Sediment components and standalone examples for the PALEOtoolkit biogeochemical framework.
The PALEOsediment package provides an implementation of sediment transport (PALEO reaction ReactionSedimentTransport) for n x 1D sediment columns.
This can then be combined with biogeochemistry implemented by the PALEOaqchem and PALEOboxes packages and solvers from the PALEOmodel package to create either standalone sediment models or coupled water-column - sediment configurations.
The implementation of 1D sediment reaction-transport is standard (eg Van Cappellen & Wang (1996), Boudreau (1996)) and uses the PALEOtoolkit framework to provide:
- extensible configuration for biogeochemical species and reactions defined in a .yaml configuration file
- standalone and coupled sediment configurations
- fully implicit numerical solution using a combination of sparse automatic differentation to generate Jacobians, and efficient solvers including pseudo-transient-continuation for steady-state solutions.
Documentation is available online at https://paleotoolkit.github.io/PALEOsediment.jl/
The PALEOsediment Reactions are available to PALEOtoolkit when the registered PALEOsediment package is installed and loaded:
julia> Pkg.add("PALEOsediment") # install PALEOsediment package in the currently active Julia environment
julia> import PALEOsediment
To install and run the PALEOsediment examples, clone this github repository to local directory PALEOsediment and run the examples from the Julia REPL.
Quickstart assuming a recent Julia installation: from a linux bash prompt or a Windows terminal,
$ git clone https://github.com/PALEOtoolkit/PALEOsediment.jl.git PALEOsediment
Start julia and navigate to the PALEOsediment/examples folder, and run setup.jl to configure the PALEOsediment/examples
Julia environment to use the local (downloaded) version of the PALEOsediment package:
julia> cd("PALEOsediment/examples")
julia> include("setup.jl") # use the local version of PALEOsediment packages to allow local modifications
Examples are in subfolders of PALEOsediment/examples and the use the PALEOsediment/examples Julia environment.
See Installation and getting started in the PALEOtutorials repository for more details including installation and configuration of Julia.