Implement output of scraped particles at domain boundaries (#3274)

* Implement scraping from all boundaries

* Update input script

* Output all particles to the same buffer

* Dump different boundaries into different files

* Avoid writing species that are not allocated

* Improve documentation

* Allow output of some boundaries only

* Correct compilation error

* Fixes and updates to BoundaryScraping

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

1 files changed, 9 insertions, 7 deletions

diff --git a/Source/Diagnostics/WarpXOpenPMD.cpp b/Source/Diagnostics/WarpXOpenPMD.cpp
index e45b9239d..ea93ca5d8 100644
--- a/Source/Diagnostics/WarpXOpenPMD.cpp
+++ b/Source/Diagnostics/WarpXOpenPMD.cpp
@@ -552,7 +552,8 @@ WarpXOpenPMDPlot::Init (openPMD::Access access, bool isBTD)
 
 void
 WarpXOpenPMDPlot::WriteOpenPMDParticles (const amrex::Vector<ParticleDiag>& particle_diags,
-                  const bool isBTD, const bool isLastBTDFlush, const amrex::Vector<int>& totalParticlesFlushedAlready)
+                  const bool use_pinned_pc, const bool isBTD, const bool isLastBTDFlush,
+                  const amrex::Vector<int>& totalParticlesFlushedAlready)
 {
   WARPX_PROFILE("WarpXOpenPMDPlot::WriteOpenPMDParticles()");
 
@@ -561,10 +562,11 @@ WarpXOpenPMDPlot::WriteOpenPMDParticles (const amrex::Vector<ParticleDiag>& part
     WarpXParticleContainer* pc = particle_diags[i].getParticleContainer();
     PinnedMemoryParticleContainer* pinned_pc = particle_diags[i].getPinnedParticleContainer();
     PinnedMemoryParticleContainer tmp;
-    if (! isBTD) {
-        tmp = pc->make_alike<amrex::PinnedArenaAllocator>();
-    } else {
+    if (isBTD || use_pinned_pc) {
+        if (!pinned_pc->isDefined()) continue; // Skip to the next particle container
         tmp = pinned_pc->make_alike<amrex::PinnedArenaAllocator>();
+    } else {
+        tmp = pc->make_alike<amrex::PinnedArenaAllocator>();
     }
     // names of amrex::Real and int particle attributes in SoA data
     amrex::Vector<std::string> real_names;
@@ -616,7 +618,9 @@ WarpXOpenPMDPlot::WriteOpenPMDParticles (const amrex::Vector<ParticleDiag>& part
       GeometryFilter const geometry_filter(particle_diags[i].m_do_geom_filter,
                                            particle_diags[i].m_diag_domain);
 
-      if (! isBTD) {
+      if (isBTD || use_pinned_pc) {
+          tmp.copyParticles(*pinned_pc, true);
+      } else {
           using SrcData = WarpXParticleContainer::ParticleTileType::ConstParticleTileDataType;
           tmp.copyParticles(*pc,
                             [=] AMREX_GPU_HOST_DEVICE (const SrcData& src, int ip, const amrex::RandomEngine& engine)
@@ -625,8 +629,6 @@ WarpXOpenPMDPlot::WriteOpenPMDParticles (const amrex::Vector<ParticleDiag>& part
               return random_filter(p, engine) * uniform_filter(p, engine)
                      * parser_filter(p, engine) * geometry_filter(p, engine);
           }, true);
-      } else if (isBTD) {
-          tmp.copyParticles(*pinned_pc, true);
       }
 
     // real_names contains a list of all real particle attributes.