ECP-WarpX · RemiLehe · Aug 16, 2021 · Aug 11, 2021 · Aug 11, 2021 · Aug 11, 2021
diff --git a/Docs/source/dataanalysis/inputs.2d b/Docs/source/dataanalysis/inputs.2d
@@ -13,7 +13,8 @@ insitu.int = 2
 insitu.start = 0
 insitu.config = ez2d.xml
 geometry.coord_sys   = 0                  # 0: Cartesian
-geometry.is_periodic = 0 0      # Is periodic?
+boundary.field_lo = pml pml
+boundary.field_hi = pml pml
 geometry.prob_lo     = -125.e-6 -149.e-6 
 geometry.prob_hi     =  125.e-6    1.e-6 
 warpx.fine_tag_lo    =  -12.e-6 -110.e-6
@@ -29,7 +30,6 @@ algo.particle_pusher = 0
 algo.particle_shape = 3
 algo.maxwell_solver = ckc
 warpx.use_filter = 1
-warpx.do_pml = 1
 warpx.pml_ncell = 10
 warpx.cfl = .99
 warpx.do_moving_window = 1

diff --git a/Docs/source/usage/parameters.rst b/Docs/source/usage/parameters.rst
@@ -211,7 +211,7 @@ Domain Boundary Conditions
 --------------------------
 
 * ``boundary.field_lo`` and ``boundary.field_hi`` (`2 strings` for 2D, `3 strings` for 3D, `pml` by default)
-    Boundary conditions applied to field at the lower and upper domain boundaries. Depending on the type of boundary condition, the value for ``geometry.is_periodic`` will be set, overriding the user-input for the input parameter, ``geometry.is_periodic``. If not set, the default value for the fields at the domain boundary will be set to pml.
+    Boundary conditions applied to fields at the lower and upper domain boundaries. 
     Options are:
 
     * ``Periodic``: This option can be used to set periodic domain boundaries. Note that if the fields for lo in a certain dimension are set to periodic, then the corresponding upper boundary must also be set to periodic. If particle boundaries are not specified in the input file, then particles boundaries by default will be set to periodic. If particles boundaries are specified, then they must be set to periodic corresponding to the periodic field boundaries.

diff --git a/Examples/Physics_applications/plasma_acceleration/PICMI_inputs_plasma_acceleration_mr.py b/Examples/Physics_applications/plasma_acceleration/PICMI_inputs_plasma_acceleration_mr.py
@@ -35,7 +35,6 @@
                         hi = [25e-6, 25e-6, 200.e-6])
 
 solver = picmi.ElectromagneticSolver(grid=grid, cfl=1,
-                                     warpx_do_pml = True,
                                      warpx_pml_ncell = 10)
 
 beam_distribution = picmi.UniformDistribution(density = 1.e23,

diff --git a/Examples/Tests/Langmuir/PICMI_inputs_langmuir_rz_multimode_analyze.py b/Examples/Tests/Langmuir/PICMI_inputs_langmuir_rz_multimode_analyze.py
@@ -91,7 +91,7 @@
                              moving_window_zvelocity = 0.,
                              warpx_max_grid_size=64)
 
-solver = picmi.ElectromagneticSolver(grid=grid, cfl=1., warpx_do_pml=False)
+solver = picmi.ElectromagneticSolver(grid=grid, cfl=1.)
 
 ##########################
 # diagnostics

diff --git a/Examples/Tests/SilverMueller/inputs_2d_x b/Examples/Tests/SilverMueller/inputs_2d_x
@@ -23,7 +23,6 @@ warpx.verbose = 1
 
 # Algorithms
 warpx.cfl = 1.0
-warpx.do_pml = 0
 warpx.use_filter = 0
 
 warpx.do_moving_window = 0

diff --git a/Examples/Tests/SilverMueller/inputs_2d_z b/Examples/Tests/SilverMueller/inputs_2d_z
@@ -24,7 +24,6 @@ warpx.verbose = 1
 
