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compare-calibration-rounds

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Actualizado7 de julio de 2026 a las 07:52

Compare A2MC calibration rounds (R1, R2, …) against each other and the validation targets — top-N best-achievable biomass per round, per-target Morris μ* sensitivity, P-pool / cross-regime overlays. Use when the user asks to "compare rounds", "update the multi-round figure", "refresh the R1-RN comparison", "which round is best", "top sensitive parameters per round", or to regenerate any `multiround_*` / cross-round figure after new cases complete. Codifies the multiround bundle pipeline + the footguns (screening contamination, case-name patterns, μ* ranking, param-set mismatch, partial-ensemble caveats).

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jingtao-lbl/A2MC-elm

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name	compare-calibration-rounds
description	Compare A2MC calibration rounds (R1, R2, …) against each other and the validation targets — top-N best-achievable biomass per round, per-target Morris μ* sensitivity, P-pool / cross-regime overlays. Use when the user asks to "compare rounds", "update the multi-round figure", "refresh the R1-RN comparison", "which round is best", "top sensitive parameters per round", or to regenerate any `multiround_` / cross-round figure after new cases complete. Codifies the multiround bundle pipeline + the footguns (screening contamination, case-name patterns, μ ranking, param-set mismatch, partial-ensemble caveats).
modes	{"requires_fates":true,"nutrient_pathway":"any","scope":["analysis"],"summary":"Cross-round comparison of FATES Morris ensembles; requires FATES calibration rounds. Targets from the case targets.yaml."}

Compare Calibration Rounds

Cross-round comparison of A2MC calibration rounds: best-achievable biomass per round vs the validation targets, and Morris μ* sensitivity per round. The canonical bundle lives under a site's analysis dir, use_cases/<site>/analysis/multiround_*/ (self-locating scripts; figures versioned beside them; the Kougarok reference instance is multiround_top50_sensitivity_20260606/). Read README.md there + the originating dev/ana log (findings) and the originating dev/ana log (procedure) first.

When to use

"Compare the rounds", "which round is best", "update/refresh the multi-round figure".
"Top sensitive parameters per round" / cross-round sensitivity.
Regenerating a multiround_* figure after new cases complete (e.g. a round's relaunched/added cases).
P-pool or cross-regime cross-round overlays (same bundle conventions).

The bundle

multiround_top50_sensitivity_20260606/
├── scripts/
│   ├── plot_multiround_top50_overlay.py        # biomass top-50 vs 6 targets (6 panels)
│   ├── plot_multiround_sensitivity_overlay.py  # Morris μ* top params per round (grouped bars)
│   ├── build_Y_from_monthly.py                 # R2..R5 Morris Y matrices from monthly NCs
│   └── build_Y_R1.py                           # R1 (138-param)
├── screening_top50/{R1..RN}/                   # screen_ensemble.py outputs per round
├── sensitivity/{R1..RN}_{leaf,fineroot}/       # morris μ* CSVs + per-round png
├── Y_matrices/                                 # Morris inputs (for sensitivity only)
└── multiround_*.png                            # the comparison figures

Also: tools/compare_rounds.py for quantitative round-vs-round deltas.

Pipeline (to refresh a figure after new cases)

Extract the new cases (all 3 phases if the combined/sensitivity figures are needed): production tools/extract_monthly_variables_FATES.py (TRANS) or tools/extract_and_plot_selected_cases.py (extract, any phase via --phase/--year-start/--year-end, reuses process_case).
Re-screen the round: phases/phase2_screening/screen_ensemble.py --data-dir <round extract dir> --top-n 100 --output-dir screening_top50/<RN> (source that round's config so A2MC_CASE_NAME_PATTERN is right). ⚠️ see footgun #1 — filter out-of-range cases first.
Biomass figure: python scripts/plot_multiround_top50_overlay.py (reads screening_top50/*/).
Sensitivity (only if refreshing μ*): rebuild Y (build_Y_from_monthly.py) → Morris (phases/phase1_exploration/morris_sensitivity_analysis.py) → plot_multiround_sensitivity_overlay.py.

Footguns (the load-bearing part)

