing for Scientific Computing Conference, 1995. BibTeX

Evaluation of Multigrid as a Solver for Stress Analysis Problems in Semiconductor Process Simulation, Slobodan Mijalkovi\'c, Multigrid Methods VI: Proceedings of the Sixth European Multigrid Conference Held Gent, Belgium, September 27--30, 1999., Erik Dick, Kris Riemslagh, Jan Vierendeels, 2000. BibTeX

Mixed Finite Element Beam Propagation Method, Mark Bludszuweit, Journal of Lightwave Technology, 16, 7, 1336--42, 1998. BibTeX

Parallel Krylov Methods for Econometric Model Simulation, Manfred Gilli and Giorgio Pauletto, Computational Economics, 16, 173--186, 2000. BibTeX

Software Packages that use or interface to PETSc

Automating the Finite Element Method, Logg, Anders, Archives of Computational Methods in Engineering, 14, 2, 93-138, 2007. BibTeX

Solving large sparse linear systems in a grid environment: the GREMLINS code versus the PETSc library, Jezequel, Fabienne, Couturier, Raphaël, and Denis, Christophe, The Journal of Supercomputing, 59, 3, 1517-1532, 2012. BibTeX

FEAP: A Finite Element Analysis Program, FEAP Team, Uses PETSc linear solvers - iterative and direct. BibTeX

ParPre Web Page, Victor Eijkhout, University of Tennessee, This is no longer supported. A set of preconditioners built on PETSc. BibTeX

PISM: a Parallel Ice Sheet Model, The PISM Team, We have developed a numerical model of ice sheets called PISM (a Parallel Ice Sheet Model). The thickness, temperature, velocity and age of the ice are all simulated, as is the deformation of the earth underneath the ice. New techniques for fast ice dynamics, earth deformation, and verification have are included.. BibTeX

OOFEM - an object oriented finite element package, Borek Patzak. BibTeX

OpenFVM - a finite volume based general purpose CFD solver, Open source development. BibTeX

DENDRO: a parallel geometric multigrid library for trilinear finite elements on octree meshes, H. Sundar, R.S. Sampath, S.S. Adavani, C. Davatzikos, and G. Biros, University of Pennsylvania. BibTeX

A computational framework for simulation of biogeochemical tracers in the ocean, Khatiwala, S., Columbia University. BibTeX

Lecture Notes in Computer Science, Xiangmin Jiao, Xiang-Yang Li, and Xiaosong Ma, 1999. BibTeX

DistSolve: An Open Source Web Service for Solving Sparse Systems of Equations, C. S. Crow IV, Hopkins Undergraduate Research Journal, 2003. BibTeX

PETSc for Python, L. Dalcin, R. Paz, and M. Storti, International Center for Computer Methods in Engineering, Provides Python bindings for PETSc via SWIG. BibTeX

CFDShip-Iowa, Pablo M. Carrica, Robert V. Wilson, and Fred Stern, University of Iowa, CFDShip-Iowa is a multiblock free surface flow solver that uses overset structured grids, designed for ship applications. BibTeX

Multiflow, Berend van Wachem, Mechanical Engineering - Chalmers University of Technology, MultiFlow is a curvlinear, multiblock, multiprocessor flowsolver for multiphase flows.. BibTeX

FENA - A Finite Element Model for the North Atlantic, Jens Schroeter, Alfred-Wegener-Institute for Polar and Marine Research. BibTeX

The Idea and Concept of Metos3D: A Marine Ecosystem Toolkit for Optimization and Simulation in 3-D, Piwonski, J. and Slawig, T., Christian-Albrechts-Universität zu Kiel, 2010. BibTeX

Metos3D: A Marine Ecosystem Toolkit for Optimization and Simulation in 3-D, Piwonski, J. and Slawig, T., Christian-Albrechts-Universität zu Kiel. BibTeX

Magpar: Parallel Micromagnetics Code, W. Scholz, Vienna University of Technology. BibTeX

libMesh:a C++ framework for the numerical simulation of partial differential equations on serial and parallel platforms, [Online]. BibTeX

Multiphysics Object-Oriented Simulation Environment (MOOSE), David Andrs, Cody Permann, Andrew Slaughter, Richard Martineau, Derek Gaston, John Peterson, and Jason Miller, Idaho National Laboratory. BibTeX

MOOSE: A parallel computational framework for coupled systems of nonlinear equations, Gaston, D., Newman, C., Hansen, G., and Lebrun-Grandié, D., Nuclear Engineering and Design, 239, 10, 1768--1778, 2009. BibTeX

An object-oriented finite element framework for multiphysics phase field simulations, Tonks, M.R., Gaston, D., Millett, P.C., Andrs, D., and Talbot, P., Computational Materials Science, 51, 1, 20--29, 2012. BibTeX

PyLith User Manual Version 1.6.1, Brad Aagaard, Sue Kientz, Matthew G. Knepley, Surendra Somala, Leif Strand, and Charles Williams, 2011. BibTeX

PyLith, Brad Aagaard, Matthew G. Knepley, and Charles Williams, 2012. BibTeX

Gale User Manual Version 2.0.0, Walter Landry, Luke Hodkinson, and Susan Kientz, 2011. BibTeX

UnderWorld: A Geodynamics Modelling Code, Louis Moresi, Monash University. BibTeX

Computational approaches to studying non-linear dynamics of the crust and mantle, Moresi, L., Quenette, S., Lemiale, V., Meriaux, C., Appelbe, B., and Mühlhaus, H.B., Physics of the Earth and Planetary Interiors, 163, 1-4, 69--82, 2007. BibTeX

Chaste: a test-driven approach to software development for biological modelling, Pitt-Francis, J., Pathmanathan, P., Bernabeu, M.O., Bordas, R., Cooper, J., Fletcher, A.G., Mirams, G.R., Murray, P., Osborne, J.M., Walter, A., and others, Computer Physics Communications, 180, 12, 2452--2471, 2009. BibTeX

