pyiron_atomistics is an integrated environment for performing atomistic simulations and managing computational materials science workflows. It brings atomic structures, simulation codes, job management, data storage and analysis together within a common Python-based framework.
The software is designed to make computational studies easier to scale from an individual calculation to complex simulation protocols and high-throughput workloads. Jobs are represented as Python objects, allowing calculations to be created, modified, submitted, inspected and combined into larger workflows without relying solely on collections of shell scripts.
pyiron_atomistics provides interfaces to atomistic simulation packages including LAMMPS and VASP, while its structure objects are compatible with the Atomic Simulation Environment. The surrounding pyiron ecosystem adds functionality for managing computing resources and storing calculation data, making it possible to maintain a consistent workflow across local workstations and larger computing infrastructure.
Hierarchical data management is an important part of the software. Calculation inputs, outputs and metadata can be organised using storage technologies such as HDF5 and SQL-backed resources. This helps researchers retain the provenance of large collections of calculations and makes it easier to revisit or analyse previous computational results.
The framework also supports interactive work through Jupyter notebooks, structure visualisation and feedback loops for constructing dynamic simulation procedures. Its original development was motivated by complex simulation protocols required for ab initio thermodynamics, but it has expanded into a broader environment for atomistic modelling and computational materials research.
This is free and open source software.
Key Features
- Provides object-oriented job management for individual calculations and high-throughput simulations.
- Interfaces with atomistic simulation codes including LAMMPS and VASP.
- Offers atomic structure objects compatible with the Atomic Simulation Environment.
- Provides hierarchical storage of simulation data using technologies including HDF5 and SQL.
- Supports interactive workflows, feedback loops, visualisation and Jupyter-based simulation protocols.
Website: github.com/pyiron/pyiron_atomistics
Support:
Developer: Max Planck Institute for Sustainable Materials, Computational Materials Design department
License: BSD 3-Clause License
pyiron_atomistics is written in Python. Learn Python with our recommended free books and free tutorials.
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