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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

- moving the following classes over from OPAL to CLASSIC
  o OpalField       -> ClassicField
  o OpalRing        -> Ring
  o OpalRingSection -> RingSection
  o LossDataSink
- clean up
- splitting Options into classic and opal options

- 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

A loss LossDataSink is initiated with the constructor, then particles are added (and locally stored).
In the finalize method all data is written to an ASCII or H5 file, depending on the NEW option ASCIIDUMP.

Testing of this is ongoing, there are maybe some gliches, watch out. 

Regressiontest will follow!

@Yianjun: please test the CYCLOTRON related PROBES and STRIPPER element!

		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

- use forward declaration where possible
- remove unused includes