Use ORBKIT for rendering MO #orbkit #rdkit #psikit #quantum_chemistry

As you know, there many packages for quantum chemistry not only commercial software but also free tools. And each soft has own output format. So user need to understand how to use it. But it is very time consuming step I think.

ORBIKIT is a modular python toolbox for cross-platform post processing of quantum chemical wavefunction data.

The reference URL is below.
https://arxiv.org/abs/1601.03069

It seems nice isn’t it? Fortunately the source code is disclosed on github.

So I tried to use orbkit with psikit. At first, I installed orbkit while referring the original site.

At first, I installed cython, numpy, scipy, h5py with conda and mayavi installed with pip (mayavi couldn’t install with conda due to package conflicts).

Then install orbkit.

$ cd $HOME
$ git clone https://github.com/orbkit/orbkit.git
$ export ORBKITPATH=$HOME/orbkit
$ cd $ORBKITPATH
$ python setup.py build_ext --inplace clean
$ export PYTHONPATH=$PYHONPATH:$ORBKITPATH

And also I added environment variables to my .bashrc.

Now ready, let’s use orbkit. I used psikit for making fchk file for orbkit. orbkit supports many kinds of input format. If reader has interest the package, please check the original document.

Following code shows how to use psikit and visualize MO with orbkit.

After running the code, mayavi viewer launched and could get MO view, the image is shown below.

Of course current psikit has some functions for communicate pymol for rendering MO but orbkit is also useful package for quantum chemistry.

I uploaded today’s code on my github repo.

https://github.com/iwatobipen/playground/blob/master/orbkit_psikit_test.ipynb

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