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. .. figure:: img/tags-lab.png :scale: 50% :alt: Setting tags in with the JupyterLab interface. :align: center In Jupyter notebooks -------------------- In this example, we want to remove the cell entirely when rendering it as a webpage. .. figure:: img/tags-notebook.png :scale: 50% :alt: Setting tags in with the notebook interface. :align: center In ``MyST-nb`` -------------- In this example, we only want to show the *output* of executing the cell. .. code-block:: md ```{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. .. csv-table:: :widths: auto :align: center :delim: ; 9:00 - 9:10 ; Welcome and introduction to the training course 9:10 - 9:25 ; :doc:`notebooks/first-steps` 9:25 - 9:40 ; :doc:`notebooks/next-steps` 9:40 - 9:50 ; Break 9:50 - 10:50 ; :doc:`notebooks/rh-scf` 10:50 - 11:00 ; Break 11:00 - 12:00 ; :doc:`notebooks/mp2` 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. .. csv-table:: :widths: auto :align: center :delim: ; 9:00 - 9:10 ; What did we cover yesterday? 9:10 - 9:40 ; :ref:`hpc-setup` 9:40 - 9:50 ; Break 9:50 - 10:30 ; :ref:`x-ray-cpp` 10:30 - 10:40 ; Break 10:40 - 11:20 ; :ref:`exciton` 11:20 - 11:30 ; Break 11:30 - 12:10 ; :ref:`xTB-geomeTRIC` 12:10 - 12:15 ; Break 12:15 - 12:30 ; Wrap-up