 # Algorithms
 warpx.cfl = 1.0
-warpx.do_pml = 0
 warpx.use_filter = 0
 
 warpx.do_moving_window = 0

diff --git a/Examples/Tests/SilverMueller/inputs_rz_z b/Examples/Tests/SilverMueller/inputs_rz_z
@@ -27,7 +27,6 @@ warpx.n_rz_azimuthal_modes = 2
 
 # Algorithms
 warpx.cfl = 1.0
-warpx.do_pml = 0
 warpx.use_filter = 0
 
 warpx.do_moving_window = 0

diff --git a/Examples/Tests/boundaries/inputs_3d b/Examples/Tests/boundaries/inputs_3d
@@ -22,8 +22,6 @@ boundary.field_hi = pec pec periodic
 boundary.particle_lo = reflecting absorbing periodic
 boundary.particle_hi = reflecting absorbing periodic
 
-warpx.do_pml = 0
-
 # Algorithms
 algo.particle_shape = 1
 

diff --git a/Examples/Tests/galilean/inputs_rz b/Examples/Tests/galilean/inputs_rz
@@ -36,7 +36,6 @@ particles.species_names = electrons ions
 
 warpx.do_nodal = 1
 warpx.use_filter = 1
-warpx.do_pml = 0
 
 psatd.nox = 16
 psatd.noy = 16

diff --git a/Examples/Tests/multi_J/inputs_rz b/Examples/Tests/multi_J/inputs_rz
@@ -23,7 +23,6 @@ algo.particle_shape = 3
 
 # Numerics
 warpx.do_moving_window = 1
-warpx.do_pml = 0
 warpx.moving_window_dir = z
 warpx.moving_window_v = 1.
 warpx.n_rz_azimuthal_modes = 1

diff --git a/Examples/Tests/photon_pusher/analysis_photon_pusher.py b/Examples/Tests/photon_pusher/analysis_photon_pusher.py
@@ -120,10 +120,10 @@ def generate():
         f.write("amr.max_grid_size = 8\n")
         f.write("amr.plot_int = 1\n")
         f.write("geometry.coord_sys   = 0\n")
-        f.write("geometry.is_periodic = 1 1 1\n")
+        f.write("boundary.field_lo = periodic periodic periodic\n")
+        f.write("boundary.field_hi = periodic periodic periodic\n")
         f.write("geometry.prob_lo = -0.5e-6 -0.5e-6 -0.5e-6\n")
         f.write("geometry.prob_hi = 0.5e-6 0.5e-6 0.5e-6\n")
-        f.write("warpx.do_pml = 0\n")
         f.write("algo.charge_deposition = standard\n")
         f.write("algo.field_gathering = energy-conserving\n")
         f.write("warpx.cfl = 1.0\n")

diff --git a/Examples/Tests/plasma_lens/inputs_3d b/Examples/Tests/plasma_lens/inputs_3d
@@ -16,7 +16,6 @@ boundary.field_hi = pec pec pec
 boundary.particle_lo = absorbing absorbing absorbing
 boundary.particle_hi = absorbing absorbing absorbing
 
-warpx.do_pml = 0
 warpx.const_dt = 1.e-7
 warpx.do_electrostatic = labframe
 

diff --git a/Examples/Tests/radiation_reaction/test_const_B_analytical/analysis_classicalRR.py b/Examples/Tests/radiation_reaction/test_const_B_analytical/analysis_classicalRR.py
@@ -163,10 +163,10 @@ def generate():
         f.write("amr.blocking_factor = 32\n")
         f.write("amr.max_grid_size = 64\n")
         f.write("geometry.coord_sys   = 0\n")
-        f.write("geometry.is_periodic = 1 1 1\n")
+        f.write("boundary.field_lo = periodic periodic periodic\n")
+        f.write("boundary.field_hi = periodic periodic periodic\n")
         f.write("geometry.prob_lo = {} {} {}\n".format(-sim_size, -sim_size, -sim_size))
         f.write("geometry.prob_hi = {} {} {}\n".format(sim_size, sim_size, sim_size))
-        f.write("warpx.do_pml = 0\n")
         f.write("algo.charge_deposition = standard\n")
         f.write("algo.field_gathering = energy-conserving\n")
         f.write("warpx.cfl = 1.0\n")

