Broken examples

[lewisfish]

Hi MCDC team,

I've found the following examples won't run or plot correctly:

• fixed_source/pulsed_sphere gives the following error:

  mat_iron = mcdc.material(
             ^^^^^^^^^^^^^^
  File "/home/JOSS/MCDC/mcdc/input_.py", line 326, in material
  with h5py.File(dir_name + "/" + nuc_name + ".h5", "r") as f:
                 ~~~~~~~~~^~~~~
  TypeError: unsupported operand type(s) for +: 'NoneType' and 'str'

• fixed_source/inf_pin_ce has the same error as above.
• fixed_source/slab_ce has the same issue as above. This example could also benefit from more instructions (what is build_xml.py purpose?) and a mention that openmc is a dependency.
• fixed_source/slab_reed_iqmc is missing a plt.show() or savefig from the process.py file.
• eigenvalue/2d_c5g7 fails to plot with the following error. I think this is due to the "C" argument to pcolormesh only having 1 dimension

  File "/home/JOSS/MCDC/examples/eigenvalue/2d_c5g7/process.py", line 95, in <module>
  plt.pcolormesh(X, Y, phi_thermal_sd, shading="nearest")
  File "/home/anaconda3/envs/mcdc-env/lib/python3.11/site-packages/matplotlib/pyplot.py", line 3493, in pcolormesh
  __ret = gca().pcolormesh(
          ^^^^^^^^^^^^^^^^^
  File "/home/anaconda3/envs/mcdc-env/lib/python3.11/site-packages/matplotlib/__init__.py", line 1465, in inner
  return func(ax, *map(sanitize_sequence, args), **kwargs)
         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/anaconda3/envs/mcdc-env/lib/python3.11/site-packages/matplotlib/axes/_axes.py", line 6292, in pcolormesh
  X, Y, C, shading = self._pcolorargs('pcolormesh', *args,
                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/anaconda3/envs/mcdc-env/lib/python3.11/site-packages/matplotlib/axes/_axes.py", line 5815, in _pcolorargs
  nrows, ncols = C.shape[:2]
  ^^^^^^^^^^^^
  ValueError: not enough values to unpack (expected 2, got 1)

• eigenvalue/slab_kornreich_iqmc is missing a plt.show() or savefig from the process.py file.
• eigenvalue/smrg7 fails with ERROR: Particle census bank is full
• c5g7/3d/TDX the default particle number does not resolve to the reference solution.

https://github.com/openjournals/joss-reviews/issues/6415

[jpmorgan98]

The issue with the following examples:

• fixed_source/pulsed_sphere
• fixed_source/inf_pin_ce
• fixed_source/slab_ce

I believe is because the continuous energy data library is not configured. (@ilhamv please confirm). If this is the case due to legal requirements we cannot publish or distribute that data for use outside of our center. I will add a runtime error that will stop the simulation in this case and add notes to the example files themselves. See our docs. Kinda a weird place for an open source software to be but it is what it is