ecosim-h0-target-extractor - SKILL.md Agent Skill

name: ecosim-h0-target-extractor description: Extract typical annual GPP, annual evapotranspiration, mid-season LAI, mid-season root biomass, mid-season shoot biomass, median canopy height, maximum primary-root depth, Vcmax at 25oC, and Jmax at 25oC from EcoSIM h0 NetCDF output files. Use when asked to derive these EcoSIM output targets from a selected .ecosim.h0.*.nc file for model-output processing, trait checks, or benchmark summaries.

EcoSIM h0 Target Extractor

Purpose

Use this skill to summarize key ecosystem and plant physiological targets from EcoSIM h0 NetCDF output:

typical annual GPP
typical annual ET
mid-season LAI
mid-season root biomass
mid-season shoot biomass
median canopy height
maximum primary-root depth
typical Vcmax at 25oC
typical Jmax at 25oC

The default "typical" statistic is the median across complete calendar years. The script also reports year-by-year values, mean, standard deviation, minimum, and maximum.

Workflow

Locate the selected EcoSIM h0 file. If no path is given, search data/ first, then the repository, for *.ecosim.h0.*.nc.
Run the bundled extractor:

python3 .agents/skills/ecosim-h0-target-extractor/scripts/extract_h0_targets.py /absolute/path/to/FenStordIsland.ecosim.h0.2010-01-01-00000.nc --format json --output result/ecosim_h0_targets/FenStordIsland_h0_targets.json

For a human-readable table, also create Markdown:

python3 .agents/skills/ecosim-h0-target-extractor/scripts/extract_h0_targets.py /absolute/path/to/FenStordIsland.ecosim.h0.2010-01-01-00000.nc --format markdown --output result/ecosim_h0_targets/FenStordIsland_h0_targets.md

Review warnings, especially time-coordinate inference, cumulative-variable handling, and the Vcmax/Jmax weighting method.
Report each target value with its source NetCDF units and range when finite values are available. Do not summarize target values without units.

Default Variable Mapping

The extractor uses these EcoSIM h0 variables by default:

annual GPP: ECO_GPP_col
annual ET: ECO_ET_col
mid-season LAI: ECO_LAI_col
mid-season root biomass: Root_C_pft
mid-season shoot biomass: SHOOT_C_pft
median canopy height: CAN_HT_pft
maximum primary-root depth: Root1stDepz_pft
Vcmax at 25oC: VcMax25C_RUBISCO_pft
Jmax at 25oC: JMax25C_photo_pft

For Vcmax/Jmax PFT weighting, do not use LAIstk_pft by default because it includes stalk area. The default proxy is SHOOT_C_pft * SLA_pft * 1e-4, which estimates PFT leaf area index from live shoot C and specific leaf area. This is the closest PFT-resolved proxy available in many EcoSIM h0 files, but it is still a proxy because SHOOT_C_pft can include non-leaf shoot tissue. If this proxy is unavailable, use the active-PFT mean and report a warning.

Use command-line overrides such as --gpp-var, --root-var, --vcmax-var, or --capacity-weight-method active_pft_mean if a file uses different registry names or if proxy weighting is not appropriate.

Calculation Rules

Use complete calendar years only by default. A complete year must include January 1 and December 31 in the inferred or decoded date axis.
If ECO_GPP_col or ECO_ET_col is marked as cumulative, annual totals are the year-end cumulative values, not sums of daily rows. This prevents inflated carbon and water budgets.
If a cumulative variable declines after its within-year peak, report the year-end value as the net annual total and warn that the seasonal peak differs.
Mid-season defaults to July 1 through August 31. Override with --midseason-start MM-DD --midseason-end MM-DD for sites with a different growing-season window.
Root and shoot biomass are summed over active PFTs and reported as source units, usually gC/m2.
Canopy height is reported as the mid-season median of the tallest active PFT canopy height, usually in m.
Maximum primary-root depth is derived from Root1stDepz_pft by taking the maximum over primary-root axes, active PFTs, and complete-year time steps, usually in m.
Vcmax and Jmax are weighted by the shoot-C/SLA leaf-area proxy when available. If unavailable, use the active-PFT mean and report that choice.
Preserve source units and variable metadata in JSON output. Treat annual totals as source mass or water-depth units per year by temporal context, not by silently rewriting NetCDF units.
JSON output must include the top-level target_units and target_ranges lookups as well as per-metric units, min, and max fields. Markdown output must include dedicated units and range tables. CSV output must include units and range columns.

Date Handling

The script uses a real time coordinate when present. Some EcoSIM h0 files contain time_bounds but no time-coordinate units; in that case the script infers the first date from the filename pattern YYYY-MM-DD, such as FenStordIsland.ecosim.h0.2010-01-01-00000.nc. Use --start-date YYYY-MM-DD to override this inference.

Reporting

Report the output file path, selected h0 file, complete years used, mid-season window, typical median values with units and ranges, and warnings. If the annual GPP or ET method is year_end_cumulative, explicitly mention that the script did not sum daily cumulative rows.