Potential transferability and the Knowledgebase of Interatomic Models

Empirical (fitted) interatomic potentials are widely used to predict the response of materials and structures in atomistic simulations. The ability of a potential to predict behavior that it was not fitted to reproduce is referred to as its “transferability.” Despite the importance of the notion of transferability in selecting an empirical potential for a specific application, it has not yet been rigorously addressed by the materials simulation community. This is now possible due to the forthcoming Knowledgebase of Interatomic Models (https://openkim.org) which promises to serve as an abundant source of predictions of potentials and the corresponding first principles and experimental data for various material properties. Making use of this novel data resource in a cumulative manner, we compare representations of atomic environments as well as nonparametric supervised learning algorithms which can be used to systematically define and predict the transferability of empirical potentials

Knowledgebase of Interatomic Models application programming interface as a standard for molecular simulations

Nanoscale modeling of materials often involves the use of molecular simulations or multiscale methods. These approaches frequently use empirical (fitted) interatomic potentials to represent the response of the material. As part of the open Knowledgebase of Interatomic Models (KIM) project (https://openkim.org), an application programming interface (API) for interatomic potentials has been developed in consultation with key members of the materials simulation community. The KIM API is beginning to emerge as a standard for atomistic simulations of materials. This API makes it possible for any KIM-compliant (KIM API conforming) simulation code (“Simulator”) to seamlessly use any KIM-compliant potential (“Model”) obtained from https://openkim.org. The KIM API is also necessary for the KIM Processing Pipeline in https://openkim.org to automatically compute the predictions of stored Models for a variety of material properties by linking them to computer programs called “Tests” that perform these calculations. The KIM API is lightweight and efficient, supports physical unit conversion, a variety of common neighbor list and boundary conditions used in atomistic simulations, and provides multilanguage support for C++, C, Fortran 2003, Fortran 90/95, and Fortran 77, allowing Simulators and Models written in any of these languages to work together

Ensuring reliability, reproducibility and transferability in atomistic simulations: The knowledgebase of interatomic models (https://openkim.org)

Atomistic simulations using empirical interatomic potentials play a key role in realistic scientific and industrial applications. This discussion describes an NSF-funded effort to develop an open-source online tool for promoting the use and reliability of interatomic models. The Knowledgebase of Interatomic Models (https://openkim.org) allows users to compare model predictions with reference data, to generate new predictions by uploading simulation test codes, and to download models conforming to an application programming interface (API) standard that has been developed in collaboration with the atomistic simulation community. An overview will be given of the KIM project and its main components which include the KIM API, the KIM data structure for representing arbitrary material properties, the KIM processing pipeline, and the KIM visualization framework

Transferability of Empirical Potentials and the Knowledgebase of Interatomic Models (KIM)

University of Minnesota Ph.D. dissertation. April 2016. Major: Aerospace Engineering and Mechanics. Advisors: Ryan Elliott, Ellad Tadmor. 1 computer file (PDF); xii, 273 pages.Empirical potentials have proven to be an indispensable tool in understanding complex material behavior at the atomic scale due to their unrivaled computational efficiency. However, as they are currently used in the materials community, the realization of their full utility is stifled by a number of implementational difficulties. An emerging project specifically aimed to address these problems is the Knowledgebase of Interatomic Models (KIM). The primary purpose of KIM is to serve as an open-source, publically accessible repository of standardized implementations of empirical potentials (Models), simulation codes which use them to compute material properties (Tests), and first-principles/experimental data corresponding to these properties (Reference Data). Aside from eliminating the redundant expenditure of scientific resources and the irreproducibility of results computed using empirical potentials, a unique benefit offered by KIM is the ability to gain a further understanding of a Model's transferability, i.e. its ability to make accurate predictions for material properties which it was not fitted to reproduce. In the present work, we begin by surveying the various classes of mathematical representations of atomic environments which are used to define empirical potentials. We then proceed to offer a broad characterization of empirical potentials in the context of machine learning which reveals three distinct categories with which any potential may be associated. Combining one of the aforementioned representations of atomic environments with a suitable regression technique, we define the Regression Algorithm for Transferability Estimation (RATE), which permits a quantitative estimation of the transferability of an arbitrary potential. Finally, we demonstrate the application of RATE to a specific training set consisting of bulk structures, clusters, surfaces, and nanostructures of silicon. A specific analysis of the underlying quantities inferred by RATE which are used to characterize transferability is provided

