Can't run StrongTrapPlot.ipynb

[RemDelaporteMathurin]

EDIT: I'm running in the graph_scripts_and_results folder

I'm trying to run the strong trap case.

First I run StrongTrap.ipynb and it runs without issues and produces:

When running StrongTrapPlot.ipynb, this is what I obtain in the second code cell:

Then I have this error in the third code cell:

---------------------------------------------------------------------------
FileNotFoundError                         Traceback (most recent call last)
Cell In[3], [line 1](vscode-notebook-cell:?execution_count=3&line=1)
----> [1](vscode-notebook-cell:?execution_count=3&line=1) a = np.loadtxt('Flux25EvTrap2.txt')
      [2](vscode-notebook-cell:?execution_count=3&line=2) b = np.loadtxt('Strong_flux_festim.txt')
      [5](vscode-notebook-cell:?execution_count=3&line=5) strong_breakthrough = l**2 * n_t * rhow / (2 * c0m * N_Tis * D)

File ~/miniconda3/envs/titans-tt-env/lib/python3.11/site-packages/numpy/lib/npyio.py:1356, in loadtxt(fname, dtype, comments, delimiter, converters, skiprows, usecols, unpack, ndmin, encoding, max_rows, quotechar, like)
   [1353](https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/remidm/Titans_TT_codecomparison/graph_scripts_and_results/Strong_Trap/~/miniconda3/envs/titans-tt-env/lib/python3.11/site-packages/numpy/lib/npyio.py:1353) if isinstance(delimiter, bytes):
   [1354](https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/remidm/Titans_TT_codecomparison/graph_scripts_and_results/Strong_Trap/~/miniconda3/envs/titans-tt-env/lib/python3.11/site-packages/numpy/lib/npyio.py:1354)     delimiter = delimiter.decode('latin1')
-> [1356](https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/remidm/Titans_TT_codecomparison/graph_scripts_and_results/Strong_Trap/~/miniconda3/envs/titans-tt-env/lib/python3.11/site-packages/numpy/lib/npyio.py:1356) arr = _read(fname, dtype=dtype, comment=comment, delimiter=delimiter,
   [1357](https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/remidm/Titans_TT_codecomparison/graph_scripts_and_results/Strong_Trap/~/miniconda3/envs/titans-tt-env/lib/python3.11/site-packages/numpy/lib/npyio.py:1357)             converters=converters, skiplines=skiprows, usecols=usecols,
   [1358](https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/remidm/Titans_TT_codecomparison/graph_scripts_and_results/Strong_Trap/~/miniconda3/envs/titans-tt-env/lib/python3.11/site-packages/numpy/lib/npyio.py:1358)             unpack=unpack, ndmin=ndmin, encoding=encoding,
   [1359](https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/remidm/Titans_TT_codecomparison/graph_scripts_and_results/Strong_Trap/~/miniconda3/envs/titans-tt-env/lib/python3.11/site-packages/numpy/lib/npyio.py:1359)             max_rows=max_rows, quote=quotechar)
   [1361](https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/remidm/Titans_TT_codecomparison/graph_scripts_and_results/Strong_Trap/~/miniconda3/envs/titans-tt-env/lib/python3.11/site-packages/numpy/lib/npyio.py:1361) return arr

File ~/miniconda3/envs/titans-tt-env/lib/python3.11/site-packages/numpy/lib/npyio.py:975, in _read(fname, delimiter, comment, quote, imaginary_unit, usecols, skiplines, max_rows, converters, ndmin, unpack, dtype, encoding)
    [973](https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/remidm/Titans_TT_codecomparison/graph_scripts_and_results/Strong_Trap/~/miniconda3/envs/titans-tt-env/lib/python3.11/site-packages/numpy/lib/npyio.py:973)     fname = os.fspath(fname)
    [974](https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/remidm/Titans_TT_codecomparison/graph_scripts_and_results/Strong_Trap/~/miniconda3/envs/titans-tt-env/lib/python3.11/site-packages/numpy/lib/npyio.py:974) if isinstance(fname, str):
--> [975](https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/remidm/Titans_TT_codecomparison/graph_scripts_and_results/Strong_Trap/~/miniconda3/envs/titans-tt-env/lib/python3.11/site-packages/numpy/lib/npyio.py:975)     fh = np.lib._datasource.open(fname, 'rt', encoding=encoding)
    [976](https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/remidm/Titans_TT_codecomparison/graph_scripts_and_results/Strong_Trap/~/miniconda3/envs/titans-tt-env/lib/python3.11/site-packages/numpy/lib/npyio.py:976)     if encoding is None:
    [977](https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/remidm/Titans_TT_codecomparison/graph_scripts_and_results/Strong_Trap/~/miniconda3/envs/titans-tt-env/lib/python3.11/site-packages/numpy/lib/npyio.py:977)         encoding = getattr(fh, 'encoding', 'latin1')

