:/

Author: PhilipDeegan

src/amr/data/field/initializers/samrai_hdf5_field_initializer.hpp

@@ -1,30 +1,16 @@
 #ifndef _PHARE_AMR_DATA_FIELD_INITIAZILIZERS_SAMRAI_HDF5_INITIALIZER_HPP_
 #define _PHARE_AMR_DATA_FIELD_INITIAZILIZERS_SAMRAI_HDF5_INITIALIZER_HPP_
 
-#include <memory>
-#include <random>
 #include <cassert>
-#include <functional>
 
-#include "core/def.hpp"
-#include "core/logger.hpp"
 #include "core/data/grid/gridlayoutdefs.hpp"
 #include "core/data/ndarray/ndarray_vector.hpp"
-#include "core/hybrid/hybrid_quantities.hpp"
+
 #include "core/utilities/types.hpp"
-#include "core/data/ions/particle_initializers/particle_initializer.hpp"
-#include "core/data/particles/particle.hpp"
-#include "initializer/data_provider.hpp"
 #include "core/utilities/point/point.hpp"
 
-#include "hdf5/detail/h5/h5_file.hpp"
-
-
-#include "SAMRAI/hier/PatchDataRestartManager.h"
-
 #include "amr/data/initializers/samrai_hdf5_initializer.hpp"
 
-
 namespace PHARE::amr
 {
 
@@ -45,15 +31,8 @@ template<typename Field_t, typename GridLayout>
 void SamraiHDF5FieldInitializer<Field_t, GridLayout>::load(Field_t& field,
                                                            GridLayout const& layout) const
 {
-    bool static constexpr c_ordering = false;
-
-    auto const local_cell = [&](auto const& box, auto const& point) {
-        core::Point<std::uint32_t, dimension> localPoint;
-        auto localStart = layout.physicalStartIndex(core::QtyCentering::dual, core::Direction::X);
-        for (std::size_t i = 0; i < dimension; ++i)
-            localPoint[i] = point[i] - (box.lower[i] - localStart);
-        return localPoint;
-    };
+    auto const local_cell
+        = [&](auto const& box, auto const& point) { return layout.AMRToLocal(point, box); };
 
     auto const& dest_box  = layout.AMRBox();
     auto const& centering = layout.centering(field.physicalQuantity());
@@ -73,7 +52,7 @@ void SamraiHDF5FieldInitializer<Field_t, GridLayout>::load(Field_t& field,
                         src_box.upper[i] - src_box.lower[i] + (GridLayout::nbrGhosts() * 2)
                         + (centering[i] == core::QtyCentering::primal ? 1 : 0));
                 })}};
-        auto data_view = core::make_array_view<c_ordering>(data.data(), *lcl_src_box.shape());
+        auto data_view = core::make_array_view(data.data(), *lcl_src_box.shape());
         for (auto const& point : overlap_box)
             field(local_cell(dest_box, point)) = data_view(local_cell(src_box, point));
     }

src/amr/data/initializers/samrai_hdf5_initializer.hpp

@@ -2,28 +2,15 @@
 #define _PHARE_AMR_DATA_INITIAZILIZERS_SAMRAI_HDF5_INITIALIZER_HPP_
 
 #include <memory>
-#include <random>
 #include <cassert>
-#include <functional>
 
-#include "core/data/grid/gridlayoutdefs.hpp"
-#include "core/hybrid/hybrid_quantities.hpp"
-#include "core/utilities/types.hpp"
-#include "core/data/ions/particle_initializers/particle_initializer.hpp"
-#include "core/data/particles/particle.hpp"
-#include "initializer/data_provider.hpp"
-#include "core/utilities/point/point.hpp"
 #include "core/def.hpp"
-#include "core/logger.hpp"
-
+#include "core/utilities/types.hpp"
+#include "core/utilities/box/box.hpp"
 #include "hdf5/detail/h5/h5_file.hpp"
 
 #include "SAMRAI/tbox/HDFDatabase.h"
 
-#include "amr/utilities/box/amr_box.hpp"
-
-#include "SAMRAI/hier/PatchDataRestartManager.h"
-
 
 namespace PHARE::amr
 {

src/amr/data/particles/initializers/samrai_hdf5_particle_initializer.hpp

@@ -1,28 +1,15 @@
 #ifndef _PHARE_AMR_DATA_PARTICLE_INITIAZILIZERS_SAMRAI_HDF5_INITIALIZER_HPP_
 #define _PHARE_AMR_DATA_PARTICLE_INITIAZILIZERS_SAMRAI_HDF5_INITIALIZER_HPP_
 