The FEniCS project, Logg, A., Ølgaard, K., Rognes, M.E., Wells, G.N., Jansson, J., Kirby, R.C., Knepley, M.G., Lindbo, D., and Skavhaug, O., A continually updated technical report. http://fenicsproject.org, 2011. BibTeX

Snark: A suite of software for geoscientific applications and a philosophy of scientific software development, Victorian Partnership for Advanced Computing. BibTeX

Innovative Modern Object-Oriented Solving Environment - iMOOSE, Guido Arians, Thomas Bauer, Christian Kaehler, Wolfgang Mai, Christoph Monzel, Dirk van Riesen, and Christoph Schlensok, [Online]. BibTeX

FoSSI: Family of Simplified Solver Interfaces, offers scalable access to MPI-parallel solvers from CSR-matrix format frequently used in sequential/vector codes, Stephan Frickenhaus, AWI-Bremerhaven, Germanny. BibTeX

PETSC-FUN3D Benchmark Page, Dinesh Kaushik, ODU/ANL, CFD Benchmark of some solvers in PETSc. BibTeX

SCIRun, SCIRun Development Team, University of Utah, SCIRun now uses PETSc linear solvers. BibTeX

Prometheus - A scalable unstructured finite element solver, Mark F. Adams, Berkeley. BibTeX

Illuminator Distributed Visualization Library, Adam C. Powell, IV. BibTeX

RheoPlast Phase Field Multi-Physics Code, Adam Powell, David Dussault, and Bo Zhou. BibTeX

Toolkit for Advanced Optimization (TAO) Web Page, Todd Munson, Jason Sarich, Stefan Wild, Steve Benson, Lois Curfman McInnes, and Jorge Moré, Mathematics and Computer Science Division, Argonne National Laboratory. BibTeX

Toolkit for Advanced Optimization (TAO) Users Manual, Todd Munson, Jason Sarich, Stefan Wild, Steve Benson, and Lois Curfman McInnes, Argonne National Laboratory, ANL/MCS-TM-322 - Revision 3.5, 2014. BibTeX

MEF++ Web Page, Eric Chamberland, Groupe Interdisiplinaire de Recherche en Elements Finis, A finite element code for fluid dynamics, solid mechanics, thermal and multiphysics. BibTeX

Ti-PETSc - an interface to PETSc from Titanium, Berkeley. BibTeX

Multiphase flow with PETSc, Q. Zou, LANL. BibTeX

EMSolve Web page, Daniel White et al., LLNL. BibTeX

Finite element software, Kuleuven. BibTeX

PETSc Web page, Satish Balay, Shrirang Abhyankar, Mark F. Adams, Jed Brown, Peter Brune, Kris Buschelman, Victor Eijkhout, William D. Gropp, Dinesh Kaushik, Matthew G. Knepley, Lois Curfman McInnes, Karl Rupp, Barry F. Smith, and Hong Zhang, 2014. BibTeX

Debian package for PETSc, Adam C. Powell, IV. BibTeX

Cactus Website, Provides two interface to the PETSc solvers. BibTeX

PETSc-FEM: A General Purpose, Parallel, Multi-Physics FEM Program, Mario Storti and Norberto Nigro, Centro Internacional de Metodos Computacionales en Ingenieria (CIMEC). BibTeX

FIDAP 8.5, Fluent's commercial finite element fluid code uses PETSc for parallel linear solves.. BibTeX

SLEPc Homepage, Carmen Campos, José E. Rom\'an, Eloy Romero, Andrés Tom\'as, Vicente Hern\'andez, and Vicent Vidal, Scalable Library for Eigenvalue Problem Computations. BibTeX

SLEPc Users Manual, Carmen Campos, José E. Rom\'an, Eloy Romero, Andrés Tom\'as, Vicente Hern\'andez, and Vicent Vidal, DISC-II/24/02, Scalable Library for Eigenvalue Problem Computations. BibTeX

OpenFOAM, OpenFOAM is a free, open source CFD software package. It allows PETSc linear algebra and solvers to be used underneath.. BibTeX

deal.II, deal.II is a C++ library targeting adaptive finite elements and error estimation. It allows PETSc linear algebra and solvers to be used underneath.. BibTeX

deal.II---A general-purpose object-oriented finite element library, Bangerth, W., Hartmann, R., and Kanschat, G., ACM Transactions on Mathematical Software (TOMS), 33, 4, 24--es, 2007. BibTeX

Global Arrays, Jarek Nieplocha et al., Pacific Northwest National Laboratories, Global arrays can use PETSc linear solvers. BibTeX

Software Engineering

Run-time extensibility and librarization of simulation software, Jed Brown, Matthew G. Knepley, and Barry Smith, IEEE Computing in Science and Engineering, Preprint, 2014. BibTeX

Preliminary implementation of Hybrid MPI/pthread programming model in PETSc, Shrirang Abhyankar, Barry Smith, and Kerry Stevens, Argonne National Laboratory, ANL/MCS-P2011-0112, 2012. BibTeX

Solvers as Operators, Andrew Cleary and Matthew G. Knepley, Lawrence Livermore National Laboratory, UCRL-ID-135342, 1999. BibTeX

PETSc's Software Strategy for the Design Space of Composable Extreme-Scale Solvers, Barry Smith, Lois Curfman McInnes, Emil Constantinescu, Mark Adams, Satish Balay, Jed Brown, Matthew Knepley, and Hong Zhang, Argonne National Laboratory, ANL/MCS-P2059-0312, DOE Exascale Research Conference, April 16-18, 2012, Portland, OR, 2012. BibTeX

Coping at the User-Level with Resource Limitations in the Cray Message Passing Toolkit MPI at Scale, R. T. Mills, F. M. Hoffman, P. H. Worley, K. S. Pwerumalla, A. Mirin, G. E. Hammond, and B. Smith, Cray Users Group Conference, 2009. BibTeX

Engineering PFLOTRAN for Scalable Performance on Cray XT and IBM BlueGene Architectures, R. T. Mills, V. Sripathi, G. Mahinthakumar, G. Hammond, P. C. Lichtner, and B. F. Smith, Proceedings of SciDAC 2010 Annual Meeting, 2010. BibTeX

