enable h5 write, needs to be editted

src/Algorithms/ParallelTracker.cpp

@@ -861,11 +861,11 @@ void ParallelTracker::writePhaseSpace(const long long /*step*/, bool psDump, boo
         msg << level3 << "* Wrote beam statistics." << endl;
     }
 
-    /* \todo
-
     if (psDump && (itsBunch_m->getTotalNum() > 0)) {
         // Write fields to .h5 file.
-        const size_t localNum    = itsBunch_m->getLocalNum();
+        /*
+        auto pc = itsBunch_m->getParticleContainer();
+        const size_t localNum    = pc->getLocalNum();
         double distToLastStop    = stepSizes_m.getFinalZStop() - pathLength_m;
         Vector_t<double, 3> beta = itsBunch_m->RefPartP_m / Util::getGamma(itsBunch_m->RefPartP_m);
         Vector_t<double, 3> driftPerTimeStep =
@@ -909,10 +909,11 @@ void ParallelTracker::writePhaseSpace(const long long /*step*/, bool psDump, boo
         }
         if (!statDump && !driftToCorrectPosition)
             itsBunch_m->calcBeamParameters();
-
-        msg << *itsBunch_m << endl;
+        */
+        //msg << *itsBunch_m << endl;
         itsDataSink_m->dumpH5(itsBunch_m, FDext);
 
+        /*
         if (driftToCorrectPosition) {
             if (localNum > 0) {
                 itsBunch_m->R = stashedR;
@@ -924,10 +925,9 @@ void ParallelTracker::writePhaseSpace(const long long /*step*/, bool psDump, boo
 
             itsBunch_m->calcBeamParameters();
         }
-
+        */
         msg << level2 << "* Wrote beam phase space." << endl;
     }
-    */
 }
 
 void ParallelTracker::updateReference(const BorisPusher& pusher) {

src/Structure/H5PartWrapperForPT.cpp

@@ -407,10 +407,11 @@ void H5PartWrapperForPT::writeStepHeader(
 }
 
 void H5PartWrapperForPT::writeStepData(PartBunch_t* bunch) {
-    size_t numLocalParticles = bunch->getLocalNum();
+    auto pc = bunch->getParticleContainer();
+    size_t numLocalParticles = pc->getLocalNum();
 
     REPORTONERROR(H5PartSetNumParticles(file_m, numLocalParticles));
-    /* ADA
+
     std::vector<char> buffer(numLocalParticles * sizeof(h5_float64_t));
     char* buffer_ptr        = Util::c_data(buffer);
     h5_float64_t* f64buffer = reinterpret_cast<h5_float64_t*>(buffer_ptr);
@@ -418,29 +419,29 @@ void H5PartWrapperForPT::writeStepData(PartBunch_t* bunch) {
     h5_int32_t* i32buffer   = reinterpret_cast<h5_int32_t*>(buffer_ptr);
 
     for (size_t i = 0; i < numLocalParticles; ++i)
-        f64buffer[i] = bunch->R(i)(0);
+        f64buffer[i] = pc->R(i)[0];
     WRITEDATA(Float64, file_m, "x", f64buffer);
 
     for (size_t i = 0; i < numLocalParticles; ++i)
-        f64buffer[i] = bunch->R(i)(1);
+        f64buffer[i] = pc->R(i)[1];
     WRITEDATA(Float64, file_m, "y", f64buffer);
 
     for (size_t i = 0; i < numLocalParticles; ++i)
-        f64buffer[i] = bunch->R(i)(2);
+        f64buffer[i] = pc->R(i)[2];
     WRITEDATA(Float64, file_m, "z", f64buffer);
 
     for (size_t i = 0; i < numLocalParticles; ++i)
-        f64buffer[i] = bunch->P(i)(0);
+        f64buffer[i] = pc->P(i)[0];
     WRITEDATA(Float64, file_m, "px", f64buffer);
 
     for (size_t i = 0; i < numLocalParticles; ++i)
-        f64buffer[i] = bunch->P(i)(1);
+        f64buffer[i] = pc->P(i)[1];
     WRITEDATA(Float64, file_m, "py", f64buffer);
 
     for (size_t i = 0; i < numLocalParticles; ++i)
-        f64buffer[i] = bunch->P(i)(2);
+        f64buffer[i] = pc->P(i)[2];
     WRITEDATA(Float64, file_m, "pz", f64buffer);
-
+/*
     for (size_t i = 0; i < numLocalParticles; ++i)
         f64buffer[i] = bunch->Q(i);
     WRITEDATA(Float64, file_m, "q", f64buffer);
@@ -522,4 +523,4 @@ void H5PartWrapperForPT::writeStepData(PartBunch_t* bunch) {
         reportOnError(herr, __FILE__, __LINE__);
     }
     */
-}
\ No newline at end of file
+}

[sadr_m]

@adelmann There are some transformations on the particle position before writing hdf5 file that I commented out for now. It looks like OPAL allocates memory to store the old values, stashedR.create(localNum);, then does some operations on R before writing to a file, resets R to the stashed values, and then deletes the allocated memory after dumpH5 call. Should I replicate that? Or, we can just write phase space as it is without these transformations, and leave this post-processing task to the user.

[sadr_m]

@adelmann should I replace these with kokkos for loops? I am a bit confused. Is f64buffer on the host or device? Should I deep copy views from device to the host, and then pass it to WRITEDATA in the following line.

[adelmann]

yes we need a buffer. You can look in my branch fixSolverUnits and mybe just cheery pick this one. I know I should merge to the master ...

[adelmann]

and no there are no transformation on the data, just pain write