#	Footgun	Guard
1	CROSS-round screening must cap the case number. `screen_ensemble.py` matches `PtCNPEn(\d+)<suffix>_TRANS` for any digits, so out-of-Morris-range experiment cases (e.g. H1 clumping #5001/5005/5006) sitting in a shared extract dir get swept in and can rank as "best". (This made the R5 biomass figure briefly show best #5001 instead of #1304, 2026-06-10.)	Pass `screen_ensemble.py --max-case-num <ensemble max>` (e.g. `4890`) for cross-round comparison — it drops out-of-range cases and prints how many. Verify `# Sets:` in `_results.txt` = expected. NOTE: leave `--max-case-num` UNSET for a single round's own whole-ensemble summary graph — those legitimately exceed the Morris size (e.g. R3 + reruns = 4941).
2	Read `_results.txt` Sim_ columns + `screening_result.json` `best_case_num`, NOT `screening_top50_indices.txt`. The indices file mislabels case numbers on partial ensembles and isn't always rewritten (can be stale).	The overlay scripts already do this; don't "trust" the indices file.
3	Morris CSV `rank` column is by `mu`, not `mu_star`.	Re-sort by `mu_star` (Morris importance) for selecting/ranking top params.
4	Sensitivity file prefix is unreliable. Older runs (R1–R4, 6/6) named both organs `morris_leafbiomass_` (the `--output-var` quirk); newer runs (R5, 6/10) correctly use `morris_finerootbiomass_` for fineroot. So a dir can hold either prefix. The directory `{Rn}_{organ}` is the source of truth for the organ; content is correct per dir.	Map organ by directory, never by filename prefix. Glob `morris_PFT{X}_2.csv` (matches both); ensure one file per PFT so `sorted()[-1]` is unambiguous.
5	Param-set mismatch across rounds. R1 used 138 params; R2+ used 162.	Align on shared names; show "no bar"/blank for params absent in a round; note it in the caption.
6	Partial-ensemble rounds. Screening/ranking is valid on a partial ensemble (dead cases get finite high cost), but Morris μ is NOT reliable* until the ensemble is reasonably complete.	Include a partial round in the biomass top-N figure (label it), but exclude it from the sensitivity overlay until a full Y-rebuild + Morris re-run.

Conventions

Filenames embed round + axis-mode + case count: R{N}_{TRANS,combined}_{count}cases_ensemble.png, multiround_top50_biomass_vs_6targets_R1-RN.png, multiround_top_sensitive_params_bars_R1-RN.png (per feedback_plot_filename_convention).
Biomass overlay bands: grey ±20% acceptance band + light-blue ±1 SD observation band (SD often exceeds the mean → floor the lower SD edge at 0). SD values from validation_targets_leafroot.txt.
Whole-ensemble (not top-N) cross-round plots use tools/plot_ensemble_cases.py + regen_ensemble_milestone_plot.sh (different from this bundle's top-50 overlay).
NERSC: scratch (symlink dirs, filtered sets) under $HOME/repo tmp/ only — never /tmp,/scratch.

Cross-references

Worked examples: the originating dev/ana log (procedure), 20260610b (refresh + H1 catch), the originating dev/ana log (findings).
Tools: phases/phase2_screening/screen_ensemble.py, phases/phase1_exploration/morris_sensitivity_analysis.py, tools/{compare_rounds,extract_and_plot_selected_cases,plot_ensemble_cases}.py.

Changelog

2026-06-17: ## Changelog convention adopted (see .claude/skills/README.md). Earlier history: git log + memory/dev_logs/.

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Log interactive calibration work for a site under use_cases/{site}/memory/logs/. Two log types — a PHASE log (a diagnosis, screening, experiment design/result, refinement — recorded the same way the autonomous agent does, via PhaseLogger, so both modes' logs synthesize together) or a free-form SESSION log (exploratory work that does not map to a specific phase). Use when the user wants to record calibration or exploration work — "log this", "log this phase / diagnosis / experiment", "log this calibration session", "write a session log", "record what I explored".

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name	compare-calibration-rounds
description	Compare A2MC calibration rounds (R1, R2, …) against each other and the validation targets — top-N best-achievable biomass per round, per-target Morris μ* sensitivity, P-pool / cross-regime overlays. Use when the user asks to "compare rounds", "update the multi-round figure", "refresh the R1-RN comparison", "which round is best", "top sensitive parameters per round", or to regenerate any `multiround_` / cross-round figure after new cases complete. Codifies the multiround bundle pipeline + the footguns (screening contamination, case-name patterns, μ ranking, param-set mismatch, partial-ensemble caveats).
modes	{"requires_fates":true,"nutrient_pathway":"any","scope":["analysis"],"summary":"Cross-round comparison of FATES Morris ensembles; requires FATES calibration rounds. Targets from the case targets.yaml."}

Compare Calibration Rounds

When to use

"Compare the rounds", "which round is best", "update/refresh the multi-round figure".
"Top sensitive parameters per round" / cross-round sensitivity.
Regenerating a multiround_* figure after new cases complete (e.g. a round's relaunched/added cases).
P-pool or cross-regime cross-round overlays (same bundle conventions).

The bundle

multiround_top50_sensitivity_20260606/
├── scripts/
│   ├── plot_multiround_top50_overlay.py        # biomass top-50 vs 6 targets (6 panels)
│   ├── plot_multiround_sensitivity_overlay.py  # Morris μ* top params per round (grouped bars)
│   ├── build_Y_from_monthly.py                 # R2..R5 Morris Y matrices from monthly NCs
│   └── build_Y_R1.py                           # R1 (138-param)
├── screening_top50/{R1..RN}/                   # screen_ensemble.py outputs per round
├── sensitivity/{R1..RN}_{leaf,fineroot}/       # morris μ* CSVs + per-round png
├── Y_matrices/                                 # Morris inputs (for sensitivity only)
└── multiround_*.png                            # the comparison figures

Also: tools/compare_rounds.py for quantitative round-vs-round deltas.

