pyMolDyn

pyMolDyn is a viewer for atomic clusters, crystalline and amorphous materials in a unit cell corresponding to one of the seven 3D Bravais lattices. The program calculates cavities (vacancies, voids) according to three definitions.

pyMolDyn GUI

Features

  • Interactive viewer based on GR3
  • Computation of cavities in all seven 3D Bravais lattice systems
  • Creation of high resolution images appropriate for publications
  • Video creation from a set of input frames to analyze cavity changes in materials over time
  • Statistics including
    • Surfaces, volumes and surface/volume ratios of cavities and domains
    • Pair distribution functions (including cavities), bonds, bond (dihedral) angles
    • Gyration tensor, asphericity, acylindricity
  • Filter for atoms and cavities
  • Batch mode for simultaneous processing of multiple files

Documentation

Further information on supported input formats and the Bravais lattice systems can be found on the pyMolDyn documentation page.

Short introductions to the gui version and the command line interface are also available.

Download

Current version: 0.11.1

At PGI/JCNS pyMolDyn is installed centrally on all Linux machines and Macs. For other users, we offer

  • pip installable wheels on PyPI,
  • a Windows installer,
  • a macOS DMG image for Intel and AppleSilicon chipsets,
  • packages for several Linux distributions and
  • a GitHub source code repository.

Python wheels

If you already have a working Python installation (Python version >= 3.9), you can install pyMolDyn with pip or pipx:

python3 -m pip install pymoldyn

We offer pre-compiled wheels for

  • Windows x86_64,
  • macOS x86_64 / arm64,
  • Linux x86_64

and Python versions 3.9 or newer.

Windows

For Windows users without a local Python installation, we provide an MSI installer, bundled with all needed dependencies.

macOS

We provide a universal Apple DMG installer for Intel and AppleSilicon CPUs.

The DMG installer contains all needed pyMolDyn dependencies, so no additional libraries need to be installed.

By default, macOS blocks downloaded foreign applications from being executed. In this case, please go to System Settings, switch to Privacy & Security in the sidebar and click on the Open Anyway button next to the pyMolDyn installer.

Linux

We provide pre-built DEB and RPM packages for the x86_64 architecture for the following Linux distributions:

For Arch Linux and its derivatives (e.g. Manjaro), you can use our AUR package:

yay -S pymoldyn

If your distribution is not in the list above or you prefer sandboxed application we also provide a flatpack.

After the package installation, pyMolDyn can be started from a terminal window with

pymoldyn

for the GUI version or

pymoldyn --batch

to invoke the batch CLI mode.

Source Code

For obtaining source code tarballs, please visit our public git repository at https://github.com/sciapp/pyMolDyn.

Running the development version

  • Install python3 with header files, pip and venv (e.g. python-dev, python-pip and python-venv on Debian/Ubuntu).

  • Clone pyMolDyn source code:

    git clone https://github.com/sciapp/pyMolDyn.git
cd pyMolDyn
git switch develop

  • Create a virtual environment and install pyMolDyn in editable mode:

    python3 -m venv env
source env/bin/activate
pip install -e .

  • Now apply your code changes.

  • In order to test pyMolDyn:

    pymoldyn

How to cite

I. Meyer, F. Rhiem, F. Beule, D. Knodt, J. Heinen, R. O. Jones: pyMolDyn: Identification, structure, and properties of cavities/vacancies in condensed matter (J. Comput. Chem. 2017, 38, 389–394. DOI: 10.1002/jcc.24697)

pyMolDyn at EuroScipy 2016

A poster about the implemented pyMolDyn algorithms was presented at the EuroScipy 2016.

Contact

For questions please contact Ingo Meyer (software maintainer).

Please use the GitHub issue tracker for bug reports and feature requests.