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Fix #19

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Fix #19

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Fix bugs, Load Active Particles and Derived Fields

Doc

  • Fix the link.
  • Explain the usage of sm,pt2pt.

Bugs

  • Change user-parameter Gamma to gamma, since enzo's yt frontend reads ds.gamma.
  • Fix yt-parameter velocity_unit, magnetic_unit, periodicity.
  • Map EYT_PINT to YT_LONGLONG when -DCONFIG_PINT_8. (Note that in this setting, MPI is mapped to MPI_LONG_LONG_INT.)

Derived Fields

  • Generate derived fields (Temperature, Cooling_Time) and assign them as enzo inline fields. This avoids looking up grid ID when using libyt's generating data from C-function.

Active Particles

  • Load active particles to libyt.
  • When mapping the particle attributes data type to yt datatype, we use the hdf5 data type as an indicator. This avoids including libyt.h in ParticleAttributeHandler.h. And because hdf5 is a mandatory dependency, using hdf5 data type to map to yt data type won't have any conflict.
  • GetParticleAttributeNames, GetParticleAttributes, and GetParticleAttributesHDF5DataType are created in ActiveParticleHelpers namespace. They are used in libyt only. Since the active particle is created via a register_ptype function layer, adding them here will not alter the original behavior of the active particle.
    • GetParticleAttributes allocates a new data buffer and calls GetAttribute to fill in the buffer. These buffers will be freed after libyt is done. Currently, we only get the attributes that have 1 dimension. (Notice that GetAttribute shifts the buffer pointer when returning.)

cindytsai added 28 commits June 14, 2024 11:45
@cindytsai
Try generating Temperature / Cooling_Time in enzo and pass to libyt a…
9c76126 
…s inline field.
@cindytsai
typo.
9466985
@cindytsai
typo
01c13a2
@cindytsai
typo
bbce99e
@cindytsai
typo.
8bba70c
@cindytsai
forgot to clear all pointer once freed.
565d2bb
@cindytsai
The Cooling_Time field unit computed from ComputeCoolingTime is cod…
0861427 
…e_time.
@cindytsai
Change Gamma to gamma, since yt reads ds.gamma.
3c3fd42
@cindytsai
Follow how New_Grid_WriteGrid output grid.
bd63595
@cindytsai
Fix velocity units.
4bb7c6a
@cindytsai
Fix magnetic_unit.
4488ffa
@cindytsai
Fix periodicity.
8ea3272
@cindytsai
typo.
a631777
@cindytsai
try to fix it through adding new method.
6a3769e
@cindytsai
Make sure the lifetime of attribute name exist througout the entire i…
39f7350 
…n situ.

We need this because libyt does not make a copy of the names.
@cindytsai
Map hdf5 type to yt_dtype (have error when compiling)
305c532
@cindytsai
Using if-else instead of switch, can compile and run.
c73ead2
@cindytsai
Remove commented out USE_LIBYT.
9bc581b
@cindytsai
Load active particle count.
91af696 
I don't know why there is two grid showing active particle count = 1.
There should only be one particle in this run, not sure if it overlapped.
@cindytsai
Rename GetParticleAttributes to GetParticleAttributeNames.
7ee8926
@cindytsai
Fill in particle buffer, and ignore multi-dimensional array for now
e82b0f5 
It pre-allocates buffers to store a copy of attribute data. They will free them when libyt ends.
@cindytsai
Typo.
07f52d9
@cindytsai
Get attribute value and pass to libyt. (The attributes read in libyt …
5380a50 
…are not correct)

The attributes are put in a new allocated buffer.
It will be freed when in situ analysis are done.
@cindytsai
Pass in the correct pointer for libyt.
202be41 
This is caused by GetAttribute _shifts_ the pointer passed in when returning.
@cindytsai
This should match to YT_LONGLONG
2248391
@cindytsai
Update link and version requirement.
cded658
@cindytsai
Clarify one-sided mpi sm,pt2pt settings.
0b99fd5
@cindytsai
Remove TODOs, and rename libyt_generated_derived_field to *_data.
ca79996
@cindytsai cindytsai requested a review from matthewturk June 14, 2024 17:30
cindytsai
cindytsai commented Jun 14, 2024
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@matthewturk , I totally forget about this PR.

This PR supports active particles and derived fields (though limited to Temperature and CoolingTime` only) in Enzo and fixes some bugs.

matthewturk
matthewturk reviewed Sep 6, 2024
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minor feedback otherwise LGTM

@cindytsai
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@matthewturk I have fixed the issues.

@cindytsai
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I think I should also update the version of libyt in the doc.

@cindytsai
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Done!

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@cindytsai @matthewturk