Fix and standardize parameters.md — notation, tables, units, and row numbering by ayushman1210 · Pull Request #203 · PecanProject/sipnet

ayushman1210 · 2025-12-10T12:38:28Z

##Summary:

Cleaned and standardized [parameters.md]
Fixed notation, LaTeX unit formatting, and inconsistent subscripts/superscripts.
Consolidated and renumbered run-time parameter tables (rows 1–79).
Added missing parameter symbols and parameter names; clarified definitions and notes.

##What I changed (high level):

Notation
Added/matched flux symbols (Rh, Ra, ET, T) and parameter symbol SLW.
Added superscript exception note and X_HC subscript definition.
Tables and formatting
Converted mixed/broken sections to consistent Markdown long tables.
Standardized use of \text{...} in LaTeX math and fixed malformed subscripts (e.g., K_{VPD,exp}, Q_{10,\text{soil}}).
Fixed units to LaTeX math format throughout.
Run-time parameters
Sequential Row column added and numbered 1..79 for all run-time parameters.
Assigned parameter configuration names (camelCase) where missing.
Consolidated autotrophic/heterotrophic respiration, photosynthesis, litter, allocation, nitrogen, methane, water, and tree physiology sections.
-Minor
Clarified notes on units and internal conversions (e.g., year^-1 → per-day conversion).
Kept Hard-coded Values section unchanged except formatting consistency.

fixes #81

… splitting

… numbering

ayushman1210 · 2025-12-13T09:30:07Z

hi @dlebauer please let me know if anything else needed to update in this pr #203
thanks !!

ayushman1210 · 2026-01-12T14:12:57Z

hey @dlebauer please review this pr
thanks !!

mswilburn · 2026-01-20T00:43:14Z

Looking at this PR, it has a commit that splits maintenance respiration, so it modifies state.h and sipnet.c. Should those changes be included in this PR?

ayushman1210 · 2026-01-20T17:48:58Z

Hi @mswilburn
file state.h and sipnet.c
changes are necessary to fix the conflation of soil and microbial maintenance respiration in the documentation. Without these code clarifications, the documentation can't accurately reflect how respiration is currently handled.

dlebauer

@ayushman1210 - I've asked @mswilburn to review this PR, and it seems like she is wrapping up her review. I haven't done a complete review yet, but wanted to add a few notes and questions that came up during my initial pass. Thanks again for this effort!

mswilburn

Some changes requested. Additional comment - please review superscript notation in all parameter tables. Some are not resolving as superscripts such as Initial Nitrogen Content units in Initial State Values table. There are other places where this happening.

…ers.md

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dlebauer · 2026-02-21T05:12:30Z

A few more updates; documented the leaf-water cap and fixed units (mm-->cm) in docs and source

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…ructure

ayushman1210 · 2026-02-21T15:04:01Z

hi @dlebauer i have updated the parameter.md and model.md as per your suggestion
let me know anything else needed to update
thanks !!

mswilburn · 2026-02-23T15:34:37Z

+|                           | $SLW$      | Specific Leaf Weight (leaf carbon per unit leaf area)  |

-### Subscripts (Temporal, Spatial, or Contextual Identifiers)
+**Note on superscripts:** Most variables use superscripts for process context (e.g., $X^{\text{growth}}$ for growth respiration). However, certain fluxes follow established scientific conventions and are written without superscripts: carbon fluxes ($NPP$, $GPP$, $R_H$, $R_A$) and water fluxes ($ET$, $T$). These terms are widely used in the scientific literature as standard measurements and retain this notation even when combined with subscripts (e.g., $R_{H,\text{litter}}$).


Transpiration is now using flux notation, please remove $T$ as an example of water flux.

done c6a7dc5

mswilburn · 2026-02-23T15:40:36Z

+| Symbol                      | Parameter Name        | Definition                                                      | Units    | Notes              |
+| --------------------------- | --------------------- | --------------------------------------------------------------- | -------- | ------------------ |
+| $\alpha_{\text{fine root}}$ | fineRootAllocation    | Fraction of $NPP$ allocated to fine roots                       | unitless |                    |
+| $\alpha_{\text{coarse root}}$ |                      | Fraction of $NPP$ allocated to coarse roots                     | unitless | Calculated internally from remainder: $\alpha_{\text{coarse root}} = 1 - \alpha_{\text{leaf}} - \alpha_{\text{wood}} - \alpha_{\text{fine root}}$ |


Named coarseRootAllocation

fixed in c6a7dc5

Mikki approved today; its not easy to find and resolve outstanding change requests but the changes have been implemented.

dlebauer · 2026-02-23T21:11:06Z

That was a big effort and a huge improvement in our documentation. Thanks you @ayushman1210 and @mswilburn!

mswilburn · 2026-02-23T23:20:39Z

Woohoo! It looks great!

ayushman1210 · 2026-02-26T02:10:19Z

Happy to contribute and excited to keep contributing more in the future !!
thank-u @mswilburn and @dlebauer for guidance

ayushman1210 added 3 commits December 10, 2025 14:44

fixes the conflation of soil and microbial maintenance respiration by…

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formated the file with clang

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Fix and standardize parameters.md — notation, tables, units, and row…

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… numbering

ayushman1210 requested review from Alomir, dlebauer, infotroph, mdietze and mswilburn as code owners December 10, 2025 12:38

ayushman1210 added 2 commits January 4, 2026 14:35

Merge branch 'master' into fix/docs

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Merge branch 'master' into fix/docs

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dlebauer mentioned this pull request Jan 7, 2026

Corrections and clarifications to heterotrophic respiration scheme #219

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ayushman1210 and others added 3 commits January 12, 2026 18:26

Merge branch 'master' into fix/docs

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Merge branch 'master' into fix/docs

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dlebauer self-assigned this Jan 12, 2026

Merge branch 'master' into fix/docs

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dlebauer mentioned this pull request Jan 17, 2026

SIP211 context metadata cleanup #225

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Merge branch 'master' into fix/docs

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ayushman1210 added 2 commits January 21, 2026 21:27

Merge branch 'master' into fix/docs

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ayushman1210 added 2 commits January 27, 2026 23:31

All missing parameter symbols have been successfully added to paramet…

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…ers.md

Fix clang-format alignment on soilMaintRespiration assignment (lines …

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dlebauer and others added 2 commits February 20, 2026 14:52

Update docs/parameters.md

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capitalize "notes"

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dlebauer and others added 4 commits February 20, 2026 16:12

replace degree symbol with \circ

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fix eqn refs

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consistent caps for RH RA

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Clarify transpiration notation and leaf-water cap docs

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Update docs/parameters.md

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Update docs/parameters.md

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changes as suggested by maintainer updated parameters.md and model-st…

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dlebauer approved these changes Feb 22, 2026

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mswilburn reviewed Feb 23, 2026

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Address unresolved PR 203 notation and parameter doc comments

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dlebauer merged commit b27a8fa into PecanProject:master Feb 23, 2026
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