Package: pyiron-atomistics
pyiron - an integrated development environment (IDE) for computational materials science. It combines several tools in a common platform:Atomic structure objects – compatible to theAtomic Simulation Environment (ASE).Atomistic simulation codes – likeLAMMPSandVASP.Feedback Loops – to construct dynamic simulation life cycles.Hierarchical data management – interfacing with storage resources like SQL andHDF5.Integrated visualization – based onNGLview.Interactive simulation protocols - based onJupyter notebooks.Object oriented job management – for scaling complex simulation protocols from single jobs to high-throughput simulations.pyiron (called pyron) is developed in theComputational Materials Design departmentofJoerg Neugebauerat theMax 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 theInterdisciplinary 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.
See theDocumentationpage for more details.InstallationYou can test pyiron onMybinder.org (beta).
For a local installation we recommend to install pyiron inside ananacondaenvironment:conda install -c conda-forge pyironAfter 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 theDocumentation-Installationpage for more details.ExampleAfter the successful configuration you can start your first pyiron calculation. Navigate to the projects directory and start a jupyter notebook or jupyter lab session correspondingly:cd ~/pyiron/projects
jupyter notebookOpen 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_atomistics 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:License and Acknowledgmentspyironis licensed under the BSD license.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},
}