SedTrace

A Julia package to generate and run models of marine sediment diagenesis.

Documentation	Build Status

Installation

Download and install Julia at https://julialang.org/downloads. Julia version should be 1.7 or above to use SedTrace. SedTrace is not registered with the Julia package manager. Install it directly from the GitHub repository. From the Julia terminal (aka the REPL), type ] to enter the package management mode and run

pkg> add https://github.com/JianghuiDu/SedTrace.jl.git

This will also install all the dependency packages. I also suggest installing the MKL package if you want to accelerate model simulation (at the moment this may not work on macOS with Apple silicon chips).

I suggest using Julia for Visual Studio Code as the language editor. Check the link to see how to install and configure the Julia language extension in Visual Studio Code. After installation, make sure you tell the path of Julia executable to Visual Studio Code. To do so, open Visual Studio Code, go to Settings and search for Julia: Executable Path. The path should look like C:/Users/username/AppData/Local/Programs/julia-1.9.2/bin/julia.exe on Windows, or /Applications/Julia-1.9.app/Contents/Resources/julia/bin/julia on macOS, if you have chosen the default settings when installing Julia.

SedTrace has been tested on Windows, Linux and macOS (X86 only). It has not been tested on Cygwin or other virtual machines.

First example

Now you can use the pre-included examples to see how SedTrace works. Go to the directory where Julia packages are installed. Normally this should be /users/username/.julia/packages/SedTrace. Copy the sub-directory /SedTrace/examples to a directory of your own choice (/mydirector/examples), otherwise you won't be able to execute the examples. Make sure you don't modify anything in the /.julia directory.

Now use Visual Studio Code to open the directory containing the example that you want to check, for example, /mydirectory/examples/SimpleFe. Before generating the model, remove all the pre-generated files, including the .jl files except main.SimpleFe.jl, the .xlsx files except model_config.SimpleFe.xlxs file, and anything inside the /SimpleFe/plots sub-directory (if there is one). Those files were pre-generated by the package creator and you will be able to generate them again later. If you don't remove them you will not be able to overwrite them during code generation because of ownership issues.

Now open main.SimpleFe.jl, this is where you call SedTrace to generate code and run model simulations based on the inputs from model_config.SimpleFe.xlxs. Execute the code in the script line by line. Model code and output will be generated and saved in the /mydirectory/examples/SimpleFe directory (i.e., the same ones you just deleted).

For more information, see Documentation below.

Documentation

• STABLE — documentation of the most recent version.

Project Status

The paper describing this package is published on Geoscientific Model Development.

The released versions with citable doi links are available at the Zenodo repository.

Funding information

This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 891489. This work was supported by an ETH Zurich Postdoctoral Fellowship 19-2 FEL-32.