Following tutorial directions produces broken .vol file

Issue #12 resolved
Robert Welch created an issue

To reproduce, simply follow the instructions in the tutorial, using tetgen instead of netgen. Tetgen will issue the following error:

PLC Error:  A segment and a facet intersect at point (118.263,111.252,193.039).
  Segment: [226,227] #-1 (-1)
  Facet:   [2,259,236] #-1
A self-intersection was detected. Program stopped.
Hint: use -d option to detect all self-intersections.

Running the program with the -d option does produce a .vol file, but warns that 74 pairs of faces are intersecting, and will crash voltoffea at the next step

ACTION = 'voltoffea' => Using command 'python /localhome/py12rw/Software/LocalInstall/usr/local/lib/python2.7/FFEA_initialise/FFEA_convert_from_volume/FFEA_convert_from_volumetric_mesh.py --mesh emd_5043_10ang.vol -density 1.5e3 -shear_visc 1e-3 -bulk_visc 1e-3 -shear_mod 5.5e8 -bulk_mod 2.2e9 -dielec 1.0 -make_script'

Loading FFEA node file...
Loading FFEA topology file...
Loading FFEA surface file...
Error. This topology cannot be paired with this surface.
Loading FFEA surface file...
    File '' not found. Returning empty object...
Loading FFEA material file...
    File '' not found. Returning empty object...
Loading FFEA pin file...
    File '' not found.
Traceback (most recent call last):
  File "/localhome/py12rw/Software/LocalInstall/usr/local/lib/python2.7/FFEA_initialise/FFEA_convert_from_volume/FFEA_convert_from_volumetric_mesh.py", line 123, in <module>
    vdw = FFEA_vdw.FFEA_vdw()
TypeError: __init__() takes exactly 2 arguments (1 given)

I spent part of this morning installing Netgen and found that the .vol file generated by tetgen segfaults netgen. However, loading the .stl file into netgen and using netgen does not result in a problem. If you can reproduce this problem then I would reccomend removing references to tetgen from the documentation, otherwise flagging up the issue in the documentation and letting users know how it's solved.

This is still not an ideal solution, because netgen is a pain in the ass to install (it needed well in excess of 500mb of development libraries installed, and the instructions and error messages did not give a good description of which ones it actually needed - the only way to install it is trial and error). I'm not sure if it will ever install on my workstation because it has a problem with the 64-bit version of the OpenGL Mesa libraries (I think?).

I've attached the non-broken .stl file and the broken .vol file.

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