Implement pure-SoA HDF5 particle IO

[atmyers]

This closes #5152. Although it's a bit worse than that issue indicated, HDF5 particle IO wasn't implemented for pure SoA at all. This PR does so.

The proposed changes:

• fix a bug or incorrect behavior in AMReX
• add new capabilities to AMReX
• changes answers in the test suite to more than roundoff level
• are likely to significantly affect the results of downstream AMReX users
• include documentation in the code and/or rst files, if appropriate

[ax3l]

@atmyers @WeiqunZhang I see in HPSF CI on H100 issues with:

The following tests FAILED:
93 - Particles_CheckpointRestartDualGridHDF5SOA_2d (Failed)
94 - Particles_CheckpointRestartDualGridHDF5SOA_3d (Failed)
96 - Particles_CheckpointRestartDualGridSOA_2d (Failed)
97 - Particles_CheckpointRestartDualGridSOA_3d (Failed)

Could this be from this PR?

[WeiqunZhang]

The failure can probably be reproduced locally. The issue is probably single precision build trying to read double precision data. If we cannot fix them quickly on Monday 3/30, maybe we can disable them for single precision so that we don't release 26.04 with known CTest issues.

[WeiqunZhang]

$ cd Tests/Particles/CheckpointRestartDualGridSOA/
$ make -j6 PRECISION=FLOAT USE_SINGLE_PRECISION_PARTICLES=TRUE
$ mpiexec -n 2 ./main3d.gnu.FLOAT.TPROF.MPI.ex
Initializing AMReX (26.03-107-g112b2d362859)...
MPI initialized with 2 MPI processes
MPI initialized with thread support level 0
AMReX (26.03-107-g112b2d362859) initialized
Test 1: restart with fewer levels than checkpoint
  PASSED
Test 2: restart with more levels than checkpoint
1::Assertion `sm_orig == sm_new' failed, file "main.cpp", line 133, Msg: Int component sum mismatch after restart (comp 0) !!!
SIGABRT
0::Assertion `sm_orig == sm_new' failed, file "main.cpp", line 133, Msg: Int component sum mismatch after restart (comp 0) !!!
SIGABRT
See Backtrace.1 file for details
See Backtrace.0 file for details

@atmyers

[WeiqunZhang]

I think the issue is casting int to float for reduction.

[WeiqunZhang]

#5255