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This reverts commit e1a01d62.

This reverts commit 69985bb1.

- additional OPAL input option: AMR

Modified files:

modified:   src/AbstractObjects/OpalData.cpp
modified:   src/AbstractObjects/OpalData.h
modified:   src/Algorithms/AutophaseTracker.h
modified:   src/Algorithms/BeamBeam3D.cpp
modified:   src/Algorithms/BeamBeam3D.h
modified:   src/Algorithms/CavityAutophaser.cpp
modified:   src/Algorithms/MPSplitIntegrator.cpp
modified:   src/Algorithms/MPSplitIntegrator.h
modified:   src/Algorithms/NilTracker.h
modified:   src/Algorithms/ParallelCyclotronTracker.cpp
modified:   src/Algorithms/ParallelCyclotronTracker.h
modified:   src/Algorithms/ParallelTTracker.cpp
modified:   src/Algorithms/ParallelTTracker.h
modified:   src/Algorithms/ThickTracker.cpp
modified:   src/Algorithms/ThickTracker.h
modified:   src/Algorithms/bet/EnvelopeBunch.cpp
modified:   src/Algorithms/bet/EnvelopeBunch.h
modified:   src/BasicActions/Option.cpp
modified:   src/Classic/AbsBeamline/Collimator.cpp
modified:   src/Classic/AbsBeamline/Collimator.h
modified:   src/Classic/AbsBeamline/Component.cpp
modified:   src/Classic/AbsBeamline/Component.h
modified:   src/Classic/AbsBeamline/Integrator.h
modified:   src/Classic/AbsBeamline/Probe.cpp
modified:   src/Classic/AbsBeamline/Probe.h
modified:   src/Classic/AbsBeamline/Ring.cpp
modified:   src/Classic/AbsBeamline/Ring.h
modified:   src/Classic/AbsBeamline/Septum.cpp
modified:   src/Classic/AbsBeamline/Septum.h
modified:   src/Classic/AbsBeamline/Source.cpp
modified:   src/Classic/AbsBeamline/Stripper.cpp
modified:   src/Classic/AbsBeamline/Stripper.h
modified:   src/Classic/Algorithms/AmrPartBunch.cpp
modified:   src/Classic/Algorithms/AmrPartBunch.h
modified:   src/Classic/Algorithms/MapIntegrator.cpp
modified:   src/Classic/Algorithms/MapIntegrator.h
modified:   src/Classic/Algorithms/OrbitTracker.cpp
modified:   src/Classic/Algorithms/PBunchDefs.h
modified:   src/Classic/Algorithms/PartBunch.cpp
modified:   src/Classic/Algorithms/PartBunch.h
modified:   src/Classic/Algorithms/PartBunchBase.h
modified:   src/Classic/Algorithms/PartBunchBase.hpp
modified:   src/Classic/Algorithms/ThinTracker.cpp
modified:   src/Classic/Algorithms/ThinTracker.h
modified:   src/Classic/Algorithms/Tracker.cpp
modified:   src/Classic/Algorithms/Tracker.h
modified:   src/Classic/Solvers/CSRIGFWakeFunction.cpp
modified:   src/Classic/Solvers/CSRIGFWakeFunction.hh
modified:   src/Classic/Solvers/CSRWakeFunction.cpp
modified:   src/Classic/Solvers/CSRWakeFunction.hh
modified:   src/Classic/Solvers/CollimatorPhysics.cpp
modified:   src/Classic/Solvers/CollimatorPhysics.hh
modified:   src/Classic/Solvers/GreenWakeFunction.cpp
modified:   src/Classic/Solvers/GreenWakeFunction.hh
modified:   src/Classic/Solvers/SurfacePhysicsHandler.hh
modified:   src/Classic/Solvers/WakeFunction.hh
modified:   src/Classic/Utilities/Options.cpp
modified:   src/Classic/Utilities/Options.h
modified:   src/Distribution/Distribution.cpp
modified:   src/Distribution/Distribution.h
modified:   src/Expressions/Expressions.cpp
modified:   src/Solvers/AmrPoissonSolver.h
modified:   src/Solvers/FFTBoxPoissonSolver.h
modified:   src/Solvers/FFTPoissonSolver.h
modified:   src/Solvers/MGPoissonSolver.h
modified:   src/Solvers/P3MPoissonSolver.cpp
modified:   src/Solvers/P3MPoissonSolver.h
modified:   src/Solvers/PoissonSolver.h
modified:   src/Structure/BoundaryGeometry.cpp
modified:   src/Structure/BoundaryGeometry.h
modified:   src/Structure/DataSink.cpp
modified:   src/Structure/DataSink.h
modified:   src/Structure/FieldSolver.cpp
modified:   src/Structure/FieldSolver.h
modified:   src/Structure/H5PartWrapper.h
modified:   src/Structure/H5PartWrapperForPC.cpp
modified:   src/Structure/H5PartWrapperForPC.h
modified:   src/Structure/H5PartWrapperForPS.cpp
modified:   src/Structure/H5PartWrapperForPS.h
modified:   src/Structure/H5PartWrapperForPT.cpp
modified:   src/Structure/H5PartWrapperForPT.h
modified:   src/Track/Track.cpp
modified:   src/Track/Track.h
modified:   src/Track/TrackRun.cpp
modified:   src/Track/TrackSave.cpp
modified:   src/Track/TrackStart.cpp

