[Show abstract][Hide abstract] ABSTRACT: Empirical interatomic potentials are widely used in atomistic simulations due to their ability to compute the total energy and interatomic forces quickly relative to more accurate quantum calculations. The functional forms in these potentials are sometimes stored in a tabulated format, as a collection of data points (argument–value pairs), and a suitable interpolation (often spline-based) is used to obtain the function value at an arbitrary point. We explore the effect of these interpolations on the potential predictions by calculating the quasi-harmonic thermal expansion and finite-temperature elastic constant of a one-dimensional chain compared with molecular dynamics simulations. Our results show that some predictions are affected by the choice of interpolation regardless of the number of tabulated data points. Our results clearly indicate that the interpolation must be considered part of the potential definition, especially for lattice dynamics properties that depend on higher-order derivatives of the potential. This is facilitated by the Knowledgebase of Interatomic Models (KIM) project, in which both the tabulated data (‘parameterized model’) and the code that interpolates them to compute energy and forces (‘model driver’) are stored and given unique citeable identifiers. We have developed cubic and quintic spline model drivers for pair functional type models (EAM, FS, EMT) and uploaded them to the OpenKIM repository (https://openkim.org).
Modelling and Simulation in Materials Science and Engineering 10/2015; 23(7). DOI:10.1088/0965-0393/23/7/074008 · 2.17 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Fourier's law leads to a diffusive model of heat transfer in which a thermal signal propagates infinitely fast and the only material parameter is the thermal conductivity. In micro- and nano-scale systems, non-Fourier effects involving coupled diffusion and wavelike propagation of heat can become important. An extension of Fourier's law to account for such effects leads to a Jeffreys-type model for heat transfer with two relaxation times. We propose a new Thermal Parameter Identification (TPI) method for obtaining the Jeffreys-type thermal parameters from molecular dynamics simulations. The TPI method makes use of a nonlinear regression-based approach for obtaining the coefficients in analytical expressions for cosine and sine-weighted averages of temperature and heat flux over the length of the system. The method is applied to argon nanobeams over a range of temperature and system sizes. The results for thermal conductivity are found to be in good agreement with standard Green-Kubo and direct method calculations. The TPI method is more efficient for systems with high diffusivity and has the advantage, that unlike the direct method, it is free from the influence of thermostats. In addition, the method provides the thermal relaxation times for argon. Using the determined parameters, the Jeffreys-type model is able to reproduce the molecular dynamics results for a short-duration heat pulse where wavelike propagation of heat is observed thereby confirming the existence of second sound in argon. An implementation of the TPI method in MATLAB is available as part of the online supplementary material.
[Show abstract][Hide abstract] ABSTRACT: The direct method for computing
thermal conductivity in nonequilibrium molecular dynamics gives rise to an artificial Kapitza resistance at the interface between thermostatted and unthermostatted regions. This resistance, which depends on the system size and the thermostat parameters, creates discontinuous jumps in the temperature and heat flux across the interface and therefore affects the measured thermal conductivity. In this paper, we propose a phenomenological relation for the Kapitza resistance that can be used to extract a value for the bulk thermal conductivity, which is independent of the system size and thermostat details. The paper also provides insight into the Kapitza phenomenon resulting from numerical thermostatting.
[Show abstract][Hide abstract] ABSTRACT: The quasicontinuum (QC) method, in its local (continuum) limit, is applied to materials with a multilattice crystal structure. Cauchy–Born (CB) kinematics, which accounts for the shifts of the crystal motif, is used to relate atomic motions to continuum deformation gradients. To avoid failures of CB kinematics, QC is augmented with a phonon stability analysis that detects lattice period extensions and identifies the minimum required periodic cell size. This approach is referred to as Cascading Cauchy–Born kinematics (CCB). In this paper, the method is described and developed. It is then used, along with an effective interaction potential (EIP) model for shape-memory alloys, to simulate the shape-memory effect and pseudoelasticity in a finite specimen. The results of these simulations show that (i) the CCB methodology is an essential tool that is required in order for QC-type simulations to correctly capture the first-order phase transitions responsible for these material behaviors, and (ii) that the EIP model adopted in this work coupled with the QC/CCB methodology is capable of predicting the characteristic behavior found in shape-memory alloys.
