Support Ghost Zone

[cindytsai]

Support Ghost Zone

Definitions and Terms

• Ghost cell are defined inside yt_field struct.
  • We assume that different fields can have different ghost cell in each dimension of the data array.
  • Field in different grids must have the same number of ghost cell.
  • short field_ghost_cell[6] is defined as number of cells to ignore at the beginning and the end of the data in each dimensions. Which means field_ghost_cell[0] is number of cells to ignore at the beginning of 0-dim of the data, and field_ghost_cell[1] is number of cells to ignore at the end of 0-dim.
• We don't pass ghost cell in hierarchy.
• We load them to python along with loading field_list dictionary.
• grid_dimensions and data_dim:
  • Ghost cell does not include in grid_dimension, they are just dimensions read by yt.
  • data_dim define in yt_data are the actual data dimension of the data_ptr to be wrapped, it contains ghost cell.
  • API:
    • grid_dimensions: [x][y][z] dimension read by yt. (yt_getGridInfo_Dimensions API)
    • data_dim: The actual data dimension of the pointer. (yt_getGridInfo_FieldData API)

TODOs

• Define ghost cell inside yt_field.
  • Each side can have different number of ghost zone.
  • Update yt_type_field.h.
• Remove redundant assignment, since new call for constructor on initialization.
• Wrap the data array correctly. (append_grid.cpp)
• Pass in ghost cell in field_list in libyt.param_yt dictionary.
• For derived_func, they should only generate grid without ghost zone.
  • No need to update yt_getGridInfo, since we define grid_dimension and data_dim in yt_data separately.
    • grid_dimensions: [x][y][z] dimension read by yt. (yt_getGridInfo_Dimensions API)
    • data_dim: The actual data dimension of the pointer. (yt_getGridInfo_FieldData API)
  • Check gamer derived function. (No need to change, but still ...)
• yt_rma_field transfer full grid, including ghost zone.
  • yt_rma_grid_info should change as well.
  • Be aware of yt_rma_field::prepare_data, the data dimension should include ghost cell.
• Add MPI_PATH to Makefile.
• Update libyt yt frontend.

Test Run

• libyt/example
  • ProjectionPlot
  • SlicePlot

Related Issue

• Support Enzo #4

[cindytsai]

Done 🎉 !
I'll start the PR when libyt Documents are done.