modified:   BoundaryGeometry.cpp
modified:   BoundaryGeometry.h
modified:   DataSink.cpp
modified:   DataSink.h
modified:   FieldSolver.cpp
modified:   FieldSolver.h
modified:   H5PartWrapper.cpp
modified:   H5PartWrapper.h
modified:   H5PartWrapperForPC.cpp
modified:   H5PartWrapperForPC.h
modified:   H5PartWrapperForPS.cpp
modified:   H5PartWrapperForPS.h
modified:   H5PartWrapperForPT.cpp
modified:   H5PartWrapperForPT.h
modified:   PriEmissionPhysics.cpp
modified:   PriEmissionPhysics.h
modified:   SecondaryEmissionPhysics.cpp
modified:   SecondaryEmissionPhysics.h

ParallelTTracker. Particle-Matter interaction doesn't work either at the moment.

I hope that I didn't create too much of a mess when merging!

- pass Vector_t as reference not as value in several methods

- emitSecondaryFurmanPivi(): interface changed

- interface of emitSecondaryVaughan() changed

- getPoint(): assert testing vertex ID added

- doBGphysics() renamed to emitSecondaryNone(),
  emitSecondaryFurmanPivi() resp. emitSecondaryVaughan()
- cleanup

- remove 'using namespace' from header files
- remove 'using std::string' and 'using std::abs' from header files

For reason see:
o http://stackoverflow.com/questions/5849457/using-namespace-in-c-headers

- bugfix in orienting the triangles: the STL set-intersection doesn't work
  as expected with unordered sets.
- multi-parted meshes are now supported (but not yet tested)
- several variables and methods refactored to improve readability.

BoundaryGeometry: fastIsInside(): return 1 without further tests if point is outside bbox, pass args as reference; all functions: use gsl_fcmp() to compare floating point numbers

BoundaryGeometry: pass args by reference in intersection tests; in intersectRayBoundary(): use a box which is smaller than the voxel mesh but largen than bbox of the geometry for computing the intersection with the bbox of the geometry; print a warning, if mapPoint2VoxelIndices() is called for a point outside the bbox of the voxel mesh

BoundaryGeometry: bugfix in counting intersections in intersectTinyLineSegmentBoundary(). This actually fixes an issue wih fastIsInside(); Faster mesh voxelization.

BoundaryGeometry: private method intersectLineSegmentBoundary4PartInside() removed; private method intersectTinyLineSegmentBoundary() for testing small line segments added

BoundaryGeometry: change type of structure to store the voxelization from std::set to std::unordered_set and renamed to boundaryVoxelIDs_m

BoundaryGeometry: public method intersectRayBoundary() added, private method intersectLineSegmentBoundary() added, PartInside() is now using this private methode