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modified:   Algorithms/ParallelCyclotronTracker.cpp
modified:   Algorithms/ParallelCyclotronTracker.h
modified:   Classic/Algorithms/PartBunchBase.hpp
modified:   Structure/CMakeLists.txt
modified:   Structure/MultiBunchDump.cpp
modified:   Structure/MultiBunchDump.h

MultipoleT now converges for curved magnets
MultipoleT is split into three derived classed and a base class

renaming Collimator to CCollimator where C stands for cyclotron; all other collimators are implemented using FlexibleCollimator; This also fixes #224

first version of multi-slit/pepperpot/what ever aka flexible collimator. However way to slow to be practical

Avoids having n + 1 bunches in memory where n is the
number of bunches the user wants.

modified:   src/Algorithms/ParallelCyclotronTracker.cpp
modified:   src/Algorithms/ParallelCyclotronTracker.h

This reverts commit 69985bb1.

modified:   Algorithms/NilTracker.h
modified:   Algorithms/ParallelCyclotronTracker.cpp
modified:   Algorithms/ParallelCyclotronTracker.h
modified:   Algorithms/ParallelTTracker.cpp
modified:   Algorithms/ParallelTTracker.h
modified:   Algorithms/ThickTracker.cpp
modified:   Algorithms/ThickTracker.h
modified:   Classic/Algorithms/ThinTracker.cpp
modified:   Classic/Algorithms/ThinTracker.h
modified:   Classic/Algorithms/Tracker.cpp
modified:   Classic/Algorithms/Tracker.h
modified:   Track/TrackRun.cpp

- 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

 moving startTimer/stopTimer outside loop over particles and - avoiding string
 comparison inside loops over particles

Revert "In case a distribution has OFFSET, in OPAL-cycl the referernce particle has to be adjusted."

This reverts commit 20d8e10d.

Need this for OPAL-t, OPAL-cycl coupling in lieu of gantry simulations (Jozef).

Brought back saving in local frame for cyclotron tracker. Reverted the way mean E is calculated in PartBunch. Hopefully, restarts in local as well as in global frame now work in the cyclotron tracker.

- 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

Fixed small issue with singleParticleDump not working correctly in CyclotronTracker in RK-4 mode, made combined LF-2/RK-4 tracker default

*) Fixed a problem with saving the lost particles if not all processors have lost particles. \n*) Consolidated Tracker_RK4 and Tracker_LF in ParallelCyclotronTracker. Enclosed in #ifdef for now. Activate by uncommenting #define GENERICTRACKER in ParallelCyclotronTracker.h. \n*) Added the general OPAL OPTION boundpdestroyfreq for Cyclotron Tracker.

Cosmetics, Typos and a bugfix in calculateBeamParameters_cycl() where the energy would always be 0 and thus the emittance inf

Major Changes: 1. No more dumping or restarting in LOCAL frame. 2. OPAL-CYCL now recalculates reference* variables before dump and saves in H5 file. 3. OPAL correctly reads reference* values and calculates beta*gamma correctly from Ekin (was factor 1000 wrong before) Note: Transformation of bunch data into local frame must now be done in POSTPROCESSING -> upgrade H5root