Currently, if all the damping coefficients are zero,
the initialization is stopped in between which is not
intended.

Modifications are made to continue initialization of
the rest of the FE mode if all damping coefficients are zero.

Adds option to start the simulation manager with
the simulation either in RUNNING or PAUSED mode
and the viewer in DEBUG or SIMULATION mode.

Other changes:
1. enforce const correctness
2. add comments to the member functions
3. add overload function to retrieve scene manager by scene object
4. rename 'current' scene to 'active' scene

Co-Authored-by: Alexis Girault <alexis.girault@kitware.com>

Adds deformable-rigid penalty collision handling. Unifies all the
penalty collision handling classes into one.

Co-Authored-by: Alexis Girault <alexis.girault@kitware.com>

- default LinearSolver tolerance = 1.0e-4
- default IterativeLinearSolver maxIterations = 100
- remove those default values in ConjugateGradient constructor
as they are initialized in the parent constructors
- consistent use of this pointer

Written-by: Sreekanth Arikatla <sreekanth.arikatla@kitware.com>

Written-by: Sreekanth Arikatla <sreekanth.arikatla@kitware.com>

Makes the update of LHS and RHS updateType dependent. For now only deltaVelocity type update is supported.
Clean up and renaming

Written-by: Sreekanth Arikatla <sreekanth.arikatla@kitware.com>

1. Fixs the fully implicit nonlinear Newton solver
2. Completes implementation of Newton solver that can be either semi implicit (SI) or fully implicit (FI)
3. Adds options to set the solver to either SI or FI
4. Default is SI
5. Now the lamda function computing the internal forces needs to know if it is SI or FI
6. Prints warning if the FI Newton solver does not converge within max iterations set

Written-by: Sreekanth Arikatla <sreekanth.arikatla@kitware.com>

Get rid of m_tmpStorage

Written-by: Sreekanth Arikatla <sreekanth.arikatla@kitware.com>

- use m_vegaPhysicsMesh within initializeDampingMatrix
- consider all damping coefficients

Written-by: Sreekanth Arikatla <sreekanth.arikatla@kitware.com>

Written-by: Sreekanth Arikatla <sreekanth.arikatla@kitware.com>

- Invert parameters order in getInternalForce
- Only multiply by dT at the end

Written-by: Sreekanth Arikatla <sreekanth.arikatla@kitware.com>

1. Make solve in solverBase class pure virtual
2. Rename DeformableObject to FEMDeformableObject and files accordingly
3. Efficient way to do checks in FEMDeformableObject::initialize() and pbdObject::initialize()
4. Add variable to address which map to apply for the visual geometry

1. Adds self update to the scene objects. The objects now can update themselves instead of explicit way of updating in the sceneManager class.
2. Clear warnings in PbdVolumeeConstraint, DeformableModel, PbdModel, NewtonMethod classes
3. Clean the main() in the sandbox example

Place all dynamicalModel related into separate folder.
SceneElements now has just the tangable and intangable objects.

1. Dynamical object classes are templated with the problem state
   (Deformable bodies use vectorized state. Pbd objects use pbdState.)
2. Pbd state is refactored to have only the current state
3. Rename deformableBodyState to VectorizedState which can be used in
   future by all the finite element and vectorized formulations
4. Remove unnecessary mappnig for the cloth example
5. Adds queries to sceneobject for visible, collidable and physics
6. Optional allocation of internal states for pbdState
7. Removes the specialized calls in the sceneManager::runModule.
   This will be further cleaned.
8. Correct ifdef in imstkNewmarkBeta.h

Rename DeformableBodyState to VectorizedState
Make the ifDefs consistent in style
Place and correct the headers in some files. This has to be done for all files at some point.

Clean the pbdState to just have body states.
All the physics related parameters, time step size and time
integration routines are moved to pbdModel

Style enforcement and add comments over the entire code

Adds updateFunction to the NL system. Some style cleanup.

Vega filename was hardcoded in DeformableBodyModel.

In VegaMeshReader, keep a pointer to the vega mesh
within the volumetricMesh class, and use it when
initialising the deformable body model.

Move force models implementation to ccp files

Adjust camera position and plane scale

Adds solver, maps to scene manager pipeline.
Enables different types of state updates.
Improves the example.

Adds unknown vector to nonlinear system.
Adds simplified nonlinear solver for testing

Adds connection b/n vega and deformable model tangent stiffness matrics

Clears runtime error that shows failure to create eigen vectors in problemState.
Small formatting changws.

Clears linker errors in solvers and force model.
Adds comments in the time integrator classes.

Clears compilation and linker errors in solver and TI modules.
Moved the code in TI to cpp.

Clears compilation errors in force model. Implements getForceAndMatrix in force models.
Adds get type in dynamical model. Adds get and set dynamic model in dynamic object.
Removes raw pointers in nonLinearSystem class.

Adds penalty based mesh to rigid contact handling. Adds contact force vector to deformable body model

Adds driver code to test deformable models.
Clears a bunch of compiler errors in force model module.

Add initialization of Stiffness, damping, mass matrices and vectors.
Add updates for Stiffness, damping, mass matrices and vectors.
Adds update body states given the solution vector.
Adds loading initial states
Builds effective stiffness matrix

Implements API for deformable Model: Initialization, read configuration, returning LHS and RHS of the system