Resources

Freely-available* atomistic and multiscale software and Information

*free access may be limited to academic institutions

• MultiBench is a general purpose concurrent multiscale program which implements fourteen approaches published in the literature for coupling an atomistic region modeled using standard MS with a continuum region modeled using a nonlinear FEM. The results of a benchmark problem tested with this program are described in an article by Tadmor and Miller (Modell. Simul. Mater. Sci. Eng., 17:053001, 2009) and in Chapter 12 of the MM book. The MultiBench program is based on the QC code mentioned above and is written in Fortran 90. It can be downloaded from the QC website.

• Knowledgebase of Interatomic Models (KIM) is a project funded by the U.S. National Science Foundation (NSF) for developing standards for atomistic simulations involving interatomic potentials. The project has the following main objectives:

  • Development of an online open resource for standardized testing and long-term warehousing of interatomic models (potentials and force fields) and data.

  • Development of an application programming interface (API) standard for atomistic simulations, which will allow any interatomic model to work seamlessly with any atomistic simulation code.

  • Development of a quantitative theory of transferability of interatomic models to provide guidance for selecting application-appropriate models based on rigorous criteria, and error bounds on results.

The KIM project is open to all researchers interested in atomistic simulations. More information is available at the KIM project website: https://openkim.org

• ColabFit aims to create a framework to facilitate the training and use of machine learning (ML) models in materials science including interatomic potentials. This includes an online exchange for datasets used to train ML models and a portable format for deploying ML models to simulation platforms using the OpenKIM system. More information is available at the ColabFit project website: https://colabfit.org

• Atomistic visualization programs

  • AtomEye – Atomistic configuration viewer (MIT)

  • AViz – Atomistic Vizualization software (Technion)

  • Avogadro – Advanced molecule editor and visualizer

  • iMol – Molecular visualizer for Mac OS X

  • Jmol – An open-source Java viewer for chemical structures in 3D.

  • OVITO – Open VIsualization TOol (TU Darmstadt)

  • PyMOL – PYthon-based MOLecular visualization system (DeLano Scientific LLC)

  • RasM0l – Molecular graphics visualization tool (ARCiB Laboratory, Downling College)

  • VMD – Visual Molecular Dynamics (U. Illinois)

• Atomistic simulation framworks

  • ASE – Python-based Atomistic Simulation Environment (TU Denmark)

  • CP2K – Fortran 95 package for classical and quantum calculations

  • QUIP/libAtoms – QUantum and Interatomic Potentials MD framework (University of Cambridge)

• Classical molecular dynamics (MD) programs

  • ASAP – As Soon As Possible MD program (TU Denmark)

  • DL_POLY – Daresbury Laboratory POLY (=many) tools MD program (STFC/Daresbury Lab, UK)

  • GROMACS – GROningen MAchine for Chemical Simulation (CBR, Stockholm)

  • HALMD – (GPU based) Highly Accelerated Large-scale Molecular Dynamics (University of Munich, Germany)

  • HOOMD-blue – (GPU based) Highly Optimized Object-oriented Many-particle Dynamics (U. Michigan)

  • IMD – The ITAP Molecular Dynamics program (ITAP, U. Stuttgart/MPI)

  • LAMMPS – Large-scale Atomic/Molecular Massively Parallel Simulator (Sandia)

  • MiniMol – MINImal MOLecular simulation code (Modeling Materials)

  • MOLDY – MOLecular DYnamics (U. Oxford)

  • NAMD – Not (just) Another Molecular Dynamics program (U. Illinois)

  • OpenMM – OPEN source library for Molecular Modeling simulations (Stanford University)

• Density functional theory (DFT) programs

  • ABINIT – AB INITio (Université Catholique de Louvain, Corning Inc., et al.)

  • BigDFT – massively parallel electronic structure code with GPU support

  • ESPRESSO – opEn Source Package for Research in Electronic Structure, Simulation and Optimization

  • GPAW – Grid-based Projector-Augmented Wave method (TU Denmark)

  • NWChem – NorthWest computational Chemistry (PNNL)

  • Qbox – scalable parallel first principles MD code written in C++/MPI (UC Davis)

  • Quickstep – DFT using mixed Gaussian and plane waves approach (part of CP2K package, see above)

  • SeqQuest – QUantum Electronic STructure (Sandia)

  • SIESTA – Spanish Initiative for Electronic Simulations with Thousands of Atoms

• Information resources

  • KIM REVIEW – An online open access journal that publishes commentaries on important articles related to classical molecular simulations of hard and soft matter materials and invites community participation through forum discussion.

  • MatSci.org – A community forum for the discussion of anything materials science, with a focus on computational materials science research. Its members are typically from academic research institutions and universities.

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