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.

1. Seperate files for separate Pbd colliison constrain classes
2. Preincrement lop variables
3. Refactor collision constraint classes: remove raw pointers, using auto, style corrections
4. Move pbd constraints to seperate folder within constraint folder
5. Clears warnings in Physics module

convert tabs to 4 spaces

Adds basic plot generator scripts for vectors for Matlab and Matlibplot

Style enforcement and add comments over the entire code

Trigger compilation error on macOSx

Adds comments in scene class and format changes

Move linear solver tolerance to base class. The tolerance is automatically set to machine precision.
Add API to query if a solver is iterative or not.

sreekanth.arikatla@kitware.com authored 8 years ago and Sreekanth Arikatla committed 8 years ago

Adds sparse LU and Cholesky factorization based direct dense matrix solver for linear system of equations

Add classes for nonlinear and linear systems

1.  Add kinematic state class which stores the state of the body at a particular time
2. Make member variable naming consistent in imstkDeformableBodyModel.h

1. Merge CollidingSceneObject into SceneObject. SceneObject is now optionally viewable
and collideable but not movable. SceneObject class has all the functionality of a static object.
2. Rename imstkLigUtility to imstkLogger
3. Rename virtualCouplingObject to virtualToolObject
4. Consistency with brackets for imstk namespace
5. Move enums that  into imstk scope unless if the enum has no meaning outside the class

Adds stopwatch class which measures wallclock time.
Adds cpu timer utility
Fixes bug in timeIntegrator class

in Module, sleep for a duration of loopdelay minus
the time elapsed while running once in the loop.

Did not support colors in standard output,
use std::cout and std::cerr instead.

In release, the empty while loop were stuck. Making
m_status volatile would fix the issue, but here we
are dealing with a variable handled by multiple threads,
so making it atomic makes the most sense.

- Add imstk::Mat4f and imstk::Mat4d
- Add imstk::MAX_D and imstk::MIN_D
- Remove 'Map' from GeometryMap functions
- Reorder functions in a consistent manner
- Correct reference returns
- remove unnecessary ismtk:: due to namespace
- rename vertex/triangle/hexadron/tetrahedron composed
methods with their plural form when needed
- follow style rule with return type on a line and
function name on the following one during declaration
- move print() to geometryMap base class and use it in
override functions
- use for each c++11 architecture when possible
- correct wrong iteration in HexahedralMesh::getVolume
- place conditions for return at the top of functions
- declare WeightsArray in TetrahedralMesh instead of
TetraTriangleMap
- Rename findEclosingTetrahedra to findEnclosingTetrahedra
- add override on virtual functions in child classes
- correct test function name in Sandbox

Also merge Utility within Core.

Light still a WIP

Changes the name of math constants to be consistent

Changes names of math constants

Adds geometry map base class and isometriMap

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

- Remove PThreads on Linux
- Correct CMake output directories in case of single
configuration type (not MSVC)

Conflict existed within VTK.

Use config based on https://gist.github.com/mkroman/1372117

Also remove headers in cmake files

Adding project name (iMSTK)