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to increase it by one for the scSolveFreq and amrRegridFreq if-statement

to increase it by one for the scSolveFreq and amrRegridFreq if-statement

- set level and grid to zero for new created particles
- additional error check
- write Yt output for each bin

This reverts commit 69985bb1.

Latest AMReX commit
-------------------

commit 207c75da3ad51deb2da1ba20bf8ce0a86264332a
Date:   Thu Nov 2 12:55:13 2017 -0600

    Use amrex_constants_module in amrex_filcc_2d

Affected files
--------------

modified:   ../../../../CMakeLists.txt
modified:   ../AmrOpal.cpp
modified:   ../AmrOpal.h
modified:   ../Distribution.cpp
modified:   ../Distribution.h
modified:   ../MGTSolver.cpp
modified:   ../MGTSolver.h
modified:   ../Solver.cpp
modified:   ../Solver.h
modified:   ../amrex-only/AssignMultiLevelDensity.cpp
modified:   ../amrex-only/CMakeLists.txt
modified:   ../amrex-only/Solver.cpp
modified:   ../amrex-only/testDeposition.cpp
modified:   ../amrex-only/testDepositionFail.cpp
modified:   ../amrex-only/testGeometry.cpp
modified:   ../amrex-only/testSolverFail.cpp
modified:   ../helper_functions.h
modified:   AmrParticleBase.h
modified:   AmrParticleBase.hpp
modified:   CMakeLists.txt
modified:   PartBunchAmr.h
modified:   ParticleAmrLayout.h
modified:   ParticleAmrLayout.hpp
modified:   testAmrPartBase.cpp
modified:   testCRTP.cpp
modified:   testDomainTransformSolve.cpp
modified:   testGaussian.cpp
modified:   testInitGuessSolver.cpp
modified:   testInitialBox.cpp
modified:   testLayout.cpp
modified:   testNewTracker.cpp
modified:   testPerformance.cpp
modified:   testPlasma.cpp
modified:   testReal.cpp
modified:   testScatterAMReX.cpp
modified:   testTagging.cpp
modified:   testUnifSphere.cpp
modified:   ../ippl-bunch/CMakeLists.txt
modified:   ../ippl-bunch/PartBunchBase.h
modified:   ../ippl-bunch/testAdapterPattern.cpp
modified:   ../trilinos/AmrBoundary.h
modified:   ../trilinos/AmrDirichletBoundary.h
modified:   ../trilinos/AmrLagrangeInterpolater.h
modified:   ../trilinos/AmrLagrangeInterpolater.hpp
modified:   ../trilinos/AmrMultiGridCore.h
modified:   ../trilinos/AmrMultiGridLevel.h
modified:   ../trilinos/AmrMultiGridLevel.hpp
modified:   ../trilinos/AmrOpenBoundary.h
modified:   ../trilinos/AmrTrilinearInterpolater.hpp
modified:   ../trilinos/AmrTrilinos.cpp
modified:   ../trilinos/AmrTrilinos.h
modified:   ../trilinos/CMakeLists.txt
modified:   ../trilinos/IrregularDomain.h
modified:   ../trilinos/build.h
modified:   ../trilinos/testAmrMultigrid.cpp
modified:   ../trilinos/testBoundaryMatrix.cpp
modified:   ../trilinos/testBoundaryVector.cpp
modified:   ../trilinos/testCopy.cpp
modified:   ../trilinos/testInterpolationMatrix.cpp
modified:   ../trilinos/testLagrange.cpp
modified:   ../trilinos/testNoFine.cpp
modified:   ../trilinos/testPoissonMatrix.cpp
modified:   ../trilinos/testRestrictionMatrix.cpp
modified:   ../trilinos/testSmootherMatrix.cpp
modified:   ../trilinos/testSolverComparison.cpp
modified:   ../trilinos/testSpecialPoissonMatrix.cpp
modified:   ../trilinos/testTrilinosGeometry.cpp
modified:   ../trilinos/testTrilinosSolver.cpp
modified:   ../trilinos/testWithFine.cpp
modified:   ../trilinos/tools.h
modified:   ../writePlotFile.H
modified:   ../../../../src/Amr/AmrBoxLib.cpp
modified:   ../../../../src/Amr/AmrPythonWriter.cpp
modified:   ../../../../src/Amr/AmrYtWriter.cpp
modified:   ../../../../src/Amr/BoxLibLayout.hpp
modified:   ../../../../src/Solvers/BoxLibSolvers/FMGPoissonSolver.cpp
modified:   ../../../../src/Solvers/BoxLibSolvers/FMGPoissonSolver.h

The computed total charge on the grid was not exactly the same as the total charge obtained
by multiplying the total number of particles with the charge per particle. For a slightly bigger box it's fine.

- code cleaning

We are now able to iterate over particles of a certain level.

modified:   BoxLibLayout.h
modified:   BoxLibLayout.hpp

modified:   src/Amr/BoxLibLayout.h
modified:   src/Amr/BoxLibLayout.hpp
modified:   src/Classic/Algorithms/AmrPartBunch.cpp

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

In case of "int" we can have only the same refinement in all directions. So, don't use
the functions from ParGDB.H. We use the ones from AmrCore.H

modified:   src/Amr/AmrBoxLib.cpp
modified:   src/Amr/AmrBoxLib.h
modified:   src/Amr/BoxLibLayout.h
modified:   src/Amr/BoxLibLayout.hpp

Work to be done: Code cleaning.

modified:   ippl/test/AMR/AmrOpal.cpp
modified:   ippl/test/AMR/ippl-amr/testAmrPartBase.cpp
modified:   ippl/test/AMR/ippl-amr/testInitialBox.cpp
new file:   ippl/test/AMR/ippl-bunch/testCRTP.cpp
modified:   src/Amr/AmrBoxLib.cpp
modified:   src/Amr/AmrBoxLib.h
modified:   src/Amr/BoxLibLayout.h
modified:   src/Amr/BoxLibLayout.hpp
modified:   src/Amr/BoxLibParticle.h
modified:   src/Classic/Algorithms/AmrPartBunch.cpp
modified:   src/Classic/Algorithms/AmrPartBunch.h
modified:   src/Solvers/BoxLibSolvers/FMGPoissonSolver.cpp
modified:   src/Structure/FieldSolver.cpp

modified:   src/Amr/AmrBoxLib.cpp
modified:   src/Amr/AmrBoxLib.h
modified:   src/Amr/BoxLibLayout.h
modified:   src/Amr/BoxLibLayout.hpp
modified:   src/Structure/FieldSolver.cpp

The particles cannot live without a box. Therefore, we initialize
a default box when initializing a bunch. This can still be changed
later on through the ParGDB class (i.e. BoxLibLayout).

modified:   Amr/BoxLibLayout.h
modified:   Amr/BoxLibLayout.hpp