reST cheat sheet¶

External links¶

This `Search engine <https://duckduckgo.com>`__ creates an external link like this: Search engine

This `<https://duckduckgo.com>`__ creates an external link like this: https://duckduckgo.com

Internal links¶

For internal links standard reST labels are used. The are two ways of doing this:

• If you place a label directly before a section title, you can reference to it with :ref:`label-name`. For example.

  .. _label-name:
  
  Section to cross-reference
  --------------------------
  
  This is the text of the section.
  
  It refers to the section itself, see :ref:`label-name`.
  

• Labels that aren’t placed before a section title can still be referenced, but you must give the link an explicit title, using this syntax

  .. _label-name:
  
  Some random text, see :ref:`link title <label-name>`.
  

Inter-project links¶

# -*- coding: utf-8 -*-

from global_conf import *

project, htmlhelp_basename, latex_documents = set_project_specific_var("Workflows")

html_logo = None

extensions += ["sphinx.ext.autodoc", "sphinx.ext.intersphinx", "sphinx.ext.viewcode", "sphinx_copybutton"]

# If true, the current module name will be prepended to all description
# unit titles (such as .. function::).
add_module_names = False


autodoc_default_options = {"members": True, "private-members": True, "special-members": True}
autodoc_member_order = "bysource"
autodoc_typehints = "none"

intersphinx_mapping = {
    "AMS": ("../AMS/", "../build/AMS/objects.inv"),
    "MLPotential": ("../MLPotential/", "../build/MLPotential/objects.inv"),
    "Tutorials": ("../Tutorials/", "../build/Tutorials/objects.inv"),
    "params": ("../params/", "../build/params/objects.inv"),
}

intersphinx_disabled_reftypes = ["*"]

Link to a page in the Tutorials: `AMS Tutorial <../Tutorials/AMS/ZN-PES-Scan_TST.html>`__

Citations / References¶

For citations we use footnotes.

Example:

Cite a paper here [#ref1]_ and another one here [#ref2]_.

.. Then, at the bottom of the page:

.. [#ref1] \G. te Velde, F.M. Bickelhaupt, E.J. Baerends, C. Fonseca Guerra, S.J.A. van Gisbergen, J.G. Snijders, T. Ziegler, *Chemistry with ADF*, `Journal of Computational Chemistry 22, 931 (2001) <https://doi.org/10.1002/jcc.1056>`__

.. [#ref2] \E. J. Baerends and P. Ros, *Evaluation of the LCAO Hartree-Fock-Slater method: Applications to transition-metal complexes*, `International Journal of Quantum Chemistry 14, S12, 169 (1978) <https://doi.org/10.1002/qua.560140814>`__

Result: Cite a paper here 1 and another one here 2.

Equations¶

For equation we use MathJax. The syntax is essentially the same as for latex equations.

Example:

The current :math:`I(V)` can be computed using the following equation:

.. math::

  I(V) = \frac{2e}{h} \int_{-\infty}^\infty T(E,V) f(E) dE

Result:

The current \(I(V)\) can be computed using the following equation:

Images¶

For images we use the figure directive. Simple usage:

.. figure:: Images/NEGF.png

Example (with some options):

.. figure:: Images/NEGF.png
  :width: 80%
  :align: center

  Optionally, you can put your caption here.

Result:

File download¶

Example:

Download the file :download:`link-title <downloads/file.txt>`

Result: Download the file link-title

Videos¶

This is how you can embed videos:

.. raw:: html

  <center>
    <video controls src="../_downloads/burning_isooctane.mp4"></video>
  </center>

You can download the movie :download:`here </downloads/burning_isooctane.mp4>`.

You must include a have a download link to the video file, otherwise the video will not be copied over when the documentation is built. (also, note that there is an underscore in the video controls link)

Index¶

Before section titles you generally want to use many index directives with plausible alternative names.

Example:

.. index:: Excitations
.. index:: TDDFT
.. index:: UV/Vis
.. index:: Other reasonable names people might search for...

Excitations with TDDFT
----------------------

Tables¶

For tables I advise using csv-table (they are much easier to maintain than grid tables and Simple tables). See also http://www.sphinx-doc.org/en/master/usage/restructuredtext/basics.html#tables. Example:

Example:

.. csv-table:: Optional title
   :header: "Animal", "Furry", "Pettability [a.u.]"

   "Cat", "Yes", 9
   "Dog", "Yes", 9
   "Naked mole rat", "No",  5

Result:

Code and input snippets¶

For snippets of code or run-scripts use the code-block directive.

Example:

Some python code:

.. code-block:: python
  :emphasize-lines: 3,4

  def some_function():
    interesting = False
    print 'This line is highlighted.'
    print 'This one as well...'
    print '...but not this one.'

Some ADF input block example:

.. code-block:: none

  Excitations
    Lowest 5
    FullKernel
    OnlySing
  End

Result:

Some python code:

def some_function():
  interesting = False
  print 'This line is highlighted.'
  print 'This one as well...'
  print '...but not this one.'

Some ADF input block example:

Excitations
  Lowest 5
  FullKernel
  OnlySing
End

1

G. te Velde, F.M. Bickelhaupt, E.J. Baerends, C. Fonseca Guerra, S.J.A. van Gisbergen, J.G. Snijders, T. Ziegler, Chemistry with ADF, Journal of Computational Chemistry 22, 931 (2001)

2

E. J. Baerends and P. Ros, Evaluation of the LCAO Hartree-Fock-Slater method: Applications to transition-metal complexes, International Journal of Quantum Chemistry 14, S12, 169 (1978)