[small] Inject Particles from openPMD in RZ

Docs/source/running_cpp/parameters.rst

@@ -331,7 +331,7 @@ Particle initialization
       ``<species_name>.z_shift`` (`double`) optional (default is no shift) when set this value will be added to the longitudinal, ``z``, position of the particles.
       The external file must include the species ``openPMD::Record``s labeled ``position`` and ``momentum`` (`double` arrays), with dimensionality and units set via ``openPMD::setUnitDimension`` and ``setUnitSI``.
       If the external file also contains ``openPMD::Records``s for ``mass`` and ``charge`` (constant `double` scalars) then the species will use these, unless overwritten in the input file (see ``<species_name>.mass``, ```<species_name>.charge`` or ```<species_name>.species_type``).
-      The ``external_file`` option is currently implemented for 2D and 3D geometries, with record components ``x``, ``z`` and ``y`` for 3D.
+      The ``external_file`` option is currently implemented for 2D, 3D and RZ geometries, with record components in the cartesian coordinates ``(x,y,z)`` for 3D and RZ, and ``(x,z)`` for 2D.
       For more information on the `openPMD format <https://github.com/openPMD>`__ and how to build WarpX with it, please visit :doc:`../building/openpmd`.
 
 * ``<species_name>.num_particles_per_cell_each_dim`` (`3 integers in 3D and RZ, 2 integers in 2D`)

Source/Initialization/PlasmaInjector.cpp

@@ -254,18 +254,16 @@ PlasmaInjector::PlasmaInjector (int ispecies, const std::string& name)
         parseDensity(pp);
         parseMomentum(pp);
     } else if (part_pos_s == "external_file") {
-#ifdef WARPX_DIM_RZ
-        amrex::Abort("The option of reading particle data from an external "
-                     "file has not been implemented nor tested in RZ geometry");
-#endif
-        pp.query("q_tot", q_tot); // optional
 #ifndef WARPX_USE_OPENPMD
         amrex::Abort("WarpX has to be compiled with USE_OPENPMD=TRUE to be able"
                      " to read the external openPMD file with species data");
 #endif
         external_file = true;
         std::string str_injection_file;
         pp.get("injection_file", str_injection_file);
+        // optional parameters
+        pp.query("q_tot", q_tot);
+        pp.query("z_shift",z_shift);
 
 #ifdef WARPX_USE_OPENPMD
         if (ParallelDescriptor::IOProcessor()) {
@@ -327,8 +325,6 @@ PlasmaInjector::PlasmaInjector (int ispecies, const std::string& name)
                 double const mass_unit = ps["mass"][openPMD::RecordComponent::SCALAR].unitSI();
                 mass = p_m * mass_unit;
             }
-
-            pp.query("z_shift",z_shift);
         } // IOProcessor
 
         // Broadcast charge and mass to non-IO processors

Source/Particles/PhysicalParticleContainer.H

@@ -174,6 +174,16 @@ public:
     // Inject particles in Box 'part_box'
     virtual void AddParticles (int lev);
 
+    /**
+     * Create new macroparticles for this species, with a fixed
+     * number of particles per cell (in the cells of `part_realbox`).
+     * The new particles are only created inside the intersection of `part_realbox`
+     * with the local grid for the current proc.
+     * @param[in]  lev the index of the refinement level
+     * @param[in] part_realbox the box in which new particles should be created
+     * (this box should correspond to an integer number of cells in each direction,
+     * but its boundaries need not be aligned with the actual cells of the simulation)
+    */
     void AddPlasma (int lev, amrex::RealBox part_realbox = amrex::RealBox());
 
     void MapParticletoBoostedFrame (amrex::Real& x, amrex::Real& y, amrex::Real& z, std::array<amrex::Real, 3>& u);
@@ -185,7 +195,6 @@ public:
         const amrex::Real q_tot, long npart, const int do_symmetrize);
 
