Advanced Formatting

Overview¶

Teaching: 10 min
Exercises: 0 min

Questions

What formatting options are available that go beyond those of the 'Carpentries' framework?

Objectives

Add objectives to this episode (FIXME)

Mathematical Equations¶

This style has KaTeX enabled, allowing for writing mathematical expressions in LaTeX math notation.

Using Block Syntax¶

Blocks must be enclosed in $$...$$ or \[...\] on separate lines:

block syntax

$$
V_{LJ}(r)=\frac{C12}{r^{12}}-\frac{C6}{r^{6}}
$$

$$ V_{LJ}(r)=\frac{C12}{r^{12}}-\frac{C6}{r^{6}} $$

Using inline block syntax¶

Inline blocks must be enclosed in $...$ or $...$:

block syntax

The Pythagorean theorem $a^2+b^2=c^2$ can be rearranged to $ c = \sqrt{a^2 + b^2} $

The Pythagorean theorem $a^2+b^2=c^2$ can be rearranged to $ c = \sqrt{a^2 + b^2} $

Example¶

The simplest way to write the time-independent Schrödinger equation is $H\psi = E\psi$, however, with the Hamiltonian operator expanded it becomes:

\[ -\frac{\hbar^2}{2m} \frac{d^2 \psi}{dx^2} + V\psi = E\psi\\ \]

Mermaid Diagrams¶

Mermaid is a JavaScript library that can be used to write various graphs and flow-charts within Markdown and render them on a website. This template has Mermaid support enabled and can be used as shown below.

Flowchart¶

Documentation for Mermaid Flowchart

 ``` mermaid
 graph LR
    A[Hard edge] -->|Link text| B(Round edge)
    B --> C{Decision}
    C -->|One| D[Result one]
    C -->|Two| E[Result two]
 ```

graph LR
    A[Hard edge] -->|Link text| B(Round edge)
    B --> C{Decision}
    C -->|One| D[Result one]
    C -->|Two| E[Result two]

Git Graph¶

Documentation for Mermaid gitGraph

 ``` mermaid
 gitGraph
   commit id: "C1"
   commit id: "C2"
   branch develop
   checkout develop
   commit id: "C3"
   commit id: "C4"
   checkout main
   merge develop
   commit id: "C5"
   commit id: "C6"
 ```

gitGraph
   commit id: "C1"
   commit id: "C2"
   branch develop
   checkout develop
   commit id: "C3"
   commit id: "C4"
   checkout main
   merge develop
   commit id: "C5"
   commit id: "C6"

Instructor View¶

Some lessons are rather complex and require a lot of information, which can result in long blocks of text that are needed for self-study as well as new instructors that need to familiarize themselves with the material.
In a workshop or presentation setting however it's difficult to pick out the talking points and having key information in bullet-points would be much better.

A solution to this is to introduce an "Instructor View" that will hide paragraphs that have been marked as /// html | div[class="learner"] and instead show paragraphs marked as /// html | div[class="instructor"], which are otherwise hidden.

The instructor view can be enabled in the mkdocs.yml file with:

instructor_view_enable: true

If enabled, one the following toggle icons will appear in the Navigation bar at the top to indicate which view is active and to toggle between them:

Learner view active:
Instructor view is active:

The state of the toggle is persistent for some time (by default 7 days) by setting a cookie, however this duration can be customized by a variable in mkdocs.yml:

instructor_view_cookie_lifetime: 3

Example:

/// html | div[class="learner"]
This is a long text that describes a complex topic in detail. 
This contains information that the instructor explains in detail.   
_Lorem ipsum dolor sit amet,[...] sunt in culpa qui officia deserunt mollit anim id est laborum._
///

/// html | div[class="instructor"]
* talking points for instructor
* easier to read during the workshop
///

Will be shown as:

This is a long text that describes a complex topic in detail. This contains information that the instructor explains in detail.
Lorem ipsum dolor sit amet,[...] sunt in culpa qui officia deserunt mollit anim id est laborum.

talking points for instructor
easier to read during the workshop

Custom code blocks¶

s = loadpdb protein.pdb
set {s.20 s.26} name "ASH"
savepdb s protonated.pdb
quit

trajin mdcrd_nowat.nc
trajout mdcrd_nowat.xtc
go

cd ~/scratch/workshop/pdb/6N4O/simulation/sim_pmemd/4-production
mol new prmtop_nowat.parm7
mol addfile mdcrd_nowat.xtc step 5

~/.vmdrc

# VMD settings: file ~/.vmdrc

# Turning-on of menus
menu main on

# Change display defaults
display reposition 100 600
display resize 672 682
display projection Orthographic
display depthcue off
display rendermode GLSL
display ambientocclusion on
axes location Off
color Display Background white

# Default material
mol default material Diffuse

# Configure keyboard shortcuts
user add key o {display projection orthographic} 
user add key p {display projection perspective}

Key Points¶