Parallel algorithms for hyperdynamics and local hyperdynamics

Plimpton, Steven J.; Perez, Danny; Voter, Arthur F.

doi:10.1063/5.0014448

Parallel algorithms for hyperdynamics and local hyperdynamics

Journal Article · Wed Aug 05 00:00:00 EDT 2020 · Journal of Chemical Physics

DOI:https://doi.org/10.1063/5.0014448· OSTI ID:1668355

^[1]; Perez, Danny ^[2]; ^[2]

Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)
Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

Hyperdynamics (HD) is a method for accelerating the timescale of standard molecular dynamics (MD). It can be used for simulations of systems with an energy potential landscape that is a collection of basins, separated by barriers, where transitions between basins are infrequent. HD enables the system to escape from a basin more quickly while enabling a statistically accurate renormalization of the simulation time, thus effectively boosting the timescale of the simulation. In [Kim, Perez, Voter, J Chem Phys, 139:144110, 2013)1, a local version of HD was formulated, which exploits the intrinsic locality characteristic typical of most systems to mitigate the poor scaling properties of standard HD as the system size is increased. In this paper, we discuss how both HD and local HD can be formulated to run efficiently in parallel. We have implemented these ideas in the LAMMPS MD code, which means HD can be used with any interatomic potential LAMMPS supports. Together, these parallel methods allow simulations of any size to achieve the time acceleration offered by HD (which can be orders of magnitude), at a cost 3-5x that of standard MD. As examples, we performed two simulations of a million-atom system to model the diffusion and clustering of Pt adatoms on a large patch of Pt(100) surface for 80 and 160 μs.

View Accepted Manuscript (DOE)

Research Organization:: Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States)

Sponsoring Organization:: USDOE National Nuclear Security Administration (NNSA); USDOE Office of Science (SC)

Grant/Contract Number:: AC04-94AL85000

OSTI ID:: 1668355

Alternate ID(s):: OSTI ID: 1645148

Report Number(s):: SAND--2020-4952J; 686012

Journal Information:: Journal of Chemical Physics, Journal Name: Journal of Chemical Physics Journal Issue: 5 Vol. 153; ISSN 0021-9606

Publisher:: American Institute of Physics (AIP)Copyright Statement

Country of Publication:: United States

Language:: English

References (36)

Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing Pande, Vijay S.; Baker, Ian; Chapman, Jarrod Biopolymers, Vol. 68, Issue 1 https://doi.org/10.1002/bip.10219	journal	December 2002
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
Frequency factors and isotope effects in solid state rate processes Vineyard, George H. Journal of Physics and Chemistry of Solids, Vol. 3, Issue 1-2 https://doi.org/10.1016/0022-3697(57)90059-8	journal	January 1957
The parallel replica dynamics method – Coming of age Perez, Danny; Uberuaga, Blas P.; Voter, Arthur F. Computational Materials Science, Vol. 100 https://doi.org/10.1016/j.commatsci.2014.12.011	journal	April 2015
Accelerated molecular dynamics simulations for characterizing plastic deformation in crystalline materials with cracks Chakraborty, Subhendu; Zhang, Jiaxi; Ghosh, Somnath Computational Materials Science, Vol. 121 https://doi.org/10.1016/j.commatsci.2016.04.026	journal	August 2016
gen.parRep: A first implementation of the Generalized Parallel Replica dynamics for the long time simulation of metastable biochemical systems Hédin, Florent; Lelièvre, Tony Computer Physics Communications, Vol. 239 https://doi.org/10.1016/j.cpc.2019.01.005	journal	June 2019
Multiscale diffusion method for simulations of long-time defect evolution with application to dislocation climb Baker, K. L.; Curtin, W. A. Journal of the Mechanics and Physics of Solids, Vol. 92 https://doi.org/10.1016/j.jmps.2016.04.006	journal	July 2016
Markov state models of biomolecular conformational dynamics Chodera, John D.; Noé, Frank Current Opinion in Structural Biology, Vol. 25 https://doi.org/10.1016/j.sbi.2014.04.002	journal	April 2014
Brownian motion in a field of force and the diffusion model of chemical reactions Kramers, H. A. Physica, Vol. 7, Issue 4 https://doi.org/10.1016/s0031-8914(40)90098-2	journal	April 1940
Accelerated Molecular Dynamics Methods: Introduction and Recent Developments Perez, Danny; Uberuaga, Blas P.; Shim, Yunsic Annual Reports in Computational Chemistry, Vol. 5, p. 79-98 https://doi.org/10.1016/s1574-1400(09)00504-0	book	January 2009
Long-Time Dynamics through Parallel Trajectory Splicing Perez, Danny; Cubuk, Ekin D.; Waterland, Amos Journal of Chemical Theory and Computation, Vol. 12, Issue 1 https://doi.org/10.1021/acs.jctc.5b00916	journal	December 2015
Adaptive Accelerated ReaxFF Reactive Dynamics with Validation from Simulating Hydrogen Combustion Cheng, Tao; Jaramillo-Botero, Andrés; Goddard, William A. Journal of the American Chemical Society, Vol. 136, Issue 26 https://doi.org/10.1021/ja5037258	journal	June 2014
Markov State Models: From an Art to a Science Husic, Brooke E.; Pande, Vijay S. Journal of the American Chemical Society, Vol. 140, Issue 7 https://doi.org/10.1021/jacs.7b12191	journal	February 2018
Accelerated molecular dynamics with the bond-boost method Miron, Radu A.; Fichthorn, Kristen A. The Journal of Chemical Physics, Vol. 119, Issue 12 https://doi.org/10.1063/1.1603722	journal	September 2003
Accelerated molecular dynamics: A promising and efficient simulation method for biomolecules Hamelberg, Donald; Mongan, John; McCammon, J. Andrew The Journal of Chemical Physics, Vol. 120, Issue 24 https://doi.org/10.1063/1.1755656	journal	June 2004
Parallel replica dynamics with a heterogeneous distribution of barriers: Application to n -hexadecane pyrolysis Kum, Oyeon; Dickson, Brad M.; Stuart, Steven J. The Journal of Chemical Physics, Vol. 121, Issue 20 https://doi.org/10.1063/1.1807823	journal	November 2004
A method for accelerating the molecular dynamics simulation of infrequent events Voter, Arthur F. The Journal of Chemical Physics, Vol. 106, Issue 11 https://doi.org/10.1063/1.473503	journal	March 1997
Temperature-accelerated dynamics for simulation of infrequent events So/rensen, Mads R.; Voter, Arthur F. The Journal of Chemical Physics, Vol. 112, Issue 21 https://doi.org/10.1063/1.481576	journal	June 2000
Local hyperdynamics Kim, Soo Young; Perez, Danny; Voter, Arthur F. The Journal of Chemical Physics, Vol. 139, Issue 14 https://doi.org/10.1063/1.4824389	journal	October 2013
