ameriflux-bif-ecosim-mgmt

name

ameriflux-bif-ecosim-mgmt

description

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.

AmeriFlux BIF To EcoSIM Management

Overview

Use this skill to convert AmeriFlux BADM/BIF management metadata into two editable EcoSIM workbooks:

• *_plant_mgmt.xlsx, matching $ecosim-natural-plant-mgmt.
• *_soil_mgmt.xlsx, matching $ecosim-soil-mgmt.

The extractor also writes companion JSON files and a *_management_extraction_review.xlsx workbook. Always review assumptions before converting the generated Excel files to NetCDF, because many AmeriFlux management quantities are stored in free-text comments.

Read references/mapping_rules.md when you need the exact parsing and default mapping rules.

Workflow

1. Inspect the BIF workbook if needed. Prefer the AMF-BIF sheet.
2. Run the bundled extractor with the repo Python environment so it can read both XLSX and the PFT parameter NetCDF:

.venv-cmip6/bin/python \
  .agents/skills/ameriflux-bif-ecosim-mgmt/scripts/extract_bif_mgmt_to_ecosim_excel.py \
  /path/to/AMF_SITE_BIF_YYYYMMDD.xlsx \
  --pftpar-nc /path/to/ecosim_pftpar_YYYYMMDD.nc \
  --koppen-code 41 \
  --out-dir result/SITE/ecosim_mgmt_from_bif

3. Open the review workbook and check:
   • crop-to-PFT mapping (corn=maiz41, soybean=soyb41 by default);
   • parsed planting populations from seed rates;
   • fertilizer N rates and product split among NH4Soil, NH3Soil, UreaSoil, and NO3Soil;
   • tillage depth/type defaults;
   • harvest defaults and FractionCut assumptions.
4. Edit the generated plant/soil Excel workbooks if needed.
5. Convert reviewed workbooks to NetCDF using the existing bridge skills:

.venv-cmip6/bin/python .agents/skills/ecosim-natural-plant-mgmt/scripts/plant_mgmt_excel_bridge.py \
  xlsx-to-nc SITE_plant_mgmt.xlsx SITE_pft_mgmt.nc --json-output SITE_pft_mgmt.json

.venv-cmip6/bin/python .agents/skills/ecosim-soil-mgmt/scripts/soil_mgmt_excel_bridge.py \
  xlsx-to-nc SITE_soil_mgmt.xlsx SITE_soil_mgmt.nc --json-output SITE_soil_mgmt.json

Useful Options

• --start-year and --end-year: limit the output years.
• --pftpar-nc: EcoSIM PFT parameter NetCDF used to validate pft_type against pfts.
• --koppen-code: two-digit EcoSIM climate number used to compose <pfts_short><koppen>.
• --crop-pft-map crop=pftcode: explicit crop mapping override, repeatable.
• --planting-depth-m: default planting depth used when BIF only provides seed rate.
• --topo NH1,NV1,NH2,NV2: set EcoSIM topo-unit bounds.
• --default-fertilizer-n-g-m2: placeholder N rate when a fertilizer event lacks a parseable rate.
• --tillage-depth-m and --tillage-type: placeholders for BIF tillage records.

Output Contract

The plant workbook has the exact sheets required by plant_mgmt_excel_bridge.py: control, topo_units, pft_years, and management.

The soil workbook has the exact sheets required by soil_mgmt_excel_bridge.py: control, topo_units, year_selectors, event_files, fertilizer, tillage, and irrigation.

The review workbook is not consumed by EcoSIM. It exists to protect unit consistency and mass-flow assumptions before NetCDF conversion.