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Sort EcoSIM run folders for a set of sites into one project directory with input/<SITE_ID>/ and run_dir/<SITE_ID>/ subdirectories and a project manifest. Use when asked to create EcoSIM run folders, runs, or cases for several sites at once ("create ecosim run folders for US-UMB, US-xGR, and US-Ha1", "set up a multi-site EcoSIM project"), or to add, refresh, or summarize sites in such a project.

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Track and report progress of a request to create and run an EcoSIM case for a site ("create an ecosim run for site US-UMB", "set up and run EcoSIM at <site>"). Records four stages — data preparation, namelist creation, model simulation, and output evaluation — in result/<SITE_ID>/progress.json and PROGRESS.md, derives step status from files and quality reports on disk, and records manual results such as the executable, test run, and evaluation verdicts. Use at the start of such a request, after each stage, and whenever the user asks where a site run stands.

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Inventory staged local EcoSIM data at project startup and validate input readiness for a selected site, simulation period, and preprocessing or analysis workflow. Use before data-dependent work or when relevant inputs change.

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Convert AmeriFlux ERA5 half-hourly meteorological CSV files into EcoSIM hourly climate forcing NetCDF files, compare generated forcing against overlapping measured tower meteorology when a FULLSET file is available, and report large biases or errors. Use when preparing or validating EcoSIM climate inputs for AmeriFlux sites, checking ERA5 against in situ records, diagnosing forcing discrepancies, or writing climate-quality reports. For non-AmeriFlux paper sites that need a fresh Copernicus CDS ERA5 point download by longitude/latitude, use era5-cds-point-download first.

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Extract AmeriFlux site metadata and map it to EcoSIM JSON variables. Use when a task needs site latitude, longitude, elevation, mean annual temperature, Koppen climate code, or vegetation type for an AmeriFlux site ID or flux-site name.

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Extract point-scale CMIP6 historical and SSP future climate data from the Pangeo Google Cloud catalog and convert them into bias-corrected additive or multiplicative anomalies for LSM or EcoSIM climate forcing. Use when a task needs site latitude/longitude, scenario-specific CMIP6 variables, vapor pressure derived from huss and ps, calendar-aware day-of-year climatologies, or projected change summaries for the 2050s and 2090s.

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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.

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Prepare, validate, and edit EcoSIM plant management inputs using pft_mgmt_in NetCDF, editable Excel workbooks, and optional PlantMgmtWriter.py JSON files. Use when creating or checking natural PFT management data, converting pft-mngt NetCDF to an Excel sheet for editing, converting edited Excel back to JSON or NetCDF, validating pft_type/pft_pltinfo/pft_mgmt entries, or preparing PlantMgmtWriter.py inputs for EcoSIM.

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Extract and update the EcoSIM output-variable catalog from Fortran history-field registration calls such as hist_addfld1d and hist_addfld2d. Use only when explicitly asked to update, regenerate, refresh, or rebuild the list of EcoSIM output variables from HistDataType.F90 or related F90 source; do not invoke for ordinary EcoSIM output analysis unless the variable list itself must be updated.

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Read-only sanity-check of EcoSIM plant_trait.*.desc parameter values for the first grid. Use when validating plant trait description files, enforcing clean C3/C4 physiological parameterization, reviewing photosynthetic kinetics, active leaf/root protein allocation, and root hydraulics such as RSRR, RVSR, and ARSRA, or checking ranges, units, and woody/herbaceous block consistency before running EcoSIM. Never edit or replace the `.desc` file.

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Download NASA GES DISC NLDAS_FORA0125_H version 2.0 primary hourly forcing data for a point location. Use when Codex needs to retrieve NLDAS File A meteorological forcing from the GES DISC API or HTTPS archive for a longitude/latitude pair, including Earthdata username/password authentication, hourly URL generation, nearest-grid-point extraction, CSV output, or EcoSIM climate-forcing preprocessing.

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Extract study sites, observational variables, coordinates, climate-forcing sources, and cited data sources from ecosystem-modeling papers, PDFs, supplements, or article text, then plan or create EcoSIM simulation workflows and run folders for those sites. Use when Codex is asked to read a paper for EcoSIM feasibility, including requests phrased as "read paper for ecosim feasibility"; read a paper for sites/data availability; reproduce a published site simulation in EcoSIM; compare EcoSIM outputs to paper observations; or convert paper-derived AmeriFlux, FLUXNET, US NLDAS-domain, non-US ERA5, crop, peatland, forest, grassland, wetland, or unmanaged field-site information into EcoSIM inputs and runnable cases.

