GitLab

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

- assertion expression fixed in Fieldmap::readHeader(),

- include check_adapter.hpp from boost see also: https://github.com/headmyshoulder/odeint-v2/commit/b816e93fcfd099fdd33e9f3caa6dc5d57b83f8d7

- removed from version control

- option USE_H5HUT2 added

modified:   classic/src/Algorithms/PartBunch.h

Code cleaning:
	The following in OPAL unused functions and variables of PartBunch are removed:

	void stash()
	void pop()
	Vector_t getStashIniP() const
	UnitState_t getUnitState() const
	void makHistograms()
	double getRho(NDIndex<3> e)
	bool itIsMyTurn(int *n)
	bool hasZeroNLP()
	void set_nBinsLineDensity(int n)
	void setGridIsFixed()
	double getRebinEnergy()
	void weHaveNOBins()
	double calcTimeDelay(const double &jifactor)
	void moveBunchToCathode(double &t)
	void printBinHist()
	void updatePartInBin(size_t countLost[])
	void updateBinStructure()
	void reportParticleLoss()
	double getMaxdEBins()
	virtual void setKR(Vector_t value, int i)
	virtual void setKT(Vector_t value, int i)
	virtual void BetOut(FILE *dat, FILE *sli)
	virtual void plotR()
	void beamEllipsoid(FVector<double, 6>   &centroid, FMatrix<double, 6, 6> &moment)
	void calcWeightedAverages(Vector_t &CentroidPosition, Vector_t &CentroidMomentum) const
	bool isZPeriodic() const
	double getGaBeLa() const
	double getZPos()
	void getXBounds(Vector_t &xMin, Vector_t &xMax)
	double   get_phase() const
	double* get_energy()
	void set_hr(Vector_t h)
	double get_meshEnlargement() const
	size_t getMinLocalNum()
	void calcBeamParametersLight()
	inline bool hasLowParticleCount()
	size_t getNumPartInBin(int BinID) const
	bool resetPartBinID()
	double getTBin()
	bool isDcBeam()
	Field_t tmpFieldZ_m
	Vector_t csBeta_m
	Vector_t csAlpha_m
	Vector_t stash_iniP_m