Fejl på kildeled rettet

.gitignore

@@ -2,6 +2,7 @@
 playground
 shared/BOUT-dev/
 plots*
+cached_data/*
 
 # Ignore log files
 *.log

ReadMe.md

@@ -1,5 +1,9 @@
 # North Simulation
-Numerical model for a magnetically confined plasma in the NORTH tokamak. Note: The bout++ model was developed at DTU Physics by the Plasma Physics and Fusion Energy group. We use [BOUT++](http://boutproject.github.io/) for numerical simulation.
+Numerical reduced fluid model of perpendicular dynamics a magnetically confined plasma in the NORTH tokamak. We use [BOUT++](http://boutproject.github.io/) for numerical simulation. Note: The bout++ model is an implementation of the ESEL equations, developed at DTU Physics by the Plasma Physics and Fusion Energy group.
+
+The results can be seen in the folder [presentation of main results](https://github.com/PPFE-Turbulence/north-simulation/tree/master/presentation%20of%20main%20results).
+
+To reproduce the main results of the data analysis, open and run the iPython Notebook `main_results.ipynb`. Note: It requires data from a simulation run. See the documentaion below on how to run simulations either on the Niflheim environment or (perhaps easier for a start) on your personal computer.
 
 ## Getting started
 ---------------------------------------------------------
@@ -15,7 +19,12 @@ cd ./north-simulation
 ```
 . ./install_bout_env_niflheim.sh north-simulation
 ```
-3. Navigate to the shared directory and clone and compile the Bout-dev git (make sure the path `~/north-simulation` equals the path to the repo directory):
+3. Install python-requirements to the python venv with pip:
+```
+. ~/local/venv/north-simulation/bin/activate
+pip install -r requirements.txt
+```
+4. Navigate to the shared directory and clone and compile the Bout-dev git (make sure the path `~/north-simulation` equals the path to the repo directory):
 ```
 module restore bout
 cd ~/north-simulation/shared
@@ -39,6 +48,52 @@ make
 ``` 
 ./north_full_ESEL
 ```
+**NOTE:** The command above starts simulations directly on the node, which is not recommended (but it's useful for verifying that the code will evens start running). Instead you should queue the simulations using slurm:
+
+### Niflheim: Slurm Commands
+I've included the script `./shared/NORTH/sbatch_north_full_ESEL.sh` which takes care of queuing simulations using SLURM. Here is how to do it:
+- Before running the sbatch script: Navigate to `shared/NORTH/`. In there, create a directory for output logs:
+```
+mkdir slurm_out
+```
+- Submit batch job (look at Slurm Batch job script in `shared/NORTH/` for how to write a sbatch file):
+```
+sbatch sbatch_north_full_ESEL.sh
+```
+- show your queue
+```
+squeue -u $USER
+```
+- Cancel all your jobs:
+```
+scancel -u $USER
+```
+- Cancel all pending jobs:
+```
+scancel -t PD
+```
+- Stop job gracefully (run file with `stopCheck=true` as is done in the slurm sbatch script), then add `BOUT.stop` file:
+```
+touch ./data/BOUT.stop
+```
+
+### Niflheim/VSCode: Trouble-Shooting
+**bash: fork: retry: No child processes**
+
+If VSCode causes a [fork bomb](https://stackoverflow.com/questions/47143093/linux-ssh-bash-fork-retry-no-child-processes) with the error message: `bash: fork: retry: No child processes`, simply open up a terminal and write
+```
+kill -9 -1
+```
+
+**Python Interpreter Problems**
+
+If the VSCode Python Extension won't recognize your Python Interpreter. Pressing cmd/ctrl + shift P with the following command names are useful:
+- `Python: Create Terminal`
+- `Python: Run Python File in Terminal`
+- `Python: Select Interpreter` > Enter Interpreter Path (e.g. `~/local/venv/north-simulation/bin/python`). If this doesn't work:
+- `Python: Clear Workspace Interpreter Settings`
+
+Alternatively, try downgrading the Python Extension by going to Extensions > Python (SSH - Installed, not Local - Installed) > click the down arrow next to the uninstall button and choose "Install another version" > 2022.18.2
 
 ---------------------------------------------------------
 ### Personal Computer: First time setup
@@ -126,7 +181,7 @@ conda activate north-simulation
 pip install -r requirements.txt
 ```
 
-Run the file `data_analysis.py` to reproduce the main results.
+To reproduce the main results of the data analysis, refer to the iPython Notebook `main_results.ipynb`.
 
 ## Usefull commands
 here are some usefull commands. If you're on your personal computer, I assume you have Docker running, started a Docker container and navigated to the north directory.
@@ -143,26 +198,4 @@ here are some usefull commands. If you're on your personal computer, I assume yo
 - Help on command line options
 ```
 ./north_full_ESEL -h
-```
-
-### Niflheim: Slurm Commands
-- Submit batch job (look at Slurm Batch job script in `shared/NORTH/` for how to write a sbatch file):
-```
-sbatch sbatch_north_full_ESEL.sh
-```
-- show your queue
-```
-squeue -u $USER
-```
-- Cancel all your jobs:
-```
-scancel -u $USER
-```
-- Cancel all pending jobs:
-```
-scancel -t PD
-```
-- Stop job gracefully (run file with `stopCheck=true` as is done in the slurm sbatch script), then add `BOUT.stop` file:
-```
-touch ./data/BOUT.stop
 ```