Add runtime particle components to HDF5 wrapper

[jordanm304]

Summary

Add runtime components when computing the sizes/offsets for particle HDF5 files.

Additional background

Checklist

The proposed changes:

• [ x] 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

[atmyers]

@houjun Does this change look correct to you? Is there a similar change that needs to be made in RestartHDF5 to read the runtime components back in?

[houjun]

@atmyers, I just checked the code and this fix looks correct.
The restart code uses "NStructReal + NumRealComps()", and NumRealComps() = NArrayReal + NumRuntimeRealComps(). So no need to change RestartHDF5.
I don't remember why "NStructInt" and "NStructReal" were used, likely a copy-paste error from an earlier version of AMReX.

@jordanm304, to make things consistent, I'd recommend changing the fix to:

int_size  = count[grid] * (2 + NStructInt + NumIntComps());
real_size = count[grid] * (AMREX_SPACEDIM + NStructReal + NumRealComps());