Aquatic biogeochemistry components for the PALEOtoolkit biogeochemical model framework.
The PALEOaqchem package implements biogeochemistry components that provide:
- representation of organic matter phases (as discrete reactivity fractions or as a reactive-continuum model) and remineralization by oxygen, nitrogen, manganese, iron, sulphur and disproportionation to methane.
- generic equilibrium, kinetic, and precipitation-dissolution reactions, which can be configured into reaction networks using the PALEO YAML configuration file.
- pre-packaged reactions to simplify implementation of marine carbonate chemistry and a subset of secondary redox reactions, including support for carbon and sulphur isotope systems.
It can be used in two main ways:
- to construct arbitrary aqueous biogeochemical models, including equilibrium, kinetic and precipitation-dissolution reactions for a configurable set of solute and solid-phase species.
- to construct more-or-less standard ocean or sediment biogeochemical models (with commonly used carbonate chemistry, primary and secondary redox reactions) out of predefined components.
The PALEOaqchem Reactions are available to the PALEOtoolkit framework when the registered PALEOaqchem package is installed and loaded:
julia> Pkg.add("PALEOaqchem") # install PALEOaqchem in currently active Julia environment
julia> import PALEOaqchem
Documentation is available online at https://paleotoolkit.github.io/PALEOaqchem.jl/
The PALEOtutorials repository includes a minimal model of the marine carbonate system implementated using PALEOaqchem generic chemistry.
The PALEOocean and PALEOsediment include examples of water column and sediment biogeochemistry.
The PALEOcarbchem carbonate chemistry equilibrium code originally based on Matlab CO2SYS v1.1 (van Heuven et al 2011, Lewis and Wallace 1998) and refactored for speed and extensibility.
Please see https://github.com/jamesorr/CO2SYS-MATLAB for the current version of CO2SYS-MATLAB, history, and full citation information.
The license for CO2SYS-MATLAB is included as file LICENSE_CO2SYS.md.