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Publications

ENZO: An Adaptive Mesh Refinement Code for
Astrophysics (Version 2.6)

2019

Corey Brummel-Smith, Greg Bryan, Iryna Butsky, Lauren Corlies, Andrew Emerick, John Forbes, Yusuke Fujimoto, Nathan J. Goldbaum, Philipp Grete, Cameron B. Hummels, Ji-hoon Kim, Daegene Koh, Miao Li, Yuan Li, Xinyu Li, Brian O’Shea, Molly S. Peeples, John A. Regan, Munier Salem, Wolfram Schmidt, Christine M. Simpson, Britton D. Smith, Jason Tumlinson, Matthew J. Turk, John H. Wise, Tom Abel, James Bordner, Renyue Cen, David C. Collins, Brian Crosby, Philipp Edelmann, Oliver Hahn, Robert Harkness, Elizabeth Harper-Clark, Shuo Kong, Alexei G. Kritsuk, Michael Kuhlen, James Larrue, Eve Lee, Greg Meece, Michael L. Norman, Jeffrey S. Oishi, Pascal Paschos, Carolyn Peruta, Alex Razoumov, Daniel R. Reynolds, Devin Silvia, Samuel W. Skillman, Stephen Skory, Geoffrey C. So, Elizabeth Tasker, Rick Wagner, Peng Wang, Hao Xu, and Fen Zhao, "ENZO: An Adaptive Mesh Refinement Code for Astrophysics (Version 2.6)," Journal of Open Source Software, 2019.

published article

SUNDIALS Multiphysics+MPIManyVector Performance Testing

2019

Daniel R. Reynolds, David J. Gardner, Cody J. Balos and Carol S. Woodward, "SUNDIALS Multiphysics+MPIManyVector Performance Testing," LLNL Technical Report LLNL-TR-791538, 2019.

arXiv eprint

Evaluation of Implicit-Explicit Additive Runge-Kutta Integrators for the HOMME-NH Dynamical Core

2019

Christopher J. Vogl, Andrew Steyer, Daniel R. Reynolds, Paul A. Ullrich and Carol S. Woodward, "Evaluation of Implicit-Explicit Additive Runge-Kutta Integrators for the HOMME-NH Dynamical Core," Journal of Advances in Modeling Earth Systems, accepted, 2019.

 

arXiv preprint

A New Class of High-Order Methods for Multirate Differential Equations

2019 (submitted)

Vu Thai Luan, Rujeko Chinomona and Daniel R. Reynolds, "A New Class of High-Order Methods for Multirate Differential Equations," submitted to SIAM J. Sci. Comput., 2019.


arXiv preprint

Relaxed Multirate Infinitesimal Step Methods

2018 (submitted)

Jean M. Sexton and Daniel R. Reynolds, "Relaxed Multirate Infinitesimal Step Methods," submitted to J. Comput. Appl. Math., 2018.


arXiv preprint

Cyclically Parallelized Treecode for Fast Computations of Electrostatic Interactions on Molecular Surfaces

2018 (submitted)

Jiahui Chen, Weihua Geng and Daniel R. Reynolds, "Cyclically Parallelized Treecode for Fast Computations of Electrostatic Interactions on Molecular Surfaces," submitted to Computer Physics Communications, 2018.

Further development of efficient and accurate time integration schemes for meteorological models

2019

Vu Thai Luan, Janusz A. Pudykiewicz and Daniel R. Reynolds, "Further development of efficient and accurate time integration schemes for meteorological models," J. Computational Physics, 376:817-837, 2019.

published article     arXiv preprint

Impacts and importance of diffusion on the spectral element method: A linear analysis

2018

Paul A. Ullrich, Daniel R. Reynolds, Jorge E. Guerra and Mark A. Taylor, "Impacts and importance of diffusion on the spectral element method: A linear analysis," J. Computational Physics, 375:427-446, 2018.

published article

Implicit-Explicit (IMEX) Runge-Kutta methods for non-hydrostatic atmospheric models

2018

David J. Gardner, Jorge E. Guerra, Francois P. Hamon, Daniel R. Reynolds, Paul A. Ullrich and Carol S. Woodward, "Implicit-Explicit (IMEX) Runge-Kutta methods for non-hydrostatic atmospheric models," Geoscientific Model Development, 11:1497-1515, 2018.

published article

Filters for improvement of multiscale data from atomistic simulations

2017

David J. Gardner and Daniel R. Reynolds, "Filters for improvement of multiscale data from atomistic simulations," SIAM J. Multiscale Model. Simul., 15:1-28, 2017.

published article

Implicit integration methods for dislocation dynamics

2015

David J. Gardner, Carol S. Woodward, Daniel R. Reynolds, Gregg Hommes, Sylvie Aubry and A. Tom Arsenlis, "Implicit integration methods for dislocation dynamics," Modelling and Simulation in Materials Science and Engineering, 23:025006, 2015.

