From rapid prototyping to high performance computing in material science
| Website 🌐 | Documentation 📚 | Workshops 🧑🏫 | Questions 💬 |
|---|---|---|---|
| pyiron.org | pyiron.readthedocs.io | workshop.pyiron.org | pyiron/FAQs |
The stable pyiron version is developed based on the generic job object class to handle the execution and storage of atomistic calculations and their post-processing. Two primary packages are available:
| Repository | Description | Coverage | Documentation | Conda Package |
|---|---|---|---|---|
| pyiron_atomistics | An interface to atomistic simulation codes including but not limited to GPAW, LAMMPS, S/Phi/nX and VASP. |  |
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| pyiron_base | A package for the core components e.g. the job management, data storage and resource management. |  |
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To increase the maintainability of the pyiron project, there is a continuous release of spin-off packages which are used inside pyiron, but which can also be used as stand-alone packages:
| Repository | Description | Coverage | Documentation | Conda Package |
|---|---|---|---|---|
| atomistics | Interfaces for atomistic simulation codes and workflows |  |
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| conda_subprocess | Run a subprocess or python function in a separate conda environment. |  |
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| executorlib | Scale serial and MPI-parallel python functions over hundreds of compute nodes all from within a jupyter notebook or serial python process. |  |
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| pyfileindex | Pythonic file system index |  |
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| pyiron_ontology | Leveraging ontologies for dynamic typing and guided workflow design |  |
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| pylammpsmpi | Parallel Lammps Python interface - control a mpi4py parallel LAMMPS instance from a serial python process or a Jupyter notebook. |  |
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| pysqa | Simple HPC queuing system adapter for Python on based jinja templates to automate the submission script creation. |  |
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| structuretoolkit | Build, analyse and visualise atomistic structures for materials science. |  |
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Beyond the application to atomistic simulation as part of the pyiron_atomistics package, the workflow manager pyiron_base is not limited to atomistic simulation. So the team of pyiron developers in collaboration with MaterialDigital and NFDI Matwerk developed a series of pyiron extensions for different application in materials science.
| Repository | Description | Coverage | Documentation | Conda Package |
|---|---|---|---|---|
| pyiron | A meta package which seamlessly loads all the pyiron plugins installed on a given system. |  |
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| pyiron_continuum | Modules for pyiron supporting continuum scale simulations and workflows. |  |
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| pyiron_contrib | A package to collect contributions from the community and/or bleeding edge developments. |  |
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| pyiron_dpd | Automated Defect Phase Diagrams and Workflow Prototypes. |  |
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| pyiron_electrochemistry | Workflows and analysis tools for computational electrochemistry using pyiron. |  |
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| pyiron_experimental | Post processing workflows for experimental applications. |  |
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| pyiron_gpl | A package for all interfaces which require a GPL license (default for pyiron is BSD). |  |
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| pyiron_gui | Extended graphical user interface (GUI) for the stable pyiron version |  |
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| pyiron_potentialfit | Fit machine learning interatomic potentials using pyiron. |  |
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Based on the experience with the stable pyiron version and the success of the stand-alone packages, the pyiron framework continues to innovate in the field of workflows for materials science. At the current stage pyiron_workflow is planned to be the future replacement of pyiron_base towards a more functional approach to workflows:
| Repository | Description | Coverage | Documentation | Conda Package |
|---|---|---|---|---|
| ironflow | Prototype of a graphical user interface for pyiron (not under active development) |  |
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| pyiron_workflow | Graph-and-node based workflows |  |
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In addition to the pyiron software packages in this organisation, there are a couple of repositories to automate the maintainence of the pyiron project:
| Repository | Description |
|---|---|
| actions | A centralized location for our GitHub actions |
| docker-stacks | Ready-to-run Docker images containing pyiron applications |
| pyiron-installer | pyiron installer based on conda constructor |
| pyiron_module_template | A template to generate a new pyiron module. |
| pyiron-publication-template | Template repository - how to publish your pyiron workflow |
| pyiron-resources | Resource folder for pyiron - an integrated development environment (IDE) for computational materials science. |
Example publication demonstrating how pyiron accelerates research and covers the whole simulation life cycle up to the publication of the results:
| Repository | Title | Authors | Journal |
|---|---|---|---|
| pyiron_meltingpoint | A fully automated approach to calculate the melting temperature of elemental crystals | Li-Fang Zhu, Jan Janssen, Shoji Ishibashi, Fritz Körmann, Blazej Grabowski and Joerg Neugebauer | Computational Materials Science 187, 110065 |
| pyiron_generalized_dipole | Generalized dipole correction for charged surfaces in the repeated-slab approach | Christoph Freysoldt, Arpit Mishra, Michael Ashton and Joerg Neugebauer | Physical Review B 102, 045403 |
| pyiron_md_montecarlo | Interplay of Chemistry and Faceting at Grain Boundaries in a Model Al Alloy | Huan Zhao, Liam Huber, Wenjun Lu, Nicolas J. Peter, Dayong An, Frédéric De Geuser, Gerhard Dehm, Dirk Ponge, Joerg Neugebauer, Baptiste Gault and Dierk Raabe | Physical Review Letters 124, 106102 |
