pyiron - an integrated development environment (IDE) for computational materials science.
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pyiron - an integrated development environment (IDE) for computational materials science. It combines several tools in a common platform:
Atomic Simulation Environment (ASE)_.
LAMMPS_ and
VASP_.
HDF5_.
NGLview_.
Jupyter notebooks_.
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. See the
Documentation_ page for more details.
You can test pyiron on
Mybinder.org (beta). For a local installation we recommend to install pyiron inside an
anacondaenvironment::
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_ page for more details.
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()
Test pyiron with mybinder:
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pyironis 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}, }