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.

pyiron (called pyron) is developed in the

Computational Materials Design department 

Joerg Neugebauer 

Max Planck Institut für Eisenforschung (Max Planck Institute for iron research) 

Interdisciplinary Centre for Advanced Materials Simulation (ICAMS) 

Documentation 

.. note:: pyiron: This is the documentation page for the pyiron meta package, that combines the other packages in a common interface. The API documentation for

pyiron_base 

pyiron_atomistics 

Installation

You can test pyiron on

Mybinder.org (beta) 

anaconda 

conda install -c conda-forge pyiron

After the installation of pyiron you need to configure pyiron. The default configuration can be generated automatically. Start a new Python session and import pyiron::

import pyiron pyiron.install()

It appears that pyiron is not yet configured, do you want to create a default start configuration (recommended: yes). [yes/no]: yes exit()

See the

Documentation-Installation 

Example

After the successful configuration you can start your first pyiron calculation. Navigate to the the projects directory and start a jupyter notebook or jupyter lab session correspondingly::

cd ~/pyiron/projects
jupyter notebook

Open a new jupyter notebook and inside the notebook you can now validate your pyiron calculation by creating a test project, setting up an initial structure of bcc Fe and visualize it using NGLview::

from pyiron import Project
pr = Project('test')
structure = pr.create_structure('Fe', 'bcc', 2.78)
structure.plot3d()

Finally a first lammps calculation can be executed by::

job = pr.create_job(job_type=pr.job_type.Lammps, job_name='lammpstestjob')
job.structure = structure
job.potential = job.list_potentials()[0]
job.run()

Getting started:

Test pyiron with mybinder:

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License and Acknowledgments

pyiron

If you use pyiron in your scientific work,

please consider citing 

@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}, }