PALEOcopse.jl

Julia version of the COPSE (Carbon, Oxygen, Phosphorus, Sulphur and Evolution) biogeochemical model.

The model predicts the coupled histories and controls on atmospheric O2, CO2 and ocean composition over Phanerozoic time, and is described in the following publications:

Bergman, N. M., Lenton, T. M., & Watson, A. J. (2004). COPSE: A new model of biogeochemical cycling over Phanerozoic time. American Journal of Science, 304(5), 397–437. https://doi.org/10.2475/ajs.304.5.397

Mills, B., Daines, S. J., & Lenton, T. M. (2014). Changing tectonic controls on the long-term carbon cycle from Mesozoic to present. Geochemistry, Geophysics, Geosystems, 15(12), 4866–4884. https://doi.org/10.1002/2014GC005530

Lenton, T. M., Dahl, T. W., Daines, S. J., Mills, B. J. W., Ozaki, K., Saltzman, M. R., & Porada, P. (2016). Earliest land plants created modern levels of atmospheric oxygen. Proceedings of the National Academy of Sciences, 113(35), 9704–9709. https://doi.org/10.1073/pnas.1604787113

Lenton, T. M., Daines, S.J., Mills, B. J. W. (2018). COPSE reloaded: An improved model of biogeochemical cycling over Phanerozoic time. Earth Science Reviews, 178, 1-28. https://10.1016/j.earscirev.2017.12.004

Julia implementation

The Julia version of COPSE uses the PALEOboxes coupler and PALEOmodel solvers.

The COPSE model is componentized into land, atmosphere, ocean, oceanfloor and sedcrust Domains with explicit transfer of biogeochemical fluxes between them, allowing the PALEO Reactions for each Domain to be reused to create a hierarchy of coupled models eg including a spatially-resolved ocean component.

The implementation is mathematically equivalent to the Matlab version and is tested against archived model output.

Installation and running the model

Installation

NB: requires Julia 1.9 or later. To check the Julia version:

julia> versioninfo()

Clone this github repository to local directory PALEOcopse: from a linux bash prompt or a Windows terminal,

$ git clone https://github.com/PALEOtoolkit/PALEOcopse.jl.git PALEOcopse

Start julia and navigate to the PALEOcopse/examples folder, and run setup.jl to configure the PALEOcopse/examples Julia environment to use the local (downloaded) version of the PALEOcopse package:

julia> cd("PALEOcopse/examples")
julia> include("setup.jl") # use the local version of PALEOcopse packages to allow local modifications

Running the model

Start julia and navigate to the PALEOcopse folder, then:

julia> cd("examples/COPSE")
julia> import Pkg
julia> Pkg.activate("..") # use the PALEOcopse/examples environment

julia> include("COPSE_reloaded_reloaded.jl")

Evaluation data

Datasets are not part of the public release but are available on request from the authors.

Using PALEOcopse Reactions from other models

The PALEO Reactions comprising the COPSE model are available when the registered PALEOcopse package is loaded (without downloading the repository), ie

julia> Pkg.add("PALEOcopse")
julia> import PALEOcopse