The OpenKIM processing pipeline: A cloud-based automatic material property computation engine.

The Open Knowledgebase of Interatomic Models (OpenKIM) is a framework intended to facilitate access to standardized implementations of interatomic models for molecular simulations along with computational protocols to evaluate them. These protocols include tests to compute material properties predicted by models and verification checks to assess their coding integrity. While housing this content in a unified, publicly available environment constitutes a major step forward for the molecular modeling community, it further presents the opportunity to understand the range of validity of interatomic models and their suitability for specific target applications. To this end, OpenKIM includes a computational pipeline that runs tests and verification checks using all available interatomic models contained within the OpenKIM Repository at https://openkim.org. The OpenKIM Processing Pipeline is built on a set of Docker images hosted on distributed, heterogeneous hardware and utilizes open-source software to automatically run test-model and verification check-model pairs and resolve dependencies between them. The design philosophy and implementation choices made in the development of the pipeline are discussed as well as an example of its application to interatomic model selection.

Stress and heat flux for arbitrary multibody potentials: a unified framework.

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.

Finite-temperature quasicontinuum: molecular dynamics without all the atoms.

Using a combination of statistical mechanics and finite-element interpolation, we develop a coarse-grained (CG) alternative to molecular dynamics (MD) for crystalline solids at constant temperature. The new approach is significantly more efficient than MD and generalizes earlier work on the quasicontinuum method. The method is validated by recovering equilibrium properties of single crystal Ni as a function of temperature. CG dynamical simulations of nano-indentation reveal a strong dependence on temperature of the critical stress to nucleate dislocations under the indenter.