Preliminary Implementation of PETSc Using GPUs, Victor Minden, Barry F. Smith, and Matthew G. Knepley, GPU Solutions to Multi-scale Problems in Science and Engineering, David A. Yuen, Long Wang, Xuebin Chi, Lennart Johnsson, Wei Ge, and Yaolin Shi, 131--140, 2013. BibTeX

Why Scientists and Engineers need GPUs today, Matthew G. Knepley and David A. Yuen, GPU Solutions to Multi-scale Problems in Science and Engineering, David A. Yuen, Long Wang, Xuebin Chi, Lennart Johnsson, Wei Ge, and Yaolin Shi, 131--140, 2013. BibTeX

Accurate Evaluation of Local Averages on GPGPUs, Dmitry A. Karpeev, Matthew G. Knepley, and Peter R. Brune, GPU Solutions to Multi-scale Problems in Science and Engineering, David A. Yuen, Long Wang, Xuebin Chi, Lennart Johnsson, Wei Ge, and Yaolin Shi, 487--501, 2013. BibTeX

GPU Implementation of Multigrid Solver for Stokes Equation with Strongly Variable Viscosity, Liang Zheng, Taras Gerya, Matthew G. Knepley, David A. Yuen, Huai Zhang, and Yaolin Shi, GPU Solutions to Multi-scale Problems in Science and Engineering, David A. Yuen, Long Wang, Xuebin Chi, Lennart Johnsson, Wei Ge, and Yaolin Shi, 321--333, 2013. BibTeX

Implementation of a multigrid solver on GPU for Stokes equations with strongly variable viscosity based on Matlab and CUDA, Liang Zheng, Taras Gerya, Matthew G. Knepley, David A. Yuen, Huai Zhang, and Yaolin Shi, IJHPCA, http://hpc.sagepub.com/content/early/2013/03/03/1094342013478640.abstract, 2013. BibTeX

Encyclopedia of Parallel Computing, B. Smith, 2011. BibTeX

Computación cient\'ifica en paralelo con interfaz MATLAB a PETSc, Carlos D. Acosta and Carlos E. Mejía, Lecturas Matemáticas, 27, 213--224, 2006. BibTeX

Explaining StGermain: An aspect oriented environment for building extensible computational mechanics modeling software, Steve Quenette, Louis Moresi, P. D. Sunter, and Bill F. Appelbe, Parallel and Distributed Processing Symposium, IPDPS 2007, 1--8. BibTeX

Vectorized sparse matrix multiply for compressed row storage format, E. F. D'Azevedo, M. R. Fahey, and R. T. Mills, Lecture Notes in Computer Science, 3514, 99--106, 2005. BibTeX

The COOLFluiD Framework: Design Solutions for High Performance Object Oriented Scientific Computing Software, Andrea Lani, Tiago Quintino, Dries Kimpe, Herman Deconinck, Stefan Vandewalle, and Stefaan Poedts, Computational Science ICCS 2005: 5th International Conference, Lecture Notes in Computer Science, 2005. BibTeX

Desarrollo de Aplicaciones Paralelas en Python, L. Dalcin, R. Paz, and M. Storti, Proceedings of *XIV Congress on Numerical Methods and its Applications (ENIEF). Bariloche, Argentina, 2004. BibTeX

MPI for Python, L. Dalcin, R. Paz, and M. Storti, Journal of Parallel and Distributed Computing, 2005. BibTeX

SLEPc: Scalable Library for Eigenvalue Problem Computations, V. Hernandex, J. E. Roman, and V. Vidal, Submited to VecPar 2002, 2002. BibTeX

Block Locally Optimal Preconditioned Eigenvalue Xolvers (BLOPEX) in Hypre and PETSc, Knyazev, A. V., Argentati, M. E., Lashuk, I., and Ovtchinnikov, E. E., SIAM Journal on Scientific Computing, 29, 2224-2239, 2007. BibTeX

Time Dependent Solution of the Schrodinger Equation for Parallel Computers, Asbjorn Hoiland Aarrestad, Implemented Runge-Kutta methods using PETSc, 2003. BibTeX

Performance Modeling and Prediction for the Scalable Solution of Partial Differential Equations on Unstructured Grids, D. K. Kaushik, 2002. BibTeX

Object Oriented Implementation of a General Finite Element Code, Rickard Bergstrom, Chalmers Finite Element Center, Chalmers University of Technology, 2002-13, Discribes a finite element software package that uses PETSc for its solvers, 2002. BibTeX

A Parallel General Purpose Finite Element System, Enzo A. Dari, Gustavo C. Buscaglia, and Adrian J. Lew, IX SIAM Conference on Parallel Processing for Scientific Computing, Describes software that uses PETSc for its parallel linear solves, 1999. BibTeX

Parallel Components for PDEs and Optimization: Some Issues and Experiences, B. Norris, S. Balay, S. Benson, L. Freitag, P. Hovland, L. McInnes, and B. Smith, Parallel Computing, 28 (12), 1811--1831, 2002. BibTeX

Making Automatic Differentiation Truly Automatic: Coupling PETSc with ADIC, Paul Hovland, Boyana Norris, and Barry Smith, Future Generation Computer Systems, 21, 8, 1426--1438, 2005. BibTeX

Remote Access to Mathematical Software, Elizabeth Dolan, Paul Hovland, Jorge Moré;, Boyana Norris, and Barry Smith, Mathematics and Computer Science Division, Argonne National Laboratory, ANL/MCS-P889-0601, 2001. BibTeX

Exploiting Existing Software in Libraries: Successes, Failures, and Reasons Why, William D. Gropp, Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable Scientific and Engineering Computing, 21-29, 1999. BibTeX

Algorithm Development for Large Scale Computing, Matthew Knepley and Vivek Sarin, Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable Scientific and Engineering Computing, http://books.google.com/books?id=2Da5OcnjPSgC&lpg=PA58&ots=TJCK64BUeg&dq=Bill%20Gropp%20Science%20Engineering%20Object%20Oriented&pg=PA138#v=onepage&q&f=false, 1999. BibTeX