diff --git a/Examples/Tests/radiation_reaction/test_const_B_analytical/inputs_3d b/Examples/Tests/radiation_reaction/test_const_B_analytical/inputs_3d
@@ -10,7 +10,6 @@ amr.max_grid_size = 64
 geometry.coord_sys   = 0
 geometry.prob_lo = -8e-07 -8e-07 -8e-07
 geometry.prob_hi = 8e-07 8e-07 8e-07
-warpx.do_pml = 0
 algo.charge_deposition = standard
 algo.field_gathering = energy-conserving
 warpx.cfl = 1.0

diff --git a/Python/pywarpx/picmi.py b/Python/pywarpx/picmi.py
@@ -525,7 +525,6 @@ class ElectromagneticSolver(picmistandard.PICMI_ElectromagneticSolver):
     def init(self, kw):
         assert self.method is None or self.method in ['Yee', 'CKC', 'PSATD'], Exception("Only 'Yee', 'CKC', and 'PSATD' are supported")
 
-        self.do_pml = kw.pop('warpx_do_pml', None)
         self.pml_ncell = kw.pop('warpx_pml_ncell', None)
 
         if self.method == 'PSATD':
@@ -539,7 +538,6 @@ def initialize_inputs(self):
 
         self.grid.initialize_inputs()
 
-        pywarpx.warpx.do_pml = self.do_pml
         pywarpx.warpx.pml_ncell = self.pml_ncell
         pywarpx.warpx.do_nodal = self.l_nodal
 

diff --git a/Source/WarpX.H b/Source/WarpX.H
@@ -433,6 +433,7 @@ public:
     void DampJPML (int lev, PatchType patch_type);
 
     void CopyJPML ();
+    bool isAnyBoundaryPML();
 
     /**
      * \brief Synchronize the nodal points of the PML MultiFabs

diff --git a/Source/WarpX.cpp b/Source/WarpX.cpp
@@ -666,14 +666,13 @@ WarpX::ReadParameters ()
             }
         }
 
-        pp_warpx.query("do_pml", do_pml);
         pp_warpx.query("pml_ncell", pml_ncell);
         pp_warpx.query("pml_delta", pml_delta);
         pp_warpx.query("pml_has_particles", pml_has_particles);
         pp_warpx.query("do_pml_j_damping", do_pml_j_damping);
         pp_warpx.query("do_pml_in_domain", do_pml_in_domain);
 
-        if (do_multi_J && do_pml)
+        if (do_multi_J && isAnyBoundaryPML())
         {
             amrex::Abort("Multi-J algorithm not implemented with PMLs");
         }
@@ -737,38 +736,8 @@ WarpX::ReadParameters ()
         }
 
 #ifdef WARPX_DIM_RZ
-        AMREX_ALWAYS_ASSERT_WITH_MESSAGE( do_pml==0,
-            "PML are not implemented in RZ geometry ; please set `warpx.do_pml=0`");
-#endif
-        // setting default to 0
-        Vector<int> parse_do_pml_Lo(AMREX_SPACEDIM,0);
-        // Switching pml lo to 1 when do_pml = 1 and if domain is non-periodic
-        // Note to remove this code when new BC API is fully functional
-        if (do_pml == 1) {
-            for (int idim = 0; idim < AMREX_SPACEDIM; ++idim) {
-                if ( Geom(0).isPeriodic(idim) == 0) parse_do_pml_Lo[idim] = 1;
-            }
-        }
-        pp_warpx.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
-        // setting default to 0
-        Vector<int> parse_do_pml_Hi(AMREX_SPACEDIM,0);
-        // Switching pml hi to 1 when do_pml = 1 and if domain is non-periodic
-        // Note to remove this code when new BC API is fully functional
-        if (do_pml == 1) {
-            for (int idim = 0; idim < AMREX_SPACEDIM; ++idim) {
-                if ( Geom(0).isPeriodic(idim) == 0) parse_do_pml_Hi[idim] = 1;
-            }
-        }
-        pp_warpx.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];
+        AMREX_ALWAYS_ASSERT_WITH_MESSAGE( isAnyBoundaryPML() == false,
+            "PML are not implemented in RZ geometry; please set a different boundary condition using boundary.field_lo and boundary.field_hi.");
 #endif
 
