Soil biogeochemical testbed

Code Repository

Created by Will Wieder, Melannie Hartman, Ben Sulman, Emily Kyker-Snowman, Brooke Eastman, & Ying-Ping Wang:

Updated Feb 10, 2023 Aug. 29, 2018

User’s manual and technical documentation for the biogeochemical testbed in published in:

• Wieder et al. Global Change Biology, 2018.
• Wieder et al. Geophysical Reserach Letters, 2019 The biogeochemical testbed code base used in these simulations is included (commit 26b4630).
• Eastman et al. Biogeoscciences 2023
• Wieder et al. JAMES, Submitted 2023

Feb 2023 updates include: 

• Representation of coupled C-N biogeochemistry for MIMICS, 
• Representation of root exudation, currently set to zero for all simulation
• Switch to using input data from CLM5-SP with GSWP3 forcing
• This code base was used in single point simulations at the Fernow Experimental Forest by Eastman et al (2023) and global simulations by Wieder et al. (2023).

Aug 2018 updates include:

• Updates to the code base address issues documented here and include modifications to CORPSE parameterization and the addition of a soil moisture scalar to MIMICS. Updates to the Example_Grid also simulate RCP4.5 and 8.5 through 2100 for each model.

Licence

The MIT License (MIT)

Copyright (c) 2017 Will Wieder, Melannie Hartman, Ben Sulman, & Ying-Ping Wang:

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

To get started using this repo:

Fork this repository to your personal repo (fork button in the upper right)

Then, from the local directory you want to work from you can use the following commands

This will clone your remote repository (now called origin) to your local directory

git clone https://github.com/`user`/biogeochem_testbed_1.1.git

cd biogeochem_testbed_1.1

Then you can link to the main, remote repo & call this upstream

git remote add upstream https://github.com/wwieder/biogeochem_testbed_1.1.git

git remote -v

Let's create a branch

git checkout --no-track -b Testbed_CN origin/Testbed_CN

• or maybe this would be better not sure it works?

git checkout -b --track Testbed_CN upstream/Testbed_CN

It's a good idea to periodically look for changes to the upstream master (or branch)

git status upstream/master

git pull upstream master

git merge

If there are conflicts you can needed you can rebase your repo

git rebase upstream/master

Then you can bring in files you may want to use, create new directoryies, etc

mkdir POINT

mv file_x POINT/.

At some point you may want to add & commit new filese & directories to your local repo

git status (are there any files to track or add?)

git add POINT

git status (now the directory point is staged for commit)

git commit (this will open up a text file where you can add comments

You can get a nice visual on the status of your work

git log --decorate --oneline --graph

Create and check out new branch, best to start from the latest upstream/master

This example makes a branch from remote (not local) master or branch

git checkout --no-track -b mybranch upstream/master

git fetch --all

Create a new branch has same name as remote branch & switch to it

git checkout --track upstream/Testbed_CN
git checkout Testbed_CN

To update your local branch to the remote repo just try

git pull

to make a new branch within your own code...

This is a good idea if you're going to make code modifications!

git -b Testbed_CN_v2 Testbed_CN