Mesh refinement: initialize the plasma on the correct level

docs/source/run/parameters.rst

@@ -156,6 +156,9 @@ plasma parameters for each plasma are specified via `<plasma name>.plasma_proper
     Since in a quasi-static code, there is only a 2D plasma slice evolving along the longitudinal
     coordinate, there is no need to specify a number of particles per cell in z.
 
+* ``<plasma name>.level`` (`integer`) optional (default `0`)
+    Level of mesh refinement to which the plasma is assigned.
+
 * ``<plasma name>.radius`` (`float`) optional (default `infinity`)
     Radius of the plasma. Set a value to run simulations in a plasma column.
 

src/Hipace.cpp

@@ -236,7 +236,7 @@ Hipace::InitData ()
     AmrCore::InitFromScratch(0.0); // function argument is time
     constexpr int lev = 0;
     m_multi_beam.InitData(geom[lev]);
-    m_multi_plasma.InitData(lev, m_slice_ba[lev], m_slice_dm[lev], m_slice_geom[lev], geom[lev]);
+    m_multi_plasma.InitData(m_slice_ba, m_slice_dm, m_slice_geom, geom);
     m_adaptive_time_step.Calculate(m_dt, m_multi_beam, m_multi_plasma.maxDensity());
 #ifdef AMREX_USE_MPI
     m_adaptive_time_step.WaitTimeStep(m_dt, m_comm_z);

src/particles/MultiPlasma.H

@@ -19,14 +19,14 @@ public:
 
     /** \brief Loop over plasma species and initialize them.
      *
-     * \param[in] lev MR level
      * \param[in] slice_ba slice boxarray, on which plasma particles are defined
      * \param[in] slice_dm DistributionMapping of the transverse slice domain
      * \param[in] slice_gm slice geometry
      * \param[in] gm Geometry of the simulation, to get the cell size
      */
-    void InitData (int lev, amrex::BoxArray slice_ba, amrex::DistributionMapping slice_dm,
-                   amrex::Geometry slice_gm, amrex::Geometry gm);
+    void InitData (amrex::Vector<amrex::BoxArray> slice_ba,
+                   amrex::Vector<amrex::DistributionMapping> slice_dm,
+                   amrex::Vector<amrex::Geometry> slice_gm, amrex::Vector<amrex::Geometry> gm);
 
 
     /** Loop over plasma species and depose their currents into the current 2D slice in fields

src/particles/MultiPlasma.cpp

@@ -16,14 +16,15 @@ MultiPlasma::MultiPlasma (amrex::AmrCore* amr_core)
 }
 
 void
-MultiPlasma::InitData (int lev, amrex::BoxArray slice_ba,
-                       amrex::DistributionMapping slice_dm, amrex::Geometry slice_gm,
-                       amrex::Geometry gm)
+MultiPlasma::InitData (amrex::Vector<amrex::BoxArray> slice_ba,
+                       amrex::Vector<amrex::DistributionMapping> slice_dm,
+                       amrex::Vector<amrex::Geometry> slice_gm, amrex::Vector<amrex::Geometry> gm)
 {
     for (auto& plasma : m_all_plasmas) {
-        plasma.SetParticleBoxArray(lev, slice_ba);
-        plasma.SetParticleDistributionMap(lev, slice_dm);
-        plasma.SetParticleGeometry(lev, slice_gm);
+        const int lev = plasma.m_level;
+        plasma.SetParticleBoxArray(lev, slice_ba[lev]);
+        plasma.SetParticleDistributionMap(lev, slice_dm[lev]);
+        plasma.SetParticleGeometry(lev, slice_gm[lev]);
         plasma.InitData();
 
         if(plasma.m_can_ionize) {
@@ -35,7 +36,7 @@ MultiPlasma::InitData (int lev, amrex::BoxArray slice_ba,
             }
             AMREX_ALWAYS_ASSERT_WITH_MESSAGE(plasma_product != nullptr,
                 "Must specify a valid product plasma for Ionization using ionization_product");
-            plasma.InitIonizationModule(gm, plasma_product);
+            plasma.InitIonizationModule(gm[lev], plasma_product);
         }
     }
 }

src/particles/PlasmaParticleContainer.H

@@ -90,7 +90,7 @@ public:
                            Fields& fields);
 
     amrex::Real m_density {0}; /**< Density of the plasma */
-    int m_MR_level {0}; /**< mesh refinement level on which the plasma lives */
+    int m_level {0}; /**< mesh refinement level on which the plasma lives */
     /** maximum weighting factor gamma/(Psi +1) before particle is regarded as violating
      *  the quasi-static approximation and is removed */
     amrex::Real m_max_qsa_weighting_factor {35.};

src/particles/PlasmaParticleContainer.cpp

@@ -70,7 +70,7 @@ PlasmaParticleContainer::ReadParameters ()
     }
     pp.query("ionization_product", m_product_name);
     pp.query("density", m_density);
-    pp.query("MR_level", m_MR_level);
+    pp.query("level", m_level);
     pp.query("radius", m_radius);
     pp.query("hollow_core_radius", m_hollow_core_radius);
     AMREX_ALWAYS_ASSERT_WITH_MESSAGE(m_hollow_core_radius < m_radius,

src/particles/PlasmaParticleContainerInit.cpp

@@ -17,7 +17,7 @@ InitParticles (const amrex::IntVect& a_num_particles_per_cell,
 {
     HIPACE_PROFILE("PlasmaParticleContainer::InitParticles");
 
-    const int lev = 0;
+    const int lev = m_level;
     const auto dx = ParticleGeom(lev).CellSizeArray();
     const auto plo = ParticleGeom(lev).ProbLoArray();
     const amrex::RealBox a_bounds = ParticleGeom(lev).ProbDomain();

src/particles/deposition/PlasmaDepositCurrent.cpp

@@ -22,7 +22,7 @@ DepositCurrent (PlasmaParticleContainer& plasma, Fields & fields,
     " (WhichSlice::Next) or for the ion charge deposition (WhichSLice::RhoIons)");
 
     // only deposit plasma currents on their according MR level
-    if (plasma.m_MR_level != lev) return;
+    if (plasma.m_level != lev) return;
 
     // Extract properties associated with physical size of the box
     amrex::Real const * AMREX_RESTRICT dx = gm.CellSize();

src/particles/pusher/PlasmaParticleAdvance.cpp

@@ -19,7 +19,7 @@ AdvancePlasmaParticles (PlasmaParticleContainer& plasma, Fields & fields,
     using namespace amrex::literals;
 
     // only push plasma particles on their according MR level
-    if (plasma.m_MR_level != lev) return;
+    if (plasma.m_level != lev) return;
 
     // Extract properties associated with physical size of the box
     amrex::Real const * AMREX_RESTRICT dx = gm.CellSize();