Methods, software, and benchmarks for modeling long timescale dynamics in solid-state atomic systems

textThe timescale of chemical reactions in solid-state systems greatly exceeds what may be modeled by direct integration of Newton's equation of motion. This limitation spawned the development of many different methods such as (adaptive) kinetic Monte Carlo (A)KMC, (harmonic) transition state theory (H)TST, parallel replica dynamics (PRD), hyperdynamics (HD), and temperature accelerated dynamics. The focus of this thesis was to (1) implement many of these methods in a single open-source software package (2) develop standard benchmarks to compare their accuracy and computational cost and (3) develop new long timescale methods. The lack of a open-source package that implements long timescale methods makes it difficult to directly evaluate the quality of different approaches. It also impedes the development of new techniques. Due to these concerns we developed Eon, a program that implements several long timescale methods including PRD, HD, and AKMC as well as global optimization algorithms basin hopping, and minima hopping. Standard benchmarks to evaluate the performance of local geometry optimization; global optimization; and single-ended and double-ended saddle point searches were created. Using Eon and several other well known programs, the accuracy and performance of different algorithms was compared. Important to this work is a website where anyone may download the code to repeat any of the numerical experiments. A new method for long timescale simulations is also introduced: molecular dynamics saddle search adaptive kinetic Monte Carlo (AKMC-MDSS). AKMC-MDSS improves upon AKMC by using short high-temperature MD trajectories to locate the important low-temperature reaction mechanisms of interest. Most importantly, the use of MD enables the development of a proper stopping criterion for the AKMC simulation that ensures that the relevant reaction mechanisms at the low temperature have been found. Important to the simulation of any material is knowledge of the experimental structure. Extended x-ray absorption fine structure (EXAFS) is a technique often used to determine local atomic structure. We propose a technique to quantitatively measure the accuracy of the commonly used fitting models. This technique reveals that the fitting models interpreted nanoparticles as being significantly more ordered and of much shorter bond length than they really are.Chemistr

ATK-ForceField: A New Generation Molecular Dynamics Software Package

ATK-ForceField is a software package for atomistic simulations using classical interatomic potentials. It is implemented as a part of the Atomistix ToolKit (ATK), which is a Python programming environment that makes it easy to create and analyze both standard and highly customized simulations. This paper will focus on the atomic interaction potentials, molecular dynamics, and geometry optimization features of the software, however, many more advanced modeling features are available. The implementation details of these algorithms and their computational performance will be shown. We present three illustrative examples of the types of calculations that are possible with ATK-ForceField: modeling thermal transport properties in a silicon germanium crystal, vapor deposition of selenium molecules on a selenium surface, and a simulation of creep in a copper polycrystal.Comment: 28 pages, 9 figure

QuantumATK: An integrated platform of electronic and atomic-scale modelling tools

QuantumATK is an integrated set of atomic-scale modelling tools developed since 2003 by professional software engineers in collaboration with academic researchers. While different aspects and individual modules of the platform have been previously presented, the purpose of this paper is to give a general overview of the platform. The QuantumATK simulation engines enable electronic-structure calculations using density functional theory or tight-binding model Hamiltonians, and also offers bonded or reactive empirical force fields in many different parametrizations. Density functional theory is implemented using either a plane-wave basis or expansion of electronic states in a linear combination of atomic orbitals. The platform includes a long list of advanced modules, including Green's-function methods for electron transport simulations and surface calculations, first-principles electron-phonon and electron-photon couplings, simulation of atomic-scale heat transport, ion dynamics, spintronics, optical properties of materials, static polarization, and more. Seamless integration of the different simulation engines into a common platform allows for easy combination of different simulation methods into complex workflows. Besides giving a general overview and presenting a number of implementation details not previously published, we also present four different application examples. These are calculations of the phonon-limited mobility of Cu, Ag and Au, electron transport in a gated 2D device, multi-model simulation of lithium ion drift through a battery cathode in an external electric field, and electronic-structure calculations of the composition-dependent band gap of SiGe alloys.Comment: Submitted to Journal of Physics: Condensed Matte

A Theoretical and Experimental Examination of Systematic Ligand-Induced Disorder in Au Dendrimer-Encapsulated Nanoparticles

In this paper we present a new methodology for the analysis of 1-2 nm nanoparticles using extended X-ray absorption fine structure (EXAFS) spectroscopy. Different numbers of thiols were introduced onto the surfaces of dendrimer-encapsulated Au nanoparticles, consisting of an average of 147 atoms, to systematically tune the nanoparticle disorder. An analogous system was investigated using density functional theory molecular dynamics (DFT-MD) simulations to produce theoretical EXAFS signals that could be directly compared to the experimental results. Validation of the theoretical results by comparing to experiment allows us to infer previously unknown details of structure and dynamics of the nanoparticles. Additionally, the structural information that is learned from theoretical studies can be compared with traditional EXAFS fitting results to identify and rationalize any errors in the experimental fit. This study demonstrates that DFT-MD simulations accurately depict complex experimental systems in which we have control over nanoparticle disorder, and shows the advantages of using a combined experimental/theoretical approach over standard EXAFS fitting methodologies for determining the structural parameters of metallic nanoparticles.Chemical Sciences, Geosciences, and Biosciences Division, Office of Basic Energy Sciences, Office of Science, U. S. Department of Energy DE-FG02-09ER16090Robert A. Welch Foundation F-0032Department of Energy DE-FG02-03ER15476U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences DE-AC02-98CH10886Synchrotron Catalysis Consortium, U. S. Department of Energy DE-FG02-05ER15688National Institute on Minority Health and Health Disparities from the National Institutes of Health G12MD007591Chemistr