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cfrankencfranken
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Fixed major GCHP implementation bug
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‎.claude/.nfs00000001e56c9fd600001e40‎

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{
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"env": {
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"JULIA_MCP_API_KEY": "kaimon_52d97e7eaf81a66178ae5516a4690c8b7bd01762",
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"JULIA_MCP_PORT": "1206",
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"JULIA_MCP_REPL_ID": "AtmosTransportModel"
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},
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"permissions": {
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"allow": [
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"WebFetch(domain:kahliburke.github.io)",
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"Bash(gh api:*)",
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"Bash(curl:*)",
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"Bash(grep:*)",
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"Bash(~/.juliaup/bin/julia:*)",
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"Read(//home/cfranken/data/**)",
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"Read(//kiwi-data/Data/groupMembers/cfranken/AtmosTransport/catrine/**)",
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"Bash(ls:*)",
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"Bash(do echo:*)",
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"mcp__julia__julia_eval",
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"Bash(ncdump:*)",
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"Bash(/tmp/analyze_halo_coverage.jl:*)",
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"Bash(/tmp/check_stencil_requirements.jl:*)",
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"WebSearch",
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"WebFetch(domain:www.gfdl.noaa.gov)",
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"WebFetch(domain:noaa-emc.github.io)",
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"WebFetch(domain:raw.githubusercontent.com)",
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"WebFetch(domain:arxiv.org)",
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"WebFetch(domain:www.sciencedirect.com)",
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"mcp__julia__julia_restart",
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"WebFetch(domain:data.nas.nasa.gov)",
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"Bash(julia:*)",
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"Bash(AT_DIR=/temp2/catrine-runs/output/linrood OUT_GIF=catrine_linrood_vs_geoschem_fossil_co2.gif julia:*)",
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"Bash(AT_DIR=/temp2/catrine-runs/output/linrood OUT_GIF=catrine_linrood_vs_geoschem_co2.gif julia:*)"
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]
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},
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"enableAllProjectMcpServers": true,
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"enabledMcpjsonServers": [
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"kaimon",
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"julia"
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]
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}

‎.mcp.json‎

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{
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"mcpServers": {
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"julia": {
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"command": "/home/cfranken/.local/bin/uv",
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"args": ["run", "--directory", "/home/cfranken/code/gitHub/julia-mcp", "python", "server.py", "--startup-file=yes"]
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}
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}
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}

‎.vscode/settings.json‎

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{
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"fortran.fortls.disabled": true
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}
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{
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"vscode-remote-control.allowedCommands": [
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"workbench.action.files.saveAll",
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"editor.action.formatDocument",
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"workbench.action.debug.start"
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]
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}

‎CLAUDE.md‎

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‎README.md‎

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# AtmosTransport.jl
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> **Work in Progress.** This project is under rapid active development. We regularly break things and fix them afterwards. The code is not yet intended for external users — APIs, file formats, and physics implementations may change without notice. If you are interested in contributing or following along, feel free to open an issue.
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[![Documentation](https://img.shields.io/badge/docs-dev-blue.svg)](https://RemoteSensingTools.github.io/AtmosTransport/dev/)
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A Julia-based atmospheric transport model for GPU and CPU, inspired by TM5 and designed with

‎config/preprocessing/catrine_spectral_dec2021.toml‎

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# ===========================================================================
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# Spectral mass-flux preprocessing — ERA5 CATRINE December 2021
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#
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# Converts ERA5 spectral VO/D/LNSP GRIB data to mass fluxes on a regular
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# lat-lon grid for the first month of CATRINE D7.1.
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#
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# Usage:
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# julia --project=. -p 8 scripts/preprocessing/preprocess_spectral_massflux.jl \
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# config/preprocessing/catrine_spectral_dec2021.toml
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# ===========================================================================
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[input]
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spectral_dir = "~/data/AtmosTransport/met/era5/spectral"
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coefficients = "config/era5_L137_coefficients.toml"
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surface_dir = "~/data/AtmosTransport/met/era5/surface"
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cmfmc_dir = "~/data/AtmosTransport/met/era5/cmfmc"
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[output]
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directory = "/temp1/atmos_transport/era5_spectral_catrine"
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[grid]
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nlon = 720 # target longitude count (720 → 0.5°)
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nlat = 361 # target latitude count (361 → 0.5°)
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level_top = 1 # topmost model level (1 = TOA)
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level_bot = 137 # bottommost model level (137 = surface)
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[numerics]
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float_type = "Float32"
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dt = 900.0 # advection sub-step [s]
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met_interval = 21600.0 # met data interval [s] (6-hourly)

