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Make the book as consistent as reasonable

Need to be a bit flexible, as full consistency is not always preferable

  • Check units and notation
  • Nonzero (not non-zero)
  • Ionization energy (not ionization potential)
  • Wave function (not wavefunction)
  • Use bold or italics for introducing terms
  • Text in equations: $E_{\mathrm{HF}}$
  • Generally include visualization of molecule considered, using cell with remove-input
  • Avoid commas and colons before (and in) equations

Refer to parts of the book as

  • part
    • chapter
      • section
        • subsection

Figures and tables

  • Avoid caption if possible (describe in text around instead)
  • Static images and Python cells if too expensive
  • Figures in png 300 dpi (potentially svg)
  • Typical sizes
    • matplotlib: 6x4 or 12x12
    • py3Dmol: 400x300
  • Typical py3Dmol style
    • viewer.setViewStyle({"style": "outline", "width": 0.05})
    • viewer.setStyle({"stick":{},"sphere": {"scale":0.25}})

Non-executed parts of notebook

Relevant for, e.g.

  • High-cost calculations (with Python script as static text)
  • Examples to be filled in by students
    • Potentially with pseudocode/partially filled out

Need to havs some accompanying calculations to make sure that the examples runs correct

  • Smaller examples which are invisible to the user (remove-cell)
  • Hidden boxes (hide-cell)

Make sure that all parts of the book are tested at least once!

Standards

scf_results = scf_drv(...)
molecule = vlx.Molecule.read_xyz_string(...)
basis = vlx.MolecularBasis.read(...)

Package abbreviations

import veloxchem as vlx
import numpy as np
import matplotlib.pyplot as plt
import multipsi as mtp
import py3Dmol as p3d
import adcc
import gator

References

The file references.bib in the top directory is a regular BIBTEX file. Add your references in this file (in alphabetic order and with consistent format to existing references). A citation in the text is added with

{cite}`Wang2016, Schlegel2011`

Multiple lists of references are possible but not yet properly implemented.

Add to .bib (in chronological order) and include URL to create links in the references

@article{Sellers1993,
author  = {Sellers, Harrell},
title   = {The C2-DIIS convergence acceleration algorithm},
journal = {Int. J. Quant. Chem.},
volume  = {45},
pages   = {31-41},
url     = {https://doi.org/10.1002/qua.560450106},
year    = {1993}
}