phase3-diagnosis

Diagnose root causes of failing calibration targets in the A2MC workflow.

Updated Aug 28, 2026
One-click install
npx skills add https://github.com/jingtao-lbl/A2MC --skill phase3-diagnosis-jingtao-lbl
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: phase3-diagnosis
Source: https://github.com/jingtao-lbl/A2MC/tree/main/.claude/skills/phase3-diagnosis
Command: npx skills add https://github.com/jingtao-lbl/A2MC --skill phase3-diagnosis-jingtao-lbl

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve? After a screening round of environmental model calibration, some validation targets still miss their observations, and it is unclear why. This Skill runs Phase 3 (DIAGNOSIS) of the A2MC calibration workflow as the offline agent, systematically root-causing why the screening ensemble misses its targets and producing a structured diagnosis for the next phase. ## Core Features & Use Cases - Ensemble-level diagnosis: Analyzes the top-N leader cases as a set, grouping them by miss pattern rather than fixating on the single best case, using phase3 diagnostic tools (compare_targets, check_edge_parameters, carbon/nutrient/mortality analyzers). - Evidence-grounded reasoning: Pulls context from RAG/GraphRAG, the model knowledge base (five surfaces), and per-site Adaptive Memory before asserting any mechanism, and verifies every mechanism claim at file:line in the checked-out model source. - Structured handoff: Produces ranked root causes, severity-classified failing targets, parameter recommendations, selected base cases, and testable hypotheses, logged via PhaseLogger and handed to Phase 4. - Use Case: After Phase 2 screening of an EcoSIM or FATES calibration round, ask the agent to diagnose why the leaders miss standing carbon while matching production; it gathers diagnostics, checks Memory for failed directions, and returns a ranked root-cause diagnosis with base cases for Phase 4 experiments. ## Quick Start Ask the agent to run Phase 3 and diagnose why the current screening round's targets are not calibrating, using the existing ensemble outputs.

Frequently Asked Questions about phase3-diagnosis

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

FAQPage Schema
How do I diagnose why calibration targets are failing in A2MC?▼

Run Phase 3 diagnosis after Phase 2 screening hands off a ranked ensemble. The skill gathers diagnostics with phase3 tools, pulls RAG and Adaptive Memory evidence, and produces ranked root causes, parameter recommendations, and hypotheses for Phase 4.

What is the difference between phase3-diagnosis and diagnose-forensics?▼

phase3-diagnosis is the systematic phase routine that diagnoses every failing target from a screening round. diagnose-forensics is reactive triage for a single suspicious case or anomaly; run forensics first if one result looks like contamination or an infrastructure artifact.

Does phase3-diagnosis work with non-FATES models like PFLOTRAN?▼

Yes, but most FATES-shaped tools (PFT collapse, mortality, nutrient pools) have no analog for non-vegetation models. Only backend-dispatching tools like compare_targets.py apply directly; build the diagnosis from the model's own outputs and sim-vs-obs time series instead.

Why must mechanisms be verified in model source code during diagnosis?▼

Parameter descriptions and long_name attributes have repeatedly contradicted actual Fortran behavior in this workflow. The skill requires confirming every mechanism claim at file:line in the checked-out source after consulting the knowledge base, because a wrong mechanism costs hours of misdirected experiments.

What inputs does Phase 3 diagnosis require before it can run?▼

It needs Phase 1 sensitivity rankings, Phase 2 top-N cases with per-target errors, and optionally Phase 6 rethink pathways on later cycles. It reads existing simulation outputs only and never launches new simulations itself.