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Fix and standardize parameters.md — notation, tables, units, and row numbering#203

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ayushman1210 wants to merge 23 commits intoPecanProject:masterfrom
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Fix and standardize parameters.md — notation, tables, units, and row numbering#203
ayushman1210 wants to merge 23 commits intoPecanProject:masterfrom
ayushman1210:fix/docs

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@ayushman1210 ayushman1210 commented Dec 10, 2025 •
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##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

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ayushman1210 commented Dec 13, 2025

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

@dlebauer dlebauer mentioned this pull request Jan 7, 2026
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ayushman1210 commented Jan 12, 2026

hey @dlebauer please review this pr
thanks !!

@dlebauer dlebauer self-assigned this Jan 12, 2026
@dlebauer dlebauer mentioned this pull request Jan 17, 2026
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mswilburn commented Jan 20, 2026

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?

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ayushman1210 commented Jan 20, 2026

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
dlebauer reviewed Jan 27, 2026
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@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
mswilburn requested changes Jan 27, 2026
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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.

ayushman1210 and others added 5 commits January 27, 2026 23:42
@ayushman1210
Fix clang-format continuation indentation on soilMaintRespiration ass…
3d6931f 
…ignment

Use ContinuationIndentWidth (base + 4 spaces) instead of AlignOperands
for multi-line assignment continuation on lines 1178-1179.
@ayushman1210
Fix clang-format style: operator-first continuation line formatting
0a0af99 
Move the * operator to the start of the continuation line (lines 1178-1179)
to comply with clang-format style guidelines.
@ayushman1210
Merge branch 'master' into fix/docs
bf2f442
@ayushman1210
fixes
5e7425c
@ayushman1210
clang-format
a777f94
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ayushman1210 commented Jan 29, 2026

Hey @mswilburn and @dlebauer,
I’ve made the changes you suggested. Whenever you have some free time, could you please review the PR?
Thanks!

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ayushman1210 commented Feb 3, 2026

Hey @dlebauer , Whenever you have some free time, could you please review this PR? I’ve made the changes in the code as suggested.
Thanks!

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@Alomir Alomir Awaiting requested review from Alomir Alomir is a code owner

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Ensure documentation of parameters and model structure is consistent and complete.

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