CRPC Handbook of Parallel Computing, S. Balay, W. D. Gropp, L. C. McInnes, and B. F. Smith, 2002. BibTeX

Developing a Derivative-Enhanced Object-Oriented Toolkit for Scientific Computations, Paul Hovland, Boyana Norris, Lucas Roh, and Barry Smith, Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable Scientific and Engineering Computing, 129-137, also available as Argonne preprint ANL/MCS-P731-1098, 1999. BibTeX

Efficient Management of Parallelism in Object Oriented Numerical Software Libraries, Satish Balay, William D. Gropp, Lois Curfman McInnes, and Barry F. Smith, Modern Software Tools in Scientific Computing, E. Arge, A. M. Bruaset, and H. P. Langtangen, 163--202, 1997. BibTeX

PETSc Users Manual, Satish Balay, Shrirang Abhyankar, Mark F. Adams, Jed Brown, Peter Brune, Kris Buschelman, Victor Eijkhout, William D. Gropp, Dinesh Kaushik, Matthew G. Knepley, Lois Curfman McInnes, Karl Rupp, Barry F. Smith, and Hong Zhang, Argonne National Laboratory, ANL-95/11 - Revision 3.5, 2014. BibTeX

PETSc Developers Manual, Satish Balay, Shrirang Abhyankar, Mark F. Adams, Jed Brown, Peter Brune, Kris Buschelman, Victor Eijkhout, William D. Gropp, Dinesh Kaushik, Matthew G. Knepley, Lois Curfman McInnes, Karl Rupp, Barry F. Smith, and Hong Zhang, Argonne National Laboratory, 2011. BibTeX

The ALICE Memory Snooper, Ibrahima Ba and Barry F. Smith, 1999. BibTeX

Rozwiazywanie ukladow rownan przy pomocy pakietu PETSc, Marcin Bojko and Piotr Krzyzanowski, Instytut Matematyki, Stosowanej i Mechaniki, Uniwersytet Warszawski, An introduction to PETSc in Polish, 1998. BibTeX

Integrating Automatic Differentiation with Object-Oriented Toolkits for High-Performance Scientific Computing, J. Abate, S. Benson, L. Grignon, P. Hovland, L. C. McInnes, and B. Norris, Automatic Differentiation of Algorithms: From Simulation to Optimization, George Corliss, Christèle Faure, Andreas Griewank, Laurent Hascoët, and Uwe Naumann, 2002. BibTeX

PETSc 2.0: A Case Study of Using MPI to Develop Numerical Software Libraries, Lois Curfman McInnes and Barry F. Smith, Proceedings of the MPI Developers Conference, Notre Dame, IN, 1995. BibTeX

Scalable, Extensible, and Portable Numerical Libraries, William D. Gropp and Barry F. Smith, Proceedings of the Scalable Parallel Libraries Conference, 87--93, 1994. BibTeX

Scalable Libraries for Solving Systems of Nonlinear Equations and Unconstrained Minimization Problems, William D. Gropp, Lois Curfman McInnes, and Barry F. Smith, Proceedings of the Scalable Parallel Libraries Conference, 60-67, 1995. BibTeX

The Design of Data-structure-neutral Libraries for the Iterative Solution of Sparse Linear Systems, Barry F. Smith and William D. Gropp, Scientific Programming, 5, 329--336, 1996. BibTeX

A Microkernel Design for Component-based Parallel Numerical Software Systems, Satish Balay, William D. Gropp, Lois Curfman McInnes, and Barry F. Smith, Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable Scientific and Engineering Computing, 58-67, also available as Argonne preprint ANL/MCS-P727-0998, 1998. BibTeX

A Comparison of the PETSc Library and HPF Implementations of an Archetypal PDE Computation, M. E. Hayder, D. E. Keyes, and P. Mehrotra, Advances in Engineering Software, 29, 415-424, 1998. BibTeX

Infrastructure and Interfaces for Large-Scale Numerical Software, L. A. Freitag, W. D. Gropp, P. D. Hovland, L. C. McInnes, and B. F. Smith, Mathematics and Computer Science Division, Argonne National Laboratory, ANL/MCS-P751-0599, to appear in the Proceedings of the 1999 International Conference on Parallel and Distributed Processing Techniques and Applications, June 28 - July 1, 1999, Las Vegas, Nevada, 1999. BibTeX

On Combining Computational Differentiation and Toolkits for Parallel Scientific Computing, C. H. Bischof, H. M. Bücker, and P. D. Hovland, Euro-Par 2000 -- Parallel Processing, Proceedings of the 6th International Euro-Par Conference, Munich, Germany, August/September 2000, A. Bode, T. Ludwig, W. Karl, and R. Wismüller, 86--94, 2000. BibTeX

PETSc and Overture: Lessons Learned Developing an Interface between Components, K. R. Buschelman, W. D. Gropp, L. C. McInnes, and B. F. Smith, Proceedings of the International Federation for Information Processing Working Conference on Software Architectures for Scientific Computing, Kluwer, 57--68, 2000. BibTeX

An Interface for Efficient Vector Scatters and Gathers on Parallel Machines, Barry F. Smith, Mathematics and Computer Science Division, Argonne National Laboratory, ANL/MCS-P701. BibTeX

The Transition of Numerical Software: From Nuts-and-Bolts to Abstraction, Barry Smith, SIGNUM Newsletter, 1998. BibTeX

Using ADIFOR and ADIC to Provide a Jacobian for the SNES Component of PETSc, Christian Bischof, Paul Hovland, and Po-Ting Wu, ANL, ANL/MCS-TM-233, 1997. BibTeX

Algorithm design and analysis

Agglomeration-based physical frame dG discretizations: An attempt to be mesh free, Bassi, Francesco, Botti, Lorenzo, and Colombo, Alessandro, Mathematical Models and Methods in Applied Sciences, 24, 08, 1495--1539, 2014. BibTeX

