1 files changed, 99 insertions, 36 deletions

diff --git a/Source/Diagnostics/WarpXIO.cpp b/Source/Diagnostics/WarpXIO.cpp
index 186a8d45e..869d3580e 100644
--- a/Source/Diagnostics/WarpXIO.cpp
+++ b/Source/Diagnostics/WarpXIO.cpp
@@ -11,6 +11,8 @@
 #include <AMReX_AmrMeshInSituBridge.H>
 #endif
 
+#include "SliceDiagnostic.H"
+
 #ifdef AMREX_USE_ASCENT
 #include <ascent.hpp>
 #include <AMReX_Conduit_Blueprint.H>
@@ -84,11 +86,11 @@ WarpX::WriteWarpXHeader(const std::string& name) const
 
 	// Geometry
 	for (int i = 0; i < AMREX_SPACEDIM; ++i) {
-            HeaderFile << Geometry::ProbLo(i) << ' ';
+            HeaderFile << Geom(0).ProbLo(i) << ' ';
 	}
         HeaderFile << '\n';
         for (int i = 0; i < AMREX_SPACEDIM; ++i) {
-            HeaderFile << Geometry::ProbHi(i) << ' ';
+            HeaderFile << Geom(0).ProbHi(i) << ' ';
 	}
         HeaderFile << '\n';
 
@@ -283,7 +285,7 @@ WarpX::InitFromCheckpoint ()
 	    }
 	}
 
-	Geometry::ProbDomain(RealBox(prob_lo,prob_hi));
+        ResetProbDomain(RealBox(prob_lo,prob_hi));
 
 	for (int lev = 0; lev < nlevs; ++lev) {
 	    BoxArray ba;
@@ -422,14 +424,14 @@ WarpX::GetCellCenteredData() {
         AverageAndPackVectorField( *cc[lev], Efield_aux[lev], dcomp, ng );
         dcomp += 3;
         // then the magnetic field
-        AverageAndPackVectorField( *cc[lev], Efield_aux[lev], dcomp, ng );
+        AverageAndPackVectorField( *cc[lev], Bfield_aux[lev], dcomp, ng );
         dcomp += 3;
         // then the current density
         AverageAndPackVectorField( *cc[lev], current_fp[lev], dcomp, ng );
         dcomp += 3;
+        // then the charge density
         const std::unique_ptr<MultiFab>& charge_density = mypc->GetChargeDensity(lev);
         AverageAndPackScalarField( *cc[lev], *charge_density, dcomp, ng );
-
         cc[lev]->FillBoundary(geom[lev].periodicity());
     }
 
@@ -612,37 +614,7 @@ WarpX::WritePlotFile () const
         }
     }
 
-    Vector<std::string> particle_varnames;
-    particle_varnames.push_back("weight");
-
-    particle_varnames.push_back("momentum_x");
-    particle_varnames.push_back("momentum_y");
-    particle_varnames.push_back("momentum_z");
-
-    particle_varnames.push_back("Ex");
-    particle_varnames.push_back("Ey");
-    particle_varnames.push_back("Ez");
-
-    particle_varnames.push_back("Bx");
-    particle_varnames.push_back("By");
-    particle_varnames.push_back("Bz");
-
-#ifdef WARPX_RZ
-    particle_varnames.push_back("theta");
-#endif
-
-    if (WarpX::do_boosted_frame_diagnostic && WarpX::do_boosted_frame_particles)
-    {
-        particle_varnames.push_back("xold");
-        particle_varnames.push_back("yold");
-        particle_varnames.push_back("zold");
-
-        particle_varnames.push_back("uxold");
-        particle_varnames.push_back("uyold");
-        particle_varnames.push_back("uzold");
-    }
-
-    mypc->WritePlotFile(plotfilename, particle_plot_flags, particle_varnames);
+    mypc->WritePlotFile(plotfilename);
 
