AddPlasmaFromFile fix for periodic boundaries (#1089)

* Added description of singleparticle particle injection style

* Revert "Added description of singleparticle particle injection style"

This reverts commit f02d842.

* Tried to inject particles only in simulation Box

* Added Todo for multiple levels of mesh refinement

* Explain todo better

* Added x and y_shifts and replaced cascading ifs by bools and continue

* Replaced cascading ifs by bools and continue

* Replaced TODO by FIXME as reviewer suggested

* Made the insidebounds function use box limits as defaults

* Fixed identation issue

* Fixed identation issue

* Fixed identation issue

* Added to Docs the default for xmin,xmax and other dirs

* Fix missing y and z dirs

* Update Source/Initialization/PlasmaInjector.cpp

* Fixed PlasmaInjector limits with periodic condition

* Removed check if 3D because now ylims are +/-inf

* Restored if to check for y velocity also in 2D/RZ

* Fixed Docs to recent changes

* Update Source/Initialization/PlasmaInjector.cpp

* Fix extra bracket

* Tiny bool cleanup

Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>

Docs/source/running_cpp/parameters.rst

@@ -288,6 +288,13 @@ Particle initialization
     The mass of one `physical` particle of this species.
     If ``species_type`` is specified, the mass will be set to the physical value and ``mass`` is optional.
 
+* ``<species_name>.xmin,ymin,zmin`` (`float`) optional (default unlimited)
+    When ``<species_name>.xmin`` and ``<species_name>.xmax`` (see below) are set, they delimit the region within which particles are injected.
+    The same is applicable in the other directions.
+    If periodic boundary conditions are used in direction ``i``, then the default (i.e. if the range is not specified) range will be the simulation box, ``[geometry.prob_hi[i], geometry.prob_lo[i]]``.
+
+* ``<species_name>.xmax,ymax,zmax`` (`float`) optional (default unlimited)
+
 * ``<species_name>.injection_style`` (`string`)
     Determines how the particles will be injected in the simulation.
     The options are:

Source/Initialization/PlasmaInjector.cpp

@@ -79,7 +79,7 @@ PlasmaInjector::PlasmaInjector (int ispecies, const std::string& name)
     pp.query("radially_weighted", radially_weighted);
     AMREX_ALWAYS_ASSERT_WITH_MESSAGE(radially_weighted, "ERROR: Only radially_weighted=true is supported");
 
-    // parse plasma boundaries
+    // Unlimited boundaries
     xmin = std::numeric_limits<amrex::Real>::lowest();
     ymin = std::numeric_limits<amrex::Real>::lowest();
     zmin = std::numeric_limits<amrex::Real>::lowest();
@@ -88,6 +88,30 @@ PlasmaInjector::PlasmaInjector (int ispecies, const std::string& name)
     ymax = std::numeric_limits<amrex::Real>::max();
     zmax = std::numeric_limits<amrex::Real>::max();
 
+    // NOTE: When periodic boundaries are used, default injection range is set to mother grid dimensions.
+    const Geometry& geom = WarpX::GetInstance().Geom(0);
+    if( geom.isPeriodic(0) ) {
+        xmin = geom.ProbLo(0);
+        xmax = geom.ProbHi(0);
+    }
+
+    if( geom.isPeriodic(1) ) {
+#       ifndef WARPX_DIM_3D
+        zmin = geom.ProbLo(1);
+        zmax = geom.ProbHi(1);
+#       else
+        ymin = geom.ProbLo(1);
+        ymax = geom.ProbHi(1);
+#       endif
+    }
+
+#   ifdef WARPX_DIM_3D
+    if( geom.isPeriodic(2) ) {
+        zmin = geom.ProbLo(2);
+        zmax = geom.ProbHi(2);
+    }
+#   endif
+
     pp.query("xmin", xmin);
     pp.query("ymin", ymin);
     pp.query("zmin", zmin);

Source/Particles/PhysicalParticleContainer.cpp

@@ -374,9 +374,9 @@ PhysicalParticleContainer::AddPlasmaFromFile(ParticleReal q_tot,
                     uy = ptr_uy.get()[i]*momentum_unit_y/PhysConst::m_e;
                 }
                 CheckAndAddParticle(x, y, z, { ux, uy, uz}, weight,
-                particle_x,  particle_y,  particle_z,
-                particle_ux, particle_uy, particle_uz,
-                particle_w);
+                                    particle_x,  particle_y,  particle_z,
+                                    particle_ux, particle_uy, particle_uz,
+                                    particle_w);
             }
         }
         auto const np = particle_z.size();