skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Multiply accelerated ReaxFF molecular dynamics: coupling parallel replica dynamics with collective variable hyper dynamics

Abstract

To address the time scales required to study complex chemical reactions, methods performing accelerated molecular dynamics are necessary even with the recent advancement in high-performance computing. A number of different acceleration techniques are available. Here we explore potential synergies between two popular acceleration methods – Parallel Replica Dynamics (PRD) and Collective Variable Hyperdynamics (CVHD), by analysing the speedup obtained for the pyrolysis of n-dodecane. We determine that PRD + CVHD provides additional speedup to CVHD by reaching the required time scales for the reaction at an earlier wall-clock time. Although some speedup is obtained with the additional replicas, we found that the effectiveness of the inclusion of PRD is depreciated for systems where there is a dramatic increase in reaction rates induced by CVHD. Similar observations were made in the simulation of ethylene-carbonate/Li system, which is inherently more reactive than pyrolysis, suggest that the speedup obtained via the combination of the two acceleration methods can be generalised to most practical chemical systems.

Authors:
 [1];  [1];  [1]
+ Show Author Affiliations
  1. Pennsylvania State Univ., University Park, PA (United States)
Publication Date:
Research Org.:
Energy Frontier Research Centers (EFRC) (United States). Fluid Interface Reactions, Structures and Transport Center (FIRST). Multi-Scale Fluid-Solid Interactions in Architected and Natural Materials (MUSE); Univ. of Utah, Salt Lake City, UT (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES); US Army Research Laboratory (ARO); National Science Foundation (NSF)
OSTI Identifier:
1596124
Grant/Contract Number:  
SC0019285; W911NF-12-2-0023
Resource Type:
Accepted Manuscript
Journal Name:
Molecular Simulation
Additional Journal Information:
Journal Volume: 45; Journal Issue: 14-15; Journal ID: ISSN 0892-7022
Publisher:
Taylor & Francis
Country of Publication:
United States
Language:
English
Subject:
42 ENGINEERING; Parallel replica dynamics; collective variable hyperdynamics; pyrolysis; battery electrolytes; ReaxFF

Citation Formats

Ganeshan, Karthik, Hossain, Md. Jamil, and van Duin, Adri C. T. Multiply accelerated ReaxFF molecular dynamics: coupling parallel replica dynamics with collective variable hyper dynamics. United States: N. p., 2019. Web. doi:10.1080/08927022.2019.1646911.
Copy to clipboard
Ganeshan, Karthik, Hossain, Md. Jamil, & van Duin, Adri C. T. Multiply accelerated ReaxFF molecular dynamics: coupling parallel replica dynamics with collective variable hyper dynamics. United States. doi:https://doi.org/10.1080/08927022.2019.1646911
Copy to clipboard
Ganeshan, Karthik, Hossain, Md. Jamil, and van Duin, Adri C. T. Thu . "Multiply accelerated ReaxFF molecular dynamics: coupling parallel replica dynamics with collective variable hyper dynamics". United States. doi:https://doi.org/10.1080/08927022.2019.1646911. https://www.osti.gov/servlets/purl/1596124.
Copy to clipboard
@article{osti_1596124,
title = {Multiply accelerated ReaxFF molecular dynamics: coupling parallel replica dynamics with collective variable hyper dynamics},
author = {Ganeshan, Karthik and Hossain, Md. Jamil and van Duin, Adri C. T.},
abstractNote = {To address the time scales required to study complex chemical reactions, methods performing accelerated molecular dynamics are necessary even with the recent advancement in high-performance computing. A number of different acceleration techniques are available. Here we explore potential synergies between two popular acceleration methods – Parallel Replica Dynamics (PRD) and Collective Variable Hyperdynamics (CVHD), by analysing the speedup obtained for the pyrolysis of n-dodecane. We determine that PRD + CVHD provides additional speedup to CVHD by reaching the required time scales for the reaction at an earlier wall-clock time. Although some speedup is obtained with the additional replicas, we found that the effectiveness of the inclusion of PRD is depreciated for systems where there is a dramatic increase in reaction rates induced by CVHD. Similar observations were made in the simulation of ethylene-carbonate/Li system, which is inherently more reactive than pyrolysis, suggest that the speedup obtained via the combination of the two acceleration methods can be generalised to most practical chemical systems.},
doi = {10.1080/08927022.2019.1646911},
journal = {Molecular Simulation},
number = 14-15,
volume = 45,
place = {United States},
year = {2019},
month = {8}
}
Copy to clipboard
Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI:  https://doi.org/10.1080/08927022.2019.1646911
Copyright Statement
Other availability
Search WorldCat Search WorldCat to find libraries that may hold this journal
Citation Metrics:
Cited by: 3 works
Citation information provided by
Web of Science
Save / Share:
Export Metadata
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.