‎config/runs/catrine_era5_spectral_1week.toml‎

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# ===========================================================================
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# CATRINE D7.1 — ERA5 Spectral 0.5° Lat-Lon (1-Week Test)
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#
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# 4-tracer intercomparison: CO2, fossil CO2, SF6, 222Rn
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# Period: 1 Dec 2021 — 7 Dec 2021 (28 windows = 7 days × 4 windows/day)
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# Met data: ERA5 spectral mass fluxes, preprocessed to 720×361×137
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# Output: 3-hourly, full 3D fields + column mass (BinaryOutputWriter)
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#
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# Preprocessing:
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# julia --project=. scripts/preprocessing/preprocess_spectral_massflux.jl \
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# config/preprocessing/catrine_spectral_dec2021.toml
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#
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# Usage:
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# julia --threads=2 --project=. scripts/run.jl \
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# config/runs/catrine_era5_spectral_1week.toml
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# ===========================================================================
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[architecture]
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use_gpu = true
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float_type = "Float32"
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[grid]
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type = "latlon"
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met_source = "era5"
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size = [720, 361, 137] # 0.5° × 0.5°, full 137 levels
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[met_data]
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driver = "preprocessed_latlon"
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directory = "/temp1/atmos_transport/era5_spectral_catrine"
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dt = 300 # advection sub-step [s] (Prather needs CFL<1)
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max_windows = 28 # 7 days × 4 windows/day
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# --- Initial conditions ---
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# CO2 and SF6 from LSCE inversions (1 Dec 2021 00:00 UTC)
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# Bilinear horizontal + log-pressure vertical interpolation
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# from LMDZ 360×180×79 → ERA5 720×361×137
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# fossil_co2 and rn222 start from zero (no IC entry needed)
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[initial_conditions]
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co2.file = "~/data/AtmosTransport/catrine/InitialConditions/startCO2_202112010000.nc"
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co2.variable = "CO2"
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sf6.file = "~/data/AtmosTransport/catrine/InitialConditions/startSF6_202112010000.nc"
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sf6.variable = "SF6"
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# --- Tracers ---
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[tracers.co2]
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emission = "prebuilt"
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file = "~/data/AtmosTransport/catrine/output/era5_spectral_1week/emissions_prebuild/co2_720x361.bin"
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species = "co2"
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[tracers.fossil_co2]
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emission = "prebuilt"
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file = "~/data/AtmosTransport/catrine/output/era5_spectral_1week/emissions_prebuild/fossil_co2_720x361.bin"
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species = "fossil_co2"
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[tracers.sf6]
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emission = "edgar_sf6"
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file = "~/data/AtmosTransport/catrine/Emissions/edgar_v8/v8.0_FT2022_GHG_SF6_2022_TOTALS_emi.nc"
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noaa_growth_file = "~/data/AtmosTransport/catrine/Emissions/sf6_gr_gl.txt"
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year = 2022
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scale_year = 2022
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[tracers.rn222]
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emission = "prebuilt"
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file = "~/data/AtmosTransport/catrine/output/era5_spectral_1week/emissions_prebuild/rn222_720x361.bin"
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chemistry = "decay"
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half_life = 330350.4 # 3.8235 days in seconds
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# --- Chemistry (222Rn radioactive decay) ---
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[chemistry]
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type = "composite"
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# --- Advection ---
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[advection]
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scheme = "slopes"
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# --- Convection ---
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# NOTE: Tiedtke convection requires CMFMC fields, which are not yet merged
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# into the preprocessed spectral mass flux files. Enable once surface fields
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# are integrated via merge_era5_surface_to_massflux.jl.
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#[convection]
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#type = "tiedtke"
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# --- Diffusion ---
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[diffusion]
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type = "pbl"
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beta_h = 15.0
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Kz_bg = 0.1
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Kz_min = 0.01
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#Kz_max = 500.0
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# --- Output (3-hourly, full 3D + column mass) ---
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[output]
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filename = "~/data/AtmosTransport/catrine/output/era5_spectral_1week/catrine_era5_week"
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interval = 10800 # 3 hours
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auto_convert = true
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format = "binary"
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split = "daily"
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[output.fields]
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co2_3d = {type = "full_3d", species = "co2"}
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fossil_co2_3d = {type = "full_3d", species = "fossil_co2"}
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sf6_3d = {type = "full_3d", species = "sf6"}
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rn222_3d = {type = "full_3d", species = "rn222"}
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co2_column_mass = {type = "column_mass", species = "co2"}
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fco2_column_mass = {type = "column_mass", species = "fossil_co2"}
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sf6_column_mass = {type = "column_mass", species = "sf6"}
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rn222_column_mass = {type = "column_mass", species = "rn222"}
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surface_pressure = "surface_pressure"
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[buffering]
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strategy = "double"

