changes made after merging with lastest dev version

1 files changed, 40 insertions, 5 deletions

diff --git a/Source/Particles/PhysicalParticleContainer.cpp b/Source/Particles/PhysicalParticleContainer.cpp
index a1d4e1319..8ef4c13a9 100644
--- a/Source/Particles/PhysicalParticleContainer.cpp
+++ b/Source/Particles/PhysicalParticleContainer.cpp
@@ -82,6 +82,40 @@ PhysicalParticleContainer::PhysicalParticleContainer (AmrCore* amr_core, int isp
     pp.query("do_splitting", do_splitting);
     pp.query("split_type", split_type);
     pp.query("do_continuous_injection", do_continuous_injection);
+    // Whether to plot back-transformed (lab-frame) diagnostics 
+    // for this species.
+    pp.query("do_boosted_frame_diags", do_boosted_frame_diags);
+
+    pp.query("plot_species", plot_species);
+    int do_user_plot_vars;
+    do_user_plot_vars = pp.queryarr("plot_vars", plot_vars);
+    if (not do_user_plot_vars){
+        // By default, all particle variables are dumped to plotfiles,
+        // including {x,y,z,ux,uy,uz}old variables when running in a 
+        // boosted frame
+        if (WarpX::do_boosted_frame_diagnostic && do_boosted_frame_diags){
+            plot_flags.resize(PIdx::nattribs + 6, 1);
+        } else {
+            plot_flags.resize(PIdx::nattribs, 1);
+        }
+    } else {
+        // Set plot_flag to 0 for all attribs
+        if (WarpX::do_boosted_frame_diagnostic && do_boosted_frame_diags){
+            plot_flags.resize(PIdx::nattribs + 6, 0);
+        } else {
+            plot_flags.resize(PIdx::nattribs, 0);
+        }
+        // If not none, set plot_flags values to 1 for elements in plot_vars.
+        if (plot_vars[0] != "none"){
+            for (const auto& var : plot_vars){
+                // Return error if var not in PIdx. 
+                AMREX_ALWAYS_ASSERT_WITH_MESSAGE( 
+                    ParticleStringNames::to_index.count(var), 
+                    "plot_vars argument not in ParticleStringNames");
+                plot_flags[ParticleStringNames::to_index.at(var)] = 1;
+            }
+        }
+    }
 }
 
 PhysicalParticleContainer::PhysicalParticleContainer (AmrCore* amr_core)
@@ -185,7 +219,7 @@ PhysicalParticleContainer::AddGaussianBeam(Real x_m, Real y_m, Real z_m,
             attribs[PIdx::uz] = u[2];
             attribs[PIdx::w ] = weight;
 
-            if (WarpX::do_boosted_frame_diagnostic && WarpX::do_boosted_frame_particles)
+            if (WarpX::do_boosted_frame_diagnostic && do_boosted_frame_diags)
             {
                 auto& particle_tile = DefineAndReturnParticleTile(0, 0, 0);
                 particle_tile.push_back_real(particle_comps["xold"], x);
@@ -469,7 +503,7 @@ PhysicalParticleContainer::AddPlasmaCPU (int lev, RealBox part_realbox)
                     attribs[PIdx::uy] = u[1];
                     attribs[PIdx::uz] = u[2];
                     
-                    if (WarpX::do_boosted_frame_diagnostic && WarpX::do_boosted_frame_particles)
+                    if (WarpX::do_boosted_frame_diagnostic && do_boosted_frame_diags)
                     {
                         auto& particle_tile = DefineAndReturnParticleTile(lev, grid_id, tile_id);
                         particle_tile.push_back_real(particle_comps["xold"], x);
@@ -711,7 +745,7 @@ PhysicalParticleContainer::AddPlasmaGPU (int lev, RealBox part_realbox)
                     attribs[PIdx::uz] = u[2];
 
                     // note - this will be slow on the GPU, need to revisit
-                    if (WarpX::do_boosted_frame_diagnostic && WarpX::do_boosted_frame_particles)
+                    if (WarpX::do_boosted_frame_diagnostic && do_boosted_frame_diags)
                     {
                         auto& particle_tile = DefineAndReturnParticleTile(lev, grid_id, tile_id);
                         particle_tile.push_back_real(particle_comps["xold"], x);
@@ -801,7 +835,6 @@ FieldGatherES (const amrex::Vector<std::array<std::unique_ptr<amrex::MultiFab>,
             const auto& particles = pti.GetArrayOfStructs();
             int nstride = particles.dataShape().first;
             const long np  = pti.numParticles();
-
             auto& attribs = pti.GetAttribs();
             auto& Exp = attribs[PIdx::Ex];
             auto& Eyp = attribs[PIdx::Ey];
@@ -1686,7 +1719,7 @@ PhysicalParticleContainer::PushPX(WarpXParIter& pti,
     auto& Bzp = attribs[PIdx::Bz];
     const long np  = pti.numParticles();
 
-    if (WarpX::do_boosted_frame_diagnostic && WarpX::do_boosted_frame_particles)
+    if (WarpX::do_boosted_frame_diagnostic && do_boosted_frame_diags)
     {
         auto& xpold    = pti.GetAttribs(particle_comps["xold"]);
         auto& ypold    = pti.GetAttribs(particle_comps["yold"]);
@@ -1831,6 +1864,8 @@ void PhysicalParticleContainer::GetParticleSlice(const int direction, const Real
     // Note the the slice should always move in the negative boost direction.
     AMREX_ALWAYS_ASSERT(z_new < z_old);
 
+    AMREX_ALWAYS_ASSERT(do_boosted_frame_diags == 1);
+
     const int nlevs = std::max(0, finestLevel()+1);
 
     // we figure out a box for coarse-grained rejection. If the RealBox corresponding to a