fastatomstruct 1.5.1

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Fast calculation of structural and dynamical parameters

fastatomstruct is a Python package (mostly written in Rust) that includes functions to calculate atomic structural quantities. If possible, thread-based parallelization (using rayon) is employed to speed up calculations and take advantage of multicore processors.

Citation

If you use fastatomstruct in your research, please cite the following paper:

Documentation

The documentation can be found here.

What can this package do?

The package can currently calculate the following quantities:

• Structural
  • Atomic distances
  • Coordination numbers
  • Finding bonds
  • Nearest neighbours
  • Radial distribution function
  • Static structure factor
  • Bond orientational parameter (Steinhardt et al.) and Bond Order Correlation parameter
  • Tetrahedral and octahedral order parameters
  • Three-body correlation (TBC) - simple, angular-limited, and angular-resolved
  • Bond length ratio (BLR)
  • Bond angle distribution
  • Angular-resolved RDF with local coordinate systems
  • Local environment characterization (Cartesian and cylindrical coordinates)
  • Peierls distortion analysis
• Dynamical
  • Mean squared displacement
  • Non-gaussian parameter
  • Overlap q
  • Four-point correlation functions
  • Current correlation functions
  • Velocity autocorrelation
  • Vibrational density of states
  • Viscosity
  • Intermediate scattering functions
  • Participation ratio from dynamical matrices
  • Phase quotient analysis
  • Mode-weighted quantities

Example usage

This example uses the Atomic Simulation Environment, which can also be installed using pip (pip install ase) and is a dependency of fastatomstruct.

from ase.build import bulk
from fastatomstruct import all_distances, coordination_numbers

# Lithium in the BCC phase with the unit cell repeated
# 10x10x10 times
atoms = bulk("Li", "bcc", 3.45).repeat((10, 10, 10))

# Atomic distances
dists = all_distances(atoms)

# Coordination numbers with a cutoff of 3 A
coordination = coordination_numbers(atoms, 3)

More examples can be found in the documentation.

Example usage in Rust

fastatomstruct can also be used in Rust projects. You can find the documentation for the Rust API here. Examples can be found here.

Installation

From PyPI

fastatomstruct can be installed from the Python Package Index. Currently, Windows (x86_64), Linux (x86_64, aarch64), and Mac OS X (x86_64, aarch64) with a Python version >= 3.8 are supported. In addition, your x86_64 processor has to support AVX2 instructions. Most processors since 2015 should meet those criteria. If your system doesn't, you can still install fastatomstruct from source (see next subsection).

To run the installation, use

pip install fastatomstruct

Image parallelization

If you want to use image parallelization with fastatomstruct.ipar (see documentation), you should also install mpi4py. Please consult the corresponding documentation for installation instructions and prerequisites.

From source

Installing fastatomstruct from source requires

• Python >= 3.8
• pip
• a working Rust installation (1.87 and newer), including cargo (installation instructions can be found here)
• maturin, a Python package that can e.g. be installed using pip3 install --upgrade maturin

To build the Python wheel, run

maturin build --release

The resulting wheel will be located in target/wheels/. You can install it using

python3 -m pip install target/wheels/fastatomstruct-version.whl

Replace "version" with your actual Python version. The package can then be used in Python using e.g. from fastatomstruct import coordination_numbers.

Running tests

You can run the tests using

cargo test

Additional regression tests are implemented using the pytest framework. To run them, you need to install pytest (e.g. using pip install pytest) and then run

pytest

Contributing

We welcome contributions to fastatomstruct. To contribute, please follow these steps:

1. Fork the repository on GitLab.
2. Create a new branch with a descriptive name for your feature or bugfix.
3. Make your changes and commit them with clear and concise commit messages.
4. Push your changes to your forked repository.
5. Open a merge request on the original repository and provide a detailed description of your changes.

Reporting Issues

If you encounter any issues or bugs while using fastatomstruct, please report them on our GitLab issues page. Provide as much detail as possible, including steps to reproduce the issue and any relevant error messages.

Seeking Support

For support and questions, you can also use the GitLab issues page. We will do our best to assist you in a timely manner.