Merge pull request #259 from ablelly/choose_pml_direction

Choose pml direction

Author: MaxThevenet

Docs/source/running_cpp/parameters.rst

@@ -661,6 +661,12 @@ Boundary conditions
     The characteristic depth, in number of cells, over which
     the absorption coefficients of the PML increases.
 
+* ``warpx.do_pml_Lo`` (`2 ints in 2D`, `3 ints in 3D`; default: `1 1 1`)
+    The directions along which one wants a pml boundary condition for lower boundaries on mother grid.
+
+* ``warpx.do_pml_Hi`` (`2 floats in 2D`, `3 floats in 3D`; default: `1 1 1`)
+    The directions along which one wants a pml boundary condition for upper boundaries on mother grid.
+
 Diagnostics and output
 ----------------------
 

Source/BoundaryConditions/PML.H

@@ -101,7 +101,8 @@ public:
 #ifdef WARPX_USE_PSATD
          amrex::Real dt, int nox_fft, int noy_fft, int noz_fft, bool do_nodal,
 #endif
-         int do_dive_cleaning, int do_moving_window);
+         int do_dive_cleaning, int do_moving_window,
+         const amrex::IntVect do_pml_Lo, const amrex::IntVect do_pml_Hi);
 
     void ComputePMLFactors (amrex::Real dt);
 
@@ -172,7 +173,9 @@ private:
 #endif
 
     static amrex::BoxArray MakeBoxArray (const amrex::Geometry& geom,
-                                         const amrex::BoxArray& grid_ba, int ncell);
+                                         const amrex::BoxArray& grid_ba, int ncell,
+                                         const amrex::IntVect do_pml_Lo,
+                                         const amrex::IntVect do_pml_Hi);
 
     static void Exchange (amrex::MultiFab& pml, amrex::MultiFab& reg, const amrex::Geometry& geom);
 };

Source/BoundaryConditions/PML.cpp

@@ -319,11 +319,12 @@ PML::PML (const BoxArray& grid_ba, const DistributionMapping& grid_dm,
 #ifdef WARPX_USE_PSATD
           Real dt, int nox_fft, int noy_fft, int noz_fft, bool do_nodal,
 #endif
-          int do_dive_cleaning, int do_moving_window)
+          int do_dive_cleaning, int do_moving_window,
+          const amrex::IntVect do_pml_Lo, const amrex::IntVect do_pml_Hi)
     : m_geom(geom),
       m_cgeom(cgeom)
 {
-    const BoxArray& ba = MakeBoxArray(*geom, grid_ba, ncell);
+    const BoxArray& ba = MakeBoxArray(*geom, grid_ba, ncell, do_pml_Lo, do_pml_Hi);
     if (ba.size() == 0) {
         m_ok = false;
         return;
@@ -399,7 +400,7 @@ PML::PML (const BoxArray& grid_ba, const DistributionMapping& grid_dm,
 
         BoxArray grid_cba = grid_ba;
         grid_cba.coarsen(ref_ratio);
-        const BoxArray& cba = MakeBoxArray(*cgeom, grid_cba, ncell);
+        const BoxArray& cba = MakeBoxArray(*cgeom, grid_cba, ncell, do_pml_Lo, do_pml_Hi);
 
         DistributionMapping cdm{cba};
 
@@ -438,12 +439,18 @@ PML::PML (const BoxArray& grid_ba, const DistributionMapping& grid_dm,
 }
 
 BoxArray
-PML::MakeBoxArray (const amrex::Geometry& geom, const amrex::BoxArray& grid_ba, int ncell)
+PML::MakeBoxArray (const amrex::Geometry& geom, const amrex::BoxArray& grid_ba, int ncell,
+                   const amrex::IntVect do_pml_Lo, const amrex::IntVect do_pml_Hi)
 {
     Box domain = geom.Domain();
     for (int idim = 0; idim < AMREX_SPACEDIM; ++idim) {
         if ( ! geom.isPeriodic(idim) ) {
-            domain.grow(idim, ncell);
+            if (do_pml_Lo[idim]){
+                domain.growLo(idim, ncell);
+            }
+            if (do_pml_Hi[idim]){
+                domain.growHi(idim, ncell);
+            }
         }
     }
 

