abort for openpmd bp backend if species is selected. Also write parti…

…cle output for BTD only if write_species is 1
ECP-WarpX · Oct 25, 2021 · bd81754 · bd81754
1 parent dd2c6d6
commit bd81754
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Showing 4 changed files with 41 additions and 20 deletions.
diff --git a/Source/Diagnostics/BTDiagnostics.cpp b/Source/Diagnostics/BTDiagnostics.cpp
@@ -110,16 +110,6 @@ void BTDiagnostics::DerivedInitData ()
     m_output_species.resize(m_num_buffers);
     m_totalParticles_flushed_already.resize(m_num_buffers);
     m_totalParticles_in_buffer.resize(m_num_buffers);
-    for (int i = 0; i < m_num_buffers; ++i) {
-        m_particles_buffer[i].resize(m_output_species_names.size());
-        m_totalParticles_flushed_already[i].resize(m_output_species_names.size());
-        m_totalParticles_in_buffer[i].resize(m_output_species_names.size());
-        // initialize these values to 0
-        for (int isp = 0; isp < m_totalParticles_flushed_already[i].size(); ++isp) {
-            m_totalParticles_flushed_already[i][isp] = 0;
-            m_totalParticles_in_buffer[i][isp] = 0;
-        }
-    }
 }
 
 void
@@ -664,9 +654,12 @@ BTDiagnostics::Flush (int i_buffer)
     // Reset the buffer counter to zero after flushing out data stored in the buffer.
     ResetBufferCounter(i_buffer);
     IncrementBufferFlushCounter(i_buffer);
-    UpdateTotalParticlesFlushed(i_buffer);
-    ResetTotalParticlesInBuffer(i_buffer);
-    ClearParticleBuffer(i_buffer);
+    // if particles are selected for output then update and reset counters
+    if (m_output_species_names.size() > 0) {
+        UpdateTotalParticlesFlushed(i_buffer);
+        ResetTotalParticlesInBuffer(i_buffer);
+        ClearParticleBuffer(i_buffer);
+    }
 }
 
 void BTDiagnostics::MergeBuffersForPlotfile (int i_snapshot)
@@ -933,6 +926,9 @@ BTDiagnostics::InitializeParticleBuffer ()
     auto& warpx = WarpX::GetInstance();
     const MultiParticleContainer& mpc = warpx.GetPartContainer();
     for (int i = 0; i < m_num_buffers; ++i) {
+        m_particles_buffer[i].resize(m_output_species_names.size());
+        m_totalParticles_flushed_already[i].resize(m_output_species_names.size());
+        m_totalParticles_in_buffer[i].resize(m_output_species_names.size());
         for (int isp = 0; isp < m_particles_buffer[i].size(); ++isp) {
             m_totalParticles_flushed_already[i][isp] = 0;
             m_totalParticles_in_buffer[i][isp] = 0;

diff --git a/Source/Diagnostics/Diagnostics.cpp b/Source/Diagnostics/Diagnostics.cpp
@@ -199,12 +199,18 @@ Diagnostics::InitData ()
             InitializeFieldBufferData(i_buffer, lev);
         }
     }
-    // When particle buffers, m_particle_boundary_buffer are included,
-    // they will be initialized here
-    InitializeParticleBuffer();
-    InitializeParticleFunctors();
 
     amrex::ParmParse pp_diag_name(m_diag_name);
+    // default for writing species output is 1
+    int write_species = 1;
+    pp_diag_name.query("write_species", write_species);
+    if (write_species == 1) {
+        // When particle buffers, m_particle_boundary_buffer are included,
+        // they will be initialized here
+        InitializeParticleBuffer();
+        InitializeParticleFunctors();
+    }
+
     amrex::Vector <amrex::Real> dummy_val(AMREX_SPACEDIM);
     if ( queryArrWithParser(pp_diag_name, "diag_lo", dummy_val, 0, AMREX_SPACEDIM) ||
          queryArrWithParser(pp_diag_name, "diag_hi", dummy_val, 0, AMREX_SPACEDIM) ) {
@@ -221,9 +227,6 @@ Diagnostics::InitData ()
         amrex::Print() << " WARNING: For full diagnostics on a reduced domain, particle io is not supported, yet! Therefore, particle-io is disabled for this diag " << m_diag_name << "\n";
     }
 
-    // default for writing species output is 1
-    int write_species = 1;
-    pp_diag_name.query("write_species", write_species);
     if (write_species == 0) {
         if (m_format == "checkpoint"){
             amrex::Abort("For checkpoint format, write_species flag must be 1.");

diff --git a/Source/Diagnostics/FlushFormats/FlushFormatOpenPMD.cpp b/Source/Diagnostics/FlushFormats/FlushFormatOpenPMD.cpp
@@ -82,6 +82,26 @@ FlushFormatOpenPMD::FlushFormatOpenPMD (const std::string& diag_name)
     operator_type, operator_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

diff --git a/Source/Diagnostics/WarpXOpenPMD.H b/Source/Diagnostics/WarpXOpenPMD.H
@@ -142,6 +142,8 @@ public:
               bool isBTD = false,
               const amrex::Geometry& full_BTD_snapshot=amrex::Geometry() ) const;
 
+  /** Return OpenPMD File type ("bp" or "h5" or "json")*/
+  std::string OpenPMDFileType () {return m_OpenPMDFileType;}
 
 private:
   void Init (openPMD::Access access, bool isBTD);