- In case of Edison and Cori we should not
  call the find_package(Trilinos) command
  otherwise it uses the wrong
  TRILINNOS_TPL_LIBRARIES (i.e. instead
  of cray-tpsl/16.07.1 [that we need to load]
  it uses cray-tpsl/16.06.1 linked libs).
  This leads obviously to linker problems.
- Fix if-statement bug in src/CMakeLists.txt

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

modified:   src/CMakeLists.txt

- check ${HOSTNAME} for compilation.
- h5file_t cast.

modified:   CMakeLists.txt
modified:   H5Reader.h

     to compile with the "amrcore" branch of BoxLib.

We had to comment several lines of the following files:

modified:   src/Algorithms/ParallelTTracker.cpp
modified:   src/Solvers/amr/ElectroMagneticParticleClass.H
modified:   src/Solvers/amr/Electrostatic.cpp
modified:   src/Solvers/amr/ParticleDerive.cpp
modified:   src/Track/TrackRun.cpp

- tracking of beam

modified:   CMakeLists.txt
modified:   PoissonProblems.cpp
modified:   testAmrPartBunch.cpp
modified:   visualize.py

- units in yt
- tagging in single Gaussian example

modified:   AmrOpal.cpp
modified:   PoissonProblems.cpp
modified:   PoissonProblems.h
modified:   error.cpp
modified:   visualize.py

- PoissonProblems: In case of Gaussian distribution
  mean and standard deviation can be set at runtime
- usage of 1 / (4*pi*\epsilon_0) in
  PoissonProblems::doSolveParticlesReal

modified:   CMakeLists.txt
modified:   H5Reader.cpp
modified:   PoissonProblems.cpp
modified:   PoissonProblems.h
modified:   error.cpp
modified:   visualize.py

- allow non-cubic domain

modified:   PoissonProblems.cpp
modified:   PoissonProblems.h
modified:   error.cpp

- reading charge from H5 file
- tagging in error.cpp
- change tagging criteria in AmrOpal.cpp due to real distribution.

modified:   AmrOpal.cpp
modified:   Distribution.cpp
modified:   Distribution.h
modified:   H5Reader.cpp
modified:   H5Reader.h
modified:   PoissonProblems.cpp
modified:   PoissonProblems.h
modified:   error.cpp

- Doxygen documentation

modified:   Tagging_nd.f90
new file:   analyse.py
modified:   error.cpp
modified:   vis_iter.py
modified:   visualize.py

- start with AMR example.

modified:   CMakeLists.txt
modified:   PoissonProblems.cpp
modified:   PoissonProblems.h
modified:   error.cpp

- bug fix in Distribution reading from H5 file

modified:   Distribution.cpp

- Doxygen documentation

modified:   AmrOpal.h
modified:   AmrOpal_F.h
modified:   AmrPartBunch.h
modified:   Distribution.h
modified:   H5Reader.h
modified:   PartBunch.h
modified:   PartBunchBase.h
modified:   PoissonProblems.h
modified:   Solver.cpp
modified:   Solver.h
modified:   error.cpp
modified:   iterative.cpp
modified:   testSolver.cpp
modified:   writePlotFile.H

- put different Poisson problems into class
  --> less redundant coding (error.cpp)
- split up Solver.h into *.h and *.cpp file

modified:   CMakeLists.txt
new file:   PoissonProblems.cpp
new file:   PoissonProblems.h
copied:     Solver.h -> Solver.cpp
modified:   Solver.h
modified:   error.cpp
modified:   writePlotFile.H

- split Distribution.h into *.h and *.cpp file (cleaner)
- implement reading of H5 files (cyclotron) based on
  code in OPAL, i.e. src/Structure/H5PartWrapper and
  src/Structure/H5PartWrapperForPC
- add test file for reading H5 file

modified:   CMakeLists.txt
new file:   Distribution.cpp
modified:   Distribution.h
new file:   H5Reader.cpp
new file:   H5Reader.h
new file:   testH5Read.cpp

- ParallelCyclotronTracker::Tracker_RK4(): add missing curly brackets

- ParticleSpatialLayout<T,Dim,Mesh,CachingPolicy>::update() fix wrong indentation

- Distribution::WriteOutFileInjection(): fix bug in calling Ippl::myNode()

- OpalBeamline::getFieldAt(): add parenthesis around bit-wise

- add missing type cast in assertion to test return value of 'H5OpenFile()'

- fixed bug in Distribution.h: Instead of a Gaussian distribution
  a uniform was generated.
- error.cpp: Multiple ways of solver: with and without particles,
	     uniform and gaussian distribution.

modified:   CMakeLists.txt
modified:   Distribution.h
modified:   error.cpp
modified:   testAmrPartBunch.cpp

- additional test for studying convergence of solver.

modified:   CMakeLists.txt

	- code cleaning

modified:   error.cpp
modified:   testSolver.cpp

- solver refinement over whole domain

modified:   testSolver.cpp

- bug fix in Solver.h (forgot to uncomment if-statement)

modified:   Solver.h
modified:   error.cpp

- solver L2 error norm test: no refinement vs. refinement.

modified:   README
modified:   Solver.h
new file:   error.cpp
modified:   iterative.cpp
modified:   testSolver.cpp

- Dirichlet BC on edge (an not on nodal point).

modified:   iterative.cpp

descriptor has been return by H5OpenFile()

	- bug fixes

modified:   AmrOpal.cpp
modified:   AmrOpal.h
modified:   AmrPartBunch.h
modified:   testAmrPartBunch.cpp