Formatting your documents

Companion documents: Improving your writing, Making a figure

Why should I read this?

For better or worse, the quality of your figures correlates with the perceived quality of your work. Just like the grammatical correctness of your writing, one might wonder if someone is sufficiently careful with their scientific work if they aren't very careful with their figures and presentation. I am putting some "rules" below for how to format your documents and figures.

Consistency

One should keep styles consistent within a manuscript. You might be forgiven for esoteric style choices if they are employed consistently. From here:

A clear and consistent design in the figures in your scientific paper will make it easy for your reader to gather the presented information. For this, I suggest to use the same colour and symbols for each variable throughout all your scientific figures. Sample 1 is displayed as red triangles in Figure 1? Make sure it is in Figure 5 too.

Compiling and other boilerplate

• Use LaTeX for all of your documents.
• Make sure your documents do not compile with errors, especially if you are using Overleaf!
• If you have warnings, understand where they warnings come from. They may be signaling something important!
• On my local computer, I like using latexmk for compilation.
• Put each sentence on one line of source .tex code

Preamble and packages

Always structure your document so that the preamble is separate from the main text (two separate files). You can connect them by placing \input{preamble.tex} at the top of your main text file main.tex, right after the latex \documentclass[11pt,sort&compress]{elsarticle} clause.

In the preamble file, you should include some packages. Here are some examples. Please look them up to see what they do.

