RXMD: A scalable reactive molecular dynamics simulator for optimized time-to-solution

Nomura, Ken-ichi; Kalia, Rajiv K.; Nakano, Aiichiro; Rajak, Pankaj; Vashishta, Priya

doi:10.1016/j.softx.2019.100389

Title: RXMD: A scalable reactive molecular dynamics simulator for optimized time-to-solution

Journal Article · 31 December 2019 · SoftwareX

DOI: https://doi.org/10.1016/j.softx.2019.100389 · OSTI ID:1580550

Nomura, Ken-ichi; Kalia, Rajiv K.; Nakano, Aiichiro; Rajak, Pankaj; Vashishta, Priya

Not Available

View Journal Article

Cite

Export

Save

Sponsoring Organization:: USDOE

OSTI ID:: 1580550

Journal Information:: SoftwareX, Journal Name: SoftwareX Journal Issue: C Vol. 11; ISSN 2352-7110

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: English

References (37)

QM/MM Methods for Biomolecular Systems Senn, Hans Martin; Thiel, Walter Angewandte Chemie International Edition, Vol. 48, Issue 7 https://doi.org/10.1002/anie.200802019	journal	January 2009
Fast Parallel Algorithms for Short-Range Molecular Dynamics Plimpton, Steve Journal of Computational Physics, Vol. 117, Issue 1 https://doi.org/10.1006/jcph.1995.1039	journal	March 1995
Theoretical studies of enzymic reactions: Dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme Warshel, A.; Levitt, M. Journal of Molecular Biology, Vol. 103, Issue 2 https://doi.org/10.1016/0022-2836(76)90311-9	journal	May 1976
Hybrid finite-element/molecular-dynamics/electronic-density-functional approach to materials simulations on parallel computers Ogata, Shuji; Lidorikis, Elefterios; Shimojo, Fuyuki Computer Physics Communications, Vol. 138, Issue 2 https://doi.org/10.1016/S0010-4655(01)00203-X	journal	August 2001
Hybrid quantum mechanical/molecular dynamics simulation on parallel computers: density functional theory on real-space multigrids Ogata, Shuji; Shimojo, Fuyuki; Kalia, Rajiv K. Computer Physics Communications, Vol. 149, Issue 1 https://doi.org/10.1016/S0010-4655(02)00612-4	journal	November 2002
A scalable parallel algorithm for large-scale reactive force-field molecular dynamics simulations Nomura, Ken-ichi; Kalia, Rajiv K.; Nakano, Aiichiro Computer Physics Communications, Vol. 178, Issue 2 https://doi.org/10.1016/j.cpc.2007.08.014	journal	January 2008
An extended-Lagrangian scheme for charge equilibration in reactive molecular dynamics simulations Nomura, Ken-ichi; Small, Patrick E.; Kalia, Rajiv K. Computer Physics Communications, Vol. 192 https://doi.org/10.1016/j.cpc.2015.02.023	journal	July 2015
Shift/collapse on neighbor list (SC-NBL): Fast evaluation of dynamic many-body potentials in molecular dynamics simulations Kunaseth, Manaschai; Hannongbua, Supa; Nakano, Aiichiro Computer Physics Communications, Vol. 235 https://doi.org/10.1016/j.cpc.2018.09.021	journal	February 2019
PuReMD-GPU: A reactive molecular dynamics simulation package for GPUs Kylasa, S. B.; Aktulga, H. M.; Grama, A. Y. Journal of Computational Physics, Vol. 272 https://doi.org/10.1016/j.jcp.2014.04.035	journal	September 2014
Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques Aktulga, H. M.; Fogarty, J. C.; Pandit, S. A. Parallel Computing, Vol. 38, Issue 4-5 https://doi.org/10.1016/j.parco.2011.08.005	journal	April 2012
eReaxFF: A Pseudoclassical Treatment of Explicit Electrons within Reactive Force Field Simulations Islam, Md Mahbubul; Kolesov, Grigory; Verstraelen, Toon Journal of Chemical Theory and Computation, Vol. 12, Issue 8 https://doi.org/10.1021/acs.jctc.6b00432	journal	July 2016
