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.<experiment>/ ├── 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 [<1 MB] │ ├── fields_rokgem_2d.nc 2-D weathering fields (NetCDF) │ ├── rokgem_series_*.res Weathering time series (ASCII) │ └── RokGeM_DATA_GLOBAL_*.res Global weathering snapshots ├── embm/ Energy-moisture balance atmosphere (EMBM) restart files ├── goldstein/ Ocean circulation (GOLDSTEIN) restart files │ └── rst.* Restart fields (streamfunction, T, S, density, overturning) ├── goldsteinseaice/ Sea-ice model restart files ├── atchem/ Atmospheric chemistry restart file ├── data_BIOGEM/ FORTRAN namelist for BioGeM ├── data_ECOGEM/ FORTRAN namelist for EcoGeM ├── data_SEDGEM/ FORTRAN namelist for SedGeM ├── data_ROKGEM/ FORTRAN namelist for RokGeM ├── data_EMBM/ FORTRAN namelist for EMBM ├── data_GEM/ FORTRAN namelist for GEM framework ├── data_GEMLITE/ FORTRAN namelist for GEMLite ├── data_ATCHEM/ FORTRAN namelist for atmospheric chemistry ├── data_GOLD/ FORTRAN namelist for GOLDSTEIN ocean ├── data_goldSIC/ FORTRAN namelist for sea-ice model └── data_genie FORTRAN namelist for the GENIE framework Key Output Files Used in the Analysis The analysis scripts primarily read three NetCDF files per experiment, plus selected time series: NetCDF timeslice files (spatial fields at saved time steps) File Variables used Description ecogem/fields_ecogem_2d.nc Individual PFT biomass (PFTs 1-112), eco2D_Plankton_Chl_Total, eco2D_Plankton_C_Total, eco2D_Uptake_Fluxes_C, eco2D_Size_Mean Plankton ecosystem: biomass per functional type, chlorophyll, carbon, net primary production, mean cell size biogem/fields_biogem_2d.nc ocn_sur_temp, ocn_sur_PO4, ocn_sur_TDFe, phys_MLD, phys_fxsw, bio_fexport_POC, bio_fpart_POC, misc_pH, carb_sur_pHsws, carb_ohm_cal, carb_ohm_arg, phys_cost Surface ocean fields: temperature, nutrients, mixed layer depth, PAR, POC export, pH, carbonate saturation biogem/fields_biogem_3d.nc ocn_DIC_13C, carb_pHsws, ocn_PO4, ocn_O2, phys_u, phys_v, misc_rho, phys_opsi, phys_opsia, phys_opsip 3-D ocean fields: carbon isotopes, pH, nutrients, oxygen, currents, overturning circulation Time series files (ASCII, global means over time) File Description biogem/biogem_series_ocn_temp.res Global mean ocean temperature biogem/biogem_series_ocn_PO4.res Global mean phosphate biogem/biogem_series_misc_insol.res Global mean insolation biogem/biogem_series_misc_surpH.res Global mean surface pH biogem/biogem_series_fexport_POC.res Global POC export flux biogem/biogem_series_ocn_DIC_13C.res Global mean DIC delta-13C biogem/biogem_series_ocn_O2.res Global mean dissolved oxygen biogem/biogem_series_ocn_ALK.res Global mean alkalinity Ecosystem trait files File Description ecogem/Plankton_params.txt Plankton functional type parameters (cell volume, carbon quota coefficients, trophic strategy) Scripts to plot the model outputs The analysis scripts (Jupyter notebooks) and auxiliary data are available in the associated code repository: https://github.com/ruiying-ocean/kpg_selectivity. Here is just for description and might be outdated. Main manuscript figures Script Figure Experiments required plot_timeseries.ipynb Environmental and biological time series (Fig. 1) main, Danian, noextinction, size_effect, solar, CO2 plot_diversity_timeseries.ipynb Plankton richness (Fig. 2) main plot_extinction_maps.ipynb Geographic extinction maps (Fig. 3) main, solar, CO2, forcePAR, forceSST plot_lat_selectivity.ipynb Latitudinal selectivity patterns (Fig. 4) main, solar, CO2, forcePAR, forceSST Supplementary/extended figures Script Content Experiments required plot_allometric_traits.ipynb Allometric trait relationships (Fig. S1) None (theoretical curves only) plot_cretaceous_climate.ipynb Pre-impact (Maastrichtian) climate baseline SPIN plot_maps.ipynb Environmental change maps (SST, pH, nutrients, PAR) main plot_Danian.ipynb Post-extinction recovery dynamics SPIN, main, Danian plot_photoacclimation.ipynb Chlorophyll:carbon ratio (photoacclimation) main plot_sensitivity_experiment.ipynb Individual extinction driver analysis main, solar, CO2, forcePAR, forceSST plot_threshold_sensitivity.ipynb Extinction threshold sensitivity main plot_alternative_extinction_threshold.ipynb Robustness of extinction criteria main plot_foram_distribution.ipynb Foraminifera biogeography main plot_mld_validation.ipynb Mixed layer depth model validation main plot_modern_validation.ipynb Modern ocean circulation validation main