Data

Tools

Indexes

Applications

Experiments

Open Source Science

chirpy

A python package for chirality, dynamics, and molecular vibrations.

https://github.com/sjaehnigen/chirpy

Science Score: 57.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 6 DOI reference(s) in README
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (13.7%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

A python package for chirality, dynamics, and molecular vibrations.

Basic Info
  • Host: GitHub
  • Owner: sjaehnigen
  • License: gpl-3.0
  • Language: Python
  • Default Branch: master
  • Homepage:
  • Size: 9.89 MB
Statistics
  • Stars: 2
  • Watchers: 2
  • Forks: 1
  • Open Issues: 0
  • Releases: 0
Created about 3 years ago · Last pushed 7 months ago
Metadata Files
Readme License Citation Authors

README.md

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 >= 3.13 - pip >= 25.1 - packmol >= 20.0 (optional)

You can also use Anaconda to create a chirpy environment from the delivered conda_env.yml file: shell conda env create -f conda_env.yml

In the parent directory, run: shell pip install .

ChirPy has now been installed and can be imported within a python environment: python import chirpy as cp

Check that you installation is correct by running from a bash terminal the test suite in tests/: shell python run_tests.py or shell ./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.

Owner

  • Name: Sascha Jähnigen
  • Login: sjaehnigen
  • Kind: user

Citation (CITATION.bib) 

@misc{ChirPy,
  title = {{C}hirPy -- {A} python package for chirality, dynamics, and molecular vibrations},
  author = {J{\"a}hnigen, Sascha},
  year = {2022},
  doi = {10.5281/zenodo.4775330},
  url = {https://github.com/sjaehnigen/chirpy}
  howpublished = {\url{https://github.com/sjaehnigen/chirpy}},
}

GitHub Events

Total
  • Issues event: 2
  • Watch event: 1
  • Issue comment event: 1
  • Push event: 3
  • Fork event: 1
  • Create event: 2
Last Year
  • Issues event: 2
  • Watch event: 1
  • Issue comment event: 1
  • Push event: 3
  • Fork event: 1
  • Create event: 2