Database of atomistic reaction mechanisms with application to kinetic Monte Carlo

Terrell, Rye; Welborn, Matthew; Chill, Samuel T.; Henkelman, Graeme

doi:10.1063/1.4730746

Cited by 14 publications

(12 citation statements)

References 21 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Finding stationary points (SPs) of a multivariate nonlinear function is a frequently arising problem in many areas of science. For example, locating SPs provides the foundations for global optimisation, [1][2][3] thermodynamic sampling to overcome broken ergodicity, [4][5][6][7] and rare event dynamics [8][9][10][11][12][13][14][15] within the framework of potential energy landscape theory. 16 Knowledge of the SPs of the potential energy function, V (x), with x = (x 1 , .…”

Section: Introductionmentioning

confidence: 99%

An inversion-relaxation approach for sampling stationary points of spin model Hamiltonians

Hughes

Mehta

Wales

2014

The Journal of Chemical Physics

View full text Add to dashboard Cite

Sampling the stationary points of a complicated potential energy landscape is a challenging problem. Here we introduce a sampling method based on relaxation from stationary points of the highest index of the Hessian matrix. We illustrate how this approach can find all the stationary points for potentials or Hamiltonians bounded from above, which includes a large class of important spin models, and we show that it is far more efficient than previous methods. For potentials unbounded from above, the relaxation part of the method is still efficient in finding minima and transition states, which are usually the primary focus of attention for atomistic systems.

show abstract

Section: Introductionmentioning

confidence: 99%

An inversion-relaxation approach for sampling stationary points of spin model Hamiltonians

Hughes

Mehta

Wales

2014

The Journal of Chemical Physics

View full text Add to dashboard Cite

show abstract

“…80 KMC and its variants are well established simulation methods for studying complex chemistry at the nanoscale. [37][38][39][40][41][42][43]76,79,[81][82][83][84][85][86][87][88][89][90] We employ a local KMC model, where one molecule moves at an instance in time, and extend it with a method known as τ -leaping, based on the Gillespie algorithm. 91 The extension offers an efficient choice of the next molecular move and the most probable time step.…”

Section: General Methodologymentioning

confidence: 99%

Kinetics of Molecular Diffusion and Self-Assembly: Glycine on Cu{110}

Rommel

Wales

2017

J. Phys. Chem. C

View full text Add to dashboard Cite

Nanofabrication and the growth of self-assembled monolayers (SAM) of organic molecules are increasingly important in various industries, including microelectronics and health care. Glycine adsorbed on Cu{110} provides a good model with a rich phenomenological space to explore and understand the self-assembly of more complex amino acids. We focus on (a) the dynamics exhibited by glycine molecules already adsorbed on Cu{110} when diffusing on the metal surface, and (b) the chemical kinetics of how these molecules form clusters, networks, and islands. The stochastic discrete event algorithm we employ can be viewed as a multiscale approach, based on density functional energies and transition barriers. The method covers from the femtosecond timescale of molecular rotations to the microsecond range of molecular self-assembly. Hydrogen-bonds and van der Waals forces play a crucial role in pattern formation. Investigations of chemical kinetics show that enantiopure, homochiral islands are an intermediate step during the formation process of larger stable racemic, heterochiral islands, especially when two islands merge. At lower temperature, defects stabilise mainly homochiral clusters, and prevent the molecules from synchronising their footprint orientation, in contrast to higher temperature. On the way we solve the long standing puzzle of how the pseudo-centered (3×2) enantiopure clusters can have glide plane symmetry. We end with a comparison to similar amino acids, such as alanine and proline. The results provide insight into mechanisms for fine-tuning the self-organisation of organic molecules on metal surfaces.

show abstract

“…Thus, the kinetics of dopant cluster formation and break-up is of interest to the semiconductor industry. The details of the DFT calculation and how the initial configuration was created have been reported previously [38].…”

Section: Breakup Of a Boron Cluster In Bulk Siliconmentioning

confidence: 99%

EON: software for long time simulations of atomic scale systems

Chill¹,

Welborn²,

Terrell³

et al. 2014

Modelling Simul. Mater. Sci. Eng.

Self Cite

View full text Add to dashboard Cite

The EON software is designed for simulations of the state-to-state evolution of atomic scale systems over timescales greatly exceeding that of direct classical dynamics. States are defined as collections of atomic configurations from which a minimization of the potential energy gives the same inherent structure. The time evolution is assumed to be governed by rare events, where transitions between states are uncorrelated and infrequent compared with the timescale of atomic vibrations. Several methods for calculating the state-to-state evolution have been implemented in EON, including parallel replica dynamics, hyperdynamics and adaptive kinetic Monte Carlo. Global optimization methods, including simulated annealing, basin hopping and minima hopping are also implemented. The software has a client/server architecture where the computationally intensive evaluations of the interatomic interactions are calculated on the client-side and the state-to-state evolution is managed by the server. The client supports optimization for different computer architectures to maximize computational efficiency. The server is written in Python so that developers have access to the high-level functionality without delving into the computationally intensive components. Communication between the server and clients is abstracted so that calculations can be deployed on a single machine, clusters using a queuing system, large parallel computers using a message passing interface, or within a distributed computing environment. A generic interface to the evaluation of the interatomic interactions is defined so that empirical potentials, such as in LAMMPS, and density functional theory as implemented in VASP and GPAW can be used interchangeably. Examples are given to demonstrate the range of systems that can be modeled, including

show abstract

Database of atomistic reaction mechanisms with application to kinetic Monte Carlo

Cited by 14 publications

References 21 publications

An inversion-relaxation approach for sampling stationary points of spin model Hamiltonians

An inversion-relaxation approach for sampling stationary points of spin model Hamiltonians

Kinetics of Molecular Diffusion and Self-Assembly: Glycine on Cu{110}

EON: software for long time simulations of atomic scale systems

Contact Info

Product

Resources

About