Extension of the Polarizable Charge Equilibration Model to Higher Oxidation States with Applications to Ge, As, Se, Br, Sn, Sb, Te, I, Pb, Bi, Po, and At Elements Oppenheim, Julius J.; Naserifar, Saber; Goddard, William A. The Journal of Physical Chemistry A, Vol. 122, Issue 2 https://doi.org/10.1021/acs.jpca.7b06612	journal	November 2017
Polarizable Charge Equilibration Model for Transition-Metal Elements Kwon, Soonho; Naserifar, Saber; Lee, Hyuck Mo The Journal of Physical Chemistry A, Vol. 122, Issue 48 https://doi.org/10.1021/acs.jpca.8b07290	journal	November 2018
Chemical Vapor Deposition Synthesis of MoS 2 Layers from the Direct Sulfidation of MoO 3 Surfaces Using Reactive Molecular Dynamics Simulations Hong, Sungwook; Sheng, Chunyang; Krishnamoorthy, Aravind The Journal of Physical Chemistry C, Vol. 122, Issue 13 https://doi.org/10.1021/acs.jpcc.7b12035	journal	March 2018
Computational Synthesis of MoS ₂ Layers by Reactive Molecular Dynamics Simulations: Initial Sulfidation of MoO ₃ Surfaces Hong, Sungwook; Krishnamoorthy, Aravind; Rajak, Pankaj Nano Letters, Vol. 17, Issue 8 https://doi.org/10.1021/acs.nanolett.7b01727	journal	July 2017
Charge equilibration for molecular dynamics simulations Rappe, Anthony K.; Goddard, William A. The Journal of Physical Chemistry, Vol. 95, Issue 8 https://doi.org/10.1021/j100161a070	journal	April 1991
Electronegativity-equalization method for the calculation of atomic charges in molecules Mortier, Wilfried J.; Ghosh, Swapan K.; Shankar, S. Journal of the American Chemical Society, Vol. 108, Issue 15 https://doi.org/10.1021/ja00275a013	journal	July 1986
ReaxFF: A Reactive Force Field for Hydrocarbons van Duin, Adri C. T.; Dasgupta, Siddharth; Lorant, Francois The Journal of Physical Chemistry A, Vol. 105, Issue 41 https://doi.org/10.1021/jp004368u	journal	October 2001
The ReaxFF reactive force-field: development, applications and future directions Senftle, Thomas P.; Hong, Sungwook; Islam, Md Mahbubul npj Computational Materials, Vol. 2, Issue 1 https://doi.org/10.1038/npjcompumats.2015.11	journal	March 2016
Multiobjective genetic training and uncertainty quantification of reactive force fields Mishra, Ankit; Hong, Sungwook; Rajak, Pankaj npj Computational Materials, Vol. 4, Issue 1 https://doi.org/10.1038/s41524-018-0098-3	journal	August 2018
Nanocarbon synthesis by high-temperature oxidation of nanoparticles Nomura, Ken-ichi; Kalia, Rajiv K.; Li, Ying Scientific Reports, Vol. 6, Issue 1 https://doi.org/10.1038/srep24109	journal	April 2016
Inertial extended-Lagrangian scheme for solving charge equilibration models Leven, Itai; Head-Gordon, Teresa Physical Chemistry Chemical Physics, Vol. 21, Issue 34 https://doi.org/10.1039/C9CP02979F	journal	January 2019
GULP: A computer program for the symmetry-adapted simulation of solids Gale, Julian D. Journal of the Chemical Society, Faraday Transactions, Vol. 93, Issue 4 https://doi.org/10.1039/a606455h	journal	January 1997
Reactive nanojets: Nanostructure-enhanced chemical reactions in a defected energetic crystal Nomura, Ken-ichi; Kalia, Rajiv K.; Nakano, Aiichiro Applied Physics Letters, Vol. 91, Issue 18 https://doi.org/10.1063/1.2804557	journal	October 2007
Mechanochemistry of shock-induced nanobubble collapse near silica in water Nomura, K.; Kalia, R. K.; Nakano, A. Applied Physics Letters, Vol. 101, Issue 7 https://doi.org/10.1063/1.4746270	journal	August 2012
Energy conserving, linear scaling Born-Oppenheimer molecular dynamics Cawkwell, M. J.; Niklasson, Anders M. N. The Journal of Chemical Physics, Vol. 137, Issue 13 https://doi.org/10.1063/1.4755991	journal	October 2012
