Software and Projects Using KIM

Software

• - As Soon As Possible (ASAP) is a calculator for doing large-scale classical molecular dynamics within the Atomic Simulation Environment (ASE). ASAP has full support for KIM Portable Models (KIM API v2) as of version 3.11.3. The ASAP manual can be found here and installation instructions here.

• – The Atomic Simulation Environment (ASE) is a set of tools and Python modules for setting up, manipulating, running, visualizing and analyzing atomistic simulations. ASE supports various simulators using "calculators" that provide an interface to these codes. A KIM calculator for running Portable Models and Simulator Models (for simulators that have an ASE calculator) is available in ASE as of version 3.19.0. See here for instructions and examples.

• – DL_POLY is a general purpose classical molecular dynamics simulation software developed at Daresbury Laboratory in the UK. DL_POLY has support for KIM API v2 (released Sep 2000). For more information on DL_POLY and to obtain the code, visit the DL_POLY website.

• – GULP is a molecular simulation program emphasizing analytical solutions based on lattice dynamics, but also including a molecular dynamics mode. GULP provides full support for KIM Portable Models as of version 4.2. To use KIM with GULP you must add the flag -DKIM to DEFS in getmachine so that the code that supports KIM is enabled during compilation. Models are then specified using the kim\_model option. At present only a single type of each element is supported when using KIM and so species types are ignored when being passed to KIM models.

• – The KIM-based learning-integrated fitting framework (KLIFF) is a package for fitting analytic and machine learning interatomic potentials (IPs). Trained IPs are compatible with the KIM API and can be used with other codes that are compatible with KIM (such as those listed on this page). KLIFF is written in Python with computationally intensive components implemented in C++. The code is modular by design enabling a flexible approach to fitting incorporating different components: atomic environment descriptors, functional forms, loss functions, optimizers, and quality analyzers. The package is available through GitHub with extensive documentation and examples available here. An article describing the KLIFF packages is available here.

• – The molecular dynamics program LAMMPS has full support for the KIM API v2 as of 28 Feb 2019. This support is implemented in the KIM package in LAMMPS. See the general instructions for building LAMMPS and specific instructions for building LAMMPS with KIM support. To run LAMMPS with a KIM interatomic potential, install it (see instructions on how to do this on the Obtaining KIM Models page). Then follow the instructions in the LAMMPS documentation on how to use KIM Models in LAMMPS.

• – The libAtoms+QUIP molecular dynamics package has implemented partial support for the KIM API and is currently working towards full KIM compliance. For more information on this, contact us.

• - MDStressLab is a package for post-processing molecular dynamics or molecular statics results to obtain stress fields using different definitions of the atomistic stress tensor. MDStressLab currently supports KIM API v2. Both Fortran and C++ versions are available. For more information, contact the developers.

• – Potfit is a free implementation of the force-matching algorithm to generate effective potentials from ab-initio reference data. Potfit provides support for KIM API v2 as of version 20190325.

• - Pyiron is an integrated development environment (IDE) for computational materials science focused on simplifying the development of simulation protocols. It enables users to quickly iterate over all KIM potentials to test and validate their simulation protocols, by leveraging the LAMMPS KIM interface. (See here for examples of using pyiron with KIM.)

• - The Simulation Environment for Atomistic and Molecular Modeling – SEAMM – is a user-friendly environment for computational molecular and materials science. SEAMM is a workflow manager composed of plug-ins that wrap popular software packages and tools allowing a user to set up and run quantum and classical molecular simulations. SEAMM is developed by the Molecular Sciences Software Institute (MolSSI).

• – The quasicontinuum (QC) method is a multiscale simulation platform in which fully-resolved atomistic regions are embedded in a coarse-grained finite element regions. A high-performance 3D version of the QC code has been developed with support for polycrystalline materials of arbitrary crystal structure (simple and complex lattices). The QC code provides full support for KIM API v2. For more information on the code and how to access it, contact the developers.

Projects

• – ColabFit is a collaborative infrastructure for the development and distribution of state-of-the-art data-driven interatomic potentials (DDIPs). ColabFit aims to create a computational framework that enables researchers to rapidly develop and deploy DDIPs for complex material systems by connecting existing cyberinfrastructure resources of first principles and experimental data with a variety of fitting frameworks, and to share developed DDIPs through OpenKIM.

• - nanoHUB.org is the premier place for computational nanotechnology research, education, and collaboration. KIM is collaborating with nanoHUB.org to create KIM-Compliant Tools. Here is a list of the currently available KIM-Compliant Tools:

  • LAMMPS - Run LAMMPS by uploading a data file and command script.
  • Minimal Molecular Simulation Tool - Perform simple molecular dynamics and statics simulations.

• – The Virtual Fab simulation laboratory provides an interactive platform to construct, carry out, and analyze simulations pertaining to nanoscale devices, with an emphasis on semiconductors. Virtual Fab currently offers full support for the use of KIM Models along with a visualization interface available for plotting and comparing KIM Test Results for Models relevant to a given application. Moreover, there is development underway to autogenerate KIM Tests from simulations carried out in Virtual Fab.

• – KIM is collaborating with the Computational Materials Repository (CMR) project led by the Technical University of Denmark (DTU) on automatically importing first principles data into KIM and auto-generating Tests.

• KIM is collaborating with the National Institute of Standards and Technology (NIST) on developing reproducible scientific workflows for use with KIM Tests. For more information on the collaboration between KIM and the NIST IPR and the goals of these projects, see here.