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

Authors:
; ; ; ;
Publication Date:
Sponsoring Org.:
USDOE
OSTI Identifier:
1580550
Resource Type:
Published Article
Journal Name:
SoftwareX
Additional Journal Information:
Journal Name: SoftwareX Journal Volume: 11 Journal Issue: C; Journal ID: ISSN 2352-7110
Publisher:
Elsevier
Country of Publication:
United States
Language:
English

Citation Formats

Nomura, Ken-ichi, Kalia, Rajiv K., Nakano, Aiichiro, Rajak, Pankaj, and Vashishta, Priya. RXMD: A scalable reactive molecular dynamics simulator for optimized time-to-solution. United States: N. p., 2020. Web. doi:10.1016/j.softx.2019.100389.
Nomura, Ken-ichi, Kalia, Rajiv K., Nakano, Aiichiro, Rajak, Pankaj, & Vashishta, Priya. RXMD: A scalable reactive molecular dynamics simulator for optimized time-to-solution. United States. https://doi.org/10.1016/j.softx.2019.100389
Nomura, Ken-ichi, Kalia, Rajiv K., Nakano, Aiichiro, Rajak, Pankaj, and Vashishta, Priya. Wed . "RXMD: A scalable reactive molecular dynamics simulator for optimized time-to-solution". United States. https://doi.org/10.1016/j.softx.2019.100389.
@article{osti_1580550,
title = {RXMD: A scalable reactive molecular dynamics simulator for optimized time-to-solution},
author = {Nomura, Ken-ichi and Kalia, Rajiv K. and Nakano, Aiichiro and Rajak, Pankaj and Vashishta, Priya},
abstractNote = {},
doi = {10.1016/j.softx.2019.100389},
journal = {SoftwareX},
number = C,
volume = 11,
place = {United States},
year = {2020},
month = {1}
}

Works referenced in this record:

Reactive Molecular Dynamics: Numerical Methods and Algorithmic Techniques
journal, January 2012

  • Aktulga, Hasan Metin; Pandit, Sagar A.; van Duin, Adri C. T.
  • SIAM Journal on Scientific Computing, Vol. 34, Issue 1
  • DOI: 10.1137/100808599

Nanocarbon synthesis by high-temperature oxidation of nanoparticles
journal, April 2016

  • Nomura, Ken-ichi; Kalia, Rajiv K.; Li, Ying
  • Scientific Reports, Vol. 6, Issue 1
  • DOI: 10.1038/srep24109

Energy conserving, linear scaling Born-Oppenheimer molecular dynamics
journal, October 2012

  • Cawkwell, M. J.; Niklasson, Anders M. N.
  • The Journal of Chemical Physics, Vol. 137, Issue 13
  • DOI: 10.1063/1.4755991

PuReMD-GPU: A reactive molecular dynamics simulation package for GPUs
journal, September 2014


Chemical Vapor Deposition Synthesis of MoS 2 Layers from the Direct Sulfidation of MoO 3 Surfaces Using Reactive Molecular Dynamics Simulations
journal, March 2018

  • Hong, Sungwook; Sheng, Chunyang; Krishnamoorthy, Aravind
  • The Journal of Physical Chemistry C, Vol. 122, Issue 13
  • DOI: 10.1021/acs.jpcc.7b12035

Polarizable Charge Equilibration Model for Transition-Metal Elements
journal, November 2018

  • Kwon, Soonho; Naserifar, Saber; Lee, Hyuck Mo
  • The Journal of Physical Chemistry A, Vol. 122, Issue 48
  • DOI: 10.1021/acs.jpca.8b07290

The ReaxFF reactive force-field: development, applications and future directions
journal, March 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
journal, November 2017

  • Oppenheim, Julius J.; Naserifar, Saber; Goddard, William A.
  • The Journal of Physical Chemistry A, Vol. 122, Issue 2
  • DOI: 10.1021/acs.jpca.7b06612

Charge equilibration for molecular dynamics simulations
journal, April 1991

  • Rappe, Anthony K.; Goddard, William A.
  • The Journal of Physical Chemistry, Vol. 95, Issue 8
  • DOI: 10.1021/j100161a070

Computational Synthesis of MoS 2 Layers by Reactive Molecular Dynamics Simulations: Initial Sulfidation of MoO 3 Surfaces
journal, July 2017


Extended Born-Oppenheimer Molecular Dynamics
journal, March 2008


Polarizable charge equilibration model for predicting accurate electrostatic interactions in molecules and solids
journal, March 2017

  • Naserifar, Saber; Brooks, Daniel J.; Goddard, William A.
  • The Journal of Chemical Physics, Vol. 146, Issue 12
  • DOI: 10.1063/1.4978891

Shift/collapse on neighbor list (SC-NBL): Fast evaluation of dynamic many-body potentials in molecular dynamics simulations
journal, February 2019

  • Kunaseth, Manaschai; Hannongbua, Supa; Nakano, Aiichiro
  • Computer Physics Communications, Vol. 235
  • DOI: 10.1016/j.cpc.2018.09.021

ACKS2: Atom-condensed Kohn-Sham DFT approximated to second order
journal, February 2013

