Implement pure-SoA HDF5 particle IO (#5204)

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:
- [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

Author: atmyers

Src/Extern/HDF5/AMReX_ParticleHDF5.H

@@ -138,7 +138,11 @@ void WriteHDF5ParticleDataSync (PC const& pc,
     const int NProcs = ParallelDescriptor::NProcs();
     const int IOProcNumber = ParallelDescriptor::IOProcessorNumber();
 
-    AMREX_ALWAYS_ASSERT(real_comp_names.size() == pc.NumRealComps() + NStructReal);
+    {
+        int nrc = PC::ParticleType::is_soa_particle ?
+            pc.NumRealComps() + NStructReal - AMREX_SPACEDIM : pc.NumRealComps() + NStructReal;
+        AMREX_ALWAYS_ASSERT(static_cast<int>(real_comp_names.size()) == nrc);
+    }
     AMREX_ALWAYS_ASSERT( int_comp_names.size() == pc.NumIntComps() + NStructInt);
 
 #ifdef AMREX_USE_HDF5_ASYNC
@@ -273,7 +277,7 @@ void WriteHDF5ParticleDataSync (PC const& pc,
         CreateWriteHDF5AttrString(fid, "version_name", versionName.c_str());
 
         int num_output_real = 0;
-        for (int i = 0; i < pc.NumRealComps() + NStructReal; ++i) {
+        for (int i = 0; i < static_cast<int>(write_real_comp.size()); ++i) {
             if (write_real_comp[i]) { ++num_output_real; }
         }
 
@@ -298,7 +302,7 @@ void WriteHDF5ParticleDataSync (PC const& pc,
         // Real component names
         int real_comp_count = AMREX_SPACEDIM; // position values
 
-        for (int i = 0; i < NStructReal + pc.NumRealComps(); ++i ) {
+        for (int i = 0; i < static_cast<int>(write_real_comp.size()); ++i ) {
             if (write_real_comp[i]) {
                 /* HdrFile << real_comp_names[i] << '\n'; */
                 snprintf(comp_name, sizeof comp_name, "real_component_%d", real_comp_count);

Src/Extern/HDF5/AMReX_WriteBinaryParticleDataHDF5.H

@@ -0,0 +1,12 @@
+# This test requires particle support
+if (NOT AMReX_PARTICLES)
+   return()
+endif ()
+
+foreach(D IN LISTS AMReX_SPACEDIM)
+    set(_sources main.cpp)
+
+    setup_test(${D} _sources _input_files)
+
+    unset(_sources)
+endforeach()

Tests/Particles/CheckpointRestartDualGridHDF5SOA/CMakeLists.txt

@@ -0,0 +1,34 @@
+AMREX_HOME = ../../../
+
+DEBUG	= FALSE
+
+DIM	= 3
+
+COMP    = gnu
+
+PRECISION = DOUBLE
+
+USE_MPI   = TRUE
+MPI_THREAD_MULTIPLE = FALSE
+
+USE_OMP   = FALSE
+
+TINY_PROFILE = TRUE
+
+USE_PARTICLES = TRUE
+
+USE_HDF5  = FALSE
+# Set HDF5_HOME to the root of your HDF5 installation, e.g.:
+# HDF5_HOME = /path/to/hdf5
+
+###################################################
+
+EBASE     = main
+
+include $(AMREX_HOME)/Tools/GNUMake/Make.defs
+
+include ./Make.package
+include $(AMREX_HOME)/Src/Base/Make.package
+include $(AMREX_HOME)/Src/Particle/Make.package
+
+include $(AMREX_HOME)/Tools/GNUMake/Make.rules

Tests/Particles/CheckpointRestartDualGridHDF5SOA/GNUmakefile

@@ -0,0 +1 @@
+CEXE_sources += main.cpp