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, 2 insertions, 1 deletions

diff --git a/Source/Diagnostics/FlushFormats/FlushFormatOpenPMD.cpp b/Source/Diagnostics/FlushFormats/FlushFormatOpenPMD.cpp
index e7874c4ff..4c7c9ab81 100644
--- a/Source/Diagnostics/FlushFormats/FlushFormatOpenPMD.cpp
+++ b/Source/Diagnostics/FlushFormats/FlushFormatOpenPMD.cpp
@@ -113,6 +113,7 @@ FlushFormatOpenPMD::WriteToFile (
     const amrex::Vector<ParticleDiag>& particle_diags, int output_levels,
     const std::string prefix, int file_min_digits, bool plot_raw_fields,
     bool plot_raw_fields_guards,
+    const bool use_pinned_pc,
     bool isBTD, int snapshotID, const amrex::Geometry& full_BTD_snapshot,
     bool isLastBTDFlush, const amrex::Vector<int>& totalParticlesFlushedAlready) const
 {
@@ -137,7 +138,7 @@ 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, isLastBTDFlush, totalParticlesFlushedAlready);
+    m_OpenPMDPlotWriter->WriteOpenPMDParticles(particle_diags, use_pinned_pc, isBTD, isLastBTDFlush, totalParticlesFlushedAlready);
 
     // signal that no further updates will be written to this iteration
     m_OpenPMDPlotWriter->CloseStep(isBTD, isLastBTDFlush);