Ippl refactoring

[matt-frey]

Code:

• [x] use Kokkos::View for fields (see !2)
• [x] use Kokkos::View for particles (see !3)
• [x] add more field functions (see !4)
• [x] refactoring field layouts (see !19)
• [x] refactoring particle layouts
• [x] boundary conditions for particles (see !9 and !16)
• [x] boundary conditions for fields (see !8)
• [x] new expression interface for index classes
  • [x] Index and IndexLines (see !26)
• [x] code cleaning:
  • [x] remove DataSource (see !5)
  • [x] remove SubField and SubParticle classes (see !6)
  • [x] remove deprecated Field and RNG classes (see !21)
  • [x] remove Disc* classes (see !22)
  • [x] remove *Debug files (see !23)
  • [x] remove unused AppTypes (see !24)
  • [x] remove PETE (see !28)
  • [x] remove deprecated Particle classes (see !25)
  • [x] remove IpplMessageCounter (see !27)
  • [x] major code review of Index and NDIndex class (see !59)
  • [x] remove deprecated Mesh classes (see !29)
  • [x] remove leading Kokkos_ from field class (see !30)
  • [x] remove deprecated Ippl options (see !31)
  • [x] remove IpplCounter class (see !33)
  • [x] remove deprecated Message classes (see !46)
  • [x] remove Vec.h (see !47)
  • [x] remove IpplParticleBase class (see !48)
  • [x] replace ParticleSpatialLayout and RegionLayout (see !49)
  • [x] remove deprecated DomainMap class (see !50)
  • [x] remove unused classes (see !51)
  • [x] remove deprecated IPPL tests (see !52)
  • [x] cleanup NDRegion (see !53)
  • [x] cleanup PRegion (see !54)
  • [x] rename MPI files (see !55)
  • [x] remove NamedObj.h (see !61)
  • [x] remove deprecated functions of ParticleSpatialLayout (see !63)
  • [x] cleanup UniformCartesian (see !79)
• [ ] FFT:
  • [x] link to HeFFTe (see !69)
  • [x] add FFT transform interface (see !70)
  • [ ] implement FFT transform with Kokkos
  • [x] remove deprecated FFT interface of IPPL 1.0 (see !71)
• [x] 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:
    • [x] remove CommCreator class (see !37)
    • [x] remove unused members and unused class CommSendInfo (see !38)
    • [x] use of Boost.MPI (see !39)
  • [x] sending / receiving particle data (see !43)
  • [x] sending / receiving field data
  • [x] field halo exchange (see !62)
  • [x] 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)
  • [x] make HaloCells dimension independent (see !157)
  • [x] periodic boundary condition for halo exchange (see !64)
  • [x] add boost collectives in the communicator class (we do not use Boost anymore)
• [x] enhance Timer class to catch Kokkos kernels (see !40)
• [x] use Boost program options (see !57)

Tests: (GTest: !11)

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

Documentation:

• [x] add old manual (see !10)
• [ ] Doxygen (see !56)

[matt-frey]

marked the task refactoring particle layouts as completed

[matt-frey]

marked the task remove deprecated functions of ParticleSpatialLayout (see !63) as completed

[matt-frey]

marked the task sending / receiving field data as completed

[matt-frey]

marked the task field halo exchange (see !62) as completed

[matt-frey]

In GitLab by @srikrrish on Dec 1, 2020, 17:39

marked the task add unit test for particle update (see !45) as completed

[matt-frey]

In GitLab by @srikrrish on Dec 6, 2020, 20:48

marked the task collective operations (e.g. reduce) (see !66) as completed

[matt-frey]

marked the task link to HeFFTe (see !69) as completed

[matt-frey]

marked the task add FFT transform interface (see !70) as completed

[matt-frey]

marked the task remove deprecated FFT interface of IPPL 1.0 (see !71) as completed

[matt-frey]

marked the task code cleaning: as completed

[matt-frey]

marked the task cleanup UniformCartesian (see !79) as completed

[matt-frey]

marked the task periodic boundary condition for halo exchange (see !64) as completed

[matt-frey]

marked the task add boost collectives in the communicator class (we do not use Boost anymore) as completed

[matt-frey]

marked the task make HaloCells dimension independent (see !157) as completed

[matt-frey]

In GitLab by @vinciguerra_a on May 3, 2023, 13:16

marked the task add unit tests for fields as completed