For elsarticle class files (mine is included here), which I recommend you use, you need to organize the hyper-reference coloring a bit differently, which in that example document you will see in the preamble as well the top of main.tex

```tex \documentclass[11pt,sort&compress]{elsarticle}

\input{preamble.tex}

\begin{document}

\hypersetup{ linkcolor=darkrust, citecolor=seagreen, urlcolor=darkrust, pdfauthor=author, } ```

Discussion of these colors and their definitions are included below.

Units

Always use a LaTeX package if your quantities use units. My preference is tex \usepackage{siunitx} If you do not use a LaTeX package your spacing and characters will likely be inconsistent and incorrect. Your source code will also be very verbose and hard to read. Use proper package options:

tex \sisetup{separate-uncertainty = true,print-unity-mantissa=false,per-mode=symbol,range-phrase = \text{--}} which configures the siunitx package to display units with division m/s using the slash symbol (/) instead of the reciprocal form m s^{-1}, amongst other things. See the template preamble for its use.

Math symbols

Always use consistent math symbols. I usually put all of these in a single file that is invoked in the LaTeX preamble via tex \input{mathsymbols.tex} and an example such file is in templates/paper/mathsymbols.tex in this repository.

Some notation rules you should follow

• Bold lowercase for vectors
• Bold uppercase for matrices and tensors
• Non-bold lowercase for scalars/constants

Common errors

• Dimensionless symbols like the Reynolds number should not be italic, but upright.
  • Like this \(\mathrm{Re}\)
  • Not like this \(Re\)
• Super and subscripts that denote text should not be in math/italic symbols but rather upright normal text.
  • Like this: \(c_{\mathrm{Temp.}}\) or \(\mathbf{A}_{\mathrm{Fast}}\)
  • This is also OK: \(c^{\mathrm{(Temp.)}}\) or \(\mathbf{A}^{\mathrm{(Fast)}}\)
  • But not like this: \(c_{Temp}\) or \(\mathbf{A}_{Fast}\)
• Do not use asterisks or \(\times\) for multiplication
  • Like this: \(ab\)
  • Never like this: \(a\times b\) or \(a \ast b\)
• Do not use inline math with full fractions that make your text too small to read!
  • Don't do this (inline): \(\frac{a}{b}\)
  • Do this: \(a/b\)
• Always use \left and \right for scalable delimiters around tall expressions like fractions or summations.
  • Don't do this: \((1 + a(1 + \frac{a + b}{b}))\)
  • Do this: \(\left(1 + a\left(1+ \frac{a + b}{b} \right) \right)\)
  • Note that in the incorrect version, the closing parenthesis is too small and does not scale to the height of the fraction

Scientific notation and large/small numbers

Rule: Never use the notation \(4e-5\), \(4e+05\), or the like in any paper, presentation, or figure. Always use \(4 \times 10^{-5}\). If units are involved, use siunitx and the options listed in the paper template preamble.tex.

Bibliography

Always use consistent formatting. This might mean more than it seems at first.

Some examples and common errors:

• Choose to either abbreviate journal names (using the correct abbreviation, Google it!) or use the full journal name (use camel case! Journal of Fluid Mechanics not Journal of fluid mechanics), then stick with it.

  • Like this (full names):
    • Firouznia, M., Bryngelson, S. H., Saintillan, D. (2023). A spectral boundary integral method for simulating electrohydrodynamic flows in viscous drops. Journal of Computational Physics, 489, 112248.
    • Spratt, J.-S., Rodriguez, M., Schmidmayer, K., Bryngelson, S. H., Yang, J., Franck, C., and Colonius, T. (2021). Characterizing viscoelastic materials via ensemble-based data assimilation of bubble collapse observations. Journal of the Mechanics and Physics of Solids, 152, 104455.
  • Or like this (abbreviations)
    • Firouznia, M., Bryngelson, S. H., Saintillan, D. (2023). A spectral boundary integral method for simulating electrohydrodynamic flows in viscous drops. J. Comp. Phys., 489, 112248.
    • Spratt, J.-S., Rodriguez, M., Schmidmayer, K., Bryngelson, S. H., Yang, J., Franck, C., and Colonius, T. (2021). Characterizing viscoelastic materials via ensemble-based data assimilation of bubble collapse observations. J. Mech. Phys. Solids, 152, 104455.
  • But not like this (mixed)
    • Firouznia, M., Bryngelson, S. H., Saintillan, D. (2023). A spectral boundary integral method for simulating electrohydrodynamic flows in viscous drops. Journal of Computational Physics, 489, 112248.
    • Spratt, J.-S., Rodriguez, M., Schmidmayer, K., Bryngelson, S. H., Yang, J., Franck, C., and Colonius, T. (2021). Characterizing viscoelastic materials via ensemble-based data assimilation of bubble collapse observations. J. Mech. Phys. Solids, 152, 104455.

• In an article title, only capitalize the first letter, proper nouns, abbreviations, and the first letter after a colon

  • Like this: A Gaussian moment method and its augmentation via LSTM recurrent neural networks for the statistics of cavitating bubble populations
  • Not like this: A Gaussian Moment Method and its Augmentation via LSTM Recurrent Neural Networks for the Statistics of Cavitating Bubble Populations
  • And definitely not like this: A gaussian moment method and its augmentation via lstm recurrent neural networks for the statistics of cavitating bubble populations
  • Accomplish this via the .bib entry, like this tex title = {A {G}aussian moment method and its augmentation via {LSTM} recurrent neural networks for the statistics of cavitating bubble populations},

• Book titles are usually capitalized as you enter them verbatim (capitalization and all) in the .bib file. So, be consistent when citing book titles!

  • Like this:
    • M. A. Nielsen and I. L. Chuang, Quantum Computation and Quantum Information (Cambridge University Press, 2000)
    • T. Kruger, H. Kusumaatmaja, A. Kuzmin, O. Shardt, G. Silva, and E. Viggen, The Lattice Boltzmann Method: Principles and Practice (Springer International Publishing, 2016)
  • Or like this:
    • M. A. Nielsen and I. L. Chuang, Quantum computation and quantum information (Cambridge University Press, 2000)
    • T. Kruger, H. Kusumaatmaja, A. Kuzmin, O. Shardt, G. Silva, and E. Viggen, The lattice Boltzmann method: Principles and practice (Springer International Publishing, 2016)
  • But not like this:
    • M. A. Nielsen and I. L. Chuang, Quantum Computation and Quantum Information (Cambridge University Press, 2000)
    • T. Kruger, H. Kusumaatmaja, A. Kuzmin, O. Shardt, G. Silva, and E. Viggen, The lattice Boltzmann method: Principles and practice (Springer International Publishing, 2016)

Referencing your bibliography