Modelling and Simulation in Materials Science and Engineering 05/2014; 22(5):055001. DOI:10.1088/0965-0393/22/5/055001 · 2.17 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Nanostructures are technological devices constructed on a nanometer length scale more than a thousand times thinner than a human hair. Due to the unique properties of matter at this scale, such devices offer great potential for creating novel materials and behaviors that can be leveraged to benefit mankind. This paper addresses a particular challenge involved in the design of nanostructures-their stochastic or apparently random response to external loading. This is because fundamentally the function that relates the energy of a nanostructure to the arrangement of its atoms is extremely nonconvex, with each minimum corresponding to a possible equilibrium state that may be visited as the system responds to loading. Traditional atomistic simulation techniques are not capable of systematically addressing this complexity. Instead, we construct an equilibrium map (EM) for the nanostructure, analogous to a phase diagram for bulk materials, which fully characterizes its response. Using the EM, definitive predictions can be made in limiting cases and the spectrum of responses at any desired loading rate can be obtained. The latter is important because standard atomistic methods are fundamentally limited, by computational feasibility, to simulations of loading rates that are many orders of magnitude faster than reality. In contrast, the EM-based approach makes possible the direct simulation of nanostructure experiments. We demonstrate the method's capabilities and its surprisingly complex results for the case of a nanoslab of nickel under compression.
Proceedings of the National Academy of Sciences 04/2014; 111(17). DOI:10.1073/pnas.1402029111 · 9.67 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Dislocations are line defects that play a key role in the plasticity of crystalline materials and affect their thermal, chemical, and electrical properties. Typically dislocations are treated as stable defects; e.g., the equilibrium core structure of a dislocation is obtained by minimizing the crystal potential energy with respect to atom positions. Here we show for the first time the possibility of "entropically stabilized dislocations" that exist due to entropic effects without a corresponding potential energy well. An entropically stabilized dislocation was discovered in an accelerated multiscale quasicontinuum simulation. Its entropic nature was verified with fully atomistic free energy calculations and explained by a simple continuum-based model. This result has important consequences for the study of dislocations as well as for temporal multiscale methods that use information from the potential energy surface to accelerate time in molecular simulations.
[Show abstract][Hide abstract] ABSTRACT: The quasicontinuum (QC) method is a spatial multiscale method that extends the length scales accessible to fully atomistic simulations (like molecular dynamics (MD)) by several orders of magnitude. While the recent development of the so-called “hot-QC method” enables dynamic simulations at finite temperature, the times accessible to these simulations remain limited to the sub-microsecond time scale due to the small time step required for stability of the numerical integration. To address this limitation, we develop a novel finite-temperature QC method that can treat much longer time scales by coupling the hot-QC method with hyperdynamics—a method for accelerating time in MD simulations. We refer to the new approach as “hyper-QC”. As in the original hyperdynamics method, hyper-QC is targeted at dynamical systems that exhibit a separation of time scales between short atomic vibration periods and long waiting times in metastable states. Acceleration is achieved by modifying the hot-QC potential energy to reduce the energy barriers between metastable states in a manner that ensures that the characteristic dynamics of the system are preserved. First, the high accuracy of hot-QC in reproducing rare event kinetics is demonstrated. Then, the hyper-QC methodology is validated by comparing hyper-QC results with those of hot-QC and full MD for a one-dimensional chain of atoms interacting via a Lennard–Jones potential.
Journal of the Mechanics and Physics of Solids 02/2014; 63(1):94–112. DOI:10.1016/j.jmps.2013.10.001 · 3.60 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: This paper discusses the motivation for the creation of cyberinfrastructures to enhance specific technical areas of research. It then goes onto provide a review of two cyberinfrastructures supported by the National Science Foundation, OpenKIM and CAMS, which are geared towards enhancing materials modeling at the atomic scale. Their objectives, accomplishments, and future goals are discussed. Lastly, the future outlook for cyberinfrastructures such as these to impact materials modeling is discussed.
Current Opinion in Solid State and Materials Science 12/2013; 17(6). DOI:10.1016/j.cossms.2013.10.004 · 6.24 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: A generalization of the quasi-continuum (QC) method to finite temperature is presented. The resulting "hot-QC" formulation is a partitioned domain multiscale method in which atomistic regions modeled via molecular dynamics coexist with surrounding continuum regions. Hot-QC can be used to study equilibrium properties of systems under constant or quasistatic loading conditions. Two variants of the method are presented which differ in how continuum regions are evolved. In "hot-QC-static" the free energy of the continuum is minimized at each step as the atomistic region evolves dynamically. In "hot-QC-dynamic" both the atomistic and continuum regions evolve dynamically in tandem. The latter approach is computationally more efficient, but introduces an anomalous "mesh entropy" which must be corrected. Following a brief review of related finite-temperature methods, this review article provides the theoretical background for hot-QC (including new results), discusses the implementational details, and demonstrates the utility of the method via example test cases including nanoindentation at finite temperature.
