Add option to start with non zero output iteration

docs/source/run/parameters.rst

@@ -1066,6 +1066,11 @@ Please make sure to always clear or rename the output folder before running a ne
     available. If both Adios2 and HDF5 are available, ``h5`` is used. Note that ``json`` is extremely
     slow and is not recommended for production runs.
 
+* ``hipace.output_iteration_offset`` (`integer`) optional (default `0`)
+    Iteration number of the diagnostic output of the first computed time step.
+    This applies to both openPMD and in-situ diagnostics. Useful when restarting a simulation and
+    combining the outputs when used together with ``hipace.initial_time``.
+
 Beam diagnostics
 ^^^^^^^^^^^^^^^^
 

src/Hipace.H

@@ -192,8 +192,6 @@ public:
     inline static Hipace* m_instance = nullptr;
     /** Whether to use normalized units */
     inline static bool m_normalized_units = false;
-    /** Default location for diagnostics output */
-    inline static std::string m_output_folder = "diags";
     /** All field data (3D array, slices) and field methods */
     Fields m_fields;
     /** Contains all beam species */
@@ -334,6 +332,13 @@ public:
     /** Owns data for m_grid_external_fields */
     amrex::Array<amrex::Parser, 5> m_grid_external_fields_parser;
 
+    // Diagnostic
+
+    /** Default location for diagnostics output */
+    inline static std::string m_output_folder = "diags";
+    /** iteration number written in diagnostic of first computed step */
+    inline static int m_output_iteration_offset = 0;
+
 private:
 
 #ifdef AMREX_USE_LINEAR_SOLVERS

src/Hipace.cpp

@@ -199,6 +199,8 @@ Hipace::ReadParameters ()
         "boundary.field = Dirichlet\n"
         "boundary.particle = Absorbing\n", true);
 
+    queryWithParser(pph, "output_iteration_offset", m_output_iteration_offset);
+
     amrex::ParmParse ppb("boundary");
     std::string field_boundary = "";
     getWithParser(ppb, "field", field_boundary);
@@ -1322,12 +1324,13 @@ Hipace::WriteDiagnostics (const int step)
 {
 #ifdef HIPACE_USE_OPENPMD
     if (m_diags.hasAnyFieldOutput(step, m_max_step, m_physical_time, m_max_time)) {
-        m_openpmd_writer.WriteFieldDiagnostics(m_diags.getFieldData(),
-            m_multi_laser, m_physical_time, step);
+        m_openpmd_writer.WriteFieldDiagnostics(m_diags.getFieldData(), m_multi_laser,
+            m_physical_time, step + m_output_iteration_offset);
     }
 
     if (m_diags.hasBeamOutput(step, m_max_step, m_physical_time, m_max_time)) {
-        m_openpmd_writer.WriteBeamDiagnostics(m_multi_beam, m_physical_time, step,
+        m_openpmd_writer.WriteBeamDiagnostics(m_multi_beam,
+            m_physical_time, step + m_output_iteration_offset,
             getDiagBeamNames(), m_3D_geom);
     }
 #else

src/fields/Fields.cpp

@@ -1433,6 +1433,7 @@ Fields::InSituWriteToFile (int step, amrex::Real time, const amrex::Geometry& ge
     std::ofstream ofs{m_insitu_file_prefix + "/reduced_fields." + pad_rank_num + ".txt",
         std::ofstream::out | std::ofstream::app | std::ofstream::binary};
 
