openPMD: Handle Zero Particles Well (#2980)

* openPMD: Handle Zero Particles Well

When a time step for output encounters zero particles in a species,
then we still want to dump them as "empty" species in openPMD. That
simplifies post-processing a lot and we have the mechanisms in
openPMD for it :)

* openPMD: Emtpy Particle Writes

Write empty records for iterations (steps or lab steps for BTD,
respectively) without particles in a species.

* Re-order: ED-PIC & Constant Particle Records

- set attributes once
- set constant records once
- clean up into appropriate functions

* Enable BTD for ADIOS :)

Works now as well :tada:

* Fix lingo in comments (Reva)

Thank you!! :)

Co-authored-by: Revathi  Jambunathan <41089244+RevathiJambunathan@users.noreply.github.com>

Co-authored-by: Revathi  Jambunathan <41089244+RevathiJambunathan@users.noreply.github.com>

1 files changed, 1 insertions, 21 deletions

diff --git a/Source/Diagnostics/FlushFormats/FlushFormatOpenPMD.cpp b/Source/Diagnostics/FlushFormats/FlushFormatOpenPMD.cpp
index 951013555..4c31dbecd 100644
--- a/Source/Diagnostics/FlushFormats/FlushFormatOpenPMD.cpp
+++ b/Source/Diagnostics/FlushFormats/FlushFormatOpenPMD.cpp
@@ -100,26 +100,6 @@ FlushFormatOpenPMD::FlushFormatOpenPMD (const std::string& diag_name)
     engine_type, engine_parameters,
     warpx.getPMLdirections()
   );
-
-  // Temporarily adding Abort for adios filetype if species is selected for BTD output
-  bool species_output = true;
-  int write_species = 1;
-  std::vector< std::string > output_species_names;
-  bool species_specified = pp_diag_name.queryarr("species", output_species_names);
-  if (species_specified == true and output_species_names.size() > 0) {
-      species_output = true;
-  } else {
-      // By default species output is computed for all diagnostics, if write_species is not set to 0
-      species_output = true;
-  }
-  // Check user-defined option to turn off species output
-  pp_diag_name.query("write_species", write_species);
-  if (write_species == 0) species_output = false;
-  if (diag_type_str == "BackTransformed" and species_output == true) {
-      if (m_OpenPMDPlotWriter->OpenPMDFileType() == "bp") {
-          amrex::Abort(" Currently BackTransformed diagnostics type does not support species output for ADIOS backend. Please select h5 as openpmd backend");
-      }
-  }
 }
 
 void
@@ -155,7 +135,7 @@ FlushFormatOpenPMD::WriteToFile (
         varnames, mf, geom, output_levels, output_iteration, time, isBTD, full_BTD_snapshot);
 
     // particles: all (reside only on locally finest level)
-    m_OpenPMDPlotWriter->WriteOpenPMDParticles(particle_diags, isBTD, totalParticlesFlushedAlready);
+    m_OpenPMDPlotWriter->WriteOpenPMDParticles(particle_diags, isBTD, isLastBTDFlush, totalParticlesFlushedAlready);
 
     // signal that no further updates will be written to this iteration
     m_OpenPMDPlotWriter->CloseStep(isBTD, isLastBTDFlush);