Introduction

Welcome to the Documentation Page!

On this page you will find a collection of the various notations used in the documentation.

Code Examples

Source code should always be provided using the code-block directive. The directive is followed by a blank line, after which the code is displayed with consistent indentation.

Python example:

from molecule import Simulation

sim = Simulation("water.xyz")
sim.run(steps=1000)

For inline code snippets, use double backticks, for example: Simulation.run().

Command-Line (Bash) Instructions

Terminal commands should be documented in a bash code block:

molsim prepare input.yaml
molsim run --nsteps 5000

Note: the $ prompt is omitted so that commands can be copied easily.

Input Files

Input files should be presented either in their entirety or by showing the relevant sections in a dedicated block.

Example YAML input file:

system:
  molecule: water
  charge: 0

simulation:
  method: DFT
  steps: 1000

For longer files, only the essential sections should be highlighted.

Output Files

Output files may include logs, tables, or structured data.

Example text output:

Step   Energy (Hartree)
1      -76.345
2      -76.351
...

Units and column names should always be specified.

Notes and Warnings

Important information should be highlighted using Sphinx directives:

Note

The format of input files may vary between software versions.

Warning

Large systems may require significant memory and computational time.

Summary of Conventions

Code: .. code-block:: <language> with consistent indentation
Commands: bash block without a prompt
Input/Output: complete, copyable examples
Inline code: use double backticks

This format will be applied consistently throughout all subsequent pages of the documentation.