Source/Initialization/WarpXInitData.cpp

@@ -131,21 +131,35 @@ WarpX::InitPML ()
 {
     if (do_pml)
     {
+        amrex::IntVect do_pml_Lo_corrected = do_pml_Lo;
+
+#ifdef WARPX_DIM_RZ
+        do_pml_Lo_corrected[0] = 0; // no PML at r=0, in cylindrical geometry
+#endif
         pml[0].reset(new PML(boxArray(0), DistributionMap(0), &Geom(0), nullptr,
                              pml_ncell, pml_delta, 0,
 #ifdef WARPX_USE_PSATD
                              dt[0], nox_fft, noy_fft, noz_fft, do_nodal,
 #endif
-                             do_dive_cleaning, do_moving_window));
+                             do_dive_cleaning, do_moving_window,
+                             do_pml_Lo_corrected, do_pml_Hi));
         for (int lev = 1; lev <= finest_level; ++lev)
         {
+            amrex::IntVect do_pml_Lo_MR = amrex::IntVect::TheUnitVector();
+#ifdef WARPX_DIM_RZ
+            //In cylindrical geometry, if the edge of the patch is at r=0, do not add PML
+            if ((max_level > 0) && (fine_tag_lo[0]==0.)) {
+                do_pml_Lo_MR[0] = 0;
+            }
+#endif
             pml[lev].reset(new PML(boxArray(lev), DistributionMap(lev),
                                    &Geom(lev), &Geom(lev-1),
                                    pml_ncell, pml_delta, refRatio(lev-1)[0],
 #ifdef WARPX_USE_PSATD
                                    dt[lev], nox_fft, noy_fft, noz_fft, do_nodal,
 #endif
-                                   do_dive_cleaning, do_moving_window));
+                                   do_dive_cleaning, do_moving_window,
+                                   do_pml_Lo_MR, amrex::IntVect::TheUnitVector()));
         }
     }
 }

Source/WarpX.H

@@ -496,6 +496,8 @@ private:
     int do_pml = 1;
     int pml_ncell = 10;
     int pml_delta = 10;
+    amrex::IntVect do_pml_Lo = amrex::IntVect::TheUnitVector();
+    amrex::IntVect do_pml_Hi = amrex::IntVect::TheUnitVector();
     amrex::Vector<std::unique_ptr<PML> > pml;
 
     amrex::Real moving_window_x = std::numeric_limits<amrex::Real>::max();

Source/WarpX.cpp

@@ -383,6 +383,22 @@ WarpX::ReadParameters ()
         pp.query("pml_ncell", pml_ncell);
         pp.query("pml_delta", pml_delta);
 
+        Vector<int> parse_do_pml_Lo(AMREX_SPACEDIM,1);
+        pp.queryarr("do_pml_Lo", parse_do_pml_Lo);
+        do_pml_Lo[0] = parse_do_pml_Lo[0];
+        do_pml_Lo[1] = parse_do_pml_Lo[1];
+#if (AMREX_SPACEDIM == 3)
+        do_pml_Lo[2] = parse_do_pml_Lo[2];
+#endif
+        Vector<int> parse_do_pml_Hi(AMREX_SPACEDIM,1);
+        pp.queryarr("do_pml_Hi", parse_do_pml_Hi);
+        do_pml_Hi[0] = parse_do_pml_Hi[0];
+        do_pml_Hi[1] = parse_do_pml_Hi[1];
+#if (AMREX_SPACEDIM == 3)
+        do_pml_Hi[2] = parse_do_pml_Hi[2];
+#endif
+
+
         pp.query("dump_openpmd", dump_openpmd);
         pp.query("dump_plotfiles", dump_plotfiles);
         pp.query("plot_raw_fields", plot_raw_fields);
@@ -393,7 +409,7 @@ WarpX::ReadParameters ()
         if (not user_fields_to_plot){
             // If not specified, set default values
             fields_to_plot = {"Ex", "Ey", "Ez", "Bx", "By",
-                              "Bz", "jx", "jy", "jz", 
+                              "Bz", "jx", "jy", "jz",
                               "part_per_cell"};
         }
         // set plot_rho to true of the users requests it, so that
@@ -411,9 +427,9 @@ WarpX::ReadParameters ()
         // If user requests to plot proc_number for a serial run,
         // delete proc_number from fields_to_plot
         if (ParallelDescriptor::NProcs() == 1){
-            fields_to_plot.erase(std::remove(fields_to_plot.begin(), 
-                                             fields_to_plot.end(), 
-                                             "proc_number"), 
+            fields_to_plot.erase(std::remove(fields_to_plot.begin(),
+                                             fields_to_plot.end(),
+                                             "proc_number"),
                                  fields_to_plot.end());
         }
 
@@ -497,7 +513,7 @@ WarpX::ReadParameters ()
     {
         ParmParse pp("algo");
         // If not in RZ mode, read use_picsar_deposition
-        // In RZ mode, use_picsar_deposition is on, as the C++ version 
+        // In RZ mode, use_picsar_deposition is on, as the C++ version
         // of the deposition does not support RZ
         pp.query("use_picsar_deposition", use_picsar_deposition);
         current_deposition_algo = GetAlgorithmInteger(pp, "current_deposition");