[Show abstract][Hide abstract] ABSTRACT: An objective quasicontinuum (OQC) method is developed for simulating rodlike systems that can be represented as a combination of locally objective structures. An objective structure (OS) is one for which a group of atoms, called a “fundamental domain” (FD), is repeated using specific rules of translation and rotation to build a more complex structure. An objective Cauchy-Born rule defines the kinematics of the OS atoms in terms of a set of symmetry parameters and the positions of the FD atoms. The computational advantage lies in the capability of representing a large system of atoms through a small set of symmetry parameters and FD atom positions. As an illustrative example, we consider the deformation of a copper single-crystal nanobeam which can be described as an OS. OQC simulations are performed for uniform and nonuniform bending for two different orientations (nanobeam axis oriented along  and ) and compared with elastica results. In the uniform bending case, the -oriented single-crystal nanobeam experiences elongation, while the -oriented nanobeam experiences contraction in total length. The nonuniform bending allows for stretching, contraction, and bending as deformation. Under certain loading conditions, dislocation nucleation is observed within the FD.
[Show abstract][Hide abstract] ABSTRACT: The self-consistent method of lattice dynamics (SCLD) is used to obtain an analytical solution for the free energy of a periodic, one-dimensional, mono-atomic chain accounting for fourth-order anharmonic effects. For nearest-neighbor interactions, a closed-form analytical solution is obtained. In the case where more distant interactions are considered, a system of coupled nonlinear algebraic equations is obtained (as in the standard SCLD method) however with the number of equations dramatically reduced. The analytical SCLD solutions are compared with a numerical evaluation of the exact solution for simple cases and with molecular dynamics simulation results for a large system. The advantages of SCLD over methods based on the harmonic approximation are discussed as well as some limitations of the approach.
[Show abstract][Hide abstract] ABSTRACT: 1. Introduction; Part I. Continuum Mechanics and Thermodynamics: 2.
Essential continuum mechanics and thermodynamics; Part II. Atomistics:
3. Lattices and crystal structures; 4. Quantum mechanics of materials;
5. Empirical atomistic models of materials; 6. Molecular statics; Part
III. Atomistic Foundations of Continuum Concepts: 7. Classical
equilibrium statistical mechanics; 8. Microscopic expressions for
continuum fields; 9. Molecular dynamics; Part IV. Multiscale Methods:
10. What is multiscale modeling?; 11. Atomistic constitutive relations
for multilattice crystals; 12. Atomistic/continuum coupling: static
methods; 13. Atomistic/continuum coupling: finite temperature and
dynamics; Appendix; References; Index.
[Show abstract][Hide abstract] ABSTRACT: 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. Currently, no standardized approach exists for estimating the accuracy of interatomic potentials. In addition, a lack of standardization in programming interfaces for potentials and the lack of a systematic infrastructure for archiving them makes it difficult to use potentials for new applications and to reproduce published results.
The Knowledgebase of Interatomic Models (KIM) (http://openKIM.org) is a 4-year NSF CDI program which attempts to address these limitations. One difficulty in the use of interatomic models is that simulation codes and interatomic potentials are written in a variety of programming languages. In order to allow the programs and model subroutines to be mutually compatible, it is necessary to define a robust application programming interface (API) designed to accommodate the requirements of molecular simulations. The KIM project has developed such an API in collaboration with key members of the molecular simulation community. The API is based on the concept of descriptor files, which define all variables and methods needed for input and output for a given application or model. The API addresses issues such as naming conventions for models (unique names), neighbor-list objects and their interface, system of units, unit conversion, and a complete description of variables and methods.
In this talk we will present a brief overview of the KIM framework and then provide details on the KIM API protocol. We invite the molecular simulation community to participate in the KIM project and contribute to the standardization efforts under way.