Multiscale modeling using goal-oriented adaptivity and numerical homogenization. Part II: Algorithms for the Moore-Penrose pseudoinverse, Jhurani, C. and Demkowicz, L., Computer Methods in Applied Mechanics and Engineering, 213, 418-426, 2012. BibTeX

Parallel Two-Grid Semismooth Newton-Krylov-Schwarz Method for Nonlinear Complementarity Problems, Yang, Haijian and Cai, Xiao-Chuan, J. Sci. Comput., 47, 2, 258--280, 2011. BibTeX

Parallel Iterative Substructuring in Structural Mechanics, Rheinbach, Oliver, Archives of Computational Methods in Engineering, 16, 4, 425-463, 2009. BibTeX

Finite Element Integration on GPUs, Matthew G. Knepley and Andy R. Terrel, ACM Transactions on Mathematical Software, 39, 2, http://arxiv.org/abs/1103.0066, 2013. BibTeX

Finite Element Integration with Quadrature on Accelerators, Matthew G. Knepley, Karl Rupp, and Andy R. Terrel, 2014. BibTeX

Composing Scalable Nonlinear Algebraic Solvers, Peter Brune, Mathew Knepley, Barry Smith, and Xuemin Tu, Argonne National Laboratory, ANL/MCS-P2010-0112, 2013. BibTeX

Hierarchical Krylov and Nested Krylov Methods for Extreme-Scale Computing, Lois Curfman McInnes, Barry Smith, Hong Zhang, and Richard Tran Mills, Parallel Computing, 40, 17--31, 2014. BibTeX

Hierarchical Krylov and Nested Krylov Methods for Extreme-Scale Computing, Lois Curfman McInnes, Barry Smith, Hong Zhang, and Richard Tran Mills, Argonne National Laboratory, ANL/MCS-P2097-0512, 2012. BibTeX

Composable Linear Solvers for Multiphysics, J. Brown, M. G. Knepley, D. A. May, L. C. McInnes, and B. F. Smith, Proceeedings of the 11th International Symposium on Parallel and Distributed Computing (ISPDC 2012), 55--62, 2012. BibTeX

Optimal Partitions for Eigenvalues, Blaise Bourdin, D. Bucur, and E. Oudet, SIAM J. Sci. Comput., 31, 6, 4100--4114, 2009. BibTeX

Numerical implementation of overlapping balancing domain decomposition methods on unstructured meshes, J.-H. Kimn and Blaise Bourdin, 55, 2007. BibTeX

A Technique for Accelerating the Convergence of Restarted GMRES, AH Baker, ER Jessup, and T Manteuffel, SIAM JOURNAL ON MATRIX ANALYSIS AND APPLICATIONS, 2005. BibTeX

A parallel geometric multigrid method for finite elements on octree meshes, R.S. Sampath and G. Biros. BibTeX

Bottom-up construction and 2:1 balance refinement of linear octrees in parallel, H. Sundar, R.S. Sampath, and G. Biros, SIAM Journal on Scientific Computing, 2008. BibTeX

Low-constant parallel algorithms for finite element simulations using linear octrees, H. Sundar, R.S. Sampath, S.S. Adavani, C. Davatzikos, and G. Biros, SC'07: ACM/IEEE Conference on Supercomputing, 2007. BibTeX

A Parallel Maximal Independent Set Algorithm, Adams, Mark  F., Proceedings 5th copper mountain conference on iterative methods, 1998. BibTeX

Dynamic data-driven inversion for terascale simulations: real-time identification of airborne contaminants, Ak\ccelik, V., Biros, G., Draganescu, A., Hill, J., Ghattas, O., and van Bloemen Waanders, B., Proceedings of the 2005 ACM/IEEE conference on Supercomputing, 2005. BibTeX

Frontiers of Parallel Computing, V. Akcelik, G. Biros, Omar Ghattas, J. Hill, David Keyes, and B. van Bloemen Waanders, 2006. BibTeX

Using Distributed Computers to Deterministically Approximate Higher Dimensional Convection Diffusion Equations, Matthew F. Dixon and C. J. Kenneth Tan, The Journal of Supercomputing, 28, 235--253, 2004. BibTeX

Some Parallel Linear and Nonlinear Schwarz Methods with Applications in Computational Fluid Dynamics, Feng-Nan Hwang, 2004. BibTeX

On improving the performance of the linear solver restarted GMRES, A. H. Baker, 2003. BibTeX

A Parallel Implementation of Dual-Primal FETI-DP Methods for Three Dimensional Linear Elasticity Using a Transformation of Basis, Axel Klawonn and Oliver Rheinbach, Universität Duisburg-Essen, SM-E-601, 2005. BibTeX

Inexact FETI-DP Methods, Axel Klawonn and Oliver Rheinbach, Universität Duisburg-Essen, SM-E-609, 2005. BibTeX

Robust FETI-DP Methods for Heterogeneous Three Dimensional Elasticity Problems, Axel Klawonn and Oliver Rheinbach, Universität Duisburg-Essen, SM-E-607, 2005. BibTeX

Performance of a parallel mixed finite element implementation for fourth order clamped anisotropic plate bending problems in distributed memory environments, Kshitij Kulshreshtha, Neela Nataraj, and Michael Jung, Applied Mathematics and Computation, 155, 3, 753--777, 2004. BibTeX

Using Exact Jacobians in an Implicit Newton-Krylov Method, F. D. Bramkamp, H. M. Bücker, and A. Rasch, Computers & Fluids, 35, 10, 1063--1073, 2006. BibTeX

An explicit expression for the penalty parameter of the interior penalty method, Khosro Shahbazi, Journal of Computational Physics, 205, 401--407, 2005. BibTeX

A Parallel Lanczos Algorithm for Eigensystem Calculation, Hans-Peter Kersken and Uwe Kuster, University of Stuttgart, 310, 1999. BibTeX

A component decomposition preconditioning for 3D stress analysis problems, M. D. Mihajlovi and S. Mijalkovi, Numerical Linear Algebra with Applications, 9, 567--583, 2002. BibTeX