     WriteJobInfo(plotfilename);
 
@@ -771,3 +743,94 @@ WarpX::WriteJobInfo (const std::string& dir) const
 	jobInfoFile.close();
     }
 }
+
+
+/* \brief
+ *  The slice is ouput using visMF and can be visualized used amrvis. 
+ */
+void
+WarpX::WriteSlicePlotFile () const
+{
+    if (F_fp[0] ) {
+       VisMF::Write( (*F_slice[0]), "vismf_F_slice");
+    }
+
+    if (rho_fp[0]) {
+       VisMF::Write( (*rho_slice[0]), "vismf_rho_slice");
+    }
+
+    VisMF::Write( (*Efield_slice[0][0]), amrex::Concatenate("vismf_Ex_slice_",istep[0]));
+    VisMF::Write( (*Efield_slice[0][1]), amrex::Concatenate("vismf_Ey_slice_",istep[0]));
+    VisMF::Write( (*Efield_slice[0][2]), amrex::Concatenate("vismf_Ez_slice_",istep[0]));
+    VisMF::Write( (*Bfield_slice[0][0]), amrex::Concatenate("vismf_Bx_slice_",istep[0]));
+    VisMF::Write( (*Bfield_slice[0][1]), amrex::Concatenate("vismf_By_slice_",istep[0]));
+    VisMF::Write( (*Bfield_slice[0][2]), amrex::Concatenate("vismf_Bz_slice_",istep[0]));
+    VisMF::Write( (*current_slice[0][0]), amrex::Concatenate("vismf_jx_slice_",istep[0]));
+    VisMF::Write( (*current_slice[0][1]), amrex::Concatenate("vismf_jy_slice_",istep[0]));
+    VisMF::Write( (*current_slice[0][2]), amrex::Concatenate("vismf_jz_slice_",istep[0]));
+
+}
+
+
+void 
+WarpX::InitializeSliceMultiFabs ()
+{
+
+    int nlevels = Geom().size();
+
+    F_slice.resize(nlevels);
+    rho_slice.resize(nlevels);
+    current_slice.resize(nlevels);
+    Efield_slice.resize(nlevels);
+    Bfield_slice.resize(nlevels);
+
+}
+
+
+// To generate slice that inherits index type of underlying data //
+void 
+WarpX::SliceGenerationForDiagnostics ()
+{
+
+    Vector<Geometry> dom_geom;
+    dom_geom = Geom();
+
+    if (F_fp[0] ) {
+       F_slice[0] = CreateSlice( *F_fp[0].get(), dom_geom, slice_realbox, 
+                                 slice_cr_ratio );
+    }
+    if (rho_fp[0]) {
+       rho_slice[0] = CreateSlice( *rho_fp[0].get(), dom_geom, slice_realbox, 
+                                   slice_cr_ratio );
+    }
+
+    for (int idim = 0; idim < 3; ++idim) {
+       Efield_slice[0][idim] = CreateSlice( *Efield_fp[0][idim].get(), 
+                                dom_geom, slice_realbox, slice_cr_ratio );
+       Bfield_slice[0][idim] = CreateSlice( *Bfield_fp[0][idim].get(), 
+                               dom_geom, slice_realbox, slice_cr_ratio );
+       current_slice[0][idim] = CreateSlice( *current_fp[0][idim].get(), 
+                               dom_geom, slice_realbox, slice_cr_ratio );
+    }
+
+
+}
+
+
+void 
+WarpX::ClearSliceMultiFabs ()
+{
+
+    F_slice.clear();
+    rho_slice.clear();
+    current_slice.clear();
+    Efield_slice.clear();
+    Bfield_slice.clear();
+    F_slice.shrink_to_fit();
+    rho_slice.shrink_to_fit();
+    current_slice.shrink_to_fit();
+    Efield_slice.shrink_to_fit();
+    Bfield_slice.shrink_to_fit();
+
+}
+