+    const int out_step = step + Hipace::m_output_iteration_offset;
     const int nslices_int = geom3D.Domain().length(2);
     const std::size_t nslices = static_cast<std::size_t>(nslices_int);
     const int is_normalized_units = Hipace::m_normalized_units;
@@ -1441,7 +1442,7 @@ Fields::InSituWriteToFile (int step, amrex::Real time, const amrex::Geometry& ge
     // avoid pointers to temporary objects as second argument, stack variables are ok
     const amrex::Vector<insitu_utils::DataNode> all_data{
         {"time"     , &time},
-        {"step"     , &step},
+        {"step"     , &out_step},
         {"n_slices" , &nslices_int},
         {"z_lo"     , &geom3D.ProbLo()[2]},
         {"z_hi"     , &geom3D.ProbHi()[2]},

src/laser/MultiLaser.cpp

@@ -1064,6 +1064,7 @@ MultiLaser::InSituWriteToFile (int step, amrex::Real time, int max_step, amrex::
     std::ofstream ofs{m_insitu_file_prefix + "/reduced_laser." + pad_rank_num + ".txt",
         std::ofstream::out | std::ofstream::app | std::ofstream::binary};
 
+    const int out_step = step + Hipace::m_output_iteration_offset;
     const int nslices_int = m_laser_geom_3D.Domain().length(2);
     const std::size_t nslices = static_cast<std::size_t>(nslices_int);
     const int is_normalized_units = Hipace::m_normalized_units;
@@ -1072,7 +1073,7 @@ MultiLaser::InSituWriteToFile (int step, amrex::Real time, int max_step, amrex::
     // avoid pointers to temporary objects as second argument, stack variables are ok
     const amrex::Vector<insitu_utils::DataNode> all_data{
         {"time"     , &time},
-        {"step"     , &step},
+        {"step"     , &out_step},
         {"n_slices" , &nslices_int},
         {"z_lo"     , &m_laser_geom_3D.ProbLo()[2]},
         {"z_hi"     , &m_laser_geom_3D.ProbHi()[2]},

src/particles/beam/BeamParticleContainer.cpp

@@ -634,6 +634,7 @@ BeamParticleContainer::InSituWriteToFile (int step, amrex::Real time, const amre
 
     const amrex::Real sum_w0_inv = m_insitu_sum_rdata[0] <= 0._rt ?
         0._rt : 1._rt / m_insitu_sum_rdata[0];
+    const int out_step = step + Hipace::m_output_iteration_offset;
     const std::size_t nslices = static_cast<std::size_t>(m_nslices);
     const amrex::Real normalized_density_factor = Hipace::m_normalized_units ?
         geom.CellSizeArray().product() : 1; // dx * dy * dz in normalized units, 1 otherwise
@@ -643,7 +644,7 @@ BeamParticleContainer::InSituWriteToFile (int step, amrex::Real time, const amre
     // avoid pointers to temporary objects as second argument, stack variables are ok
     amrex::Vector<insitu_utils::DataNode> all_data{
         {"time"    , &time},
-        {"step"    , &step},
+        {"step"    , &out_step},
         {"n_slices", &m_nslices},
         {"charge"  , &m_charge},
         {"mass"    , &m_mass},

src/particles/plasma/PlasmaParticleContainer.cpp

@@ -937,6 +937,7 @@ PlasmaParticleContainer::InSituWriteToFile (int step, amrex::Real time, const am
 
     const amrex::Real sum_w0_inv = m_insitu_sum_rdata[0] <= 0._rt ?
         0._rt : 1._rt / m_insitu_sum_rdata[0];
+    const int out_step = step + Hipace::m_output_iteration_offset;
     const std::size_t nslices = static_cast<std::size_t>(m_nslices);
     const amrex::Real normalized_density_factor = Hipace::m_normalized_units ?
         geom.CellSizeArray().product() : 1; // dx * dy * dz in normalized units, 1 otherwise
@@ -946,7 +947,7 @@ PlasmaParticleContainer::InSituWriteToFile (int step, amrex::Real time, const am
     // Avoid pointers to temporary objects as second argument, stack variables are ok
     const amrex::Vector<insitu_utils::DataNode> all_data{
         {"time"    , &time},
-        {"step"    , &step},
+        {"step"    , &out_step},
         {"n_slices", &m_nslices},
         {"charge"  , &m_charge},
         {"mass"    , &m_mass},