docs: standardize LaTeX math notation in model-structure.md - #280
Merged
Alomir merged 5 commits intoMar 5, 2026
Merged
Conversation
Resolve mixed use of \mathit, \mathrm, \text, and bare (no command)
for similar symbols throughout the document. The inconsistency was
most visible in CH4-related flux subscripts and water-dependency
function labels.
Notation convention applied:
- Descriptive subscript text ('litter', 'soil', 'vol', 'water', etc.):
use \text{} uniformly.
- Chemical formulas in math (CH4): use \text{CH}_4 throughout,
with the numeric subscript placed outside \text{} so it renders
as a proper mathematical subscript.
- Math operator / function names (clip): use \operatorname{} instead
of \mathrm{}, which is the semantically correct LaTeX command for
named operators and prevents incorrect italic spacing.
Specific changes:
- F^C_{CH4,litter} / F^C_{CH4,soil}: \mathit -> \text{CH}_4\text{,...}
- Section heading 'Methane Production (C -> CH4)': bare -> \text{CH}_4
- Equation (eq:ch4): \mathit{CH_4,j} -> \text{CH}_4\text{,}j for
both the flux symbol F^C and the rate parameter K.
- D_\mathrm{water, CH_4}: \mathrm -> \text{} and split to
D_{\text{water,CH}_4} for consistency with all other D_{water,...}.
- Inline prose F^C_{CH_4}, K_{\mathit{CH_4,}j}: standardized.
- F^N_\mathrm{vol} (two occurrences): \mathrm -> \text{}.
- D_{water,N_vol} subscript (heading + inline): N_vol -> N_\text{vol}.
- D_{\mathrm{water},N_{vol}} inline: \mathrm -> \text{}.
- D_{water,CH_4} heading + equation: bare CH_4 -> \text{CH}_4.
- \\$ in prose: bare -> \text{CH}_4.
- clip() function: \mathrm{clip} -> \operatorname{clip} (both sites).
man080107
requested review from
Alomir,
dlebauer,
mdietze and
mswilburn
as code owners
February 26, 2026 09:31
dlebauer
previously requested changes
Feb 28, 2026
dlebauer
left a comment
dlebauer
left a comment
Member
There was a problem hiding this comment.
This looks great, thanks! Could you please also check that parameters.md has consistent typesetting?
Contributor
Author
|
Hi @dlebauer , I've pushed the latest changes! Following your advice, I've standardized all the LaTeX math notation across both . Methane (CH₄) and Nitrous Oxide (N₂O) formulas are now properly formatted using upright roman text (\text{}), and I've replaced all instances of \textit{}, \textrm{}, and \mathfrak{} with standard \text{}. Let me know if everything looks good!" |
Alomir
reviewed
Mar 1, 2026
Contributor
Author
|
Thanks @Alomir for pointing that out. I’ve removed both rows for the initial CH₄ and N₂O soil concentrations as suggested. Please let me know if anything else needs to be adjusted. |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
3 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Summary
Standardized LaTeX notation across SIPNET documentation by resolving inconsistent use of \mathit, \mathrm, \text, and bare symbols, especially for CH₄ flux subscripts and water-dependency functions.
Changes
Motivation
Ensures consistent, semantically correct LaTeX formatting and improves documentation readability.
Testing
Built documentation locally and verified equations render correctly. Changes are documentation-only and do not affect model outputs.
Related issues
Fixes #277
Checklist