  • Verstraelen, T.; Ayers, P. W.; Van Speybroeck, V.
  • The Journal of Chemical Physics, Vol. 138, Issue 7
  • DOI: 10.1063/1.4791569

Fast Parallel Algorithms for Short-Range Molecular Dynamics
journal, March 1995


Hybrid quantum mechanical/molecular dynamics simulation on parallel computers: density functional theory on real-space multigrids
journal, November 2002


Generalized extended Lagrangian Born-Oppenheimer molecular dynamics
journal, October 2014

  • Niklasson, Anders M. N.; Cawkwell, Marc J.
  • The Journal of Chemical Physics, Vol. 141, Issue 16
  • DOI: 10.1063/1.4898803

Reactive nanojets: Nanostructure-enhanced chemical reactions in a defected energetic crystal
journal, October 2007

  • Nomura, Ken-ichi; Kalia, Rajiv K.; Nakano, Aiichiro
  • Applied Physics Letters, Vol. 91, Issue 18
  • DOI: 10.1063/1.2804557

ReaxFF:  A Reactive Force Field for Hydrocarbons
journal, October 2001

  • van Duin, Adri C. T.; Dasgupta, Siddharth; Lorant, Francois
  • The Journal of Physical Chemistry A, Vol. 105, Issue 41
  • DOI: 10.1021/jp004368u

GULP: A computer program for the symmetry-adapted simulation of solids
journal, January 1997

  • Gale, Julian D.
  • Journal of the Chemical Society, Faraday Transactions, Vol. 93, Issue 4
  • DOI: 10.1039/a606455h

Dynamic Transition in the Structure of an Energetic Crystal during Chemical Reactions at Shock Front Prior to Detonation
journal, October 2007


Hybrid finite-element/molecular-dynamics/electronic-density-functional approach to materials simulations on parallel computers
journal, August 2001


Shift-Collapse Acceleration of Generalized Polarizable Reactive Molecular Dynamics for Machine Learning-Assisted Computational Synthesis of Layered Materials
conference, November 2018

  • Liu, Kuang; Vashishta, Priya; Kunaseth, Manaschai
  • 2018 IEEE/ACM 9th Workshop on Latest Advances in Scalable Algorithms for Large-Scale Systems (scalA)
  • DOI: 10.1109/ScalA.2018.00009

Embrittlement of Metal by Solute Segregation-Induced Amorphization
journal, April 2010


Multiobjective genetic training and uncertainty quantification of reactive force fields
journal, August 2018


QM/MM Methods for Biomolecular Systems
journal, January 2009

  • Senn, Hans Martin; Thiel, Walter
  • Angewandte Chemie International Edition, Vol. 48, Issue 7
  • DOI: 10.1002/anie.200802019

Mechanochemistry of shock-induced nanobubble collapse near silica in water
journal, August 2012

  • Nomura, K.; Kalia, R. K.; Nakano, A.
  • Applied Physics Letters, Vol. 101, Issue 7
  • DOI: 10.1063/1.4746270

Sustainable Adaptive Grid Supercomputing: Multiscale Simulation of Semiconductor Processing across the Pacific
conference, November 2006

  • Takemiya, Hiroshi; Tanaka, Yoshio; Sekiguchi, Satoshi
  • ACM/IEEE SC 2006 Conference (SC'06)
  • DOI: 10.1109/SC.2006.59

Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques
journal, April 2012


Inertial extended-Lagrangian scheme for solving charge equilibration models
journal, January 2019

  • Leven, Itai; Head-Gordon, Teresa
  • Physical Chemistry Chemical Physics, Vol. 21, Issue 34
  • DOI: 10.1039/C9CP02979F

Electronegativity-equalization method for the calculation of atomic charges in molecules
journal, July 1986

  • Mortier, Wilfried J.; Ghosh, Swapan K.; Shankar, S.
  • Journal of the American Chemical Society, Vol. 108, Issue 15
  • DOI: 10.1021/ja00275a013

Collaborative Simulation Grid: Multiscale Quantum-Mechanical/Classical Atomistic Simulations on Distributed PC Clusters in the US and Japan
conference, January 2002


Coupling Length Scales for Multiscale Atomistics-Continuum Simulations: Atomistically Induced Stress Distributions in Si / Si 3 N 4 Nanopixels
journal, August 2001


eReaxFF: A Pseudoclassical Treatment of Explicit Electrons within Reactive Force Field Simulations
journal, July 2016

  • Islam, Md Mahbubul; Kolesov, Grigory; Verstraelen, Toon
  • Journal of Chemical Theory and Computation, Vol. 12, Issue 8
  • DOI: 10.1021/acs.jctc.6b00432

A scalable parallel algorithm for large-scale reactive force-field molecular dynamics simulations
journal, January 2008

  • Nomura, Ken-ichi; Kalia, Rajiv K.; Nakano, Aiichiro
  • Computer Physics Communications, Vol. 178, Issue 2
  • DOI: 10.1016/j.cpc.2007.08.014

An extended-Lagrangian scheme for charge equilibration in reactive molecular dynamics simulations
journal, July 2015

  • Nomura, Ken-ichi; Small, Patrick E.; Kalia, Rajiv K.
  • Computer Physics Communications, Vol. 192
  • DOI: 10.1016/j.cpc.2015.02.023