published article

Fully-coupled simulation of cosmic reionization I: numerical methods and tests

2015

Michael L. Norman, Daniel R. Reynolds, Geoffrey C. So, Robert P. Harkness and John H. Wise, "Fully-coupled simulation of cosmic reionization I: numerical methods and tests," The Astrophysical Journal Supplement, 216:16, 2015.

published article     arXiv preprint

Fully-coupled simulation of cosmic reionization II: recombinations, clumping factors, and the photon budget for reionization

2014

Geoffrey C. So, Michael L. Norman, Daniel R. Reynolds, and John H. Wise, "Fully-coupled simulation of cosmic reionization II: recombinations, clumping factors, and the photon budget for reionization," The Astrophysical Journal, 789:149, 2014.

published article     arXiv preprint

Enzo: an adaptive mesh refinement code for astrophysics

2014

Greg L. Bryan, Michael L. Norman, Brian W. O'Shea, Tom Abel, John H. Wise, Matthew J. Turk, Daniel R. Reynolds, David C. Collins, Peng Wang, Samuel W. Skillman, Britton Smith, Robert P. Harkness, James Bordner, Ji-Hoon Kim, Michael Kuhlen, Hao Xu, Nathan Goldbaum, Cameron Hummels, Alexei G. Kritsuk, Elizabeth Tasker, Stephen Skory, Christine M. Simpson, Oliver Hahn, Jeffrey S. Oishi, Geoffrey C. So, Fen Zhao, Renyue Cen and Yuan Li, "Enzo: an adaptive mesh refinement code for astrophysics," The Astrophysical Journal Supplement, 211:19, 2014.

published article     arXiv preprint

Multiphysics simulations: challenges and opportunities

2013

David E. Keyes et al., "Multiphysics simulations: challenges and opportunities," International Journal of High Performance Computing Applications, 27:4-83, 2013.

published article

A fully implicit Newton-Krylov-Schwarz method for tokamak MHD: Jacobian construction and preconditioner formulation

2012

Daniel R. Reynolds, Ravi Samtaney, and Hilari C. Tiedeman, "A fully implicit Newton-Krylov-Schwarz method for tokamak MHD: Jacobian construction and preconditioner formulation," Computational Science & Discovery, 5:014003, 2012.

published article

Sparse Jacobian construction for mapped grid visco-resistive magnetohydrodynamics

2012

Daniel R. Reynolds and Ravi Samtaney, "Sparse Jacobian construction for mapped grid visco-resistive magnetohydrodynamics," Lecture Notes in Computational Science and Engineering, vol. 87, 2012.

Operator-based preconditioning of stiff hyperbolic systems

2010

Daniel R. Reynolds, Ravi Samtaney and Carol S. Woodward, "Operator-based preconditioning of stiff hyperbolic systems," SIAM Journal on Scientific Computing, 32:150-170, 2010.

published article

Cosmological radiation hydrodynamics with Enzo

2009

Michael L. Norman, Daniel R. Reynolds and Geoffrey C. So, "Cosmological radiation hydrodynamics with Enzo," Recent Directions in Astrophysical Quantitative Spectroscopy and Radiation Hydrodynamics, AIP, 2009.

published article     arXiv preprint

Cosmological radiative transfer codes comparison project II: the radiation-hydrodynamic tests

2009

Ilian T. Iliev, Daniel Whalen, Kyungjin Ahn, Sunghye Baek, Nickolay Y. Gnedin, Andrey V. Kravtsov, Garrelt Mellema, Michael Norman, Milan Raicevic, Daniel R. Reynolds, Daisuke Sato, Paul R. Shapiro, Benoit Semelin, Joseph Smidt, Hajime Susa, Tom Theuns and Masayuki Umemura, "Cosmological radiative transfer codes comparison project II: the radiation-hydrodynamic tests," MNRAS, 400:1283-1316, 2009.

published article     arXiv preprint

Self-consistent solution of cosmological radiation-hydrodynamics and chemical ionization

2009

Daniel R. Reynolds, John C. Hayes, Pascal Paschos and Michael L. Norman, "Self-consistent solution of cosmological radiation-hydrodynamics and chemical ionization," Journal of Computational Physics, 228:6833-6854, 2009.

published article     arXiv preprint

Vibration damping and heat transfer using material phase changes

2009

Petr Kloucek and Daniel R. Reynolds, "Vibration damping and heat transfer using material phase changes," U.S. Patent Number 7,506,735, issued March 24, 2009.

A Newton-Krylov solver for implicit solution of hydrodynamics in core collapse supernovae

2008

Daniel R. Reynolds, F. Douglas Swesty and Carol S. Woodward, "A Newton-Krylov solver for implicit solution of hydrodynamics in core collapse supernovae," Journal of Physics: Conference Series, 125, 2008. 

published article

Panel Discusses Research Directions and Enabling Technologies for the Future

2007

Daniel R. Reynolds and Ryan Szypowski, "Panel Discusses Research Directions and Enabling Technologies for the Future," SIAM NewsMay 2007.