Use natbib via \usepackage{natbib} (it is automatically loaded when one uses the elsarticle class). I recommend the bibliography style file in the template at templates/paper/bibsty.bst. This is automatically handled if you use the paper template in this repository. This way, you will have access to text and parenthetical citations, which render as:

One can partially address this problem by working in Fourier space [1] or fitting a parametric model to approximate the eddy diffusivity operator [21, 23]. However, the former requires spatial homogeneity, and the latter's accuracy depends on the parametric model's quality. Liu et al. [17] introduces an improved model that uses the nonlocal eddy diffusivity operator's moments to approximate the operator. via the code tex One can partially address this problem by working in Fourier space or fitting a parametric model to approximate the eddy diffusivity operator~\citep{hamba04,park21}. However, the former requires spatial homogeneity, and the latter's accuracy depends on the parametric model's quality. \citet{liu21} introduces an improved model that uses the nonlocal eddy diffusivity operator's moments to approximate the operator. Note the use of \citep{ref} and \citet{ref} here. Text \citet{ref} instances can be used as nouns but parenthetical references cannot.

• This is OK (via \citet{ref}): > So and so [1] did this awesome thing.
• This is not (via \citep{ref}): > [1] did this awesome thing.

Always prevent line-breaks via tides ~ between a parenthetical reference and the text before it. For example:

• This is correct: The algorithm is fast, but not as fast as possible~\citep{ref}.
• This is not: The algorithm is fast, but not as fast as possible \citep{ref}.

We generally want our references at the end of sentences unless they are part of a long list.

• Incorrect: > The LBM method [1] is not as accurate as the finite volume method [2].
• Correct: > The LBM method is described in So and So [1]. However, is not as accurate as the finite volume method [2].
• And this is also acceptable > Cavitation is seen in many engineering applications, including submarines [1], pumps [2], and medical devices [3].

Creating your bibliography

• Use bibtool to remove unused entries from your bibliography (.bib) file

  • Remove all unused bibliography entries from your .bib file. To do this,
    • Make sure you have bibtool installed your your system
    • Copy a bibtool.config file to your document path, mine is located here
    • Compile your document (I prefer latexmk for this, but a combination of pdflatex and bibtex also works).
    • Use the command bibtool -r bibtool.config -x main.aux > test.bib
    • Now you have a file test.bib that contains only the bibliography entries in your document
    • Move the test.bib file over to your main bibliography file via something like mv test.bib ref.bib

• Use bibstyle to remove unneeded elements from your bibliography entries

  • In particular, I use the command bibtex-tidy --omit=date-added,date-modified,month,doi --curly --numeric --align=13 --sort=title --duplicates=key,citation --no-escape --sort-fields --trailing-commas --no-remove-dupe-fields test.bib
  • You can see above that it removes certain entries, sorts the document, checks for duplicates, etc.
  • It does this on test.bib in the above call. You will want to do it on whatever the bibtool output file is.

• Bibliography style file (.bst)

  • Unless the journal or conference you submit to insists otherwise, use the style file here. This style file includes the relevant information you want your entries to include (like title), but ignores others (like month of publication). It also supports author-year citations (invoked via \citet{} as above).

Colors

I like to use the following color palette in your TeX preamble: ```tex \usepackage{xcolor} \definecolor{lightblue}{rgb}{0.63, 0.74, 0.78} \definecolor{seagreen}{rgb}{0.18, 0.42, 0.41} \definecolor{orange}{rgb}{0.85, 0.55, 0.13} \definecolor{silver}{rgb}{0.69, 0.67, 0.66} \definecolor{rust}{rgb}{0.72, 0.26, 0.06} \definecolor{purp}{RGB}{68, 14, 156} \definecolor{joshua}{RGB}{251,220,127}

\colorlet{lightsilver}{silver!30!white} \colorlet{darkorange}{orange!75!black} \colorlet{darksilver}{silver!65!black} \colorlet{darklightblue}{lightblue!70!black} \colorlet{darkrust}{rust!85!black} \colorlet{darkseagreen}{seagreen!85!black} `` In particular, I usedarkrustandseagreen` quite a bit, as I find them complementary and easy on the eyes.

Setup your hyperrefs this way so that you have an attractive notation of your crossrefs in your document: tex \usepackage[colorlinks=true,linkcolor=darkrust,citecolor=darklightblue,urlcolor=darksilver]{hyperref}

Referencing equations, figures, tables, and sections

Figures, tables, sections

To keep things consistent, I recommend using the cleveref package tex \usepackage{cleveref} which is invoked for figures, tables, and sections via the commands \Cref{} and \cref{}, using the former if the reference is at the beginning of a sentence. Figures, tables, and sections are always treated as nouns. Check out the paper template in this repository for its use in the preamble.tex file.

Equations

First, labeling them appropriately as tex \begin{gather} Ax=b \label{e:lineareqn} \end{gather} and then reference then via cleveref! As \cref{e:lineareqn}.

Treat your equations as nouns, and never use the abbreviation "eqn." before it.

• Like this: The algorithm follows from reducing \eqref{e:someqn} to a first-order system.
  • Which renders as:

    The algorithm follows from reducing (1) to a first-order system.

• Not like this: The algorithm follows from reducing equation \eqref{e:someqn} to a first-order system.
• Nor like this: The algorithm follows from reducing eqn. \eqref{e:someqn} to a first-order system.

"Dashes"

Learn the difference between the hyphen (- in LaTeX), the en dash (-- in LaTeX), and the em dash (--- in LaTeX). This is easily Google-able. Here are some references:

• https://grammarist.com/usage/hyphen-en-dash-or-em-dash/
• https://www.grammarly.com/blog/hyphens-and-dashes/
• https://editorninja.com/hyphen-vs-en-dash-vs-em-dash/

Some correct examples

• Hyphen
  • Separating words, such as "over-subscribed".
  • Some last names
• En dash
  • Separating two things that are different, like "Runge--Kutta" time stepping
  • Ranges, like "Steps 5--8 are unnecessary for algorithm X".
• Em dash
  • For putting a parenthetical in a sentence, like "I went to the grocery store---one that was extremely far away---and picked up cooking supplies."
    • I recommend avoiding the use of the em dash.