Ippl refactoring

[matt-frey]

Code:

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

Tests: (GTest: !11)

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

Documentation:

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

[matt-frey]

In GitLab by @srikrrish on Oct 23, 2020, 22:41

marked the task use Kokkos::View for particles (see !3) as completed

[matt-frey]

In GitLab by @srikrrish on Oct 23, 2020, 22:41

marked the task use Kokkos::View for particles (see !3) as incomplete

[matt-frey]

In GitLab by @srikrrish on Oct 24, 2020, 15:22

marked the task use Kokkos::View for particles (see !3) as completed

[matt-frey]

In GitLab by @srikrrish on Oct 24, 2020, 15:22

marked the task add more field functions (see !4) as completed

[matt-frey]

With !11 we add the unit test environment. I propose that we implement for each new class such a test base. In addition the Doxygen documentation needs to be extended.

[matt-frey]

In GitLab by @srikrrish on Oct 26, 2020, 11:54

Great! I will add the other tests for differential operators, unary and binary also in to the gtest for fields. Same can be then done for particles.

[matt-frey]

👍
Ok, could you then approve !11. Thanks.

[matt-frey]

marked the task scatter (see !15) as completed

[matt-frey]

marked the task add unit tests for particles (see #12) as completed

[matt-frey]

marked the task boundary conditions for particles (see !9 and !16) as completed

[matt-frey]

marked the task add old manual (see !10) as completed

[matt-frey]

marked the task remove DataSource (see !5) as completed

[matt-frey]

marked the task remove SubField and SubParticle classes (see !6) as completed

[matt-frey]

marked the task remove deprecated Field and RNG classes (see !21) as completed

[matt-frey]

marked the task remove Disc classes (see !22)* as completed