Ippl refactoring

Code:

• use Kokkos::View for fields (see !2 (merged))
• use Kokkos::View for particles (see !3 (merged))
• add more field functions (see !4 (merged))
• refactoring field layouts (see !19 (merged))
• refactoring particle layouts
• boundary conditions for particles (see !9 (merged) and !16 (merged))
• boundary conditions for fields (see !8 (merged))
• new expression interface for index classes
  • Index and IndexLines (see !26 (merged))
• code cleaning:
  • remove DataSource (see !5 (merged))
  • remove SubField and SubParticle classes (see !6 (merged))
  • remove deprecated Field and RNG classes (see !21 (merged))
  • remove Disc* classes (see !22 (merged))
  • remove *Debug files (see !23 (merged))
  • remove unused AppTypes (see !24 (merged))
  • remove PETE (see !28 (merged))
  • remove deprecated Particle classes (see !25 (merged))
  • remove IpplMessageCounter (see !27 (merged))
  • major code review of Index and NDIndex class (see !59 (merged))
  • remove deprecated Mesh classes (see !29 (merged))
  • remove leading Kokkos_ from field class (see !30 (merged))
  • remove deprecated Ippl options (see !31 (merged))
  • remove IpplCounter class (see !33 (merged))
  • remove deprecated Message classes (see !46 (merged))
  • remove Vec.h (see !47 (merged))
  • remove IpplParticleBase class (see !48 (merged))
  • replace ParticleSpatialLayout and RegionLayout (see !49 (merged))
  • remove deprecated DomainMap class (see !50 (merged))
  • remove unused classes (see !51 (merged))
  • remove deprecated IPPL tests (see !52 (merged))
  • cleanup NDRegion (see !53 (merged))
  • cleanup PRegion (see !54 (merged))
  • rename MPI files (see !55 (merged))
  • remove NamedObj.h (see !61 (merged))
  • remove deprecated functions of ParticleSpatialLayout (see !63 (merged))
  • cleanup UniformCartesian (see !79 (merged))
• FFT:
  • link to HeFFTe (see !69 (merged))
  • add FFT transform interface (see !70 (merged))
  • implement FFT transform with Kokkos
  • remove deprecated FFT interface of IPPL 1.0 (see !71 (merged))
• reduction operations for particle classes (see !32 (merged))
• domain decomposition:
  • add new load balancing interface
  • remove deprecated load balancing
• inter-node communication:
  • update general MPI interface:
    • remove CommCreator class (see !37 (merged))
    • remove unused members and unused class CommSendInfo (see !38 (merged))
    • use of Boost.MPI (see !39 (merged))
  • sending / receiving particle data (see !43 (merged))
  • sending / receiving field data
  • field halo exchange (see !62 (merged))
  • collective operations (e.g. reduce) (see !66 (merged))
  • improve the way in which particle update is called
  • recursive bisection algorithm
  • non-blocking receive for particles
  • non-blocking receive for field data (halo exchange)
  • send field data as 3d data (i.e., do not serialize as 1d arrays)
  • make HaloCells dimension independent (see !157 (merged))
  • periodic boundary condition for halo exchange (see !64 (merged))
  • add boost collectives in the communicator class (we do not use Boost anymore)
• enhance Timer class to catch Kokkos kernels (see !40 (merged))
• use Boost program options (see !57 (merged))

Tests: (GTest: !11 (merged))

• add unit tests for fields (see !11 (merged), !88 (merged), !97 (merged))
• add unit tests for particles (see #12 (closed))
• add unit tests for PIC operations:
  • scatter (see !15 (merged))
  • gather (see !36 (merged))
• add unit tests for index classes
• add unit test for FFT (see !157 (merged))
• add unit test for field BCs (see !44 (merged))
• add unit test for particle update (see !45 (merged))

Documentation:

• add old manual (see !10 (merged))
• Doxygen (see !56 (merged))