Pipeline (to refresh a figure after new cases)

Extract the new cases (all 3 phases if the combined/sensitivity figures are needed): production tools/extract_monthly_variables_FATES.py (TRANS) or tools/extract_and_plot_selected_cases.py (extract, any phase via --phase/--year-start/--year-end, reuses process_case).
Re-screen the round: phases/phase2_screening/screen_ensemble.py --data-dir <round extract dir> --top-n 100 --output-dir screening_top50/<RN> (source that round's config so A2MC_CASE_NAME_PATTERN is right). ⚠️ see footgun #1 — filter out-of-range cases first.
Biomass figure: python scripts/plot_multiround_top50_overlay.py (reads screening_top50/*/).
Sensitivity (only if refreshing μ*): rebuild Y (build_Y_from_monthly.py) → Morris (phases/phase1_exploration/morris_sensitivity_analysis.py) → plot_multiround_sensitivity_overlay.py.

Footguns (the load-bearing part)

#	Footgun	Guard
1	CROSS-round screening must cap the case number. `screen_ensemble.py` matches `PtCNPEn(\d+)<suffix>_TRANS` for any digits, so out-of-Morris-range experiment cases (e.g. H1 clumping #5001/5005/5006) sitting in a shared extract dir get swept in and can rank as "best". (This made the R5 biomass figure briefly show best #5001 instead of #1304, 2026-06-10.)	Pass `screen_ensemble.py --max-case-num <ensemble max>` (e.g. `4890`) for cross-round comparison — it drops out-of-range cases and prints how many. Verify `# Sets:` in `_results.txt` = expected. NOTE: leave `--max-case-num` UNSET for a single round's own whole-ensemble summary graph — those legitimately exceed the Morris size (e.g. R3 + reruns = 4941).
2	Read `_results.txt` Sim_ columns + `screening_result.json` `best_case_num`, NOT `screening_top50_indices.txt`. The indices file mislabels case numbers on partial ensembles and isn't always rewritten (can be stale).	The overlay scripts already do this; don't "trust" the indices file.
3	Morris CSV `rank` column is by `mu`, not `mu_star`.	Re-sort by `mu_star` (Morris importance) for selecting/ranking top params.
4	Sensitivity file prefix is unreliable. Older runs (R1–R4, 6/6) named both organs `morris_leafbiomass_` (the `--output-var` quirk); newer runs (R5, 6/10) correctly use `morris_finerootbiomass_` for fineroot. So a dir can hold either prefix. The directory `{Rn}_{organ}` is the source of truth for the organ; content is correct per dir.	Map organ by directory, never by filename prefix. Glob `morris_PFT{X}_2.csv` (matches both); ensure one file per PFT so `sorted()[-1]` is unambiguous.
5	Param-set mismatch across rounds. R1 used 138 params; R2+ used 162.	Align on shared names; show "no bar"/blank for params absent in a round; note it in the caption.
6	Partial-ensemble rounds. Screening/ranking is valid on a partial ensemble (dead cases get finite high cost), but Morris μ is NOT reliable* until the ensemble is reasonably complete.	Include a partial round in the biomass top-N figure (label it), but exclude it from the sensitivity overlay until a full Y-rebuild + Morris re-run.

Conventions

Filenames embed round + axis-mode + case count: R{N}_{TRANS,combined}_{count}cases_ensemble.png, multiround_top50_biomass_vs_6targets_R1-RN.png, multiround_top_sensitive_params_bars_R1-RN.png (per feedback_plot_filename_convention).
Biomass overlay bands: grey ±20% acceptance band + light-blue ±1 SD observation band (SD often exceeds the mean → floor the lower SD edge at 0). SD values from validation_targets_leafroot.txt.
Whole-ensemble (not top-N) cross-round plots use tools/plot_ensemble_cases.py + regen_ensemble_milestone_plot.sh (different from this bundle's top-50 overlay).
NERSC: scratch (symlink dirs, filtered sets) under $HOME/repo tmp/ only — never /tmp,/scratch.

Cross-references

Worked examples: the originating dev/ana log (procedure), 20260610b (refresh + H1 catch), the originating dev/ana log (findings).
Tools: phases/phase2_screening/screen_ensemble.py, phases/phase1_exploration/morris_sensitivity_analysis.py, tools/{compare_rounds,extract_and_plot_selected_cases,plot_ensemble_cases}.py.

Changelog

2026-06-17: ## Changelog convention adopted (see .claude/skills/README.md). Earlier history: git log + memory/dev_logs/.