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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查看安装方法安装前可以查看交给 AI 代理的指令内容。
result/projects/<PROJECT>/
input/<SITE_ID>/ the site's inputs (copy of result/<SITE_ID>/input/)
run_dir/<SITE_ID>/ <SITE_ID>.namelist, input paths ../../input/<SITE_ID>/<file>
project.json manifest: per-site inputs, chronology, tracker, smoke, and trait status
PROJECT.md the manifest as a table
Each case stays self-contained: its own grid, climate, plant management, the
site-corrected PFT parameter copy, GHG, and microbial files. Backups
(*.before_*, *.orig_*, *.prev_*) are not copied.
Choose a project name (from the user, or a short descriptive one) and the site list.
Prepare every site with the single-site workflow
(ameriflux-namelist-generator references/runfolder_workflow.md), each in
result/<SITE_ID>/ with its own progress tracker: data preparation, run
folder, 2-year smoke run, and plant-trait correction. Sites are independent;
report per-site problems instead of stopping the whole project.
Assemble the project:
python .agents/skills/ecosim-multisite-project/scripts/assemble_project.py \
--project <PROJECT> --sites US-UMB US-xGR [...]
The script requires result/<SITE_ID>/input/, run_dir/<SITE_ID>.namelist,
and a passed smoke run (--allow-no-smoke to override), copies the inputs,
rewrites namelist paths to ../../input/<SITE_ID>/, checks that every path
resolves from run_dir/<SITE_ID>/, and writes project.json and
PROJECT.md. It exits nonzero if any site was skipped or has path problems.
Report from PROJECT.md: one row per site with PFTs, chronology, climate
years, stage status, smoke run, and trait findings, plus the sites left out
and why.
To add sites or pick up changes, fix them in result/<SITE_ID>/ and rerun
the script with those sites; other sites in the manifest are kept. Model
output already in a project run directory is kept unless --replace-runs.
Only on request, run each case in its project run directory:
nohup python .agents/skills/ameriflux-namelist-generator/scripts/run_site_full.py \
--site-id <SITE_ID> --run-dir result/projects/<PROJECT>/run_dir/<SITE_ID> > /dev/null 2>&1 &
The same rules apply as for single sites: one continued run on failure, then
report the error. Sites run independently; a failing site does not stop the
others. Each run writes full_run_summary.json in its run directory.
result/<SITE_ID>/ and
reassemble, so the single-site tracker, logs, and evidence stay the source of
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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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