Works referenced in this record:

Application of the Embedded-Atom Method to Covalent Materials: A Semiempirical Potential for Silicon
journal, December 1987

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

Algorithms of GPU-enabled reactive force field (ReaxFF) molecular dynamics
journal, April 2013

Determining in situ phases of a nanoparticle catalyst via grand canonical Monte Carlo simulations with the ReaxFF potential
journal, July 2014

Pyrolysis of binary fuel mixtures at supercritical conditions: A ReaxFF molecular dynamics study
journal, January 2019

Charge-optimized many-body potential for the hafnium/hafnium oxide system
journal, March 2010

Connectivity-Based Parallel Replica Dynamics for Chemically Reactive Systems: From Femtoseconds to Microseconds
journal, October 2013

  • Joshi, Kaushik L.; Raman, Sumathy; van Duin, Adri C. T.
  • The Journal of Physical Chemistry Letters, Vol. 4, Issue 21
  • DOI: 10.1021/jz4019223

Merging Metadynamics into Hyperdynamics: Accelerated Molecular Simulations Reaching Time Scales from Microseconds to Seconds
journal, September 2015

  • Bal, Kristof M.; Neyts, Erik C.
  • Journal of Chemical Theory and Computation, Vol. 11, Issue 10
  • DOI: 10.1021/acs.jctc.5b00597

Hyperdynamics: Accelerated Molecular Dynamics of Infrequent Events
journal, May 1997

A mathematical formalization of the parallel replica dynamics
journal, January 2012

  • Le Bris, Claude; Lelièvre, Tony; Luskin, Mitchell
  • Monte Carlo Methods and Applications, Vol. 18, Issue 2
  • DOI: 10.1515/mcma-2012-0003

ReaxFF Reactive Force Field for Molecular Dynamics Simulations of Hydrocarbon Oxidation
journal, February 2008

  • Chenoweth, Kimberly; van Duin, Adri C. T.; Goddard, William A.
  • The Journal of Physical Chemistry A, Vol. 112, Issue 5
  • DOI: 10.1021/jp709896w

A reactive potential for hydrocarbons with intermolecular interactions
journal, April 2000

  • Stuart, Steven J.; Tutein, Alan B.; Harrison, Judith A.
  • The Journal of Chemical Physics, Vol. 112, Issue 14
  • DOI: 10.1063/1.481208

Direct observation of realistic-temperature fuel combustion mechanisms in atomistic simulations
journal, January 2016

  • Bal, Kristof M.; Neyts, Erik C.
  • Chemical Science, Vol. 7, Issue 8
  • DOI: 10.1039/C6SC00498A

Extending the Time Scale in Atomistic Simulation of Materials
journal, August 2002

Catalyzed Growth of Carbon Nanotube with Definable Chirality by Hybrid Molecular Dynamics−Force Biased Monte Carlo Simulations
journal, October 2010

  • Neyts, Erik C.; Shibuta, Yasushi; van Duin, Adri C. T.
  • ACS Nano, Vol. 4, Issue 11
  • DOI: 10.1021/nn102095y

Accelerated dynamics: Mathematical foundations and algorithmic improvements
journal, June 2015

Adaptive Accelerated ReaxFF Reactive Dynamics with Validation from Simulating Hydrogen Combustion
journal, June 2014

  • Cheng, Tao; Jaramillo-Botero, Andrés; Goddard, William A.
  • Journal of the American Chemical Society, Vol. 136, Issue 26
  • DOI: 10.1021/ja5037258

Escaping free-energy minima
journal, September 2002

  • Laio, A.; Parrinello, M.
  • Proceedings of the National Academy of Sciences, Vol. 99, Issue 20
  • DOI: 10.1073/pnas.202427399

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

Understanding Molecular Simulation
journal, January 1997

  • Frenkel, Daan; Smit, Berend; Tobochnik, Jan
  • Computers in Physics, Vol. 11, Issue 4
  • DOI: 10.1063/1.4822570

Parallel replica method for dynamics of infrequent events
journal, June 1998

Accelerated ReaxFF Simulations for Describing the Reactive Cross-Linking of Polymers
journal, July 2018

  • Vashisth, Aniruddh; Ashraf, Chowdhury; Zhang, Weiwei
  • The Journal of Physical Chemistry A, Vol. 122, Issue 32
  • DOI: 10.1021/acs.jpca.8b03826
    [ × clear filter / sort ]

    Similar Records in DOE PAGES and OSTI.GOV collections: