Introduction to pyiron modules: pyiron_atomistics

Here, a brief introduction to pyiron_atomistics and its components is presented. In the answers/comments to this post, you can ask any questions about pyiron_atomistics, or discuss new desirable features which you think should be added to this module.

Pyiron modular structure

Pyiron is known as an IDE for material science workflows. It facilitates various types of simulation and analysis workflows across multiple scales such as DFT simulations using VASP/SPHInX, molecular dynamics simulation using LAMMPS, continuum simulation using DAMASK or FEniCS, analyzing STEM images using pySTEM library, … .

To support such multiscale/multi-purpose workflows, pyiron includes the necessary functionalities within its modular structure. The modularity is ensured via pyiron conda packages: pyiron_base, pyiron_atomistics, pyiron_continuum, pyiron_experimental, pyiron_gui, and pyiron_contrib. This structure of pyiron allows the users to obtain the required functionalities without the need to install unnecessary packages.

The objective of pyiron_atomistics

pyiron_atomistics is the module intended to manage atomistics simulation workflows. The supported simulation methods are DFT, thermodynamics integration, and molecular dynamics. Not only the module provides an interface to run the aforementioned simulations, but also it provides job classes for more complex type of atomistics workflows to calculate thermo-mechanical properties of material from atomistics simulations.

Features and components

The supported simulation software includes: VASP, LAMMPS, SPHInX-dft, GPAW, phonopy, espei, pycalphad, … . It also takes advantage of ASE and aimsgb libraries for creating atomistics structure and grain boundaries. Of course, the list of supported software is open, as the source code is available on GitHub for user’s contributions to integrate the interface to new packages.

Beside simulation software packages, pyiron_atomistics has integrated access to two large databases for interatomic potentials: NIST and OpenKIM. Moreover, pyiron_atomistics has integrated visualization tools for atomistics structure and trajectories.

Additionally, by inheriting from interactive and master/child job classes of pyiron_base, pyiron_atomistics provides the required protocols and feedback loops for high throughput simulations and machine learned simulations.

Installation and testing

You can install pyiron_atomistics from conda-forge channel via,

conda install -c conda-forge pyiron_atomistics

For an out-of-the-box experience, you can use pyiron/pyiron docker images as,

docker run -p 8888:8888 --name pyiron_atomistics_container pyiron/pyiron:latest

Source

The source of pyiron_base is available on GitHub via https://github.com/pyiron/pyiron_atomistics. Though you can contribute directly to pyiron_Tatomistics, it is recommended that the users’ contributions are introduced first in pyiron_contrib package, via https://GitHub.com/pyiron/pyiron_contrib.

Documentation

The documentation and tutorial for all pyiron packages can be found under https://pyiron.org.

More video tutorials are available via: