This repository contains the supplementary information for the paper Garduno et. al. (2023). Climate shapes the oxygenation of Earth's atmosphere across the Great Oxidation Event. EPSL.

Reproduce our results

Install PhotochemPy

To reproduce our results, you first need to install the version of PhotochemPy that we use. We made minor changes to the original code to run our simulations. Clone this version with the following command:

git clone -b experimental_daniel https://github.com/DanyIvan/PhotochemPy

Then follow the PhotochemPy installation instructions:

• Create a conda environment with all dependencies:

conda create -n photochempy -c conda-forge python numpy scipy scikit-build

• Navigate to the root directory with a terminal, activate your new conda environment, then install with setup.py:

conda activate photochempy
python setup.py install

Install extra dependencies

Some additional packages specified in the file requirements.txt are needed to run our python scripts. You can install these packages in the photochempy conda environment with:

conda install --file requirements.txt

Run scripts

The reproduce_results/ folder contains the python scripts to reproduce our result. The reproduce_results/templates/ folder contains the PhotochemPy templates we use. The reproduce_results/input_data/ folder contains the oxygen fluxes, temperature profiles, and relative humidity profiles we use.

To reproduce our results, activate the photochempy conda environment generated in the previous steps. Then navigate to the reproduce_results/ folder and run the increase_O2_flux.py or the decrease_CO_flux.py scripts. You can specify the surface temperature, surface relative humidity, and methane to oxygen flux ratio for each run from the terminal. For example:

python increase_O2_flux.py --fratio 0.3 --rh 0.6 --temp 270

In this case, you will reproduce our results for the case in which the oxygen flux increases, with a methane to oxygen flux ratio of 0.3, a surface temperature of 270, and a tropospheric relative humidity of 0.6. The model output from this run will be saved in the model_output/ folder.

Remake our plots

The plots/ folder contains a python script make_plots.py to remake all the plots we show in the manuscript and some other plots. The plots/model_output/ folder contains all the model output necessary to make these plots.

To remake our plots, navigate to the plots/ folder, activate the photochempy conda environment generated in the previous steps, and run:

python make_plots.py

Boundary Conditions

The folder boundary_conditions/ contains the species boundary conditions machine-readable files that we use in the species.dat files. We keep these boundary conditions constant for all species across all runs, except for methane, oxygen, and carbon monoxide. We specify each run's surface flux boundary conditions in CSV files for methane, oxygen, and carbon monoxide. The fluxes units are $molecules/cm^{2}/s$.

Reaction rates

The reaction_rates/ folder contains the machine-readable reaction rates file that we use. We use the reaction rates of the PhotochemPy Archean2Proterozoic templates. You can also view these rates here:

https://github.com/DanyIvan/PhotochemPy/blob/main/input/templates/Archean2Proterozoic/reactions.rx