[FIX] Jabowa: align self.grow to per-step convention#404
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Memory mortality assumes plant_module.grow stores a per-step increment (consistent with Bettina's m^3/step). Jabowa stored an annualised rate (cm/yr), causing relative_grow * steps_per_year to be inflated by steps_per_year-fold at sub-yearly time steps - Memory's threshold became effectively N times more lenient (e.g. 12x at monthly dt). Convert annualised rate to per-step in-place inside progressPlant. self.grow now stores cm/step, dbh += self.grow directly. CSV output column 'growth' also switches to cm/step for consistency across plant models (Bettina already outputs m^3/step). Documents the per-step contract explicitly in Memory.md so future plant modules cannot regress. BREAKING CHANGE: Jabowa CSV output column 'growth' semantics changes from cm/yr to cm/step. Downstream analyses that assumed cm/yr must multiply by dt_yr = time / (3600*24*365.25) to recover the old value. Reference CSVs regenerated for 12 Jabowa benchmarks. Bettina benchmarks unaffected.
mcwimm
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May 8, 2026
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I'm glad you found this bug!
Could you also please upload the non-CI reference files? Once you have done so, this PR will be ready to be merged.
- Apply suggestion in Memory.md: '**Contract for plant modules**' -> '**Note**'
- Regenerate non-CI reference CSVs for 11 Jabowa benchmarks (Default,
Aboveground/AsymmetricZOI, Belowground/{FixedSalinity, FON, SymmetricZOI,
Merge_FixedSalinity_FON, Merge_FixedSalinity_sZOI},
Mortality/{Memory, NoGrowth, Random, RandomGrowth}).
This was referenced Jun 8, 2026
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Summary
Mortality/Memoryassumes thatplant_module.growstores a per-step growth increment (consistent with Bettina'sm³/step).Jabowainstead stored an annualised rate (cm/yr), so the formulainflated the LHS by
steps_per_year-fold for Jabowa, making the mortality threshold effectivelyN×more lenient at sub-yearly time steps (e.g. 12× too lenient at monthly dt).This PR fixes the unit mismatch at its source:
Jabowa.self.growis now stored ascm/step, matching Bettina's per-step convention. TheMortality/Memoryformula is unchanged (it was correct for Bettina all along; the contract is now documented explicitly inMemory.md).Diagnosis
dt = 1 yr)relative_grow × 1 < threshold✓ correctdt = 1/12 yr)relative_grow × 12 < threshold— threshold effectively0.5%/12 ≈ 0.04%/yr✗relative_grow × 1 < threshold✓Bettina was unaffected because every Bettina intermediate (maint, ag/bg resources) explicitly multiplies by
self.time, so itsself.growis already per-step.Changes
Code
PlantModelLib/Jabowa/Jabowa.py— convert annualised rate to per-step insideprogressPlant.self.grownow storescm/step;dbh += self.growdirectly (no time rescaling).PlantModelLib/Mortality/Memory/Memory.py— comment generalised (was Bettina-only "m³ per time step").Documentation
PlantModelLib/Jabowa/Jabowa.md— Process overview reflects per-step semantics.PlantModelLib/Mortality/Memory/Memory.md— explicit per-step contract for plant modules; removed Bettina-specific "m³/m³" / "biovolume" wording.Reference CSVs (regenerated)
12 Jabowa benchmarks:
Default,Aboveground/AsymmetricZOI,Belowground/{FON, FON_MultiSpecies, FixedSalinity, SymmetricZOI, Merge_FixedSalinity_FON, Merge_FixedSalinity_sZOI},Mortality/{Memory, NoGrowth, Random, RandomGrowth}. Bettina references untouched.This unifies the output convention across plant modules.