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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Review the instructions the agent will receive before you install.
Use this skill to build, inspect, validate, or edit EcoSIM soil_mgmt_in files. Soil management files use yearly selectors (fertf, tillf, irrigf) that point to event-table variables inside the same NetCDF file. Existing NetCDF files can be exported to Excel for editing, then converted back to JSON or NetCDF.
Read references/soil_mgmt_contract.md when you need exact NetCDF dimensions, Excel sheet columns, field order, units, or Fortran reader behavior.
f90src/IOutils/ReadManagementMod.F90..nc, inspect it first:.venv-cmip6/bin/python .agents/skills/ecosim-soil-mgmt/scripts/soil_mgmt_excel_bridge.py inspect soil-mngt.nc
event_files sheet so empty but intentional variables are preserved during round trips.fertf, tillf, and irrigf entries are fixed 10-character names. Use NO for inactive management.g m-2. Convert annual or field-rate values before writing: 1 g m-2 = 10 kg ha-1.DDMMYYYY for year-specific schedules. The Fortran reader uses the year embedded in the event string for leap-year day-of-year conversion.Use the bundled bridge for NetCDF, Excel, and JSON conversions:
.venv-cmip6/bin/python .agents/skills/ecosim-soil-mgmt/scripts/soil_mgmt_excel_bridge.py nc-to-xlsx soil-mngt.nc soil-mngt.xlsx
.venv-cmip6/bin/python .agents/skills/ecosim-soil-mgmt/scripts/soil_mgmt_excel_bridge.py xlsx-to-json soil-mngt.xlsx soil-mngt.json
.venv-cmip6/bin/python .agents/skills/ecosim-soil-mgmt/scripts/soil_mgmt_excel_bridge.py xlsx-to-nc soil-mngt.xlsx soil-mngt-edited.nc --json-output soil-mngt-edited.json
JSON remains supported:
.venv-cmip6/bin/python .agents/skills/ecosim-soil-mgmt/scripts/soil_mgmt_excel_bridge.py nc-to-json soil-mngt.nc soil-mngt.json
.venv-cmip6/bin/python .agents/skills/ecosim-soil-mgmt/scripts/soil_mgmt_excel_bridge.py json-to-nc soil-mngt.json soil-mngt.nc
For fertilizer-only files, verify that:
fertf selectors point to existing fertilizer variables for every active year.tillf and irrigf are NO if there are no tillage or irrigation events.DDMMYYYY and match the selector year unless deliberately yearless.For tillage and irrigation files, also verify row counts do not exceed reader limits: fertilizer <=12, scheduled irrigation <=24, and tillage <=367.
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Extract EPA/NADP tDEP atmospheric deposition and NADP precipitation chemistry rasters for an AmeriFlux or EcoSIM site. Use when deriving atmospheric chemistry inputs such as NH4, NO3, SO4, Ca, or precipitation pH for EcoSIM forcing workflows.
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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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