[Show abstract][Hide abstract] ABSTRACT: Atomistic simulations in materials science play a key role in realistic scientific and industrial applications. However, the predictive capability of these approaches hinges on the accuracy of the model (potential or force field) used to describe the atomic interactions. Modern models are optimized to reproduce electronic structure results for a dataset of representative atomic configurations. However, no standardized approach currently exists for quantifying the range of applicability of an interatomic model or estimating the accuracy of its predictions. This makes it difficult or even impossible to select an appropriate model for a given application. A second difficulty is that since computer implementations of interatomic models do not subscribe to coding standards, it is hard to connect a given model to a desired simulation tool. This talk will describe a current NSF-CDI funded effort to create an open source online tool that addresses these limitations: the Knowledgebase of Interatomic Models (http://openKIM.org). KIM will allow users to compare model predictions with reference data, to generate new predictions by uploading simulation test codes, and to download models conforming to application programming interface (API) standards which are being developed in collaboration with atomistic simulation community. Inthis talk I will give an overview of the KIM project and describe recent developments.
[Show abstract][Hide abstract] ABSTRACT: A two-step unified framework for the evaluation of continuum field expressions from molecular simulations for arbitrary interatomic potentials is presented. First, pointwise continuum fields are obtained using a generalization of the Irving-Kirkwood procedure to arbitrary multibody potentials. Two ambiguities associated with the original Irving-Kirkwood procedure (which was limited to pair potential interactions) are addressed in its generalization. The first ambiguity is due to the nonuniqueness of the decomposition of the force on an atom as a sum of central forces, which is a result of the nonuniqueness of the potential energy representation in terms of distances between the particles. This is in turn related to the shape space of the system. The second ambiguity is due to the nonuniqueness of the energy decomposition between particles. The latter can be completely avoided through an alternate derivation for the energy balance. It is found that the expressions for the specific internal energy and the heat flux obtained through the alternate derivation are quite different from the original Irving-Kirkwood procedure and appear to be more physically reasonable. Next, in the second step of the unified framework, spatial averaging is applied to the pointwise field to obtain the corresponding macroscopic quantities. These lead to expressions suitable for computation in molecular dynamics simulations. It is shown that the important commonly-used microscopic definitions for the stress tensor and heat flux vector are recovered in this process as special cases (generalized to arbitrary multibody potentials). Several numerical experiments are conducted to compare the new expression for the specific internal energy with the original one.
The Journal of Chemical Physics 05/2011; 134(18):184106. DOI:10.1063/1.3582905 · 2.95 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Material properties emerge from phenomena on scales ranging from Angstroms to millimeters, and only a multiscale treatment can provide a complete understanding. Materials researchers must therefore understand fundamental concepts and techniques from different fields, and these are presented in a comprehensive and integrated fashion for the first time in this book. Incorporating continuum mechanics, quantum mechanics, statistical mechanics, atomistic simulations and multiscale techniques, the book explains many of the key theoretical ideas behind multiscale modeling. Classical topics are blended with new techniques to demonstrate the connections between different fields and highlight current research trends. Example applications drawn from modern research on the thermo-mechanical properties of crystalline solids are used as a unifying focus throughout the text. Together with its companion book, Continuum Mechanics and Thermodynamics (Cambridge University Press, 2011), this work presents the complete fundamentals of materials modeling for graduate students and researchers in physics, materials science, chemistry and engineering.
[Show abstract][Hide abstract] ABSTRACT: The microscopic definition for the Cauchy stress tensor has been examined in the past from many different perspectives. This has led to different expressions for the stress tensor and consequently the "correct" definition has been a subject of debate and controversy. In this work, a unified framework is set up in which all existing definitions can be derived, thus establishing the connections between them. The framework is based on the non-equilibrium statistical mechanics procedure introduced by Irving, Kirkwood and Noll, followed by spatial averaging. The Irving--Kirkwood--Noll procedure is extended to multi-body potentials with continuously differentiable extensions and generalized to non-straight bonds, which may be important for particles with internal structure. Connections between this approach and the direct spatial averaging approach of Murdoch and Hardy are discussed and the Murdoch--Hardy procedure is systematized. Possible sources of non-uniqueness of the stress tensor, resulting separately from both procedures, are identified and addressed. Numerical experiments using molecular dynamics and lattice statics are conducted to examine the behavior of the resulting stress definitions including their convergence with the spatial averaging domain size and their symmetry properties. Comment: 86 pages
Journal of Elasticity 08/2010; 100(1). DOI:10.1007/s10659-010-9249-6 · 1.35 Impact Factor