- Free memory after initialization of particles.

modified:   Distribution.h

	- particle tracking
	- multi-level (particles are initialized on single level first, after tagging
	  they should be redistributed)

modified:   AmrPartBunch.h
modified:   Distribution.h
modified:   testAmrPartBunch.cpp

- Initialize particles on multi-level
- The refined boxes have to be checked (hard-coded)

modified:   AmrPartBunch.h
modified:   testAmrPartBunch.cpp

- ParticleContainer<NR, NI>::AssignDensity is now also available for all other attributes
- ParticleContainer<NR, NI>::AssignDensitySingleLevel is now also available for all other attributes
- ParticleContainer<NR, NI>::estTimestep got removed
- ParticleContainer<NR,NI>::sumParticleMass is now also available for all other attributes

modified:   ippl/test/AMR/testAmrPartBunch.cpp
modified:   src/Solvers/amr/AccelParticles.cpp
modified:   src/Solvers/amr/Electrostatic.cpp
modified:   src/Solvers/amr/ParticleDerive.cpp

	- Bug fix: Checking number of arguments in case of IPPL.

modified:   testAmrPartBunch.cpp

	- Getter functions in AmrPartBunch
- Gaussian distribution
- Set charge-to-mass ration for AmrPartBunch in testAmrPartBunch.cpp

modified:   AmrPartBunch.h
modified:   Distribution.h
modified:   testAmrPartBunch.cpp

	- AmrPartBunch:gatherStatistics
	- Doxygen
	- Setter functions for attributes.

modified:   AmrPartBunch.h
modified:   Distribution.h
modified:   PartBunch.h
modified:   PartBunchBase.h
modified:   testAmrPartBunch.cpp

	- Initialization of particles works.

modified:   AmrPartBunch.h
modified:   Distribution.h
modified:   PartBunchBase.h
modified:   testAmrPartBunch.cpp

	- Doxygen
	- Code cleaning.
	- Distribution (still bugs)

new file:   AmrDoxyfile
modified:   AmrPartBunch.h
new file:   Distribution.h
modified:   PartBunch.h
modified:   PartBunchBase.h
modified:   testAmrPartBunch.cpp

modified:   AmrPartBunch.h
modified:   PartBunch.h
modified:   PartBunchBase.h
modified:   testAmrPartBunch.cpp

	- set up geometry
	- initialize particles
	- do particle mapping

modified:   ippl/test/AMR/AmrPartBunch.h
modified:   ippl/test/AMR/PartBunchBase.h
modified:   ippl/test/AMR/testAmrPartBunch.cpp

List of all files that had to be updated:

