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refactor code: force more structure to check routine; streamline and avoid reduce by adding reference particle type to PartBunchBase

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:   BeamBeam.cpp
modified:   BeamBeam.h
modified:   Bend.cpp
modified:   Bend.h
modified:   Collimator.cpp
modified:   Collimator.h
modified:   Component.cpp
modified:   Component.h
modified:   Corrector.cpp
modified:   Corrector.h
modified:   Cyclotron.cpp
modified:   Cyclotron.h
modified:   CyclotronValley.cpp
modified:   CyclotronValley.h
modified:   Degrader.cpp
modified:   Degrader.h
modified:   Diagnostic.cpp
modified:   Diagnostic.h
modified:   Drift.cpp
modified:   Drift.h
modified:   Integrator.h
modified:   Lambertson.cpp
modified:   Lambertson.h
modified:   Marker.cpp
modified:   Marker.h
modified:   Monitor.cpp
modified:   Monitor.h
modified:   Multipole.cpp
modified:   Multipole.h
modified:   Offset.cpp
modified:   Offset.h
modified:   ParallelPlate.cpp
modified:   ParallelPlate.h
modified:   Patch.cpp
modified:   Patch.h
modified:   Probe.cpp
modified:   Probe.h
modified:   RBend.cpp
modified:   RBend3D.cpp
modified:   RBend3D.h
modified:   RFCavity.cpp
modified:   RFCavity.h
modified:   RFQuadrupole.cpp
modified:   RFQuadrupole.h
modified:   Ring.cpp
modified:   Ring.h
modified:   SBend.cpp
modified:   SBend3D.cpp
modified:   SBend3D.h
modified:   SectorFieldMapComponent.h
modified:   Separator.cpp
modified:   Separator.h
modified:   Septum.cpp
modified:   Septum.h
modified:   Solenoid.cpp
modified:   Solenoid.h
modified:   Source.cpp
modified:   Source.h
modified:   Stripper.cpp
modified:   Stripper.h
modified:   TravelingWave.cpp
modified:   TravelingWave.h
modified:   VariableRFCavity.cpp
modified:   VariableRFCavity.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!

moving Classic into src directory and pack all objects into libOpal since Classic also depends on libOpal

- 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

		MINR, MAXR, MINZ, MAXZ. 
- if a particle is out of cyclotron aperture or out of the field map, 
   it will be deleted after this step and its parameters are recorded in the *.loss file
- change data type of particle id from int to size_t
- many minor cosmetics of display massage