Create a conda environment for the eChem book

Using the echem.yml file (stored at the root of the echem directory) to create a conda environment echem will install all needed packages to compile the book.

conda env create -f echem.yml

Commands

Run notebooks by opening jupyter-lab (or jupyter-notebook):

$ jupyter-lab

Jupyter can access folders below where it is spawned, so initiate it in, e.g. the main eChem folder. Examples on how to use Jupyter can be found here.

Build the book:

$ jupyter-book build .

Publish the html-version:

$ ghp-import -n -p -f _build/html

Alternative installation

You can manually create the environment and install the packages in several steps:

conda create -n echem -c conda-forge -c veloxchem python=3.9 veloxchem libblas=*=*mkl
conda activate echem
conda install -c conda-forge jupyter-book matplotlib ghp-import py3dmol h5py k3d
conda install -c conda-forge -c veloxchem multipsi=0.0.1
conda install -c conda-forge -c gator gator
conda install -c conda-forge -c pyscf pyscf

References

The file references.bib in the top directory is a regular BIBTEX file. Add your references in this file. A citation in the text is added with

{cite}`Wang2016, Schlegel2011`

Multiple lists of references are possible but not yet properly implemented.

Distribution of labor:

Sections to be added/expanded marked in bold.

1. Intro

   • All authors

2. Tutorials and workflows:

   • Photochemistry: MD
   • Vibrational: IEB
   • UV/vis: TF
   • Optical activity: PN
   • X-ray: TF

3. Electronic ground states:

   • Primarily PN+MD
   • MD will expand CAS parts

4. Molecular structure and dynamics:

   • Primarily IEB+MH
   • MD: TF

5. Spectra and properties:

   • Primarily PN+MD
   • TDDFT: AD (+TF)
   • ADC: IEB+MH
   • Exciton coupling: XL

6. Environment:

   • Primarily PN

7. Visualization:

   • Primarily PN+MD+TF