         if ( (do_pml_j_damping==1)&&(do_pml_in_domain==0) ){
@@ -1234,7 +1203,9 @@ WarpX::BackwardCompatibility ()
         amrex::Abort("warpx.use_kspace_filter is not supported anymore. "
                      "Please use the flag use_filter, see documentation.");
     }
-
+    if ( pp_warpx.query("do_pml", backward_int) ) {
+        amrex::Abort( "do_pml is not supported anymore. Please use boundary.field_lo and boundary.field_hi to set the boundary conditions.");
+    }
     ParmParse pp_interpolation("interpolation");
     if (pp_interpolation.query("nox", backward_int) ||
         pp_interpolation.query("noy", backward_int) ||
@@ -2305,3 +2276,13 @@ WarpX::PicsarVersion ()
     return std::string("Unknown");
 #endif
 }
+
+bool
+WarpX::isAnyBoundaryPML()
+{
+    for (int idim = 0; idim < AMREX_SPACEDIM; ++idim) {
+        if ( WarpX::field_boundary_lo[idim] == FieldBoundaryType::PML) return true;
+        if ( WarpX::field_boundary_hi[idim] == FieldBoundaryType::PML) return true;
+    }
+    return false;
+}
diff --git a/Tools/PerformanceTests/automated_test_1_uniform_rest_32ppc b/Tools/PerformanceTests/automated_test_1_uniform_rest_32ppc
@@ -23,7 +23,6 @@ boundary.particle_hi = absorbing absorbing periodic
 warpx.verbose = 1
 
 algo.particle_shape = 3
-warpx.do_pml = 0
 
 # CFL
 warpx.cfl = 1.0

diff --git a/Tools/PerformanceTests/automated_test_2_uniform_rest_1ppc b/Tools/PerformanceTests/automated_test_2_uniform_rest_1ppc
@@ -23,7 +23,6 @@ boundary.particle_hi = absorbing absorbing absorbing
 warpx.verbose = 1
 
 algo.particle_shape = 3
-warpx.do_pml = 1
 
 # CFL
 warpx.cfl = 1.0

diff --git a/Tools/PerformanceTests/automated_test_3_uniform_drift_4ppc b/Tools/PerformanceTests/automated_test_3_uniform_drift_4ppc
@@ -24,7 +24,6 @@ warpx.verbose = 1
 
 # Algorithms
 algo.particle_shape = 3
-warpx.do_pml = 0
 
 # CFL
 warpx.cfl = 1.0

diff --git a/Tools/PerformanceTests/automated_test_4_labdiags_2ppc b/Tools/PerformanceTests/automated_test_4_labdiags_2ppc
@@ -24,7 +24,6 @@ warpx.verbose = 1
 algo.particle_shape = 3
 warpx.use_filter = 1
 warpx.cfl = 1.0
-warpx.do_pml = 0
 
 # Moving window
 warpx.do_moving_window = 1

diff --git a/Tools/PerformanceTests/automated_test_5_loadimbalance b/Tools/PerformanceTests/automated_test_5_loadimbalance
@@ -22,7 +22,6 @@ boundary.particle_hi = absorbing absorbing periodic
 warpx.verbose = 1
 algo.load_balance_intervals = -5
 algo.particle_shape = 3
-warpx.do_pml = 0
 
 # CFL
 warpx.cfl = 1.0

diff --git a/Tools/PerformanceTests/automated_test_6_output_2ppc b/Tools/PerformanceTests/automated_test_6_output_2ppc
@@ -23,7 +23,6 @@ boundary.particle_hi = absorbing absorbing absorbing
 warpx.verbose = 1
 
 algo.particle_shape = 3
-warpx.do_pml = 0
 
 # CFL
 warpx.cfl = 1.0