29 个（bioepic-data 的仓库） · 按人气排序
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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Extract AmeriFlux BASE-BADM/BIF crop management records into EcoSIM-editable plant-management and soil-management Excel workbooks that can be converted to EcoSIM NetCDF files. Use when asked to derive EcoSIM planting, harvest, fertilizer, or tillage management inputs from AMF *_BIF_*.xlsx or BIF CSV files, especially for crop sites where management details live in GRP_DM_* records and DM_COMMENT fields.
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Sort AmeriFlux BASE-BADM BIF variables from Excel or CSV files into observation, management-event, static metadata, and plotting-ready target time-series tables. Use when Codex is asked to sort AmeriFlux BIF variables into time series; organize BADM/BIF variables by date; pivot AMF *_BIF_*.xlsx files by GROUP_ID; output total LAI, leaf mass per area, above-ground biomass, canopy height, fruit yield, or total yield time series; write MATLAB readers for BIF time-series plotting; or prepare dated AmeriFlux site observations and management records for EcoSIM workflows.
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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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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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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 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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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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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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Extract one EcoSIM PFT parameter record from a PFT-parameter NetCDF file into a standalone NetCDF. Use when Codex needs to isolate all parameters for a given EcoSIM six-character PFT code such as ndlf34, or a four-character pfts_short value plus Koppen climate code, while preserving all non-PFT-specific variables such as pfts_short, pfts_long, and Koppen metadata.
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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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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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Use this skill when deriving EcoSIM plant trait parameter recommendations for a named plant from web and online literature evidence, using a read-only `plant_trait.*.desc` file and the `ndlf43` tree block or `gr3s43` grass block as the starting archetype. Never edit or replace the `.desc` file.
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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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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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