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modified:   CMakeLists.txt
modified:   Doxyfile
modified:   src/Algorithms/ParallelCyclotronTracker.cpp
modified:   src/BasicActions/Option.cpp
modified:   src/Classic/Algorithms/PBunchDefs.h
modified:   src/Classic/Algorithms/Tracker.cpp
modified:   src/Classic/Utilities/Options.cpp
modified:   src/Classic/Utilities/Options.h
modified:   src/Main.cpp
modified:   src/Solvers/PoissonSolver.h
modified:   src/Structure/DataSink.cpp
modified:   src/Structure/FieldSolver.cpp
modified:   src/Structure/FieldSolver.h
modified:   src/Track/Track.cpp

in order to be a optimiser run, we now also check commandline arguments in addition to the input file

Remark: Following directories are still using BoxLib instead of AMReX:

- src/ippl/test/AMR/boxlib-amr
- src/ippl/test/AMR/boxlib-only

Updated files:

modified:   CMakeLists.txt
modified:   CMakeModules/CCSEOptions.cmake
modified:   CMakeModules/FindCCSE.cmake
modified:   ippl/src/AmrParticle/AmrParticleBase.hpp
modified:   ippl/test/AMR/AmrOpal.cpp
modified:   ippl/test/AMR/AmrOpal.h
modified:   ippl/test/AMR/AmrOpal_F.h
modified:   ippl/test/AMR/CMakeLists.txt
modified:   ippl/test/AMR/Distribution.h
modified:   ippl/test/AMR/H5Reader.cpp
modified:   ippl/test/AMR/Solver.cpp
modified:   ippl/test/AMR/Solver.h
modified:   ippl/test/AMR/helper_functions.h
modified:   ippl/test/AMR/ippl-amr/AmrParticleBase.h
modified:   ippl/test/AMR/ippl-amr/AmrParticleBase.hpp
modified:   ippl/test/AMR/ippl-amr/ParticleAmrLayout.h
modified:   ippl/test/AMR/ippl-amr/ParticleAmrLayout.hpp
modified:   ippl/test/AMR/ippl-amr/testAmrPartBase.cpp
modified:   ippl/test/AMR/ippl-amr/testInitialBox.cpp
modified:   ippl/test/AMR/ippl-amr/testNewTracker.cpp
modified:   ippl/test/AMR/ippl-amr/testPerformance.cpp
modified:   ippl/test/AMR/ippl-amr/testPlasma.cpp
modified:   ippl/test/AMR/ippl-amr/testScatterAMReX.cpp
modified:   ippl/test/AMR/ippl-amr/testTagging.cpp
modified:   ippl/test/AMR/ippl-bunch/testAdapterPattern.cpp
modified:   src/Amr/AmrBoxLib.cpp
modified:   src/Amr/AmrBoxLib.h
modified:   src/Amr/AmrBoxLib_F.h
modified:   src/Amr/AmrDefs.h
modified:   src/Amr/BoxLibLayout.h
modified:   src/Amr/BoxLibLayout.hpp
modified:   src/Amr/BoxLibParticle.h
modified:   src/Amr/BoxLibParticle.hpp
modified:   src/Classic/Algorithms/AmrPartBunch.h
modified:   src/Main.cpp
modified:   src/Solvers/BoxLibSolvers/FMGPoissonSolver.cpp
modified:   src/Solvers/BoxLibSolvers/FMGPoissonSolver.h
modified:   src/Structure/FieldSolver.cpp
modified:   src/Track/TrackRun.cpp
modified:   src/Track/TrackRun.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!

i.e. we do not create a database with BoxLib ParmParse.

modified:   src/Main.cpp

OpalData *OPAL = OpalData::getInstance();
OpalData *opal = OpalData::getInstance();

This change applies to following files:

modified:   src/AbstractObjects/BeamSequence.cpp
modified:   src/AbstractObjects/Element.cpp
modified:   src/Main.cpp
modified:   src/Match/MatchParser.cpp
modified:   src/OpalConfigure/Configure.cpp
modified:   src/Solvers/P3MPoissonSolver.cpp
modified:   src/Structure/H5PartWrapperForPS.cpp
modified:   src/Structure/H5PartWrapperForPT.cpp
modified:   src/ValueDefinitions/RealConstant.cpp
modified:   src/ValueDefinitions/StringConstant.cpp
modified:   src/opal.cpp

- revert 'chdir()' change

    - fixing number of particles when the numbers don't add up to the total due to rounding errors;
    - clean up: rename files to comply with coding guide lines;
    - improve message when field of bend overlapps;
    - warning is emitted if too few fourier coefficients are used to filter the field map;

fixing restart: can now (again) restart from any step in any H5Part file that was written for/with OPAL; SDDS file and load balance file are rewound to an s-position less or equal as in the H5file

change data type of distCorr from std::vector to tenzor; working on matched gauss distribution; adding gsl error handler