DOI: 10.5281/zenodo.17742290
title: cGENIE model outputs for KPG study

description: 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