	modified:   classic/src/Algorithms/PartBunch.h
	modified:   ippl/doc/tex/introduction.tex
	modified:   ippl/doc/tex/ippl_particles.tex
	modified:   ippl/src/DataSource/ACLVISPtclAttribDataSource.hpp
	modified:   ippl/src/DataSource/ACLVISPtclBaseDataSource.h
	modified:   ippl/src/DataSource/ACLVISPtclBaseDataSource.hpp
	modified:   ippl/src/DataSource/FilePtclBaseDataSource.h
	modified:   ippl/src/DataSource/FilePtclBaseDataSource.hpp
	modified:   ippl/src/DataSource/MakeDataSource.h
	modified:   ippl/src/DataSource/MakeDataSource.hpp
	modified:   ippl/src/DataSource/PtclAttribDataSource.cpp
	modified:   ippl/src/DataSource/PtclAttribDataSource.h
	modified:   ippl/src/DataSource/PtclBaseDataSource.cpp
	modified:   ippl/src/DataSource/PtclBaseDataSource.h
	modified:   ippl/src/DataSource/StringDataSource.hpp
	modified:   ippl/src/DataSource/inst/FileParBaseInteractDS_Cart_1D.cpp
	modified:   ippl/src/DataSource/inst/FileParBaseInteractDS_Cart_2D.cpp
	modified:   ippl/src/DataSource/inst/FileParBaseInteractDS_Cart_3D.cpp
	modified:   ippl/src/DataSource/inst/FileParBaseInteractDS_Unif_1D.cpp
	modified:   ippl/src/DataSource/inst/FileParBaseInteractDS_Unif_2D.cpp
	modified:   ippl/src/DataSource/inst/FileParBaseInteractDS_Unif_3D.cpp
	modified:   ippl/src/DataSource/inst/FileParBaseSpatialDS_Cart_1D.cpp
	modified:   ippl/src/DataSource/inst/FileParBaseSpatialDS_Cart_2D.cpp
	modified:   ippl/src/DataSource/inst/FileParBaseSpatialDS_Cart_3D.cpp
	modified:   ippl/src/DataSource/inst/FileParBaseSpatialDS_Unif_1D.cpp
	modified:   ippl/src/DataSource/inst/FileParBaseSpatialDS_Unif_2D.cpp
	modified:   ippl/src/DataSource/inst/FileParBaseSpatialDS_Unif_3D.cpp
	modified:   ippl/src/DataSource/inst/FileParBaseUniformDS_1D.cpp
	modified:   ippl/src/DataSource/inst/FileParBaseUniformDS_2D.cpp
	modified:   ippl/src/DataSource/inst/FileParBaseUniformDS_3D.cpp
	modified:   ippl/src/Ippl.h
	modified:   ippl/src/Particle/BoxParticleCachingPolicy.h
	modified:   ippl/src/Particle/CMakeLists.txt
	modified:   ippl/src/Particle/CellParticleCachingPolicy.h
	modified:   ippl/src/Particle/GenArrayParticle.h
	modified:   ippl/src/Particle/GenParticle.h
	renamed:    ippl/src/Particle/ParticleBase.h -> ippl/src/Particle/IpplParticleBase.h
	renamed:    ippl/src/Particle/ParticleBase.hpp -> ippl/src/Particle/IpplParticleBase.hpp
	modified:   ippl/src/Particle/NoParticleCachingPolicy.h
	modified:   ippl/src/Particle/ParticleBalancer.h
	modified:   ippl/src/Particle/ParticleBalancer.hpp
	modified:   ippl/src/Particle/ParticleCashedLayout.h
	modified:   ippl/src/Particle/ParticleCashedLayout.hpp
	modified:   ippl/src/Particle/ParticleInteractLayout.h
	modified:   ippl/src/Particle/ParticleInteractLayout.hpp
	modified:   ippl/src/Particle/ParticleLayoutFromGrid.cpp
	modified:   ippl/src/Particle/ParticleLayoutFromGrid.h
	modified:   ippl/src/Particle/ParticleSpatialLayout.cppNudge
	modified:   ippl/src/Particle/ParticleSpatialLayout.h
	modified:   ippl/src/Particle/ParticleSpatialLayout.hNudge
	modified:   ippl/src/Particle/ParticleSpatialLayout.hpp
	modified:   ippl/src/Particle/ParticleUniformLayout.h
	modified:   ippl/src/Particle/ParticleUniformLayout.hpp
	modified:   ippl/src/Particle/inst/ParticleBaseInteract_Cart_1D.cpp
	modified:   ippl/src/Particle/inst/ParticleBaseInteract_Cart_2D.cpp
	modified:   ippl/src/Particle/inst/ParticleBaseInteract_Cart_3D.cpp
	modified:   ippl/src/Particle/inst/ParticleBaseInteract_Unif_1D.cpp
	modified:   ippl/src/Particle/inst/ParticleBaseInteract_Unif_2D.cpp
	modified:   ippl/src/Particle/inst/ParticleBaseInteract_Unif_3D.cpp
	modified:   ippl/src/Particle/inst/ParticleBaseSpatial_Cart_1D.cpp
	modified:   ippl/src/Particle/inst/ParticleBaseSpatial_Cart_2D.cpp
	modified:   ippl/src/Particle/inst/ParticleBaseSpatial_Cart_3D.cpp
	modified:   ippl/src/Particle/inst/ParticleBaseSpatial_Unif_1D.cpp
	modified:   ippl/src/Particle/inst/ParticleBaseSpatial_Unif_2D.cpp
	modified:   ippl/src/Particle/inst/ParticleBaseSpatial_Unif_3D.cpp
	modified:   ippl/src/Particle/inst/ParticleBaseUniform_1D.cpp
	modified:   ippl/src/Particle/inst/ParticleBaseUniform_2D.cpp
	modified:   ippl/src/Particle/inst/ParticleBaseUniform_3D.cpp
	modified:   ippl/src/Utility/DiscParticle.h
	modified:   ippl/src/Utility/DiscParticle.hpp
	modified:   ippl/src/Utility/IpplStats.cpp
	modified:   ippl/src/Utility/IpplStats.h
	modified:   ippl/test/6dtrack/GTChargedParticles/GTChargedParticles.hh
	modified:   ippl/test/AMR/AmrPartBunch.h
	modified:   ippl/test/AMR/CMakeLists.txt
	modified:   ippl/test/AMR/PartBunch.h
	modified:   ippl/test/AMR/PartBunchBase.h
	modified:   ippl/test/AMR/testAmrPartBunch.cpp
	modified:   ippl/test/CavityTrack/ChargedParticles/ChargedParticles.hh
	modified:   ippl/test/PwrSpec/testPwrSpec.cpp
	modified:   ippl/test/hdf5/hdf5write-1.cpp
	modified:   ippl/test/hdf5/testHdf5-1.cpp
	modified:   ippl/test/particle/1dperiodic.cpp
	modified:   ippl/test/particle/CacheTest.cpp
	modified:   ippl/test/particle/FFTFieldSolver.cpp
	modified:   ippl/test/particle/FieldCompare.cpp
	modified:   ippl/test/particle/PIC2d.cpp
	modified:   ippl/test/particle/PIC3d-timing-1.cpp
	modified:   ippl/test/particle/PIC3d.cpp
	modified:   ippl/test/particle/PIC3dBCo-p.cpp
	modified:   ippl/test/particle/PIC3dBCo-p.cpp.nok
	modified:   ippl/test/particle/PairTest.cpp
	modified:   ippl/test/particle/neighNodeTest1.cpp
	modified:   ippl/test/particle/p3m3d.cpp
	modified:   ippl/test/particle/p3m3dHeating.cpp
	modified:   ippl/test/particle/p3m3dMicrobunching.cpp
	modified:   ippl/test/particle/pdbtest.cpp
	modified:   ippl/test/particle/salman-1.cpp
	modified:   ippl/test/particle/test-scatter-1.cpp
	modified:   ippl/test/particle/test-update-1.cpp
	modified:   ippl/test/poissonsolvers/femmgTest.cpp
	modified:   ippl/test/simple-new/id-test1.cpp
	modified:   ippl/test/simple-new/memcheck-1.cpp
	modified:   ippl/test/simple-new/memcheck-2.cpp
	modified:   ippl/test/simple/TestParticleDebug.cpp
	modified:   ippl/test/simple/TestParticleDebugParallel.cpp
	modified:   ippl/test/ttrack/GTChargedParticles/GTChargedParticles.hh
	modified:   ippl/test/twostream-1/.depend

