ecosim-trait-check-refine

Validates and refines EcoSIM per-PFT plant trait values using deterministic sanity checks.

Updated Aug 28, 2026
One-click install
npx skills add https://github.com/jingtao-lbl/A2MC --skill ecosim-trait-check-refine-jingtao-lbl
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: ecosim-trait-check-refine
Source: https://github.com/jingtao-lbl/A2MC/tree/main/.claude/skills/ecosim-trait-check-refine
Command: npx skills add https://github.com/jingtao-lbl/A2MC --skill ecosim-trait-check-refine-jingtao-lbl

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires netCDF4.

What problem does it solve? EcoSIM runs can complete successfully yet produce dead, stunted, or botanically wrong plants because the per-PFT trait VALUES in the pft_file_in NC table are physiologically inappropriate. This Skill diagnoses those value problems by running the EcoSIM developer's deterministic checker against the run's plant_trait.*.desc dump, then guides refinement of the NC input and re-verification by run. ## Core Features & Use Cases - Deterministic trait checking: Runs check_plant_trait_desc.py on a plant_trait.<year>.desc dump to flag range, fraction, sign, N/P magnitude, type-flag, and cross-parameter issues ranked ERROR to WARN. - Optional web-evidence layer: Derives literature-based trait ranges per PFT via the ecosim-trait-deriver skill and re-checks with --web-evidence for borderline magnitudes. - Refine and re-verify loop: Maps flagged .desc codes back to NC pft_file_in variables, patches values with netCDF4, re-runs on the same binary, and confirms the plant actually grows (peak SHOOT_C_pft), not just that the checker passes. - Use Case: An EcoSIM BioCON run finishes and writes output tapes, but the plant regrows smaller every spring. Use this Skill to sanity-check the trait values, test hypotheses like the RCS sign convention, and determine whether the cause is parameter values or a deeper carbon-balance issue requiring recalibration. ## Quick Start Ask the agent to sanity-check the plant trait values from my EcoSIM run's plant_trait.2000.desc file and tell me which pft input parameters look physiologically wrong.

Frequently Asked Questions about ecosim-trait-check-refine

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I check if EcoSIM plant trait values are reasonable?▼

Run check_plant_trait_desc.py from the ecosim-plant-trait-sanity-check skill on the run's plant_trait.<year>.desc dump. It flags range, fraction, sign, N/P magnitude, type-flag, and cross-parameter issues ranked ERROR to WARN, with nonzero exit if any ERROR exists.

How do I generate the plant_trait.desc file in EcoSIM?▼

Set disp_planttrait = .true. in the run namelist and run a short window. EcoSIM writes one plant_trait.<year>.desc per year to the run directory, decoding the exact per-PFT traits it used from the NC pft_file_in table.

What is the difference between ecosim-trait-check-refine and ecosim-version-drift?▼

ecosim-trait-check-refine handles value appropriateness: the run finishes and writes output, but the plant is wrong. ecosim-version-drift handles structure and completeness: missing input variables the binary requires, ENDRUN failures, or inactive-by-default target outputs.

Why does the plant still die after the trait checker passes?▼

The checker flags plausibility, not causality. If the plant fails to compound carbon year-over-year as a perennial, the bottleneck is the whole-plant annual carbon balance, which leaf-level parameters like RCS, VCMX, or CHL cannot fix; recalibration against observed targets is needed.

Should I edit the plant_trait.desc file to fix flagged values?▼

No. The .desc file is a decoded output dump, so editing it changes nothing. Map each flagged code back to its variable in the NC pft_file_in table, patch those values with netCDF4, re-run on the same binary, and re-check the new .desc.