Localized saddle-point search and application to temperature-accelerated dynamics

Shim, Yunsic; Callahan, Nathan; Amar, Jacques G.

doi:10.1063/1.4793218

Cited by 11 publications

(4 citation statements)

References 50 publications

(50 reference statements)

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“…TSSCDS is based on running high‐energy dynamics, which is a strategy similar to the temperature AD technique . However, in TSSCDS an algorithm (BBFS) is used to directly provide an initial guess for the TS structure.…”

Section: Methodsmentioning

confidence: 99%

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An automated method to find transition states using chemical dynamics simulations

2014

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A procedure to automatically find the transition states (TSs) of a molecular system (MS) is proposed. It has two components: high-energy chemical dynamics simulations (CDS), and an algorithm that analyzes the geometries along the trajectories to find reactive pathways. Two levels of electronic structure calculations are involved: a low level (LL) is used to integrate the trajectories and also to optimize the TSs, and a higher level (HL) is used to reoptimize the structures. The method has been tested in three MSs: formaldehyde, formic acid (FA), and vinyl cyanide (VC), using MOPAC2012 and Gaussian09 to run the LL and HL calculations, respectively. Both the efficacy and efficiency of the method are very good, with around 15 TS structures optimized every 10 trajectories, which gives a total of 7, 12, and 83 TSs for formaldehyde, FA, and VC, respectively. The use of CDS makes it a powerful tool to unveil possible nonstatistical behavior of the system under study.

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Section: Methodsmentioning

confidence: 99%

“…Several accelerated dynamics (AD) methods have been proposed in the literature to simulate infrequent events, and some of them have been implemented in popular molecular dynamics programs. Our method and the AD methods share in common the use of high‐energy or high‐temperature dynamics.…”

Section: Introductionmentioning

confidence: 99%

An automated method to find transition states using chemical dynamics simulations

2014

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“…48 TSSCDS has two major components: high-energy chemical dynamics (or classical trajectory) simulations, and a very efficient geometry-based algorithm to identify bond breaking/formation (BBF) processes called BBFS (S for search). Several methods proposed in the literature [49][50][51][52][53][54][55][56][57][58][59][60][61][62][63][64][65][66][67][68] share in common with TSSCDS the use of accelerated dynamics. However, the novelty of our method is the direct search of TS structures, using the BBFS, from the simulation snapshots.…”

Section: Introductionmentioning

confidence: 99%

An automated transition state search using classical trajectories initialized at multiple minima

Martı́nez-Núñez

2015

Phys. Chem. Chem. Phys.

129

186

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Very recently, we proposed an automated method for finding transition states of chemical reactions using dynamics simulations; the method has been termed Transition State Search using Chemical Dynamics Simulations (TSSCDS) (E. Martínez-Núñez, J. Comput. Chem., 2015, 36, 222-234). In the present work, an improved automated search procedure is developed, which consists of iteratively running different ensembles of trajectories initialized at different minima. The iterative TSSCDS method is applied to the complex C3H4O system, obtaining a total of 66 different minima and 276 transition states. With the obtained transition states and paths, statistical RRKM calculations and Kinetic Monte Carlo simulations are carried out to study the fragmentation dynamics of propenal, which is the global minimum of the system. The kinetic simulations provide a (three-body dissociation)/(CO elimination) ratio of 1.49 for an excitation energy of 148 kcal mol(-1), which agrees well with the corresponding value obtained in the photolysis of propenal at 193 nm (1.1), suggesting that at least these two channels: three-body dissociation (to give H2 + CO + C2H2) and CO elimination occur on the ground electronic state.

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“…Recently, we have developed a localized saddle-point (LSAD) method 52 which instead of using the whole system, uses only a small region around the transition to calculate the corresponding activation barrier. In addition, we have shown that for a fixed event size, this method leads to system-size independent scaling, while maintaining a negligibly small error.…”

Section: A Local Saddle-point Calculationsmentioning

confidence: 99%

Improved scaling of temperature-accelerated dynamics using localization

Shim

Amar

2016

The Journal of Chemical Physics

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While temperature-accelerated dynamics (TAD) is a powerful method for carrying out non-equilibrium simulations of systems over extended time scales, the computational cost of serial TAD increases approximately as N(3) where N is the number of atoms. In addition, although a parallel TAD method based on domain decomposition [Y. Shim et al., Phys. Rev. B 76, 205439 (2007)] has been shown to provide significantly improved scaling, the dynamics in such an approach is only approximate while the size of activated events is limited by the spatial decomposition size. Accordingly, it is of interest to develop methods to improve the scaling of serial TAD. As a first step in understanding the factors which determine the scaling behavior, we first present results for the overall scaling of serial TAD and its components, which were obtained from simulations of Ag/Ag(100) growth and Ag/Ag(100) annealing, and compare with theoretical predictions. We then discuss two methods based on localization which may be used to address two of the primary "bottlenecks" to the scaling of serial TAD with system size. By implementing both of these methods, we find that for intermediate system-sizes, the scaling is improved by almost a factor of N(1/2). Some additional possible methods to improve the scaling of TAD are also discussed.

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Localized saddle-point search and application to temperature-accelerated dynamics

Cited by 11 publications

References 50 publications

An automated method to find transition states using chemical dynamics simulations

An automated method to find transition states using chemical dynamics simulations

An automated transition state search using classical trajectories initialized at multiple minima

Improved scaling of temperature-accelerated dynamics using localization

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