Add new two-muscle case with prestretch only

[Lukuas31415]

Main changes of this PR

Issues that are addressed by this PR:

Features that have been added:

Additional information

Author's checklist

• I updated the documentation.
• I checked that everything compiles and runs as it should.

[carme-hp]

mechanics1_00000000.vtu is the same as prestretch1_0000001.vtu -> Hence I delete it (I think this duplicated output also appears in other examples)

[carme-hp]

I've started adding contraction.

So now in this case you can run

./muscle_contraction_with_prestretch ../settings_contraction_with_prestretch.py incompressible_mooney_rivlin 2

or
./muscle_prestretch ../settings_prestretch.py incompressible_mooney_rivlin 2

For some reason I still don't know, prestretch seems to only be applied to muscle 1.

Minor todos:

• fix number of output files during contraction (now there are way less fibers files than mechanics files)
• Change the names of bc in the prestretch only case to the ones I used for contraction (see ../settings_contraction_with_prestretch.py)

[carme-hp]

@Lukuas31415 can you check if the prestretch + contraction looks good now? I've visualized in red the muscle before prestretch and in blue the muscle after prestretch. The first output file from fibers and mechanics for contraction seem to match the geometry after prestretch

[Lukuas31415]

The prestretch looks good apart from the fact that there are 2 mechanics and 1 fiber file, but the first contraction fiber file is the prestretched one, so that looks very good. I couldn't find why the contraction mechanics is doing exactly 10 iterations per time step, and the fibers 1, as it should.
For me, both muscles are being prestretched, so that seems to work now as well.

[carme-hp]

I think that now the output frequency was set to 1, which might not be good if the two solvers use different timestep sizes. Can you compare to what was the output frequency set to in a single muscle case?

[Lukuas31415]

I have replaced the settings of the contraction part with the equivalent part of the ellipsoid contraction, and now everything works as intended. However, there are a lot of changes in the muscle contraction solver of which I don't know what they do, but it seems to work, so I left it in. Maybe you can check if this is fine this way?

[carme-hp]

Thank you, I decided to undo your last changes and push again with applying only the relevant changes at the lines. (Your commit included a lot of indentation fixes, which made it hard to find out the differences)

[carme-hp]

TO-DO:

• Check that it behaves as expected
• Modify readme to include separated instructions for prestretch only and prestretch + contraction
• Rename case, and change location if needed
• Go through issues and PR's and if they are obsolete, link them to this PR.

To do in a different PR (each, in this order)

• Connect the two muscles
• Make it possible to choose different forces for each muscle
• Add optimization file

[carme-hp]

@Lukuas31415 says it doesn't contract. Is this indeed true? Was it contracting with commit 459e5e4?
If yes,

• find the difference

If not:

• slot connectors names, do they have to be different in the prestretch than in the contraction
• prestretch looks first at muscle 2 and then at 1, while contraction does it in the opposite order

[Lukuas31415]

I found the difference. Apart from a lot of indentation differences and differences in the setup of the Dynamic Hyperelasticity Solver, the main differences were the slot names. It works now as intended, and I think this is ready to be merged.

[carme-hp]

Looks great!