comp-chem-utils 0.0.6

Utilities for computational chemistry.

CompChemUtils is a set of tools for computational chemistry workflows.

Install ccu

ccu requires: Python 3.10+ or PyPy3.

1. Run the following command in your command line:

pip install comp-chem-utils

2. Check that you’ve installed the correct version:

$ ccu --version
0.0.6

You can also install the in-development version with:

pip install git+ssh://[e-mail]/ugognw/python-comp-chem-utils.git@development

Usage

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)
True

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.        ]])

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