modified:   src/Solvers/amr/Electrostatic.cpp

The Particle attributes are now private.

modified:   PartBunch.h
modified:   PartBunchBase.h
modified:   testAmrPartBunch.cpp

modified:   AmrPartBunch.h
copied:     testAmrPartBunch.cpp -> PartBunch.h
modified:   PartBunchBase.h
modified:   testAmrPartBunch.cpp

new file:   AmrPartBunch.h
new file:   PartBunch.h
new file:   PartBunchBase.h
modified:   testAmrPartBunch.cpp

new file:   ippl/test/AMR/CMakeLists.txt
new file:   ippl/test/AMR/testAmrPartBunch.cpp

modified:   ippl/test/particle/CMakeLists.txt

- simple H5hut version check added
- set indentation to 4 spaces

modified:   CMakeLists.txt
modified:   src/Solvers/amr/Electrostatic.cpp

The dummy example Laplace(\phi) = -\rho
where \rho = 1, agrees with MATLAB solution.

modified:   src/Solvers/amr/Electrostatic.H
modified:   src/Solvers/amr/Electrostatic.cpp

Not final version since still hard-coded. In future we will
use the "OPAL-way", i.e.

double coefE = 1.0 / (4 * pi * epsilon_0);
Track::block->slbunch->setCouplingConstant(coefE);

modified:   src/Solvers/amr/Accel.H
modified:   src/Solvers/amr/Accel.cpp
modified:   src/Solvers/amr/Accel_advance.cpp
modified:   src/Solvers/amr/Electrostatic.H
modified:   src/Solvers/amr/Electrostatic.cpp
modified:   src/Structure/FieldSolver.cpp

modified:   src/Solvers/amr/Accel.H
modified:   src/Solvers/amr/Accel.cpp
modified:   src/Solvers/amr/Accel_advance.cpp
modified:   src/Structure/FieldSolver.cpp

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

modified:   src/Main.cpp

new file:   CMakeModules/CCSEOptions.cmake
new file:   CMakeModules/FindCCSE.cmake

OPAL can now be compiled with AMR enabled (default: OFF).

modified:   CMakeLists.txt
modified:   ippl/CMakeLists.txt
modified:   src/CMakeLists.txt

This change applies to

modified:   src/Track/TrackRun.cpp
modified:   src/Track/TrackRun.h

AMR: Synchronization with svn-Version (+ indentation fixing):

modified:   src/Structure/FieldSolver.cpp
modified:   src/Structure/FieldSolver.h
modified:   src/Track/TrackRun.cpp
modified:   src/Track/TrackRun.h

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

modified:   src/Solvers/amr/AccelBld.cpp
modified:   src/Solvers/amr/Accel_output.cpp
modified:   src/Solvers/amr/CMakeLists.txt
deleted:    src/Solvers/amr/ComputeStencil.cpp
modified:   src/Solvers/amr/ElectroMagneticParticleClass.H
modified:   src/Solvers/amr/Src_3d/ProbInit.f90
modified:   src/Solvers/amr/TrilinosSolver.cpp
modified:   src/Solvers/amr/TrilinosSolver.h
modified:   src/Solvers/amr/init_trilinos.cpp

- DataSink::writeSurfaceInteraction(): cast H5_ERR if compared to variable of type h5_file_t

- LossDataSink::~LossDataSink(): mark rc as unused if NDEBUG is set
- LossDataSink::openH5(): cast H5_ERR if compared to variable of type h5_file_t

- Fieldmap::readHeader():
    - compile time error fixed if NDEBUG is set
    - cast H5_ERR to h5_file_t in assert expression
    - do not query other field info than name
- break down long lines of code