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Parallelization of one loop of Law2_ScGeom_CapillaryPhys_Capillarity (see http://www.mail-archive.com/yade-dev@lists.launchpad.net/msg11238.html) and some comments

fix previous commit for case (fusionDetection && hertz model) in capillary law (re-initiate bodiesMenisciiList at first real contact) and add some comments

Removal of parallel loops in capillary Law2: needs maybe more verification, and improvements for fusion detection

Sign convention change for fCap, to be consistent with global framework. Plus other minor changes. As discussed in http://www.mail-archive.com/yade-dev@lists.launchpad.net/msg10868.html and http://www.mail-archive.com/yade-dev@lists.launchpad.net/msg10877.html

Parallelization of interaction loops in Law2_..._Capillarity (which is in fact not a LawFunctor handled by InteractionLoop). Moreover adopting the FOREACH iterator for the non-parallel flavour.

Considering simulations of a dense sample with 10000 bodies, executions of capillary Law2 took :
- before change : ~ 1700 s / 100 000 executions, whatever j option (j4 or j1 tested)
- after change : 620 s / 100 000 executions with j4 (only one run tested)

So:
- Law2_ScGeom_CapillaryPhys_Capillarity is now parallelized (thanks to InteractionLoop example...)
- approx *3 speedup is reached from j1 to j4 (better benchmark could maybe have been done)

Many years we had a symlink in build-dir "yade" which
points to a source dir. It was neccessary for scons build
system, which is not the case at the moment. All headers
must be included directly without "yade/" prefix, e.g.:

<core/Scene.hpp>
<pkg/common/Sphere.hpp>

Do not redeclare cundallInteractionPhysics and mindlinInteractionPhysics in local scopes, as they should be global. Fixes crash LP:966186.

Improvements in Law2_ScGeom_CapillaryPhys_Capillarity.cpp (included isBroken flag and updated checkFusion)

Merge the "collide" branch to trunk (branch history at https://code.launchpad.net/~bruno-chareyre/yade/collide2)

Summary:
- the stride logic is improved by using displacements instead of velocities. Reference position and sweepLength are added to bounds.
- the sweepLength of each body is updated in collider::action() according to collider's targetInterv, so that ideally all bodies leave their bounds at the same iteration (more or less the same idea as in the old velocityBin but with per-body logic)
- a number of optimizations in the collider and interaction dispatcher. Namely, the handling of virtual interactions is a lot faster, allowing a larger number of them for the optimal verletDist.
- timings reported at https://yade-dem.org/wiki/Colliders_performace (please add your reports there), roughly x3 speedup vs. bzr2999 in triaxial simulations
- A new ZECollider is introduced, using CGAL's dD intersection algorithm. It is relatively slow and therefore not recommended, but the code is very short and it may be worth a try when parallel CGAL is released.
- Added references to some CGAL packages and a few fixes in references.

- remove the if(!b) test in a few important places (proof of concept + don't waste time doing the same test twice)

- small fix in the theoretical background

- Documentation of the capillary law (warn users on distanceFactor and neverErase flags, as in http://www.mail-archive.com/yade-dev@lists.launchpad.net/msg07391.html.

Law2_ScGeom_CapillaryPhys_Capillarity can now be used with Ip2_FrictMat_FrictMat_MindlinCapillaryPhys for hertz model

- adapt TSC and TCE to new non-dynamic behaviour (more changes and cleaning planned)
- remove prevNormal and frictionAngle from FrictPhys
- Add temporary FrictPhysTransitory for compatibility of old laws
- Rename Ip2_2xCohFrictMat_CohFrictPhys for names consistency, as suggested by Janek

1. Simplify InteractionContainer, move interactions inside bodies (NOT useful for getting all interactions of a body)
2. Advance with cmake a little bit (nothing functional yet)
3. Remove YADE_REQUIRE_FEATURE, use plain #ifdefs instead (empty files will be compiled, oh well)
4. Remove a few files that were apparently not compiled for a very long time.

2. Change the directory where to install headers to not include yade version

1. Add LawTester class for prescribing displacements on interactions precisely, see scripts/test/law-test.py
2. plot now displays the last point as a bullet 
3. Rename Interaction{Geometry,Physics} to I{Geom,Phys}; rename related classes as well (functors etc)
4. Rename Interaction::interaction{Geometry,Physics} to Interaction::{geom,phys}
5. Add Vector3.normalized() to the eigen wrapper
6. Add framework for arbitrary rendering hooks (GLDrawExtra) run from OpenGLRenderer at the end of the rendering routine (not yet fully tested)

2. change attribute specification adding and additional attribute flags (read-only from python, not saved, should call postLoad after changing value from python)
3. Macros cleanup in Serializable
4. Support clang for compilation (more than 2x faster) https://yade-dem.org/wiki/Compilation_with_LLVM/clang
(documentation not yet update to reflect those changes fully, sorry)

Scene::currentIteration->Scene::iter
Scene::getSimulationTime()->Scene::time
Scene::getComputation...Time()->Scene::getComputationTime()
Scene::stopAtIteration->Scene::stopAtIter 
etc.
2. Fix bug with per-class compilation (thanks to Sega for reporting)

2. Assign Body.bounded in py/utils.py funcs (in prep for making BoundDispatcher 1d)

- Update documentation of some classes, reformat a little, and fix (again) some email adresses.