     /** Load a particle beam from an external file
-     *
      * @param[in] q_tot total charge of the particle species to be initialized
      */
     void AddPlasmaFromFile (amrex::ParticleReal q_tot,

Source/Particles/PhysicalParticleContainer.cpp

@@ -239,7 +239,7 @@ PhysicalParticleContainer::AddGaussianBeam (
             npart /= 4;
         }
         for (long i = 0; i < npart; ++i) {
-#if (defined WARPX_DIM_3D) || (WARPX_DIM_RZ)
+#if (defined WARPX_DIM_3D) || (defined WARPX_DIM_RZ)
             const Real weight = q_tot/(npart*charge);
             const Real x = distx(mt);
             const Real y = disty(mt);
@@ -328,7 +328,7 @@ PhysicalParticleContainer::AddPlasmaFromFile(ParticleReal q_tot,
         double const momentum_unit_x = ps["momentum"]["x"].unitSI();
         std::shared_ptr<ParticleReal> ptr_uz = ps["momentum"]["z"].loadChunk<ParticleReal>();
         double const momentum_unit_z = ps["momentum"]["z"].unitSI();
-#   ifdef WARPX_DIM_3D
+#   ifndef WARPX_DIM_XZ
         std::shared_ptr<ParticleReal> ptr_y = ps["position"]["y"].loadChunk<ParticleReal>();
         double const position_unit_y = ps["position"]["y"].unitSI();
 #   endif
@@ -361,10 +361,10 @@ PhysicalParticleContainer::AddPlasmaFromFile(ParticleReal q_tot,
         for (auto i = decltype(npart){0}; i<npart; ++i){
             ParticleReal const x = ptr_x.get()[i]*position_unit_x;
             ParticleReal const z = ptr_z.get()[i]*position_unit_z+z_shift;
-#   ifndef WARPX_DIM_3D
-            ParticleReal const y = 0.0_prt;
-#   else
+#   if (defined WARPX_DIM_3D) || (defined WARPX_DIM_RZ)
             ParticleReal const y = ptr_y.get()[i]*position_unit_y;
+#   else
+            ParticleReal const y = 0.0_prt;
 #   endif
             if (plasma_injector->insideBounds(x, y, z)) {
                 ParticleReal const ux = ptr_ux.get()[i]*momentum_unit_x/PhysConst::m_e;
@@ -464,16 +464,6 @@ PhysicalParticleContainer::AddParticles (int lev)
     }
 }
 
-/**
- * Create new macroparticles for this species, with a fixed
- * number of particles per cell (in the cells of `part_realbox`).
- * The new particles are only created inside the intersection of `part_realbox`
- * with the local grid for the current proc.
- * @param lev the index of the refinement level
- * @param part_realbox the box in which new particles should be created
- * (this box should correspond to an integer number of cells in each direction,
- * but its boundaries need not be aligned with the actual cells of the simulation)
- */
 void
 PhysicalParticleContainer::AddPlasma (int lev, RealBox part_realbox)
 {

Source/WarpX.cpp

@@ -554,11 +554,17 @@ WarpX::ReadParameters ()
 
         // Only needs to be set with WARPX_DIM_RZ, otherwise defaults to 1
         pp.query("n_rz_azimuthal_modes", n_rz_azimuthal_modes);
-#if (defined WARPX_DIM_RZ) && (defined WARPX_USE_PSATD)
+#if (defined WARPX_DIM_RZ)
+        AMREX_ALWAYS_ASSERT_WITH_MESSAGE( Geom(0).isPeriodic(0) == 0, "In RZ,"
+                                         " the boundary condition in r can not"
+                                         " be periodic.\nPlease change "
+                                         " `geometry.is_periodic` in the input");
+#if (defined WARPX_USE_PSATD)
         // Force do_nodal=true (that is, not staggered) and
         // use same shape factors in all directions, for gathering
         do_nodal = true;
         l_lower_order_in_v = false;
+#endif
 #endif
     }