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Use this skill when you need to derive, from web-sourced evidence, typical values for a named plant's annual GPP, LAI, specific LAI or specific leaf area, Rubisco Vcmax at 25oC, Jmax at 25oC, root-to-shoot ratio, rooting depth, leaf protein nitrogen, and leaf chlorophyll nitrogen.

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Build EcoSIM atmospheric greenhouse-gas forcing files by combining a historical monthly atmgas NetCDF with RCMIP/CMIP6 SSP concentration pathways. Use when Codex needs SSP245/SSP585 or other SSP atmospheric CO2, CH4, and N2O concentrations, key-year tables, or scenario NetCDF files spanning historical years through 2100 for EcoSIM or related biogeochemical forcing workflows.

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Create EcoSIM Fortran namelist files and workable EcoSIM run folders for AmeriFlux site runs from site-specific grid, plant management, climate forcing, and greenhouse-gas inputs. Use when preparing or updating an EcoSIM `.namelist`, run folder, runfolder, run directory, or executable-ready site case for AmeriFlux or FLUXNET sites, especially after generating `*_ecosim_grid.nc`, `*_ecosim_climate_<first>-<last>.nc`, and `*_pft_mgmt.nc` inputs.

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Edit EcoSIM PFT-parameter NetCDF files such as ecosim_pftpar_20260303.nc with the ParEditor class from applications/notebooks/scripts/ParamEditor.py. Use when asked to modify, scale, copy, compare, or delete PFT parameter records for a plant functional type (six-character pfts code such as gr3s43 or ndlf34), update microbe parameter NetCDF values, or maintain the JSONL change log that records past parameter changes. Never modify plant_trait.*.desc files; they are read-only references.

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Map observed site vegetation, species lists, land-cover descriptions, or plant management PFTs to EcoSIM vegetation codes using templates/ecosim_pftpar_20260303.nc.cdl. Use when choosing or validating EcoSIM pft_type values, pfts entries, pfts_short categories, pfts_long plant type meanings, or the combined short-code plus Koppen climate numerical code used by plant management inputs.

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Download Copernicus CDS ERA5 single-level point time-series climate forcing for non-US or non-NLDAS EcoSIM sites from longitude/latitude coordinates. Use when a paper-derived site is outside the NLDAS domain, lacks AmeriFlux/FLUXNET curated forcing, or needs global ERA5 variables such as 2m temperature, dewpoint temperature, surface pressure, solar radiation, precipitation, and 10m wind components for EcoSIM preprocessing.

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Estimate calcium-normalized Gapon selectivity coefficients from paired exchange and solution chemistry, or initialize depth-explicit EcoSIM Gapon inputs from the closest bundled ecosystem template when paired chemistry is unavailable. Use when deriving or checking EcoSIM GKC4, GKCH, GKCA, GKCM, GKCN, or GKCK values; matching a target ecosystem, climate, vegetation, and management regime to a starting profile; remapping template values to target soil layers; or documenting that template-based values require calibration or tuning.

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Run the combined AmeriFlux to EcoSIM extraction workflow for site metadata, NADP or tDEP atmospheric chemistry, gSSURGO soil data, and optional climate or grid NetCDF forcing. Use when building a complete site-specific EcoSIM input package.

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Download, screen, and map non-North-America auxiliary EcoSIM climate variables from global or regional atmospheric-chemistry data sources. Use when a non-US/non-NLDAS site needs annual EcoSIM precipitation chemistry variables such as PHRG, CN4RIG, CNORIG, CSORG, CCARG, CMGRG, CNARG, CKARG, or CCLRG; when deciding whether to use CAMS, EBAS, EANET, or MERRA-2; or when deriving site-specific auxiliary variables after ERA5 climate forcing has been prepared.

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Use this skill when you need to derive a Koppen-Geiger climate label from input latitude and longitude, then convert between the letter code such as `Csa` and the EcoSIM-style numeric code such as `34`.

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Extract dominant-component soil profile variables for EcoSIM grid or template inputs from gSSURGO, with FAO HWSD v2.0 fallback when gSSURGO data are unavailable or incomplete. Use when deriving soil depth, bulk density, field capacity, wilting point, hydraulic conductivity, texture, rock fraction, pH, CEC, or soil organic carbon; or when converting EcoSIM grid NetCDF files to editable Excel workbooks and back.

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Prepare, validate, inspect, and edit EcoSIM soil management inputs using soil_mgmt_in NetCDF, editable Excel workbooks, and optional JSON files. Use when checking fertilizer, tillage, or irrigation management data; converting soil-mngt NetCDF to Excel for editing; converting edited Excel back to JSON or NetCDF; decoding fertf/tillf/irrigf selector variables; or validating EcoSIM ReadManagementMod.F90 soil-management inputs.

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