Utilities for computational chemistry.
Project description
CompChemUtils is a set of tools for computational chemistry workflows.
Requirements
Installation
$ 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://git@gitlab.com:ugognw/python-comp-chem-utils.git
or, similarly:
$ poetry add git+ssh://git@gitlab.com:ugognw/python-comp-chem-utils.git
Documentation
Testing
To run all the tests run:
$ nox
Note, to combine the coverage data from all the nox environments run:
Windows |
set PYTEST_ADDOPTS=--cov-append nox |
---|---|
Other |
PYTEST_ADDOPTS=--cov-append nox |
Examples
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
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 (namely, “Cu-THQ.traj”) while considering the symmetry of the adsorbate and the adsorption sites.:
$ ccu adsorption place-adsorbate CO Cu-THQ.traj orientations/
Enable Shell Completion
Add this to your ~/.bashrc::
eval "$(_CCU_COMPLETE=bash_source ccu)"
Add this to ~/.zshrc::
eval "$(_CCU_COMPLETE=zsh_source ccu)"
Add this to ~/.config/fish/completions/ccu.fish::
eval (env _CCU_COMPLETE=fish_source ccu)
Project details
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