The gravitational field of a laser beam beyond the short wavelength approximation

Light carries energy, and therefore, it is the source of a gravitational field. The gravitational field of a beam of light in the short wavelength approximation has been studied by several authors. In this article, we consider light of finite wavelengths by describing a laser beam as a solution of Maxwell's equations and taking diffraction into account. Then, novel features of the gravitational field of a laser beam become apparent, such as frame-dragging due to its spin angular momentum and the deflection of parallel co-propagating test beams that overlap with the source beam. Even though the effects are too small to be detected with current technology, they are of conceptual interest, revealing the gravitational properties of light.© 2018 IOP Publishing Lt

Bayesian, frequentist, and information geometric approaches to parametric uncertainty quantification of classical empirical interatomic potentials

In this paper, we consider the problem of quantifying parametric uncertainty in classical empirical interatomic potentials (IPs) using both Bayesian (Markov Chain Monte Carlo) and frequentist (profile likelihood) methods. We interface these tools with the Open Knowledgebase of Interatomic Models and study three models based on the Lennard-Jones, Morse, and Stillinger--Weber potentials. We confirm that IPs are typically sloppy, i.e., insensitive to coordinated changes in some parameter combinations. Because the inverse problem in such models is ill-conditioned, parameters are unidentifiable. This presents challenges for traditional statistical methods, as we demonstrate and interpret within both Bayesian and frequentist frameworks. We use information geometry to illuminate the underlying cause of this phenomenon and show that IPs have global properties similar to those of sloppy models from fields such as systems biology, power systems, and critical phenomena. IPs correspond to bounded manifolds with a hierarchy of widths, leading to low effective dimensionality in the model. We show how information geometry can motivate new, natural parameterizations that improve the stability and interpretation of uncertainty quantification analysis and further suggest simplified, less-sloppy models

Type Label Framework for Bonded Force Fields in LAMMPS

New functionality is added to the LAMMPS molecular simulation package that increases the versatility with which LAMMPS can interface with supporting software and manipulate information associated with bonded force fields. We introduce the “type label” framework that allows atom types and their higher-order interactions (bonds, angles, dihedrals, and impropers) to be represented in terms of the standard atom type strings of a bonded force field. Type labels increase the human readability of input files, enable bonded force fields to be supported by the OpenKIM repository, simplify the creation of reaction templates for the REACTER protocol, and increase compatibility with external visualization tools such as VMD and OVITO. An introductory primer on the forms and use of bonded force fields is provided to motivate this new functionality and serve as an entry point for LAMMPS and OpenKIM users unfamiliar with bonded force fields. The type label framework has the potential to streamline modeling workflows that use LAMMPS by increasing the portability of software, files, and scripts for pre-processing, running, and post-processing a molecular simulation

Frequency spectrum of an optical resonator in a curved spacetime

The effect of gravity and proper acceleration on the frequency spectrum of an optical resonator—both rigid or deformable—is considered in the framework of general relativity. The optical resonator is modeled either as a rod of matter connecting two mirrors or as a dielectric rod whose ends function as mirrors. Explicit expressions for the frequency spectrum are derived for the case that it is only perturbed slightly and variations are slow enough to avoid any elastic resonances of the rod. For a deformable resonator, the perturbation of the frequency spectrum depends on the speed of sound in the rod supporting the mirrors. A connection is found to a relativistic concept of rigidity when the speed of sound approaches the speed of light. In contrast, the corresponding result for the assumption of Born rigidity is recovered when the speed of sound becomes infinite. The results presented in this article can be used as the basis for the description of optical and opto-mechanical systems in a curved spacetime. We apply our results to the examples of a uniformly accelerating resonator and an optical resonator in the gravitational field of a small moving sphere. To exemplify the applicability of our approach beyond the framework of linearized gravity, we consider the fictitious situation of an optical resonator falling into a black hole.© 2018 The Author(s