ChirPy

ChirPy (chiral python) is a python package for chirality, dynamics, and molecular vibrations.

Main features:

• Computation of vibrational circular dichroism (VCD) from molecular dynamics (MD) and time-correlation functions (TCF)
• Application of the periodic gauge for magnetic moments and crystal symmetry in solid-state
• Interpretation, processing, and creation of molecular topologies and supercells
• Analysis and visualisation of MD results

Furthermore:

• Scientific visualisation
• Interfacing with VMD
• Processing of volumetric data and vector fields

(... work in progress)

Installation

Copy or clone the repository into a local directory. Open a bash terminal and change directory to the local copy of the repository.

Make sure you have the following packages installed:

• python >= 3.10
• pip >= 22.3
• packmol >= 20.0 (optional)

You can also use Anaconda to create a chirpy environment from the delivered conda_env.yml file:

conda env create -f conda_env.yml

In the parent directory, run:

pip install .

ChirPy has now been installed and can be imported within a python environment:

import chirpy as cp

Check that you installation is correct by running from a bash terminal the test suite in tests/:

python run_tests.py

or

./run_tests.py

(optional arguments: --verbose, --scripts)

Thank you for reporting bugs and issues to the developers.

Examples

Workable binaries can be found in the folder scripts/ with some pre-implemented ChirPy features. Make sure you add this folder to PATH.

Available jupyter notebooks and data sets:

• Computation of Solid-State Vibrational Circular Dichroism in the Periodic Gauge

(... under construction)

References

1. S. Jähnigen, A. Zehnacker, and R. Vuilleumier; Computation of Solid-State Vibrational Circular Dichroism in the Periodic Gauge, J. Phys. Chem. Lett., 2021, 12 (30), 7213-7220.
2. S. Jähnigen, D. Sebastiani, R. Vuilleumier; The important role of non-covalent interactions for the vibrational circular dichroism of lactic acid in aqueous solution, Phys. Chem. Chem. Phys., 2021, 23, 17232.