comp-chem-utils 0.0.5

Description:

compchemutils 0.0.5

CompChemUtils is a set of tools for computational chemistry workflows.

Requirements

Python 3.10 or later
click (package for command line interfaces)
numpy (N-dimensional array package)
scipy (library for scientific computing)
ase (tools for atomistic simulations)



Installation
python3 -m pip install comp-chem-utils
or, if you use poetry:
poetry add comp-chem-utils
You can also install the in-development version with:
pip install git+ssh://[email protected]:ugognw/python-comp-chem-utils.git
or, similarly:
poetry add git+ssh://[email protected]:ugognw/python-comp-chem-utils.git


Usage

Example
Determine whether a water molecule is symmetric with respect to a 180 degree
rotation about its secondary orientation axis.

>>> from ase.build import molecule
>>> from ccu.structure.axisfinder import find_secondary_axis
>>> from ccu.structure.symmetry import Rotation, RotationSymmetry
>>> h2o = molecule('H2O')
>>> axis = find_secondary_axis(h2o)
>>> r = Rotation(180, axis)
>>> sym = RotationSymmetry(r)
>>> sym.check_symmetry(h2o)
True




Example
Retrieve 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. ]])



Example
Place adsorbates on a surface (namely, Cu-THQ.traj) while considering the
symmetry of the adsorbate and the adsorption sites.
ccu adsorption place-adsorbate CO Cu-THQ.traj orientations/



Documentation
View the latest version of the documentation on Read the Docs.

License

For personal and professional use. You cannot resell or redistribute these repositories in their original state.

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