Numerical experiments with parallel orderings for ILU preconditioners, M Benzi, W Joubert, and G Mateescu, Electronic Transactions on Numerical Analysis, 8, 88--114, 1999. BibTeX

Fast, High-Order Methods for Scattering by Inhomogeneous Media, EMK Hyde, 2003. BibTeX

Parallel Solution of Stochastic PDEs, A. Keese and H. G. Matthies, Proceedings in Applied Mathematics and Mechanics, 2, 485--486, 2003. BibTeX

Fast parallel algorithms for a broad class of nonlinear variational diffusion approaches, Joachim Weickert, Josef Heers, Christoph Schnorr, Karel J. Zuiderveld, Otmar Scherzer, and H. Siegfried Stiehl, Real Time Imaging, 7, 31--45, 2001. BibTeX

An Efficient Block Variant of GMRES, A. H. Baker, J. M. Dennis, and E. R. Jessup, University of Colorado, Boulder, CU-CS-957-03, 2003. BibTeX

Parallel Performance of Some Two-Level ASPIN Algorithms, Leszek Marcinkowski and Xiao-Chuan Cai, Proceedings of the 15th International Conference on Domain Decomposition Methods, 639--646, 2003. BibTeX

A Domain Decomposition Based Two-Level Newton Scheme for Nonlinear Problems, Deepak V. Kulkarni and Daniel A. Tortorelli, Proceedings of the 15th International Conference on Domain Decomposition Methods, 615--622, 2003. BibTeX

Some Computational Results for Dual-Primal FETI Methods for Elliptic Problems in 3D, Axel Klawonn, Oliver Rheinbach, and Olof B. Widlund, Proceedings of the 15th International Conference on Domain Decomposition Methods, 361--368, 2003. BibTeX

Improving Robustness and Parallel Scalability of Newton's Method Through Nonlinear Preconditioning, Feng-Nan Hwang and Xiao-Chuan Cai, Proceedings of the 15th International Conference on Domain Decomposition Methods, 201--208, 2003. BibTeX

Balancing Neumann-Neumann for (In)Compressible Linear Elasticity and (Generalized) Stokes and Parallel Implementation, P. Goldfeld, Proceedings of the 14th International Conference on Domain Decomposition Methods, I. Herrera, D. Keyes, O. Widlund, and R. Yates, 209--216, 2003. BibTeX

Toward scalable FETI algorithm for variational inequalities with applications to composites, Zdenek Dostal, David Horak, and Oldrich Vlach, Proceedings of the 14th International Conference on Domain Decomposition Methods, I. Herrera, D. Keyes, O. Widlund, and R. Yates, 395--401, 2003. BibTeX

Scalabilities of FETI for variational inequalities and contact shape optimization, Zdenek Dostal, David Horak, Jan Szweda, and Vit Vondrak, Proceedings of the 13th International Conference on Domain Decomposition Methods, N. Debit, M.Garbey, R. Hoppe, J. Periaux, D. Keyes, and Y. Kuznetsov, 359--367, 2002. BibTeX

A Nonlinear Additive Schwarz Preconditioned Inexact Newton Method for Shocked Duct Flows, Xiao-Chuan Cai, David E. Keyes, and David P. Young, Proceedings of the 13th International Conference on Domain Decomposition Methods, N. Debit, M.Garbey, R. Hoppe, J. Periaux, D. Keyes, and Y. Kuznetsov, 343--350, 2002. BibTeX

Multiplicative-additive preconditioning combination for general sparse linear systems, Li, Z., Lanteri S., and Saad, Y., 2003. BibTeX

Hessian-based model reduction for large-scale systems with initial-condition inputs, Bashir, O., Willcox, K., Ghattas, O., van Bloemen Waanders, B., and Hill, J., International journal for numerical methods in engineering, 73, 6, 844--868, 2008. BibTeX

Hessian-Based Model Reduction for Large-Scale Data Assimilation Problems, Bashir, O., Ghattas, O., Hill, J., van Bloemen Waanders, B., and Willcox, K., Computational Science--ICCS 2007, 1010--1017, 2007. BibTeX

Fast algorithms for Bayesian uncertainty quantification in large-scale linear inverse problems based on low-rank partial Hessian approximations, Ak\ccelik, V., Flath, H.P., Ghattas, O., Hill, J., van Bloemen Waanders, B., and Wilcox, L., SIAM Journal on Scientific Computing, 33, 1, 2011. BibTeX

Model Reduction for Large Scale Applications in Microsystem Technology, Abul K. M. Fahimuddin and Heike Fassbender, Proceedings of the 2004 SIAM Parallel Processing Conference, 2003. BibTeX

Parallel Computation of a Fully Implicit Finite Volume Method Using Different Ordering Strategies, Masoud Darbandi, Gerry E. Schneider, and Seyed Mehi Bostandoost, Proceedings of AIAA Conference, Reno, Nevada, 2004. BibTeX

A Comparative Study of Preconditioned Methods for Solving Fully Coupled Fluid Flow Equations, Masoud Darbandi, Gerry E. Schneider, and Soheyl Vakili, The 13th Annual Conference on Computational Fluid Dynamics, 2005. BibTeX

The Employment of Algebraic Multigrid as a Preconditioner to Solve Fully Implicit Mixed Convection Equations, Masoud Darbandi, Soheyl Vakili, and Gerry E. Schneider, The 44th AIAA Aerospace Sciences Meeting and Exhibit, 2006. BibTeX

Using Different Preconditioned Krylov Subspace Methods to Solve Coupled Fluid Flow Equations, Masoud Darbandi, Gerry E. Schneider, and Soheyl Vakili, Computational Fluid Dynamics, 15, 1, 2006. BibTeX

An Algebraic Multilevel Preconditioner for Field-Circuit Coupled Problems, Lahaye, D., Vandewalle, S., and Hameyer, K., J. Comput. Appl. Math., 168, 267--275, 2004. BibTeX

Faster PDE-based Simulations Using Robust Composite Linear Solvers, S. Bhowmick, P. Raghavan, L. McInnes, and B. Norris, ANL, ANL/MCS-P993-0902, To appear in Future Generation Computer Systems, 2002. BibTeX

