Get Started¶

Install `ccu`¶

ccu requires: Python 3.10+ or PyPy3.

Run the following command in your command line:

pip install comp-chem-utils

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://git@gitlab.com/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/