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Implement plant N pools with fixed CN ratios and N limitation #206

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Copilot AI commented Dec 17, 2025 •
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Adds nitrogen tracking to plant carbon pools (leaf, wood, fine root, coarse root) with configurable C:N ratios. Growth is now limited when soil mineral N is insufficient to meet plant N demand.

Implementation

New parameters:

  • leafCN, woodCN, fineRootCN, coarseRootCN - C:N ratios for each plant pool (g C / g N)

New state variables:

  • plantLeafN, plantWoodN, fineRootN, coarseRootN - N content in each pool (g N m⁻²)

N demand calculation (eq 12):

// For each pool i: dN_i/dt = dC_i/dt / CN_i
fluxes.leafNDemand = fluxes.leafCreation / params.leafCN;
// ... similarly for wood, fine root, coarse root

Total N demand and uptake (eq 20):

fluxes.plantNDemand = leafNDemand + woodNDemand + fineRootNDemand + coarseRootNDemand;
fluxes.plantNUptake = fmin(plantNDemand, envi.minN / climate->length);

N limitation:
When plantNDemand > plantNUptake, NPP is set to 0 by making GPP = R_A, preventing growth under N-limited conditions.

N allocation:
When supply < demand, N is allocated proportionally: k = uptake / demand, each pool receives k × demand - losses.

Changes

  • src/sipnet/state.h: Added CN parameters and plant N pool state variables
  • src/sipnet/sipnet.c:
    • Added calcPlantNDemandAndUptake() function
    • Integrated N limitation check in calculateFluxes()
    • Updated updatePoolsForSoil() to track plant N pools
    • Added CN parameter reading in initModel()
  • docs/CHANGELOG.md: Documented new features
  • docs/parameters.md: Added CN parameter definitions
  • tests/smoke/russell_2/sipnet.param: Added example CN values (25, 200, 50, 150)

Backward compatible: when nitrogen cycle is disabled or CN parameters are unspecified (0), new code has no effect.

Original prompt

This section details on the original issue you should resolve

<issue_title>Implement plant N pools, fixed CN, N demand, N limitation</issue_title>
<issue_description>plant pools (i) leaf, wood, fine root, coarse root

  • Add CN parameters for each pool
  • calculate dN_i/dt = dC_i/dt * CN_i for each pool (eq 12)
  • calculate total plant N demand (eq 20, F^N_demand = sum dN_i/dt), and subtract from N_min
    • calculate all the N demand and N supply terms in a time step, then for a particular N stock calculate k = (N demand) / (N stock + N supply), then if k < 1 each demand gets k*Ndemand
  • N limitation
    • F^N_uptake = min(N_min/dt, F^N_demand)
    • New indicator variable I_N = boolean(F^N_demand > N_min/dt)
    • if(I_N): NPP = 0; this might be done by setting GPP = R_A</issue_description>

<agent_instructions>Follow the style that exists in the current code. Use standard C constructs.</agent_instructions>

Comments on the Issue (you are @copilot in this section)

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Copilot AI self-assigned this Dec 17, 2025
Copilot AI and others added 5 commits December 17, 2025 00:30
@dlebauer
Add plant N pools, CN parameters, and N demand calculation
e144a6b 
Co-authored-by: dlebauer <464871+dlebauer@users.noreply.github.com>
@dlebauer
Add CN parameters to parameter reading and test file
e6f5a85 
Co-authored-by: dlebauer <464871+dlebauer@users.noreply.github.com>
@dlebauer
Add documentation for plant N pools and CN parameters
c28db4a 
Co-authored-by: dlebauer <464871+dlebauer@users.noreply.github.com>
@dlebauer
Address code review feedback - simplify N uptake calc and remove redu…
188137c 
…ndant nSupply

Co-authored-by: dlebauer <464871+dlebauer@users.noreply.github.com>
@dlebauer
Remove redundant totalDemand variable
91c76a3 
Co-authored-by: dlebauer <464871+dlebauer@users.noreply.github.com>
Copilot AI changed the title [WIP] Implement plant N pools with CN parameters and N limitation calculations Implement plant N pools with fixed CN ratios and N limitation Dec 17, 2025
Copilot AI requested a review from dlebauer December 17, 2025 00:43
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@dlebauer dlebauer Awaiting requested review from dlebauer dlebauer is a code owner

@Alomir Alomir Awaiting requested review from Alomir Alomir will be requested when the pull request is marked ready for review Alomir is a code owner

@mdietze mdietze Awaiting requested review from mdietze mdietze will be requested when the pull request is marked ready for review mdietze is a code owner

@infotroph infotroph Awaiting requested review from infotroph infotroph will be requested when the pull request is marked ready for review infotroph is a code owner

@mswilburn mswilburn Awaiting requested review from mswilburn mswilburn will be requested when the pull request is marked ready for review mswilburn is a code owner

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Implement plant N pools, fixed CN, N demand, N limitation

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