computational chemistry toolkit
# cctk ## Computational Chemistry Toolkit
This is a Python 3-based library for working with computational chemistry data.
- ## Contents:
- [Technical Details](#technical-details)
- [How to Cite](#how-to-cite)
cctk is an open-source Python package designed to automate generation and analysis of computational chemistry files.
- Potential uses for cctk include:
- Monitoring one or many geometry optimizations.
- Extracting geometry from output files, changing geometric parameters, and creating new input files.
- Calculating molecular properties (e.g. NICS) along a reaction coordinate.
- Screening different functionals and basis sets.
- Generating potential energy surfaces in one or more dimensions (e.g. More O’Ferrall-Jencks plots).
For examples of how cctk can be used, refer to the [tutorials](https://github.com/ekwan/cctk/tree/master/tutorial).
- ### Compatible File Types:
- Gaussian 16 .out (read) and .gjf (read/write).
- .xyz (read/write)
- .mol2 (read)
- .mae (read)
- Orca .inp (write)
#### Installing with a working Python 3.7+ environment:
Simply run: ` $ pip install cctk `
#### Installing without a working Python 3.7+ environment:
If you have a different version of Python (e.g. Python 2.7), you can use a conda environment to run cctk without breaking existing packages.
- Install [conda](https://docs.conda.io/en/latest/)/[miniconda](https://docs.conda.io/en/latest/miniconda.html).
- Use env.yml to create a Conda environment called cctk and install cctk:
` $ cd cctk $ conda env create -f env.yml `
Now, run conda activate cctk to enter the cctk Python environment (and conda deactivate to leave). (More complete guides to conda usage can be found elsewhere.)
- cctk/ contains the Python modules for cctk and the accompanying static data files.
- docs/ contains the code needed to generate the documentation.
- scripts/ contains pre-defined scripts that use cctk to quickly analyze and manipulate one or many output files.
- test/ contains code to test cctk and accompanying files.
- tutorial/ contains detailed tutorials on how to use cctk on complex, real-world problems.
To build the documentation (which requires a few extra dependencies), run:
` cd docs/ sphinx-apidoc -o . ../cctk/ make html `
The documentation files can then be found in docs/_build/html.
## Technical Details:
### External Data:
cctk depends on some external data, stored in cctk/data/: - Atomic weights are taken from the [NIST website](https://physics.nist.gov/cgi-bin/Compositions/stand_alone.pl?ele=&all=all&ascii=ascii2&isotype=some) and stored in cctk/data/isotopes.csv. - Covalent radii are taken from [Dalton Trans. 2008, 2832–2838](https://pubs.rsc.org/en/content/articlelanding/2008/dt/b801115j#!divAbstract) and stored in cctk/data/covalent_radii.csv. (When multiple atomic types were specified, the one with longer bond distances was adopted for simplicity).
cctk was written by Corin Wagen and Eugene Kwan at the Department of Chemistry and Chemical Biology at Harvard University. Please email firstname.lastname@example.org with any questions or bug reports; we will do our best!
## How to Cite:
Wagen, C.C.; Kwan, E.E. cctk 2020, [www.github.com/ekwan/cctk](www.github.com/ekwan/cctk).
This project is licensed under the Apache License, Version 2.0: see LICENSE for full terms and conditions.
Copyright 2020 by Corin Wagen and Eugene Kwan
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