The purpose of the example provided in section 4 of the manuscript is to show how to use Chempath in a 1D photochemical model, not to apply Chempath to a model in which all species match the observations. We disagree that the evaluation of Chempath is not convincing when it results in questionable values for CH3OO. The CH3OO high number density results from an incomplete representation of its chemistry in the reaction system we used, and is not a result artificially produced by Chempath. Chempath is a tool for evaluating photochemical models. The fact that our code was able to show the lack of important reactions for CH3O2 chemistry in the photochem model ModernEarth reaction system demonstrates that Chempath fulfills its purpose: to evaluate and understand the results and photochemical models. We will update the manuscript to discuss the inconsistency of CH3O2 in the photochem model and warn the reader to take our results with caution since the model we used is not intended to be a perfect representation of the modern Earth's atmosphere.

If there is a concern that our code is not working well or producing artificial results, this can be easily discarded using our input files and the reviewer’s implementation of the PAP algorithm. For example, the reviewer could use their algorithm implementation to corroborate that they get results similar to ours in the simple example we used to explain how the algorithm works. The Chempath code repository also includes an example of how to apply Chempath to a simple photochemical box model (https://github.com/DanyIvan/chempath/blob/main/examples/box_model_pathways/box_model_pathways_example.ipynb). These results could also be corroborated with the reviewer's implementation of the algorithm. Finally, our results for our the photochem model run can also be corroborated with the existing version of the PAP algorithm with the input files we used to obtain these results. These input files are available here: https://github.com/DanyIvan/chempath/tree/main/examples/photochem_modern_earth/chempath_input. 

We are preparing another publication in which we will apply Chempath to the model output of Garduno et. al. 2023 and  2024. If the editor thinks changing our example is absolutely necessary, we can try to use the output from other publications that used photochem or a similar model. However, this task is not straightforward since we would likely have to rerun the simulation to get the complete model output we need to run Chempath. Alternatively, we can modify our example to analyze only the stratosphere in the photochem model, where the reaction system we used seems to be fine, or we can try to update the reaction system to make our simulation more realistic. We are also happy to use our code in model output provided by the reviewer or the editor. Finally, we note that we used the same chemical mechanism Wogan et. al (2023) used, but we have different boundary conditions in the model.

References:

Garduno Ruiz, D., Goldblatt, C., and Ahm, A.-S.: Climate shapes the oxygenation of Earth’s atmosphere across the Great Oxidation Event, Earth and Planetary Science Letters, 607, 118 071, https://doi.org/10.1016/j.epsl.2023.118071, 2023.

Garduno Ruiz, D., Goldblatt, C., and Ahm, A.: Climate Variability Leads to Multiple Oxygenation Episodes Across the Great Oxidation Event, Geophysical Research Letters, 51, https://doi.org/10.1029/2023gl106694, 2024.

Wogan, N. F., Catling, D. C., Zahnle, K. J., and Lupu, R.: Origin-of-life Molecules in the Atmosphere after Big Impacts on the Early Earth, The Planetary Science Journal, 4, 169, https://doi.org/10.3847/psj/aced83, 2023.