- 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>

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>

In FEMForceModel and StVKForceModel

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

Its name should be "CLFEM" and not "Corotational" to return
the correct type.

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

MeshIO (input, output, convert) for (volumetric) meshes in  .msh and .veg file format

![liverScreenShot2](/uploads/f396f4cc1570700aa9c90e835dd932d2/liverScreenShot2.png)New addition(s):
1. Added `MSHMeshIO` to read a mesh in .msh file format, and instantiate `imstk::VolumetricMesh` 
2. Added a method in `VegaMeshIO` to convert `imstk::VolumetricMesh` to `vega::VolumetricMesh`
3. Added a method in `VegaMeshIO` to write `imstk::Mesh` in .veg file format.
4. Added an example `testMshandVegaIO` in `Sandbox` to test these implementations (Attached is the output with this merge request).

See merge request !112

Improve render clock

`VTKInteractorStyle::CreateRepeatingTimer` would call
`VTKInteractorStyle::OnTimer` then sleep for the period
given in ms after calling `OnTimer` again. This isn't
adapted for rendering at a uniform frame rate, because
the time spent within the `OnTimer` function is not
taken into account in the sleep time.

By using `OneShotTimer`, we can manipulate when to
render the next frame: in (period - time spent) ms
if the time spent in `OnTimer` is smaller than the period
time, or right away (period of 0 ms) if the time spent
is over the target period (late frame).

An interface is added in the `VTKInteractorStyle`,
wrapped in the `VTKViewer`, to set the target frame rate.

Also added a commit to use `DATA_DIR` defined in the Sandbox example to easily change the data directory for each user on their own machine. Any local change to the `DATA_DIR` value should not be committed in the future.

See merge request !114

vtkInteractor::CreateRepeatingTimer would call
vtkInteractorStyle::OnTimer then sleep for the period
given in ms after calling OnTimer again. This isn't
adapted for rendering at a regular framerate, because
the time taken withing the OnTimer function is not
taken into account in the sleep time.

By using OneShotTimer, we can manipulate when to
render the next frame: in (period - time spent) ms
if the time spent in OnTimer is smaller than the period
time, or right away (period of 0 ms) if the time spent
is over the target period (late frame).

An interface is added in the VTKInteractorStyle,
wrapped in the VTKViewer, to set the target framerate.

Default value is 0ms to render as fast as possible. See:
: http://gaming.stackexchange.com/questions/221423/is-there-any-reason-to-limit-my-fps

Current default to ".". Needs to be modified for each
user on their on system (do not commit changes to this line).

BUG: Fixes wrong default value for pbd tolerance

Fixes wrong default value for pbd tolerance in PbdConstraint class

See merge request !110

Fixes wrong default value for pbd tolerance in PbdConstraint class

improve module timing

@NickMilef I quickly made this based on the way you handle frequency in the logger you created. Could you give me your thoughts on what strategy would be the best between those two?


* Current implementation: using `sleep_for`
  - **pros:** will stop the thread and will not frenetically keep looping in the while loop. (does that actually matter?)
  - **cons:** might sleep too long?

* Offered implementation: this commit
  - **pros:** as soon as `elapsed > loopDelay`, run module (won't "sleep" too long)
  - **cons:** keeps rolling in the while loop. Could that be an issue?

See merge request !108

- wrapper for loopdelay
- use double precision for loopdelay and frequency to
maintain correct values for set/get after divisions by 1000

Vtk no copy

#### ENH: Align Eigen matrix allocator for stl vectors - 0fa25818
Define `StdVectorOfxxx` for all eigen matrix structures defined in `imstkMath.h` which are used in iMSTK within a `std::vector`.
See http://eigen.tuxfamily.org/dox-devel/group__TopicStlContainers.html
Requires to update SCCD to commit 645508940 which also updates its vec3 structure.


#### ENH: Use no copy data array to map vertices to VTK - 400c0987 
Update VTK mesh render delegates (SurfaceMesh, LineMesh, TetrahedralMesh) to directly map the vertices from the eigen and stl structures in iMSTK, and get rid of `VTKMappedVertexArray`. This should considerably reduce overhead calls and improve performances thanks to the no-copy operation. See http://www.vtk.org/Wiki/VTK/Tutorials/DataArrays

Add back normals generation in the `SurfaceMesh` render delegate, and update testPbdCloth to add another row of points to the cloth (made it easier to debug the initial vertex positions), as well as adding lights to better visualize correct normals.

See merge request !107

Update VTK mesh render delegates (SurfaceMesh,
LineMesh, TetrahedralMesh) to directly map the vertices
from the eigen and stl structures in iMSTK, and get rid
of VTKMappedVertexArray. This should considerably reduce
overhead calls and improve performances thanks to the
no-copy operation.

See http://www.vtk.org/Wiki/VTK/Tutorials/DataArrays

Add back normals generationin the SurfaceMesh render delegate.

Also updates testPbdCloth to add another row of points
to the cloth (made it easier to debug the initial
vertex positions), as well as add lights to better
debug normals.

define "StdVectorOfxxx" for all eigen matrix structures
used in iMSTK within std::vector.

See http://eigen.tuxfamily.org/dox-devel/group__TopicStlContainers.html

Requires to update SCCD to commit 645508940
which also updates its vec3 structure.

VTK renaming

Renamed everything that uses VTK. Some of these classes will need an interface eventually, but that can be done as the Vulkan renderer gets built so that we can abstract the important common characteristics.

See merge request !106

Refactor physics module

**Summary**:  
*  Modifies the Dynamical objects realted classes to generalize for any problem state. This allows for rigid bodies, deformable bodies using FEM and pbd under one dynamicalObject base class.
* Adds common interface for pbd solver and FE solvers to allow simpler code in SceneManager
* Refactors all the PBD classes for bugs, style, warnings and efficiency.
* Misc. modifications including rearranging folders, example codes, renaming classes and clearing some warnings.

See merge request !103

Use HTTPS for external dependencies

As noted by @NickMilef in the developers mailing list, `googletest` git repository was using the SSH protocol instead of HTTPS, which requires users to add an ssh_key on github.com.

We switch all those external projects to HTTPS protocol, but keep the ones hosted by ourselves on gitlab.kitware.com in SSH since we might be contributing back to those during development

See merge request !105

1. Enforces style to move one line code to one line
2. Move multiple lines to .cpp
3. make epsilon part of the class
4. SolvePositionConstraint in the base class is made pure virtual

googletest git repository was using the SSH protocol
instead of HTTPS, which requires users to add an
ssh_key on github.com.

We switch all those external projects to HTTPS protocol,
but keep the ones hosted by ourselves on gitlab.kitware.com
in SSH since we might be contributing back to those
during development.

Rename NewtonMethod to NewtonSolver and the files accordingly

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

Removes problemState base class
Initialize methods now return bool

Make PbdConstraint abstract base class with solvePositionConstraint to be implemted in base class

1. Template parameter in the DunamicalObject and DynamicalModel is named to StateType
2. Rename paramerts in the initialization of the pbd constraints
3. Remove unnecessary APIs in scene object hierarchy

Renames pbd constraint classes.
Renames the selfUpdate to updateGeometries

Add testing framework

Add testing with google test framework in the superbuild.

See merge request !104