ACKS2: Atom-condensed Kohn-Sham DFT approximated to second order Verstraelen, T.; Ayers, P. W.; Van Speybroeck, V. The Journal of Chemical Physics, Vol. 138, Issue 7 https://doi.org/10.1063/1.4791569	journal	February 2013
Generalized extended Lagrangian Born-Oppenheimer molecular dynamics Niklasson, Anders M. N.; Cawkwell, Marc J. The Journal of Chemical Physics, Vol. 141, Issue 16 https://doi.org/10.1063/1.4898803	journal	October 2014
Polarizable charge equilibration model for predicting accurate electrostatic interactions in molecules and solids Naserifar, Saber; Brooks, Daniel J.; Goddard, William A. The Journal of Chemical Physics, Vol. 146, Issue 12 https://doi.org/10.1063/1.4978891	journal	March 2017
Extended Born-Oppenheimer Molecular Dynamics Niklasson, Anders M. N. Physical Review Letters, Vol. 100, Issue 12 https://doi.org/10.1103/PhysRevLett.100.123004	journal	March 2008
Embrittlement of Metal by Solute Segregation-Induced Amorphization Chen, Hsiu-Pin; Kalia, Rajiv K.; Kaxiras, Efthimios Physical Review Letters, Vol. 104, Issue 15 https://doi.org/10.1103/PhysRevLett.104.155502	journal	April 2010
Coupling Length Scales for Multiscale Atomistics-Continuum Simulations: Atomistically Induced Stress Distributions in Si / Si 3 N 4 Nanopixels Lidorikis, Elefterios; Bachlechner, Martina E.; Kalia, Rajiv K. Physical Review Letters, Vol. 87, Issue 8 https://doi.org/10.1103/PhysRevLett.87.086104	journal	August 2001
Dynamic Transition in the Structure of an Energetic Crystal during Chemical Reactions at Shock Front Prior to Detonation Nomura, Ken-ichi; Kalia, Rajiv K.; Nakano, Aiichiro Physical Review Letters, Vol. 99, Issue 14 https://doi.org/10.1103/PhysRevLett.99.148303	journal	October 2007
Collaborative Simulation Grid: Multiscale Quantum-Mechanical/Classical Atomistic Simulations on Distributed PC Clusters in the US and Japan Kikuchi, H.; Kalia, R. K.; Nakano, A. ACM/IEEE SC 2002 Conference (SC'02) https://doi.org/10.1109/SC.2002.10013	conference	January 2002
Sustainable Adaptive Grid Supercomputing: Multiscale Simulation of Semiconductor Processing across the Pacific Takemiya, Hiroshi; Tanaka, Yoshio; Sekiguchi, Satoshi ACM/IEEE SC 2006 Conference (SC'06) https://doi.org/10.1109/SC.2006.59	conference	November 2006
Shift-Collapse Acceleration of Generalized Polarizable Reactive Molecular Dynamics for Machine Learning-Assisted Computational Synthesis of Layered Materials Liu, Kuang; Vashishta, Priya; Kunaseth, Manaschai 2018 IEEE/ACM 9th Workshop on Latest Advances in Scalable Algorithms for Large-Scale Systems (scalA) https://doi.org/10.1109/ScalA.2018.00009	conference	November 2018
Reactive Molecular Dynamics: Numerical Methods and Algorithmic Techniques Aktulga, Hasan Metin; Pandit, Sagar A.; van Duin, Adri C. T. SIAM Journal on Scientific Computing, Vol. 34, Issue 1 https://doi.org/10.1137/100808599	journal	January 2012

Similar Records

Scalable Reactive Molecular Dynamics Simulations for Computational Synthesis

Journal Article · 2019 · Computing in Science and Engineering · OSTI ID:1593152

Li, Ying; Nomura, Ken-ichi; Insley, Joseph; +7 more

Buckybomb: Reactive Molecular Dynamics Simulation

Journal Article · 2015 · Journal of Physical Chemistry Letters · OSTI ID:1241924

Chaban, Vitaly V.; Fileti, Eudes Eterno; Prezhdo, Oleg V.

Optimizing the Performance of Reactive Molecular Dynamics Simulations for Multi-core Architectures

Journal Article · 2015 · OSTI ID:1427253

Aktulga, Hasan Metin; Coffman, Paul; Shan, Tzu-Ray; +2 more

Title: RXMD: A scalable reactive molecular dynamics simulator for optimized time-to-solution

Citation Formats

References (37)

Similar Records

Related Subjects