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Fix typos, add hyperlink to exe docs
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Co-authored-by: SarahAlidoost <[email protected]>
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BSchilperoort and SarahAlidoost authored Jan 3, 2024
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8 changes: 4 additions & 4 deletions docs/STEMMUS_SCOPE_BMI.md
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Expand Up @@ -13,15 +13,15 @@ When starting the executable, a run-mode can be specified. The following command
./STEMMUS_SCOPE "/home/path/to/config/file.txt" full
```

(Where `./STEMMUS_SCOPE` is the path to the executable. For more info see)
(Where `./STEMMUS_SCOPE` is the path to the executable. For more info see [documentation](../run_model_on_snellius/exe/README.md))

To start BMI mode, pass anything (e.g. an empty string "") as config file, and use `bmi` to start the model in BMI-mode:

```sh
./STEMMUS_SCOPE "" bmi
```

The model will respond with `Finished command. Select run mode: `. Now you can initialize the mode:
The model will respond with `Finished command. Select run mode: `. Now you can initialize the model:

```
Finished command. Select run mode: interactive "/home/path/to/config/file.txt"
Expand All @@ -35,8 +35,8 @@ Finished model initialization

Now you can use the commands `update` to advance the model by one timestep, and `finalize` to finalize the model.

### Updating exposed variables
### Exposing variables to BMI interface

The variables which are exposed to the Python BMI are defined in `STEMMUS_SCOPE_exe.m`.
To add more variables, update the `bmiVarNames` variable.
After this, you will need to update the BMI in [PyStemmusScope](https://github.com/EcoExtreML/STEMMUS_SCOPE_Processing/) so it can make use of these exposed variables.
After this, you will need to change the BMI codes in [PyStemmusScope](https://github.com/EcoExtreML/STEMMUS_SCOPE_Processing/) so it can make use of these exposed variables.

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