nomodeco 0.2.6

a python package for the determination of optimal internal coordinate systems for molecular structures

Nomodeco.py a normal mode decomposition tool

Nomodeco.py enables the automatic determination of an optimal internal coordinate set for a given molecular structure. Using the atomic coordinates of the given molecule Nomodeco.py constructs all possible primitive internal coordinates.

Documentation

The following links provide further information and documentation about the package

decomposing vibrations-docs

How to Use:

Nomodeco can be installed using pip:

pip install nomodeco

Make sure to use a python version >=3.12.5!

For further information and a version history see:

Nomodeco on PyPI

Alternatively, Nomodeco can be installed using the github-repository. In the repository a enviroment.yml file is included which can be used to create a conda enviroment with python 3.12.5 and poetry installed.

conda env create -f enviroment.yml

Then using poetry the additional packages can be installed:

poetry update

With the usage of the enviroment.yml file also pymolpro is installed which runs jobs on the local molpro installation.

Publication for further information:

Kemal Oenen, Dennis F. Dinu, Klaus R. Liedl; Determining internal coordinate sets for optimal representation of molecular vibration. J. Chem. Phys. 7 January 2024; 160 (1): 014104. https://doi.org/10.1063/5.0180657