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fixes the conflation of soil and microbial maintenance respiration by splitting it #202

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ayushman1210 wants to merge 28 commits into from
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fixes the conflation of soil and microbial maintenance respiration by splitting it #202

ayushman1210 wants to merge 28 commits into from

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@ayushman1210 ayushman1210 commented Dec 10, 2025 •
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Summary

This update fixes the conflation of soil and microbial maintenance respiration by splitting maintRespiration into:

  • soilMaintRespiration
  • microbeMaintRespiration
    It also corrects the respiration temperature formulation by separating the base rate from the Q10 temperature effect.

Key Changes

  • Replaced maintRespiration with explicit soil and microbe maintenance fluxes.
  • Fixed incorrect mixing of base respiration rate with temperature effect.
  • Updated rSoil calculation:
    • Microbes OFF → rSoil = soilMaintRespiration
    • Microbes ON → rSoil = microbeMaintRespiration + (1 - microbeEff) * microbeIngestion
  • Updated state.h to match new flux definitions.

Testing

  • Docker build succeeds [success]
  • Model runs with --microbes [success]
  • Output (sipnet.out) generated successfully [success]

Fixes #144

ayushman1210 and others added 16 commits November 18, 2025 01:21
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Co-authored-by: David LeBauer <dlebauer@gmail.com>
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changes as per maintainer suggested
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fixes the conflation of soil and microbial maintenance respiration by…
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… splitting
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Alomir
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Thanks for putting this together, @ayushman1210! It's almost there, I have a few additions that should be made.

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ayushman1210 commented Dec 13, 2025

hey @Alomir i have made as per your suggestion
please review it
thanks !!

@ayushman1210 ayushman1210 requested a review from Alomir December 13, 2025 09:04
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ayushman1210 commented Dec 26, 2025

Hi maintainers,
Just a gentle follow-up regarding the PR #202
Whenever you get a chance, I’d really appreciate a review.
Thanks for your time!

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ayushman1210 commented Jan 7, 2026 •
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Hi @Alomir please let me know if anything else needed in this pr #202
thanks !!

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Alomir commented Jan 7, 2026

Sorry for the delay, @ayushman1210 - and again, thanks for your work here. However, I think #207 (which you are going to work on) is going to supersede this task, making it obsolete.

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Alomir commented Jan 7, 2026

I would like to leave this PR in its current state until we see how #207 works out, if you don't mind.

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ayushman1210 commented Jan 7, 2026

Got it, thanks for the update! I’ll focus on #207 then. Let me know if there’s anything specific you’d like me to prioritize.

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Alomir commented Feb 9, 2026

I think it is clear from #207 that this PR will not be needed. Thanks for your work on #207!

@Alomir Alomir closed this Feb 9, 2026
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@dlebauer dlebauer Awaiting requested review from dlebauer dlebauer is a code owner

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Split maintResp into soilMaintResp and microbeMaintResp for clarity

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