=============
CompChemUtils
=============
|ccu|_ 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
============
.. code-block:: console
python3 -m pip install comp-chem-utils
or, if you use poetry:
.. code-block:: console
poetry add comp-chem-utils
You can also install the in-development version with:
.. code-block:: console
pip install git+ssh://git@gitlab.com:ugognw/python-comp-chem-utils.git
or, similarly:
.. code-block:: console
poetry add git+ssh://git@gitlab.com:ugognw/python-comp-chem-utils.git
Usage
=====
.. admonition:: 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
.. admonition:: 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. ]])
.. admonition:: Example
Place adsorbates on a surface (namely, ``Cu-THQ.traj``) while considering the
symmetry of the adsorbate and the adsorption sites.
.. code-block:: console
ccu adsorption place-adsorbate CO Cu-THQ.traj orientations/
Documentation
=============
View the latest version of the documentation on `Read the Docs`_.
.. |ccu| replace:: ``CompChemUtils``
.. _ccu: https://gitlab.com/ugognw/python-comp-chem-utils/
.. _Python: https://www.python.org
.. |click| replace:: ``click``
.. _click: https://click.palletsprojects.com/en/8.1.x/
.. |numpy| replace:: ``numpy``
.. _numpy: https://numpy.org
.. |scipy| replace:: ``scipy``
.. _scipy: https://scipy.org
.. |ase| replace:: ``ase``
.. _ASE: https://wiki.fysik.dtu.dk/ase/index.html
.. _Read the Docs: https://python-comp-chem-utils.readthedocs.io/en/latest
.. |CO2| replace:: CO\ :sub:`2`
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