[yt-dev] Revising the skeleton frontend

[Hsi-Yu Schive]

Hi all,

I just finish the GAMER frontend for YT, and below I want to summarize some
issues and things that might be confusing in the current skeleton frontend.
I appreciate if you could help validate these issues and/or clarify some
points in the section "Things to be clarified". Hopefully it will make
frontend implementation easier in the future. I'll collect all comments and
issue a PR for the revised skeleton. It will be complementary to the recent
PR #2130 by Jonah Miller, which provides an extremely helpful example
frontend.



*Things to be clarified:*============================
1. Difference between *FieldInfoContainer.known_other_fields* and
*GridIndex._detect_output_field*:
   => known_other_fields contains fields that *might* be in an output, and
lists their units and aliases. _detect_output_fields finds the fields that
are defined in the currently loaded dataset.

2. *Dataset.unique_identifier*:
   => ??

3. Set *AMRGridPatch.Parent = None* for grids without parents, and
*AMRGridPatch.Children
= []* for grids without children

4. Field array returned by *BaseIOHandler._read_fluid_selection* should be
contiguous along the z instead of x direction. Therefore, for C-like array
with the dimension [x][y][z] and for Fortran-like array with the the
dimension (z,y,x), a matrix transpose is required (e.g., using
np_array.transpose() or np_array.swapaxes(0,2))

5. *start_index, stop_index, *and *ActiveDimension*s in the AMRGridPatch
objects
   => ??
   (1) It looks like stop_index is not used anymore
   (2) ActiveDimensions will be set by AMRGridPatch._prepare_grid. So
perhaps frontend does not need to set it explicitly anymore
   (3) It seems that start_index is also calculated automatically

6. *chunk, selector, *and *_read_chunk_data* in io.py.
   => ??
   Also the following comment about caching is confusing:
      def _read_chunk_data(self, chunk, fields):
   # This reads the data from a single chunk, and is only used for caching.

7. float type:
   (1) *GridIndex.float_type* is the float type for left and right
simulation edges and must be float64 now
   (2) *BaseIOHandler._read_fluid_selection* should always return float64
now even if the on-disk data are stored in single precision

8. Difference between *add_output_field *and *add_field *used in
FieldInfoContainer.setup_fluid_fields:

9. Dataset._parse_parameter_file: what does the following comment mean
"Note that these are all assumed to be in code units; domain_left_edge and
domain_right_edge will be updated to be in code units at a later time"
   => Perhaps it means that "domain_left_edge and domain_right_edge will be
converted to YTArray automatically at a later time"?



*Missing procedure*============================
1. Add the new frontend in *frontends/api.py*
2. Set *GridIndex.max_level*
3. Set *Dataset.refine_by*


*Bugin the current skeleton frontend*
============================
1. data_structures.py: *self.dataset* is not set in GridIndex.__init__ when
calling self.index_filename = self.dataset.parameter_filename
2. data_structures.py: replace self.Parent=[] by *self.Parent = None*
3. fields.py: the *field_list *argument is missing in
FieldInfoContainer.__init__. This issue has been fixed in Jonah's PR.
    def __init__(self, ds, field_list):
       super(SkeletonFieldInfo, self).__init__(ds, field_list)


Sincerely,
Hsi-Yu (Justin)
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