List of software projects pyiron collaborates with in alphabetical order:
The Atomic Simulation Environment (ASE) is a set of tools and Python modules for setting up, manipulating, running, visualizing and analyzing atomistic simulations. The code is freely available under the GNU LGPL license. https://wiki.fysik.dtu.dk/ase/
LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS is a classical molecular dynamics simulation code designed to run efficiently on parallel computers. It was developed at Sandia National Laboratories, a US Department of Energy facility, with funding from the DOE. It is an open-source code, distributed freely under the terms of the GNU Public License (GPL). http://lammps.sandia.gov
An IPython/Jupyter widget to interactively view molecular structures and trajectories. Utilizes the embeddable NGL Viewer for rendering. Support for showing data from the file-system, RCSB PDB, simpletraj and from objects of analysis libraries mdtraj, pytraj, mdanalysis, ParmEd, rdkit, ase, HTMD, biopython, cctbx, pyrosetta, schrodinger’s Structure. https://github.com/arose/nglview
OpenKIM is a cyberinfrastructure for improving the reliability of molecular and multiscale simulations of materials. It includes a repository of interatomic potentials that are exhaustively tested, tools to help select among existing potentials and develop new ones, and standard integration methods for using potentials in major simulation codes. Visit the OpenKIM Website.
OVITO is a scientific visualization and analysis software for atomistic and particle simulation data. It helps scientists gain better insights into materials phenomena and physical processes. The program is freely available for all major platforms under an open source license. It has served in a growing number of computational simulation studies as a powerful tool to analyze, understand and illustrate simulation results. https://www.ovito.org
S/PHI/nX is a C++ library for materials simulation, mostly electronic-structure theory. It also is a program (sphinx) to perform such simulations using density-functional theory, and k.p theory. In addition, the package offers dozens of specialized programs (add-ons) for smaller tasks related to setup, analysis, post-processing, and other types of simulations. https://sxrepo.mpie.de