cGENIE model outputs for KPG study

cGENIE Model Output for “Darkness and body size shaped End-Cretaceous marine extinction patterns” This archive contains the cGENIE Earth System Model output used to produce all figures and results in the manuscript. The analysis scripts (Jupyter notebooks) and auxiliary data are available in the associated code repository: https://github.com/ruiying-ocean/kpg_selectivity. Quick Start Clone the code repository and install dependencies (see the repository README). Place these experiment directories under model/ in the repository root so that scripts can find them at paths like ../model/muffin.u067bc.PO4Fe.main/. Open the relevant Jupyter notebook in code/ (see the figure-to-script mapping below) and run it. Experiment Descriptions Directory Description Role muffin.u067bc.PO4Fe.SPIN 10 kyr spinup with late Maastrichtian boundary conditions Baseline steady state; restart for all transient experiments muffin.u067bc.PO4Fe.main K-Pg transient experiment (100 yr): combined solar dimming + CO2 forcing + dust/iron deposition Primary experiment used by most figures muffin.u067bc.PO4Fe.Danian Extended K-Pg experiment (5 kyr continuation of main) Post-extinction ocean biogeochemistry recovery muffin.u067bc.PO4Fe.solar Solar forcing only (no CO2 increase) Sensitivity: isolating the effect of impact winter darkness muffin.u067bc.PO4Fe.CO2 CO2 forcing only (no solar dimming) Sensitivity: isolating the effect of CO2-driven warming/acidification muffin.u067bc.PO4Fe.forcePAR Main experiment with forced (prescribed Late-Cretaceous) PAR for plankton Sensitivity: decoupling light from temperature effects muffin.u067bc.PO4Fe.forceSST Main experiment with forced (prescribed Late-Cretaceous) SST for plankton Sensitivity: decoupling temperature from light effects muffin.u067bc.PO4Fe.noextinction Main experiment without the extinction mechanism Sensitivity: show the impacts of extinction on primary productivitiy muffin.u067bc.PO4Fe.size_effect Main experiment without body-size-dependent POC/DOC export ratio Sensitivity: testing the role of size collapse on carbon export Directory Structure Within Each Experiment Each experiment directory contains output from the coupled cGENIE sub-models: muffin.u067bc.PO4Fe. / ├── archive/ Model configuration files (.config, definition.xml, makefile, job script) ├── biogem/ Ocean biogeochemistry (BioGeM) output [largest component, ~228 MB] │ ├── fields_biogem_2d.nc 2-D spatial fields (NetCDF timeslices) │ ├── fields_biogem_3d.nc 3-D spatial fields (NetCDF timeslices) │ ├── biogem_series_*.res Time series (ASCII) │ ├── biogem_year_*_diag_*.res Annual diagnostic snapshots (ASCII) │ └── _restart.nc Restart file ├── ecogem/ Plankton ecosystem (EcoGeM) output [~51 MB] │ ├── fields_ecogem_2d.nc 2-D ecosystem fields (NetCDF timeslices) │ ├── Plankton_params.txt Plankton trait parameters │ ├── Plankton_params_nohead.dat Trait parameters (headerless, for parsing) │ └── Ecogem_properties.dat Ecosystem configuration properties ├── sedgem/ Sediment (SedGeM) output [~8 MB] │ ├── fields_sedgem_2d.nc 2-D sediment fields (NetCDF) │ └── seddiag_misc_*.res Sediment diagnostics (ASCII) ├── rokgem/ Rock weathering (RokGeM) output [