added openPMD-api support for I/O

Src/Base/AMReX_PlotFileUtil.H

@@ -12,6 +12,10 @@
 #include <AMReX_PlotFileUtilHDF5.H>
 #endif
 
+#ifdef AMREX_USE_OPENPMD_API
+#include <AMReX_PlotFileUtilOPENPMD.H>
+#endif
+
 #include <ostream>
 #include <string>
 #include <memory>

Src/CMakeLists.txt

@@ -200,6 +200,10 @@ if (AMReX_HDF5)
  add_subdirectory(Extern/HDF5)
 endif ()
 
+if (AMReX_OPENPMD_API)
+ add_subdirectory(Extern/openPMD-api)
+endif()
+
 #
 # Print out summary -- do it here so we already linked all
 # libs at this point

Src/Extern/openPMD-api/AMReX_ParticlesOPENPMD.H

@@ -0,0 +1,85 @@
+#ifndef AMREX_PTL_OPENPMD_API_H
+#define AMREX_PTL_OPENPMD_API_H
+
+/**
+* This file is included from AMReX_ParticleCounter.H
+* and belongs to the class ParticleContainer_impl.
+* The namespace amrex was already declared.
+*
+* Therefore all the definitions in this file belongs to namespace amrex
+*/
+
+struct AMReX_PtlCounter
+{
+ int m_MPIRank = 0;
+ int m_MPISize = 1;
+
+ unsigned long long m_Total = 0;
+
+ std::vector<unsigned long long> m_ParticleCounterByLevel;
+
+ unsigned long GetTotalNumParticles () const { return m_Total;}
+
+ std::vector<unsigned long long> m_ParticleOffsetAtRank;
+ std::vector<unsigned long long> m_ParticleSizeAtRank;
+};
+
+
+void CountParticles()
+{
+
+ m_PtlCounter.m_MPISize = amrex::ParallelDescriptor::NProcs();
+ m_PtlCounter.m_MPIRank = amrex::ParallelDescriptor::MyProc();
+
+ m_PtlCounter.m_ParticleCounterByLevel.resize(this->finestLevel()+1);
+ m_PtlCounter.m_ParticleOffsetAtRank.resize(this->finestLevel()+1);
+ m_PtlCounter.m_ParticleSizeAtRank.resize(this->finestLevel()+1);
+
+ auto lf_GetParticleOffsetOfProcessor = [&](const long& numParticles,
+ unsigned long long& offset,
+ unsigned long long& sum) -> void
+ {
+ std::vector<long> result(m_PtlCounter.m_MPISize, 0);
+ amrex::ParallelGather::Gather (numParticles, result.data(), -1, amrex::ParallelDescriptor::Communicator());
+
+ sum = 0;
+ offset = 0;
+ for (int i=0; i<result.size(); i++) {
+ sum += result[i];
+ if ( i < m_PtlCounter.m_MPIRank)
+ offset += result[i];
+ }
+ };
+
+ for (auto currentLevel = 0; currentLevel <= this->finestLevel(); currentLevel++)
+ {
+ long numParticles = 0; // numParticles in this processor
+
+ //for (ParIter pti(*this, currentLevel); pti.isValid(); ++pti) {
+ for (ParConstIterType pti(*this, currentLevel); pti.isValid(); ++pti) {
+ auto numParticleOnTile = pti.numParticles();
+ numParticles += numParticleOnTile;
+ }
+
+ unsigned long long offset=0; // offset of this level
+ unsigned long long sum=0; // numParticles in this level (sum from all processors)
+ lf_GetParticleOffsetOfProcessor(numParticles, offset, sum);
+
+ m_PtlCounter.m_ParticleCounterByLevel[currentLevel] = sum;
+ m_PtlCounter.m_ParticleOffsetAtRank[currentLevel] = offset;
+ m_PtlCounter.m_ParticleSizeAtRank[currentLevel] = numParticles;
+
+ // adjust offset, it should be numbered after particles from previous levels
+ for (auto lv=0; lv<currentLevel; lv++)
+ {
+ m_PtlCounter.m_ParticleOffsetAtRank[currentLevel] += m_PtlCounter.m_ParticleCounterByLevel[lv];
+ }
+
+ m_PtlCounter.m_Total += sum;
+ }
+}
+
+AMReX_PtlCounter m_PtlCounter;
+#endif // AMREX_PTL_OPENPMD_API_H
+
+