CompChemUtils is a set of tools for computational chemistry workflows.
Install ccu
ccu requires: Python 3.10+ or PyPy3.
Run the following command in your command line:
pip install comp-chem-utilsCheck that you’ve installed the correct version:
$ ccu --version
0.0.6You can also install the in-development version with:
pip install git+ssh://git@gitlab.com/ugognw/python-comp-chem-utils.git@developmentUsage
Determine the symmetry of a water molecule
>>> from ase.build import molecule
>>> from ccu.structure.axisfinder import find_secondary_axis
>>> from ccu.structure.symmetry import Rotation, check_symmetry
>>> h2o = molecule('H2O')
>>> axis = find_secondary_axis(h2o)
>>> r = Rotation(180, axis)
>>> check_symmetry(r, h2o)
TrueRetrieve reaction intermediates for the two-electron CO2 reduction reaction
>>> from ccu.adsorption.adsorbates import get_adsorbate
>>> cooh = get_adsorbate('COOH_CIS')
>>> cooh.positions
array([[ 0. , 0. , 0. ],
[ 0.98582255, -0.68771934, 0. ],
[ 0. , 1.343 , 0. ],
[ 0.93293074, 1.61580804, 0. ]])
>>> ocho = get_adsorbate('OCHO')
>>> ocho.positions
array([[ 0. , 0. , 0. ],
[ 1.16307212, -0.6715 , 0. ],
[ 0. , 1.343 , 0. ],
[-0.95002987, -0.5485 , 0. ]])Place adsorbates on a surface
Place adsorbates on a surface (namely, Cu-THQ.traj) while considering the symmetry of the adsorbate and the adsorption sites.
ccu adsorb CO Cu-THQ.traj orientations/
Documentation
View the latest version of the documentation on Read the Docs
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Metadata
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Release files for comp-chem-utils 0.0.6
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Source distribution (sdist)
| File | Size | Uploaded | |
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| comp_chem_utils-0.0.6.tar.gz | 6.7 MB | Details |
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| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| comp_chem_utils-0.0.6-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 8.4 MB
Release files / comp_chem_utils-0.0.6.tar.gz
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| Size | 1.6 MB |
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