save soil water stress factor and leaf water potential in outputs

[Crystal-szj]

Description

The soil water stress factor sfactorTot and leaf water potential psiLeafTot are saved in the output.mat.

• We only save additional variables rather than change physical processes. Thus, no references are needed for this issue.

relates to EcoExtreML/STEMMUS_SCOPE_Processing#102

Checklist

• Add a reference to related issues.
• @mentions of the person or team responsible for reviewing proposed changes.
• This pull request has a descriptive title.
• Code is written according to the guidelines.
• The checks by MISS_HIT style checker and linter, below the pull request, are successful (green).
• Documentation is available.
• Add changes to the changelog file under section Unreleased.
• Model runs successfully.
• Ask a meinatainer to re-generate exe file if matlab codes are changed. About how to create an exe file, see exe readme.

[Crystal-szj]

Hi @SarahAlidoost and @BSchilperoort, the soil water stress factor (sfactor) and leaf water potential (psiLeaf) are important indicators for drought effect, and should be saved into the output file for further analysis.
Here, the two variables are passed from ebal.m to STEMMUS-SCOPE.m, and the time series are assigned to variables with 'Tot' suffix (i.e. sfactorTot, and psiLeafTot).

Let me know if there were more efficient way for that!

[SarahAlidoost]

@Crystal-szj thanks for the fixes. Please see my comments and let me know if something is unclear. In addition, can you test if the model results are still the same? you can do this with notebook compare_git_branch_results.ipynb. Moreover, if you have snellius account, can you re-generate exe file at the end? Thanks.

[Crystal-szj]

Thanks for your suggestions. The soil water stress and leaf water potential are saved in two structures as WaterStressFactor.soil and WaterPotential.leaf in the code, and are saved as binary files every time step. The reason for using structures instead of variables is because the recent coupling of plant hydraulics module to the current version will output plant water stress factor, as well as root and stem water potentials.

[SarahAlidoost]

Thanks for your suggestions. The soil water stress and leaf water potential are saved in two structures as WaterStressFactor.soil and WaterPotential.leaf in the code, and are saved as binary files every time step. The reason for using structures instead of variables is because the recent coupling of plant hydraulics module to the current version will output plant water stress factor, as well as root and stem water potentials.

Is your pull request ready again for review? I run the model in your branch. The output folder does not include the csv files of WaterStressFactor and WaterPotential. Can you please check it?

[Crystal-szj]

Thanks for your suggestions. The soil water stress and leaf water potential are saved in two structures as WaterStressFactor.soil and WaterPotential.leaf in the code, and are saved as binary files every time step. The reason for using structures instead of variables is because the recent coupling of plant hydraulics module to the current version will output plant water stress factor, as well as root and stem water potentials.

Is your pull request ready again for review? I run the model in your branch. The output folder does not include the csv files of WaterStressFactor and WaterPotential. Can you please check it?

Hi @SarahAlidoost, I have just checked the repo, and the model output on my side and found that the output file name are "waterPotential.csv" and "waterStressFactor.csv" (i.e. lowercase for 'water'), Could you help to check if the file were there? cheers!

[SarahAlidoost]

@Crystal-szj well done! great that the exe file is added too 👍 . Thanks. I will merge this PR.