Instructor’s guide¶

Editing the material¶

This website uses sphinx-lesson. Pages can be added in a variety of formats:

Jupyter notebooks (.ipynb), like all the pages for Day 1.
reStructuredText (.rst), as usual for Sphinx-based documentation pages.
Markdown (.md), like all the pages for Day 2.

However, note that we do not use plain Markdown, but the MyST parser (short for Markedly Structured Text) that allows for richer content. For example, it is possible to embed Jupyter notebook input and/or output cells via MyST-nb or even write entire notebooks in plain-text!

Here are some quick guides to .rst and .md formats:

For MyST https://myst-parser.readthedocs.io/en/latest/using/syntax.html
For reStructuredText https://docutils.sourceforge.io/docs/user/rst/quickref.html
For MyST-nb https://myst-nb.readthedocs.io/en/latest/use/markdown.html

Useful notes on Jupyter notebooks¶

Sometimes it’s necessary to hide and/or remove content from a notebook when using it as training material. This can be accomplished with tags.

In JupyterLab¶

In this example, we want to remove the cell entirely when rendering it as a webpage.

Setting tags in with the JupyterLab interface.

In Jupyter notebooks¶

In this example, we want to remove the cell entirely when rendering it as a webpage.

Setting tags in with the notebook interface.

In `MyST-nb`¶

In this example, we only want to show the output of executing the cell.

```{code-block} ipython3
:tags: [remove-input]

import py3Dmol as p3d

v = p3d.view(width=400, height=400)

with open("inputs/porphyrin.xyz", "r") as fh:
    porphyrin_xyz = fh.read()

v.addModel(porphyrin_xyz, "xyz")
v.setStyle({'stick':{}})
v.zoomTo()
v.show()
```

Learning outcomes¶

Familiarize with VeloxChem

First iteration¶

Day 1 - Thursday 6 May 2021

Day 1 is based entirely on notebooks.
The first segment (up until the first break) can be conducted as a type-along with all attendees in the same room.
Subsequent segments are in breakout rooms.

9:00 - 9:10	Welcome and introduction to the training course
9:10 - 9:25	First steps with VeloxChem
9:25 - 9:40	More advanced usage of the VeloxChem API
9:40 - 9:50	Break
9:50 - 10:50	The Roothaan-Hall self-consistent field procedure
10:50 - 11:00	Break
11:00 - 12:00	Møller-Plesset perturbation theory to second order
12:00 - 12:10	Break
12:10 - 12:30	Wrap-up

Day 2 - Friday 7 February 2021

Day 2 shows how to run on HPC infrastructure and we assume that has been taken care of properly beforehand.
The first segment goes through the set up of VeloxChem. This is already part of the installation instructions, so it might be skipped.

9:00 - 9:10	What did we cover yesterday?
9:10 - 9:40	Setting up VeloxChem on a HPC cluster
9:40 - 9:50	Break
9:50 - 10:30	Complex polarization propagator in the X-ray region
10:30 - 10:40	Break
10:40 - 11:20	Exciton calculation
11:20 - 11:30	Break
11:30 - 12:10	Geometry optimizations and semiempirical Hamiltonians
12:10 - 12:15	Break
12:15 - 12:30	Wrap-up

Instructor’s guide

Contents