Unix

There are packaged versions on PyPi and conda-forge.

For the packaged version from PyPi, the following commands have to be executed:

pip install chemcoord

For the packaged version from conda-forge, the following commands have to be executed:

conda install -c conda-forge chemcoord

For the up to date development version (experimental):

git clone https://github.com/mcocdawc/chemcoord.git
cd chemcoord
pip install .

Windows

Neither installation nor running the module are tested on windows. To the best of my knowledge it should work there as well. Just use the same steps as for UNIX.

Citation and mathematical background

The theory behind chemcoord is described in this paper. If this package is used in a project that leads to a scientific publication, please acknowledge it by citing.

@article{https://doi.org/10.1002/jcc.27029,
    author = {Weser, Oskar and Hein-Janke, Björn and Mata, Ricardo A.},
    title = {Automated handling of complex chemical structures in Z-matrix coordinates—The chemcoord library},
    journal = {Journal of Computational Chemistry},
    volume = {44},
    number = {5},
    pages = {710-726},
    keywords = {analytical gradients, geometry optimization, non-linear constraints, transition state search, Z-matrix},
    doi = {10.1002/jcc.27029},
    year = {2023}
}

The redundant internal coordinate (RIC) interpolation algorithm, exposed via chemcoord.ric_functions.RIC_interpolate, is described in this paper. If you use it, please cite:

@article{whelpley_efficient_2026,
    author = {Whelpley, Noah and Van Voorhis, Troy and Weser, Oskar},
    title = {Efficient, Black-Box Estimation of Reaction Paths via Redundant Internal Coordinate Interpolation},
    year = {2026},
    journal = {ChemRxiv},
    doi = {10.26434/chemrxiv.15005488},
    url = {https://chemrxiv.org/doi/full/10.26434/chemrxiv.15005488/v1}
}

My (Oskar Weser) master thesis including a more detailed derivation of implemented equations and the mathematical background can be found here.

Acknowledgement

Zulip is an open-source modern team chat app designed to keep both live and asynchronous conversations organized, that supports the development of chemcoord with a free plan.