add plasma, fix doc

Hi-PACE · Jun 23, 2023 · 657cf39 · 657cf39
1 parent 88bb89d
commit 657cf39
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Showing 7 changed files with 41 additions and 22 deletions.
diff --git a/src/Hipace.cpp b/src/Hipace.cpp
@@ -465,7 +465,7 @@ Hipace::Evolve ()
         }
 
         m_multi_beam.InSituWriteToFile(step, m_physical_time, m_3D_geom[0], m_max_step, m_max_time);
-        m_multi_plasma.InSituWriteToFile(step, m_physical_time, m_3D_geom[0]);
+        m_multi_plasma.InSituWriteToFile(step, m_physical_time, m_3D_geom[0], m_max_step, m_max_time);
 
         // printing and resetting predictor corrector loop diagnostics
         if (m_verbose>=2 && !m_explicit) amrex::AllPrint() << "Rank " << rank <<
@@ -501,7 +501,7 @@ Hipace::SolveOneSlice (int islice, const int islice_local, int step)
 
     m_multi_beam.InSituComputeDiags(step, islice, islice_local, m_max_step,
                                     m_physical_time, m_max_time);
-    m_multi_plasma.InSituComputeDiags(step, islice);
+    m_multi_plasma.InSituComputeDiags(step, islice, m_max_step, m_physical_time, m_max_time);
 
     // Get this laser slice from the 3D array
     m_multi_laser.Copy(islice, false);

diff --git a/src/particles/beam/MultiBeam.H b/src/particles/beam/MultiBeam.H
@@ -83,10 +83,20 @@ public:
      * \param[in] step time step of simulation
      * \param[in] islice current slice, on which diags are computed.
      * \param[in] islice_local local index of the slice
+     * \param[in] max_step maximum time step of simulation
+     * \param[in] physical_time physical time at the given step
+     * \param[in] max_time maximum time of simulation
      */
     void InSituComputeDiags (int step, int islice, int islice_local,
                              int max_step, amrex::Real physical_time,
                              amrex::Real max_time);
+    /** Write reduced beam diagnostics to file
+     * \param[in] step time step of simulation
+     * \param[in] time physical time at the given step
+     * \param[in] geom Simulation geometry
+     * \param[in] max_step maximum time step of simulation
+     * \param[in] max_time maximum time of simulation
+     */
     void InSituWriteToFile (int step, amrex::Real time, const amrex::Geometry& geom,
                             int max_step, amrex::Real max_time);
     /** Loop over species and init them

diff --git a/src/particles/beam/MultiBeam.cpp b/src/particles/beam/MultiBeam.cpp
@@ -220,10 +220,10 @@ MultiBeam::InSituComputeDiags (int step, int islice, int islice_local,
                                int max_step, amrex::Real physical_time,
                                amrex::Real max_time)
 {
-    for (int i = 0; i < m_nbeams; ++i) {
-        if (utils::doOutput(m_all_beams[i].m_insitu_period, step,
+    for (auto& beam : m_all_beams) {
+        if (utils::doOutput(beam.m_insitu_period, step,
                             max_step, physical_time, max_time)) {
-            m_all_beams[i].InSituComputeDiags(islice, islice_local);
+            beam.InSituComputeDiags(islice, islice_local);
         }
     }
 }

diff --git a/src/particles/plasma/MultiPlasma.H b/src/particles/plasma/MultiPlasma.H
@@ -148,9 +148,21 @@ public:
     /** Compute reduced plasma diagnostics of current slice, store in member variable.
      * \param[in] step time step of simulation
      * \param[in] islice current slice, on which diags are computed.
+     * \param[in] max_step maximum time step of simulation
+     * \param[in] physical_time physical time at the given step
+     * \param[in] max_time maximum time of simulation
      */
-    void InSituComputeDiags (int step, int islice);
-    void InSituWriteToFile (int step, amrex::Real time, const amrex::Geometry& geom);
+    void InSituComputeDiags (int step, int islice, int max_step,
+                             amrex::Real physical_time, amrex::Real max_time);
+    /** Write reduced beam diagnostics to file
+     * \param[in] step time step of simulation
+     * \param[in] time physical time at the given step
+     * \param[in] geom Simulation geometry
+     * \param[in] max_step maximum time step of simulation
+     * \param[in] max_time maximum time of simulation
+     */
+    void InSituWriteToFile (int step, amrex::Real time, const amrex::Geometry& geom,
+                            int max_step, amrex::Real max_time);
 
