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:
-
- 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.
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. https://doi.org/10.1080/08927022.2019.1646911
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. https://doi.org/10.1080/08927022.2019.1646911. https://www.osti.gov/servlets/purl/1596124.
@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}
}
Web of Science
Figures / Tables:

Works referenced in this record:
Application of the Embedded-Atom Method to Covalent Materials: A Semiempirical Potential for Silicon
journal, December 1987
- Baskes, M. I.
- Physical Review Letters, Vol. 59, Issue 23
PuReMD-GPU: A reactive molecular dynamics simulation package for GPUs
journal, September 2014
- Kylasa, S. B.; Aktulga, H. M.; Grama, A. Y.
- Journal of Computational Physics, Vol. 272
Algorithms of GPU-enabled reactive force field (ReaxFF) molecular dynamics
journal, April 2013
- Zheng, Mo; Li, Xiaoxia; Guo, Li
- Journal of Molecular Graphics and Modelling, Vol. 41
Determining in situ phases of a nanoparticle catalyst via grand canonical Monte Carlo simulations with the ReaxFF potential
journal, July 2014
- Senftle, Thomas P.; van Duin, Adri C. T.; Janik, Michael J.
- Catalysis Communications, Vol. 52
Pyrolysis of binary fuel mixtures at supercritical conditions: A ReaxFF molecular dynamics study
journal, January 2019
- Ashraf, Chowdhury; Shabnam, Sharmin; Jain, Abhishek
- Fuel, Vol. 235
Charge-optimized many-body potential for the hafnium/hafnium oxide system
journal, March 2010
- Shan, Tzu-Ray; Devine, Bryce D.; Kemper, Travis W.
- Physical Review B, Vol. 81, Issue 12
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
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
Hyperdynamics: Accelerated Molecular Dynamics of Infrequent Events
journal, May 1997
- Voter, Arthur F.
- Physical Review Letters, Vol. 78, Issue 20
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
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
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
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
Accelerating Atomistic Simulations of Defect Dynamics: Hyperdynamics, Parallel Replica Dynamics, and Temperature-Accelerated Dynamics
journal, January 1998
- Voter, Arthur F.; Sørensen, Mads R.
- MRS Proceedings, Vol. 538
Extending the Time Scale in Atomistic Simulation of Materials
journal, August 2002
- Voter, Arthur F.; Montalenti, Francesco; Germann, Timothy C.
- Annual Review of Materials Research, Vol. 32, Issue 1
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
Accelerated dynamics: Mathematical foundations and algorithmic improvements
journal, June 2015
- Lelièvre, T.
- The European Physical Journal Special Topics, Vol. 224, Issue 12
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
Escaping free-energy minima
journal, September 2002
- Laio, A.; Parrinello, M.
- Proceedings of the National Academy of Sciences, Vol. 99, Issue 20
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
Understanding Molecular Simulation
journal, January 1997
- Frenkel, Daan; Smit, Berend; Tobochnik, Jan
- Computers in Physics, Vol. 11, Issue 4
Accelerating the Dynamics of Infrequent Events: Combining Hyperdynamics and Parallel Replica Dynamics to Treat Epitaxial Layer Growth
journal, January 1998
- Voter, A. F.; Germann, T. C.
- MRS Proceedings, Vol. 528
Parallel replica method for dynamics of infrequent events
journal, June 1998
- Voter, Arthur F.
- Physical Review B, Vol. 57, Issue 22
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
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