Adaptive Sparse Linear Solvers for Implicit CFD Using Newton-Krylov Algorithms, L. McInnes, B. Norris, S. Bhowmick, and P. Raghavan, Proceedings of the Second MIT Conference on Computational Fluid and Solid Mechanics, 2003. BibTeX

The Role of Multi-Method Linear Solvers in PDE-based Simulations, S. Bhowmick, L. McInnes, B. Norris, and P. Raghavan, Proceedings of the 2003 International Conference on Computational Science and its Applications, Lecture notes in Computer Science 2677, V. Kumar, M. L. Gavrilova, C. J. K. Tan, and P. L'Ecuyer, 828--839, 2003. BibTeX

Newton-Krylov-FAC Methods for Problems Discretized on Locally Refined Grids, M. Pernice and R. D. Hornung, Computing and Visualization in Science, 2003. BibTeX

Parallel multigrid smoothing: polynomial versus Gauss--Seidel, Adams, M. F., Brezina, M., Hu, J. J., and Tuminaro, R. S, J. Comp. Phys., 188, 2, 593-610, 2003. BibTeX

A distributed memory unstructured Gauss-Seidel algorithm for multigrid smoothers, Adams, M.F., Supercomputing, ACM/IEEE 2001 Conference, 14--14, 2001. BibTeX

Static and Dynamic Graph Partitioning. A comparative study of existing algorithms, Ulrich Elsner, 2002. BibTeX

Pseudo-Transient Continuation and Differential-Algebraic Equations, Todd S. Coffey, C. T. Kelley, and David E. Keyes, ODU, Submitted to the special issue of the SIAM Journal of Scientific Computing dedicated to papers from the 2002 Copper Mountain Conference on Iterative Methods, 2002. BibTeX

Balancing Neumann-Neumann Preconditioners for Mixed Approximations of Heterogeneous Problems in Linear Elasticity, Paulo Goldfeld, Luca F. Pavarino, and Olof B. Widlund, Numerische Mathematik, 95, 283--324, 2003. BibTeX

Scalability and FETI based algorithm for large discretized variational inequalities, Z Dostal and D Horak, Mathematics and Computers in Simulation, 61, 347--357, 2003. BibTeX

36 Scalabilities of FETI for Variational Inequalities and Contact Shape Optimization, Zdenek Dostal, David Horak, Jan Szweda, and Vit Vondrak, Proceedings of the 13th International Conference on Domain Decomposition Methods, N. Debit, M. Garbey, R. Hoppe, J. Periaus, D. Keyes, and Y. Kuznetsov. BibTeX

An Algebraic Multilevel Preconditioner for Field-Circuit Coupled Problems, Domenico Lahaye, S. Vandewalle, and K. Hameyer, IEEEMAGN, 38, 2, 413-416, 2002. BibTeX

Nonlinear additive Schwarz preconditioners and applications in computational fluid dynamics, X.-C. Cai, D. E. Keyes, and L. Marcinkowski, International Journal of Numerical Methods in Fluid Mechanics, 40, 1463--1470, 2002. BibTeX

A nonlinear additive Schwarz preconditioned inexact Newton method for shocked duct flow, X.-C. Cai, D. E. Keyes, and D. P. Young, Proceedings of the 13th International Conference on Domain Decomposition Methods, N. Debit, M. Garbey, R. Hoppe, J. Periaus, D. Keyes, and Y. Kuznetsov, 2002. BibTeX

Nonlinearly preconditioned inexact Newton algorithms, X.-C. Cai and D. E. Keyes, SIAM J. Sci. Comput., 24, 183--200, 2002. BibTeX

A parallel nonlinear additive Schwarz preconditioned inexact Newton algorithm for incompressible Navier-Stokes equations, Feng-Nan Hwang and X.-C. Cai, Journal of Computational Physics, 204, 666--691, 2005. BibTeX

A Class of Parallel Two-Level Nonlinear Schwarz Preconditioned Inexact Newton Algorithms, Feng-Nan Hwang and X.-C. Cai, Computer Methods in Applied Mechanics and Engineering, 196, 1603--1611, 2006. BibTeX

A Distributed Memory Unstructured Gauss-Seidel Algorithm for Multigrid Smoothers, Mark F. Adams, ACM/IEEE Proceedings of SC2001: High Performance Networking and Computing, 2001. BibTeX

Algebraic Multigrid for Two Dimensional Time-Harmonic Magnetic Field Computations, Domenico Lahaye, Katholieke Universiteit Leuven, 2001. BibTeX

Parallel Multigrid Solvers for 3D Unstructured Finite Element Problems in Large Deformation Elasticity and Plasticity, Adams, M. F., International Journal for Numerical Methods in Engineering, 48, 8, 1241-1262, 2000. BibTeX

Evaluation of Three Unstructured Multigrid Methods on 3D Finite Element Problems in Solid Mechanics, Adams, M. F., International Journal for Numerical Methods in Engineering, 55, 1, 519-534, 2002. BibTeX

Algebraic Multigrid for Complex Symmetric Systems, Domenico Lahaye, De Gersem, H., Vandewalle, S., and Hameyer, K., IEEEMAGN, 36, 4, 1535--1538, 2000. BibTeX

Parallel Multigrid Solver Algorithms and Implementations for 3D Unstructured Finite Element Problems, Mark F. Adams and J. Demmel, Proceedings of SC99: High Performance Networking and Computing, 1999. BibTeX

Overlapping Schwarz Methods on Unstructured Meshes using Non-matching Coarse Grids, T. Chan, B. Smith, and J. Zou, Numer. Math., 73, 149--167, 1995. BibTeX

A Parallel Maximal Independent Set Algorithm, Mark F. Adams and James Demmel, University of California, Berkeley, CSD-98-993, 1998. BibTeX

An Optimal Preconditioner for a Class of Saddle Point Problems with a Penalty Term, Axel Klawonn, New York University, TR1994-676, 1994. BibTeX