Simulating cosmological evolution with enzo

2007

Michael L. Norman, Greg L. Bryan, Robert Harkness, James Bordner, Daniel Reynolds, Brian O'Shea and Rick Wagner, "Simulating cosmological evolution with enzo," Petascale Computing: Algorithms and Applications, D. Bader (editor), CRC Press, 2007.

arXiv preprint

Implicit solvers for large-scale nonlinear problems

2006

David E. Keyes, Daniel R. Reynolds and Carol S. Woodward, "Implicit solvers for large-scale nonlinear problems," Journal of Physics: Conference Series, 46:433-442, 2006.

published article

A fully implicit numerical method for single-fluid resistive magnetohydrodynamics

2006

Daniel R. Reynolds, Ravi Samtaney and Carol S. Woodward, "A fully implicit numerical method for single-fluid resistive magnetohydrodynamics," Journal of Computational Physics, 219:144-162, 2006.

published article

On the modeling of nonlinear thermodynamics in SMA wires

2006

Petr Kloucek and Daniel R. Reynolds, "On the modeling of nonlinear thermodynamics in SMA wires," Computer Methods in Applied Mechanics and Engineering, 196:180-191, 2006.

published article

Computational modeling of vibration damping in SMA wires

2004

Petr Kloucek, Daniel R. Reynolds and Thomas I. Seidman, "Computational modeling of vibration damping in SMA wires," Continuum Mechanics and Thermodynamics, 16:495-514, 2004.

published article

On the asymptotically stochastic computational modeling of microstructures

2004

Dennis Cox, Petr Kloucek and Daniel R. Reynolds, "On the asymptotically stochastic computational modeling of microstructures," Future Generation Computer Systems, 20: 409-424, 2004.

published article

Stochastic relaxation of variational integrals with non-attainable infima

2004

Dennis D. Cox, Petr Kloucek, Daniel R. Reynolds and Pavel Solin, "Stochastic relaxation of variational integrals with non-attainable infima," in Proc.: ENUMATH 2003 European Conference on Numerical Mathematics, Springer-Verlag, Berlin, 239-249, 2004.

A nonlinear thermodynamic model for phase transitions in shape memory alloy wires

2003

Daniel R. Reynolds, "A nonlinear thermodynamic model for phase transitions in shape memory alloy wires," Ph.D. Thesis, Rice University Department of Computational and Applied Mathematics, May 2003.

published thesis

Thermal stabilization of shape memory alloy wires

2003

Petr Kloucek, Daniel R. Reynolds and Thomas I. Seidman, "Thermal stabilization of shape memory alloy wires," in Smart Structures and Materials 2003: Modeling, Signal Processing, and Control, R.C. Smith editor, Proc. of SPIE, vol. 5049, 2003.

published article

On thermodynamic active control of shape memory alloy wires

2003

Petr Kloucek, Daniel R. Reynolds and Thomas I. Seidman, "On thermodynamic active control of shape memory alloy wires," Systems and Control Letters, 48(3-4): 211-219, 2003.

published article

The computational modeling of crystalline materials using a stochastic variational principle

2002

Dennis Cox, Petr Kloucek and Daniel R. Reynolds, "The computational modeling of crystalline materials using a stochastic variational principle," in Lecture Notes in Computer Science 2330: 461-469, 2002.

published article

A subgrid projection method for relaxation of non-attainable differential inclusions

2002

Dennis Cox, Petr Kloucek and Daniel R. Reynolds, "A subgrid projection method for relaxation of non-attainable differential inclusions," in Proc.: ENUMATH 2001 European Conference on Numerical Mathematics, Springer-Verlag, Berlin, 2002.

Efficient and automatic implementation of the adjoint state method

2002

Mark S. Gockenbach, Daniel R. Reynolds, Peng Shen, and William W. Symes, "Efficient and automatic implementation of the adjoint state method," ACM Transactions on Mathematical Software, 28(1): 22-44, 2002.

published article

Second order solution of Fritz John's ultrahyperbolic PDE for volumetric computed tomography

2001

Jicun Hu, Chris Ingrassia, Svenja Lowitzsch, Jang Park, Angel Pineda, Daniel Reynolds, Nicholas Valdivia (S.K. Patch, mentor), "Second order solution of Fritz John's ultrahyperbolic PDE for volumetric computed tomography," IMA preprint 1752-4, 2001.

published article

Automatic differentiation and the adjoint state method

2001

Mark S. Gockenbach, Daniel R. Reynolds, and William W. Symes, "Automatic differentiation and the adjoint state method," in Automatic Differentiation of Algorithms: From Simulation to Optimization, Springer-Verlag, 161-165, 2001.