PALEOaqchem.jl

Aquatic biogeochemistry components for the PALEO biogeochemical model framework.

NB: work-in-progress - this repo contains an initial minimal example only to test infrastructure.

Using PALEOaqchem Reactions from other models

The PALEOaqchem Reactions are available to the PALEO framework when the registered PALEOaqchem package is loaded (without downloading the repository), ie

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

PALEOaqchem.PALEOcarbchem notes

This submodule provides a carbonate chemistry equilibrium solver 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 the file LICENSE_CO2SYS.md.

Differences from CO2SYS-MATLAB

• Refactored for speed, to allow use in numerical models.
• Based on an older (2011) version 1.1 of CO2SYS Matlab
• Uses CO2SYS Matlab equilibrium constants, with a reimplemented equilibrium calculation. NB: Although constants can be calculated for different pH scales, TAlk or pH calculations require constants to be on free pH scale.
• H2S and NH3 added from Hofman etal (2010)

References

Lewis, E. and Wallace, D. W. R. (1998) Program Developed for CO2 System Calculations, ORNL/CDIAC-105, Carbon Dioxide Inf. Anal. Cent., Oak Ridge Natl. Lab., Oak Ridge, Tenn., 38 pp., https://salish-sea.pnnl.gov/media/ORNL-CDIAC-105.pdf

van Heuven, S., D. Pierrot, J.W.B. Rae, E. Lewis, and D.W.R. Wallace (2011) MATLAB Program Developed for CO2 System Calculations. ORNL/CDIAC-105b. Carbon Dioxide Information Analysis Center, Oak Ridge National Laboratory, U.S. Department of Energy, Oak Ridge, Tennessee. https://doi.org/10.3334/CDIAC/otg.CO2SYS_MATLAB_v1.1

Hofmann AF etal (2010) AquaEnv : An Aquatic Acid–Base Modelling Environment in R. Aquatic Geochemistry, https://doi.org/10.1007/s10498-009-9084-1