‎config/runs/catrine_era5_spectral_dec2021.toml‎

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# ===========================================================================
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# CATRINE D7.1 — ERA5 Spectral 0.5° Lat-Lon (December 2021)
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#
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# 4-tracer intercomparison: CO2, fossil CO2, SF6, 222Rn
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# Period: 1 Dec 2021 — 31 Dec 2021
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# Met data: ERA5 spectral mass fluxes, preprocessed to 720x361x137
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# Output: 3-hourly, full 3D fields + column mass (BinaryOutputWriter)
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#
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# Preprocessing:
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# julia --project=. -p 8 scripts/preprocessing/preprocess_spectral_massflux.jl \
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# config/preprocessing/catrine_spectral_dec2021.toml
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#
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# Usage:
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# julia --threads=2 --project=. scripts/run.jl config/runs/catrine_era5_spectral_dec2021.toml
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# ===========================================================================
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[architecture]
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use_gpu = true
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float_type = "Float32"
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[grid]
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type = "latlon"
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met_source = "era5"
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size = [720, 361, 137] # 0.5° x 0.5°, full 137 levels
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[met_data]
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driver = "preprocessed_latlon"
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directory = "/temp1/atmos_transport/era5_spectral_catrine"
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dt = 900 # advection sub-step [s]
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# --- Initial conditions ---
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# CO2 and SF6 from LSCE inversions (1 Dec 2021 00:00 UTC)
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# fossil_co2 and rn222 start from zero (no IC entry needed)
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[initial_conditions]
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co2.file = "~/data/AtmosTransport/catrine/InitialConditions/startCO2_202112010000.nc"
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co2.variable = "CO2"
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sf6.file = "~/data/AtmosTransport/catrine/InitialConditions/startSF6_202112010000.nc"
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sf6.variable = "SF6"
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# --- Tracers ---
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[tracers.co2]
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emission = "lmdz_co2"
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dir = "~/data/AtmosTransport/catrine/Emissions/LMDZ_fluxes"
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species = "co2"
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flux_var = "flux_apos"
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start_date = "2021-12-01"
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end_date = "2021-12-31"
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[tracers.fossil_co2]
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emission = "gridfed"
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dir = "~/data/AtmosTransport/catrine/Emissions/gridfed"
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species = "fossil_co2"
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year = 2021
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[tracers.sf6]
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emission = "edgar_sf6"
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file = "~/data/AtmosTransport/catrine/Emissions/edgar_v8/v8.0_FT2022_GHG_SF6_2022_TOTALS_emi.nc"
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noaa_growth_file = "~/data/AtmosTransport/catrine/Emissions/sf6_gr_gl.txt"
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year = 2022
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scale_year = 2022
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[tracers.rn222]
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emission = "zhang_rn222"
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dir = "~/data/AtmosTransport/catrine/Emissions/ZHANG_Rn222/"
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chemistry = "decay"
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half_life = 330350.4 # 3.8235 days in seconds
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# --- Chemistry (222Rn radioactive decay) ---
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[chemistry]
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type = "composite"
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# --- Advection ---
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[advection]
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scheme = "ppm"
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ppm_order = 7
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# --- Convection ---
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# TODO: Tiedtke requires CMFMC in met data. Need to merge ERA5 CMFMC
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# into the preprocessed mass flux files or use a separate surface driver.
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#[convection]
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#type = "tiedtke"
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# --- Diffusion ---
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# TODO: PBL diffusion requires surface fields (PBLH, SSHF, T2M, U10, V10)
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# merged into the preprocessed files via merge_era5_surface_to_massflux.jl.
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#[diffusion]
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#type = "pbl"
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#beta_h = 15.0
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#Kz_bg = 0.1
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#Kz_min = 0.01
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#Kz_max = 500.0
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# --- Output (3-hourly, full 3D + column mass) ---
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[output]
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filename = "~/data/AtmosTransport/catrine/output/era5_spectral_dec2021/catrine_era5_spectral.bin"
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interval = 10800 # 3 hours
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[output.fields]
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co2_3d = {type = "full_3d", species = "co2"}
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fossil_co2_3d = {type = "full_3d", species = "fossil_co2"}
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sf6_3d = {type = "full_3d", species = "sf6"}
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rn222_3d = {type = "full_3d", species = "rn222"}
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co2_column_mass = {type = "column_mass", species = "co2"}
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fco2_column_mass = {type = "column_mass", species = "fossil_co2"}
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sf6_column_mass = {type = "column_mass", species = "sf6"}
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rn222_column_mass = {type = "column_mass", species = "rn222"}
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surface_pressure = "surface_pressure"
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[buffering]
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strategy = "double"

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