pyiron-atomistics 0.8.8

An interface to atomistic simulation codes including but not limited to GPAW, LAMMPS, S/Phi/nX and VASP.

pyiron_atomistics

pyiron_atomistics - an integrated development environment (IDE) for atomistic simulation in computational materials science. It combines several tools in a common platform:

• Atomic structure objects – compatible to the Atomic Simulation Environment (ASE).
• Atomistic simulation codes – like LAMMPS and VASP.
• Feedback Loops – to construct dynamic simulation life cycles.
• Hierarchical data management – interfacing with storage resources like SQL and HDF5.
• Integrated visualization – based on NGLview.
• Interactive simulation protocols - based on Jupyter notebooks.
• Object-oriented job management – for scaling complex simulation protocols from single jobs to high-throughput simulations.

pyiron (called pyron) is developed in the Computational Materials Design department of Joerg Neugebauer at the Max Planck Institut für Nachhaltige Materialien (Max Planck Institute for Sustainable Materials). While its original focus was to provide a framework to develop and run complex simulation protocols as needed for ab initio thermodynamics it quickly evolved into a versatile tool to manage a wide variety of simulation tasks. In 2016 the Interdisciplinary Centre for Advanced Materials Simulation (ICAMS) joined the development of the framework with a specific focus on high throughput applications. In 2018 pyiron was released as open-source project.

pyiron_atomistics: This is the documentation page for the atomistic simulation moduls of pyiron. If you're new to pyiron and want to get an overview head over to pyiron. If you're looking for the API docs of pyiron_base check pyiron_base.

Explore pyiron_atomistics

We provide various options to install, explore and run pyiron_atomistics:

• Workstation Installation (recommeded): for Windows, Linux or Mac OS X workstations (interface for local VASP executable, support for the latest jupyterlab based GUI)
• Mybinder.org (beta): test pyiron directly in your browser (no VASP license, no visualization, only temporary data storage)
• Docker (for demonstration): requires Docker installation (no VASP license, only temporary data storage)

Join the development

Please contact us if you are interested in using pyiron:

• to interface your simulation code or method
• implementing high-throughput approaches based on atomistic codes
• to learn more about method development and Big Data in material science.

Please also check out the pyiron_atomistics contributing guidelines.

Citing

If you use pyiron in your research, please consider citing the following work:

@article{pyiron-paper,
    title = {pyiron: An integrated development environment for computational materials science},
    journal = {Computational Materials Science},
    volume = {163},
    pages = {24 - 36},
    year = {2019},
    issn = {0927-0256},
    doi = {https://doi.org/10.1016/j.commatsci.2018.07.043},
    url = {http://www.sciencedirect.com/science/article/pii/S0927025618304786},
    author = {Jan Janssen and Sudarsan Surendralal and Yury Lysogorskiy and Mira Todorova and Tilmann Hickel and Ralf Drautz and Jörg Neugebauer},
    keywords = {Modelling workflow, Integrated development environment, Complex simulation protocols},
}