Fibers do not prestretch

[carme-hp]

As noted by @Lukuas31415, we observe that when we prestretch the muscle, the fibers location is not updated. Hence we start the contraction simulation with a mismatch between the mechanics and the fibers mesh.

The reason why this happens is because the prestretch simulation doesn't know anything of an existing fiber mesh.

[carme-hp]

I have pushed a solution to this problem in branch bug-prestretch. Basically I have changed the solver we use during prestretch to the one used during contraction. I changed the settings so that the mechanics solver is not dynamic and a single time-step is solved. The FastMonodomainSolver should do a single "dummy" time step as I deactivated the firing.
@Lukuas31415 Please check that it works as expected.

In blue, prestretch at time 0. In gray, contraction at time 0.

To reproduce go to bug-prestretch. You can run it using
./muscle_contraction ../settings_contraction_with_prestretch.py incompressible_mooney_rivlin 10

[carme-hp]

This is now outdated. See #11 .