Notational and Algebraic Conventions

In order to aid comprehension, this documentation strives to obey the following formatting/notation conventions.

In text:

  • Function/method parameters are set in italics.

  • When not used for emphasis, bold text is used to set apart words/phrases with specific contextual meaning.

  • Code snippets are set in fixed font, colored red, and boxed: [v for v in range(6)].

  • References to Python objects are set in fixed font, colored black (in most cases), and boxed: OpanXYZ. Where practical, they will be linked to the relevant documentation (via intersphinx).

  • Code examples are set in fixed font and boxed the full width of the page:

    from opan.utils.vector import proj
pvec = proj(vec1, vec2)

    Interactive usage examples are formatted like a Python console session, as per doctest:

    >>> 1 + 2 + 3
6

  • Where included, the key words “MUST”, “MUST NOT”, “REQUIRED”, “SHALL”, “SHALL NOT”, “SHOULD”, “SHOULD NOT”, “RECOMMENDED”, “MAY”, and “OPTIONAL” in this documentation are to be interpreted as described in RFC 2119.

  • Mathematical symbols and engineering units are set as in equations, below.

In equations:

  • Roman variables are set in serif italics: \(x + C\)
  • Lowercase Greek variables are set in italics: \(\theta + \pi \over \gamma\)
  • Uppercase Greek variables are set in upright serif: \(\Phi + \Theta\)
  • Vectors are set in bold, upright, serif Roman symbols: \(\mathbf{r}_2 - \mathbf{r}_1\)
  • Matrices are set as bold, uppercase, serif Roman or Greek symbols: \(\mathbf{M}\!^{^{^{-1}\!/_2}} \mathbf{F} \mathbf{M}\!^{^{^{-1}\!/_2}}\)
  • Engineering units are set in upright Roman (serif) equation type: \(\left(\mathrm{E_h\over B^2}\right)\)

Common symbols:

  • \(N\) – the number of atoms in the system of interest
  • \(G\) – the number of geometries in an OpenBabel XYZ file
  • \(R, S, ...\) – Arbitrary integers