     int m_sort_bin_size {32}; /**< Tile size to sort plasma particles */
 

diff --git a/src/particles/plasma/MultiPlasma.cpp b/src/particles/plasma/MultiPlasma.cpp
@@ -12,6 +12,7 @@
 #include "particles/sorting/TileSort.H"
 #include "utils/HipaceProfilerWrapper.H"
 #include "utils/DeprecatedInput.H"
+#include "utils/IOUtil.H"
 #include "Hipace.H"
 
 MultiPlasma::MultiPlasma ()
@@ -203,20 +204,24 @@ MultiPlasma::TagByLevel (const int current_N_level, amrex::Vector<amrex::Geometr
 }
 
 void
-MultiPlasma::InSituComputeDiags (int step, int islice)
+MultiPlasma::InSituComputeDiags (int step, int islice, int max_step,
+                                amrex::Real physical_time, amrex::Real max_time)
 {
     for (auto& plasma : m_all_plasmas) {
-        if (plasma.doInSitu(step)) {
+        if (utils::doOutput(plasma.m_insitu_period, step,
+                            max_step, physical_time, max_time)) {
             plasma.InSituComputeDiags(islice);
         }
     }
 }
 
 void
-MultiPlasma::InSituWriteToFile (int step, amrex::Real time, const amrex::Geometry& geom)
+MultiPlasma::InSituWriteToFile (int step, amrex::Real time, const amrex::Geometry& geom,
+                                int max_step, amrex::Real max_time)
 {
     for (auto& plasma : m_all_plasmas) {
-        if (plasma.doInSitu(step)) {
+        if (utils::doOutput(plasma.m_insitu_period, step,
+                            max_step, time, max_time)) {
             plasma.InSituWriteToFile(step, time, geom);
         }
     }

diff --git a/src/particles/plasma/PlasmaParticleContainer.H b/src/particles/plasma/PlasmaParticleContainer.H
@@ -150,7 +150,6 @@ public:
      * \param[in] geom Geometry object for the whole domain
      */
     void InSituWriteToFile (int step, amrex::Real time, const amrex::Geometry& geom);
-    bool doInSitu (int step);
 
     amrex::Parser m_parser; /**< owns data for m_density_func */
     amrex::ParserExecutor<3> m_density_func; /**< Density function for the plasma */
@@ -186,7 +185,9 @@ public:
     int m_reorder_period = 0;
     /** 2D reordering index type. 0: cell, 1: node, 2: both */
     amrex::IntVect m_reorder_idx_type = {0, 0, 0};
-
+    /** How often the insitu plasma diagnostics should be computed and written
+     * Default is 0, meaning no output */
+    int m_insitu_period {0};
 private:
     std::string m_name; /**< name of the species */
     int m_nslices; /**< number of z slices of the domain */
@@ -215,9 +216,6 @@ private:
     amrex::Vector<int> m_insitu_sum_idata;
     /** Prefix/path for the output files */
     std::string m_insitu_file_prefix = "diags/plasma_insitu";
-    /** How often the insitu plasma diagnostics should be computed and written
-     * Default is 0, meaning no output */
-    int m_insitu_period {0};
 };
 
 /** \brief Iterator over boxes in a particle container */

diff --git a/src/particles/plasma/PlasmaParticleContainer.cpp b/src/particles/plasma/PlasmaParticleContainer.cpp
@@ -431,12 +431,6 @@ IonizationModule (const int lev,
     }
 }
 
-bool
-PlasmaParticleContainer::doInSitu (int step)
-{
-    return (m_insitu_period > 0 && step % m_insitu_period == 0);
-}
-
 void
 PlasmaParticleContainer::InSituComputeDiags (int islice)
 {
-Original file line number
+Diff line change
@@ Expand Up / @@ -431,12 +431,6 @@ IonizationModule (const int lev, @@
         }
     }
-    bool
-    PlasmaParticleContainer::doInSitu (int step)
-    {
-        return (m_insitu_period > 0 && step % m_insitu_period == 0);
-    }
     void
     PlasmaParticleContainer::InSituComputeDiags (int islice)
     {
@@ Expand Down @@