diff --git a/examples/README.md b/examples/README.md index 2ef9fff..36be734 100644 --- a/examples/README.md +++ b/examples/README.md @@ -16,7 +16,7 @@ jupyter lab ``` # Outline of the examples -1. **transfer-integral-worlflow.ipynb** : Test an organic molecules HOMO/LUMO and Transfer Integral (electronic coupling) for various orenitations with morphCT. +1. **transfer-integral-workflow.ipynb** : Test an organic molecules HOMO/LUMO and Transfer Integral (electronic coupling) for various orenitations with morphCT. 2. **chromophore-picking.ipynb** : How to use VMD to select atoms from a morphology and create an array of the chosen atom's indeces to create and a array of chromophore indeces 3. **new-acceptor-molecule-workflow.ipynb** : This workflow seeks to outline the path of least resistance for investigation of a new acceptor molecule with morphCT. To predict the mobililty of in a morphology, we need 2 things: (1) a gsd of your morphology and (2) and list of atom indeces that belong to each chromophore. This workflow automates the creation of (2). I WOULD START BY RUNNING THIS TO SEE IF MORPHCT IS WORKING. 4. **workflow-itic.ipynb** : A notebook for breaking ITIC into multiple chromophores. This notebook also contains an example for creating a csv containing chromophore atom ids for using morphct-flow. @@ -25,6 +25,6 @@ jupyter lab # You can find some further (uncurated) workflows that use the morphct api here: https://github.com/JimmyRushing/thesis/tree/main/notebooks -(1) **fused-experiment.ipynb** : I used smiles strings to check out the homo-lumo gap of fused thiophens. +(1) **fused-experiment.ipynb** : I used smiles strings to check out the homo-lumo gap of fused thiophenes. (2) **voronoi_figures.ipynb** : I created a plot that visualized the voronoi analysis that takes place in the creation of neighbor lists in morphCT (3) other scratch workbooks for generating figures from morphCT data