Preconditioners for Indefinite Problems, Axel Klawonn, Westfalishen Wilhelms-Universitat Munster, 1995. BibTeX

Flexible Representation of Computational Meshes, Matthew G. Knepley and Dmitry A. Karpeev, Argonne National Laboratory, ANL/MCS-P1295-1005, ftp://info.mcs.anl.gov/pub/tech_reports/reports/P1295.pdf, 2005. BibTeX

Mesh Algorithms for PDE with Sieve I: Mesh Distribution, Matthew G. Knepley and Dmitry A. Karpeev, Argonne National Laboratory, ANL/MCS-P1455-0907, ftp://info.mcs.anl.gov/pub/tech_reports/reports/P1455.pdf, 2007. BibTeX

Mesh Algorithms for PDE with Sieve I: Mesh Distribution, Matthew G. Knepley and Dmitry A. Karpeev, Scientific Programming, 17, 3, 215--230, http://arxiv.org/abs/0908.4427, 2009. BibTeX

Computing the First Eigenpair of the p-Laplacian via Inverse Iteration of Sublinear Supersolutions, Biezuner, Rodney, Brown, Jed, Ercole, Grey, and Martins, Eder, Journal of Scientific Computing, 52, 180--201, 2012. BibTeX

Books

User friendly permeability predicting software for technical textiles, Verleye, B., Morren, G., Lomov, S.V., Sol, H., Verpoest, I., and Roose, D., status: published. BibTeX

Parallel Programming with MPI, Peter Pacheco, Morgan-Kaufmann, Devotes a couple of sections to PETSc, 1997. BibTeX

Domain Decomposition: Parallel Multilevel Methods for Elliptic Partial Differential Equations, Barry F. Smith, Petter Bjørstad, and William D. Gropp, Cambridge University Press, 1996. BibTeX

PETSc-FEM: A General Purpose, Parallel, Multi-physics FEM Program, M. Storti, N. Nigro, R. Paz, L. Dalcin, E. Lopez, L. Battaglia, G. Rodriguez, and G. Filippini. BibTeX

PETSc for Python -- Python bindings for PETSc libraries, Lisandro Dalcin, http://code.google.com/p/petsc4py/. BibTeX

libMesh: A C++ Library for Parallel Adaptive Mesh Refinement/Coarsening Simulations, B. S.~Kirk, J.~W.~Peterson, R.~H.~Stogner, and G.~F.~Carey, Engineering with Computers, 22, 3--4, 237--254, http://dx.doi.org/10.1007/s00366-006-0049-3, 2006. BibTeX

SISIPHUS: Scalable Ice-Sheet Solvers and Infrastructure for Petascale, High-Resolution, Unstructured Simulations, T. Tautges et al.. BibTeX

PFLOTRAN project, P. Lichtner et al.. BibTeX

PISM: A Parallel Ice Sheet Model, E. Bueler et al.. BibTeX

Dohp: Dual order hp-finite elements, J. Brown. BibTeX

Improving parallel scalability for edge plasma transport simulations with neutral gas species, M. McCourt, T. D. Rognlien, L. C. McInnes, and H. Zhang, Computational Science and Discovery, 5, 014012, Focus on 22nd International Conference on Numerical Simulations of Plasmas (ICNSP 2011), 2012. BibTeX

PetClaw Software, Kyle T. Mandli, David I. Ketcheson, Amal Alghamdi, and Aron Ahmadia, 2011. BibTeX

PyClaw software, Kyle T. Mandli, David I. Ketcheson, and others, 2012. BibTeX

High-order wave propagation algorithms for general hyperbolic systems, Ketcheson, David I., Parsani, Matteo, and LeVeque, Randall J., submitted, 2011. BibTeX

{Parallel Lagrange-Newton-Krylov-Schur methods for PDE constrained optimization. Part I: The Krylov-Schur solver}, Biros, G. and Ghattas, O., SIAM Journal on Scientific Computing, 27, 2, 687--713, 2005. BibTeX

Parallel Lagrange-Newton-Krylov-Schur methods for PDE-constrained optimization. Part II: The Lagrange Newton solver, and its application to optimal control of steady viscous flows, Biros, G. and Ghattas, O., SIAM Journal on Scientific Computing, 27, 2, 714--739, 2005. BibTeX

Ice Sheet System Model, Eric Larour, Mathieu Morlighem, and Helene Seroussi, \hrefhttp://issm.jpl.nasa.govissm.jpl.nasa.gov, 2010. BibTeX

Spatial patterns of basal drag inferred using control methods from a full-Stokes and simpler models for Pine Island Glacier, West Antarctica, Morlighem, M., Rignot, E., Seroussi, H., Larour, E., Dhia, H.B., and Aubry, D., Geophysical Research Letters, 37, 14, L14502, 2010. BibTeX

Multiple timescale calculations of sawteeth and other global macroscopic dynamics of tokamak plasmas, S. C. Jardin, N. Ferraro, J. Breslau, and J. Chen, Computational Science & Discovery, 5, 1, 2012. BibTeX

Analysis and Practical Use of Flexible BiCGStab, Jie Chen, Lois Curfman McInnes, and Hong Zhang, Argonne National Laboratory, ANL/MCS-P3039-0912, submitted to SIAM Journal on Scientific Computing, 2012. BibTeX

Achieving High Performance with Unified Residual Evaluation, Knepley, M. G., Brown, J., Rupp, K., and Smith, B.~F., ArXiv e-prints, 2013. BibTeX

Automated Solution of Differential Equations by the Finite Element Method: The FEniCS Book, Anders Logg, Kent-Andre Mardal, Garth Wells, Springer, 2012. BibTeX

Programming CUDA and OpenCL: A Case Study Using Modern C++ Libraries, Demidov, D., Ahnert, K., Rupp, K., and Gottschling, P., ArXiv e-prints, 2012. BibTeX

ViennaCL - A High Level Linear Algebra Library for GPUs and Multi-Core CPUs, Rupp, K., Rudolf, F., and Weinbub, J., Intl. Workshop on GPUs and Scientific Applications, 51-56, 2010. BibTeX