File ~/miniconda3/envs/titans-tt-env/lib/python3.11/site-packages/numpy/lib/_datasource.py:193, in open(path, mode, destpath, encoding, newline)
    [156](https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/remidm/Titans_TT_codecomparison/graph_scripts_and_results/Strong_Trap/~/miniconda3/envs/titans-tt-env/lib/python3.11/site-packages/numpy/lib/_datasource.py:156) """
    [157](https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/remidm/Titans_TT_codecomparison/graph_scripts_and_results/Strong_Trap/~/miniconda3/envs/titans-tt-env/lib/python3.11/site-packages/numpy/lib/_datasource.py:157) Open `path` with `mode` and return the file object.
    [158](https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/remidm/Titans_TT_codecomparison/graph_scripts_and_results/Strong_Trap/~/miniconda3/envs/titans-tt-env/lib/python3.11/site-packages/numpy/lib/_datasource.py:158) 
   (...)
    [189](https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/remidm/Titans_TT_codecomparison/graph_scripts_and_results/Strong_Trap/~/miniconda3/envs/titans-tt-env/lib/python3.11/site-packages/numpy/lib/_datasource.py:189) 
    [190](https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/remidm/Titans_TT_codecomparison/graph_scripts_and_results/Strong_Trap/~/miniconda3/envs/titans-tt-env/lib/python3.11/site-packages/numpy/lib/_datasource.py:190) """
    [192](https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/remidm/Titans_TT_codecomparison/graph_scripts_and_results/Strong_Trap/~/miniconda3/envs/titans-tt-env/lib/python3.11/site-packages/numpy/lib/_datasource.py:192) ds = DataSource(destpath)
--> [193](https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/remidm/Titans_TT_codecomparison/graph_scripts_and_results/Strong_Trap/~/miniconda3/envs/titans-tt-env/lib/python3.11/site-packages/numpy/lib/_datasource.py:193) return ds.open(path, mode, encoding=encoding, newline=newline)

File ~/miniconda3/envs/titans-tt-env/lib/python3.11/site-packages/numpy/lib/_datasource.py:533, in DataSource.open(self, path, mode, encoding, newline)
    [530](https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/remidm/Titans_TT_codecomparison/graph_scripts_and_results/Strong_Trap/~/miniconda3/envs/titans-tt-env/lib/python3.11/site-packages/numpy/lib/_datasource.py:530)     return _file_openers[ext](found, mode=mode,
    [531](https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/remidm/Titans_TT_codecomparison/graph_scripts_and_results/Strong_Trap/~/miniconda3/envs/titans-tt-env/lib/python3.11/site-packages/numpy/lib/_datasource.py:531)                               encoding=encoding, newline=newline)
    [532](https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/remidm/Titans_TT_codecomparison/graph_scripts_and_results/Strong_Trap/~/miniconda3/envs/titans-tt-env/lib/python3.11/site-packages/numpy/lib/_datasource.py:532) else:
--> [533](https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/remidm/Titans_TT_codecomparison/graph_scripts_and_results/Strong_Trap/~/miniconda3/envs/titans-tt-env/lib/python3.11/site-packages/numpy/lib/_datasource.py:533)     raise FileNotFoundError(f"{path} not found.")

FileNotFoundError: Flux25EvTrap2.txt not found.

This is because there is no file named Flux25EvTrap2.txt in the repo.

I ran this with this environment:

name: titans-tt-env
channels:
  - conda-forge
  - defaults
dependencies:
  - fenics
  - matplotlib
  - ipykernel
  - pandas
  - scipy
  - numpy<1.25
  - pip
  - pip:
      - festim==1.1.1

created with

conda env create -f environment.yml

[gabriele-ferrero]

I want to take some more time to check this issue,to reconstruct the file history (how they are produced) and names (for clarity). Together with this issue I will fix it with the typos.

[gabriele-ferrero]

check #20

[gabriele-ferrero]

Medium trap maximum timestep has been updated (otherwise there is too much error related to it if compared with other codes, there is some room to improvement there) MHIMS name was wrong causing loading issues and Typos as well