Extending atomistic simulation timescale in solid/liquid systems: Crystal growth from solution by a parallel-replica dynamics and continuum hybrid method Lu, Chun-Yaung; Voter, Arthur F.; Perez, Danny The Journal of Chemical Physics, Vol. 140, Issue 4 https://doi.org/10.1063/1.4862681	journal	January 2014
Hyperdynamics boost factor achievable with an ideal bias potential Huang, Chen; Perez, Danny; Voter, Arthur F. The Journal of Chemical Physics, Vol. 143, Issue 7 https://doi.org/10.1063/1.4928636	journal	August 2015
Large-scale conformational sampling of proteins using temperature-accelerated molecular dynamics Abrams, C. F.; Vanden-Eijnden, E. Proceedings of the National Academy of Sciences, Vol. 107, Issue 11 https://doi.org/10.1073/pnas.0914540107	journal	March 2010
Multiply accelerated ReaxFF molecular dynamics: coupling parallel replica dynamics with collective variable hyper dynamics Ganeshan, Karthik; Hossain, Md. Jamil; van Duin, Adri C. T. Molecular Simulation, Vol. 45, Issue 14-15 https://doi.org/10.1080/08927022.2019.1646911	journal	August 2019
Visualization and analysis of atomistic simulation data with OVITO–the Open Visualization Tool Stukowski, Alexander Modelling and Simulation in Materials Science and Engineering, Vol. 18, Issue 1 https://doi.org/10.1088/0965-0393/18/1/015012	journal	December 2009
Accelerated molecular dynamics simulation of low-velocity frictional sliding Kim, W. K.; Falk, M. L. Modelling and Simulation in Materials Science and Engineering, Vol. 18, Issue 3 https://doi.org/10.1088/0965-0393/18/3/034003	journal	March 2010
Embedded-atom method: Derivation and application to impurities, surfaces, and other defects in metals Daw, Murray S.; Baskes, M. I. Physical Review B, Vol. 29, Issue 12 https://doi.org/10.1103/physrevb.29.6443	journal	June 1984
Parallel replica method for dynamics of infrequent events Voter, Arthur F. Physical Review B, Vol. 57, Issue 22 https://doi.org/10.1103/physrevb.57.r13985	journal	June 1998
Heteroepitaxial growth of Co ∕ Cu ( 001 ) : An accelerated molecular dynamics simulation study Miron, Radu A.; Fichthorn, Kristen A. Physical Review B, Vol. 72, Issue 3 https://doi.org/10.1103/physrevb.72.035415	journal	July 2005
Accelerated Molecular Dynamics of Temperature-Programed Desorption Becker, Kelly E.; Mignogna, Maria H.; Fichthorn, Kristen A. Physical Review Letters, Vol. 102, Issue 4 https://doi.org/10.1103/physrevlett.102.046101	journal	January 2009
Surface self-diffusion on Pt(001) by an atomic exchange mechanism Kellogg, G. L.; Feibelman, Peter J. Physical Review Letters, Vol. 64, Issue 26 https://doi.org/10.1103/physrevlett.64.3143	journal	June 1990
Surface diffusion modes for Pt dimers and trimers on Pt(001) Kellogg, G. L.; Voter, A. F. Physical Review Letters, Vol. 67, Issue 5 https://doi.org/10.1103/physrevlett.67.622	journal	July 1991
Hyperdynamics: Accelerated Molecular Dynamics of Infrequent Events Voter, Arthur F. Physical Review Letters, Vol. 78, Issue 20 https://doi.org/10.1103/physrevlett.78.3908	journal	May 1997
Multiple-Time Scale Accelerated Molecular Dynamics: Addressing the Small-Barrier Problem Miron, Radu A.; Fichthorn, Kristen A. Physical Review Letters, Vol. 93, Issue 12 https://doi.org/10.1103/physrevlett.93.128301	journal	September 2004
Extending the Time Scale in Atomistic Simulation of Materials Voter, Arthur F.; Montalenti, Francesco; Germann, Timothy C. Annual Review of Materials Research, Vol. 32, Issue 1 https://doi.org/10.1146/annurev.matsci.32.112601.141541	journal	August 2002
A mathematical formalization of the parallel replica dynamics Le Bris, Claude; Lelièvre, Tony; Luskin, Mitchell Monte Carlo Methods and Applications, Vol. 18, Issue 2 https://doi.org/10.1515/mcma-2012-0003	journal	January 2012
Accelerating the Dynamics of Infrequent Events: Combining Hyperdynamics and Parallel Replica Dynamics to Treat Epitaxial Layer Growth Voter, A. F.; Germann, T. C. MRS Proceedings, Vol. 528 https://doi.org/10.1557/proc-528-221	journal	January 1998

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74 ATOMIC AND MOLECULAR PHYSICS
LAMMPS
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parallel algorithms

Parallel algorithms for hyperdynamics and local hyperdynamics

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