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Fix finite element deformation models and non-linear solvers

This MR does the following:

  • Fixes internal force calculation for both semi-implicit and full implicit Newton iteration
  • Fixes initialization of linear and StVK material models
  • Adds a modified conjugate gradient solver to handle fixed boundary conditions
  • Enables damping if provided in the config files
  • Enforcing code guidelines and other clean up in the related files

These fixes concludes the refactoring and bug fixes for physics module. Once these changes are merged, one should be able to create any material model with choice of semi-implicit and full implicit Newton solvers while applying Dirichlet boundary conditions. In other words, all the vega functionality (barring reduced order models) can be reproduced in iMSTK.

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