pyiron

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pyiron - an integrated development environment (IDE) for 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.

Screenshot of pyiron running inside jupyterlab.

pyiron (called pyron) is developed in the Computational Materials Design department of Joerg Neugebauer at the Max Planck Institut für Eisenforschung (Max Planck Institute for iron research). 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.

Note

pyiron_atomistics: This is the documentation page for the basic infrastructure 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

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

  • 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 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},
}

Read more about citing individual modules/ plugins of pyiron and the implemented simulation codes.