-#include <memory>
-#include <random>
 #include <cassert>
-#include <functional>
 
-#include "core/def.hpp"
-#include "core/logger.hpp"
-#include "core/utilities/box/box.hpp"
-
-#include "core/data/grid/gridlayoutdefs.hpp"
-#include "core/hybrid/hybrid_quantities.hpp"
 #include "core/utilities/types.hpp"
-#include "core/data/ions/particle_initializers/particle_initializer.hpp"
-#include "core/data/particles/particle.hpp"
-#include "initializer/data_provider.hpp"
+#include "core/utilities/box/box.hpp"
 #include "core/utilities/point/point.hpp"
-
-
-#include "hdf5/detail/h5/h5_file.hpp"
+#include "core/data/ions/particle_initializers/particle_initializer.hpp"
 
 #include "core/data/particles/particle_packer.hpp"
-#include "amr/data/field/initializers/samrai_hdf5_field_initializer.hpp"
+#include "amr/data/initializers/samrai_hdf5_initializer.hpp"
 
 
 namespace PHARE::amr

src/core/data/grid/gridlayout.hpp

@@ -802,24 +802,30 @@ namespace core
          * This method only deals with **cell** indexes.
          */
         template<typename T>
-        NO_DISCARD auto AMRToLocal(Point<T, dimension> AMRPoint) const
+        NO_DISCARD auto AMRToLocal(Point<T, dimension> const& AMRPoint,
+                                   Box<int, dimension> const& localbox) const
         {
             static_assert(std::is_integral_v<T>, "Error, must be MeshIndex (integral Point)");
             Point<std::uint32_t, dimension> localPoint;
 
             // any direction, it's the same because we want cells
             auto localStart = physicalStartIndex(QtyCentering::dual, Direction::X);
 
-            //
             for (auto i = 0u; i < dimension; ++i)
             {
-                int local = AMRPoint[i] - (AMRBox_.lower[i] - localStart);
+                int local = AMRPoint[i] - (localbox.lower[i] - localStart);
                 assert(local >= 0);
                 localPoint[i] = local;
             }
             return localPoint;
         }
 
+        template<typename T>
+        NO_DISCARD auto AMRToLocal(Point<T, dimension> const& AMRPoint) const
+        {
+            return AMRToLocal(AMRPoint, AMRBox_);
+        }
+
 
         /**
          * @brief AMRToLocal returns the local Box associated with the given AMR one.

tests/simulator/test_init_from_restart.py

@@ -15,19 +15,21 @@
 from tests.diagnostic import dump_all_diags
 
 timestep = 0.001
-first_mpi_size = 4
+time_step_nbr = 1
+first_mpi_size = 1
 ppc = 100
 cells = 200
 first_out = "phare_outputs/reinit/first"
 secnd_out = "phare_outputs/reinit/secnd"
-timestamps = np.array([timestep * 4])
+timestamps = [0]  # np.array([timestep * 2, timestep * 4])
+restart_idx = Z = 0
 simInitArgs = dict(
-    largest_patch_size=100,
-    time_step_nbr=5,
+    # largest_patch_size=100,
+    time_step_nbr=time_step_nbr,
     time_step=timestep,
     cells=cells,
     dl=0.3,
-    init_options=dict(dir=f"{first_out}/00000.00400", mpi_size=first_mpi_size),
+    init_options=dict(dir=f"{first_out}/00000.00{Z}00", mpi_size=first_mpi_size),
     diag_options=dict(format="phareh5", options=dict(dir=secnd_out, mode="overwrite")),
 )
 
@@ -38,7 +40,7 @@ def setup_model(sim):
         alpha={"mass": 4.0, "charge": 1, "nbr_part_per_cell": ppc},
     )
     ph.ElectronModel(closure="isothermal", Te=0.12)
-    dump_all_diags(model.populations, timestamps)
+    dump_all_diags(model.populations, timestamps=timestamps)
     return model
 
 
@@ -68,7 +70,7 @@ def test_reinit(self):
             phut.assert_fp_any_all_close(a, b)
 
         def get_merged(hier):
-            return single_patch_per_level_per_pop_from(datahier0)
+            return single_patch_per_level_per_pop_from(hier)
 
         ds = [get_merged(datahier0), get_merged(datahier1)]
         for key in ["alpha", "protons"]:
@@ -78,6 +80,7 @@ def get_merged(hier):
 
 
 def run_first_sim():
+    """uses params from tests_restarts.py"""
     simput = copy.deepcopy(test_restarts.simArgs)
     simput["restart_options"]["dir"] = first_out
     simput["restart_options"]["timestamps"] = timestamps
@@ -88,6 +91,7 @@ def run_first_sim():
 
 
 def launch():
+    """Launch secondary process to run first simulation to avoid initalizing MPI now"""
     cmd = f"mpirun -n {first_mpi_size} python3 -O tests/simulator/test_init_from_restart.py lol"
     proc = subprocess.run(cmd.split(" "), check=True, capture_output=True)
     return (proc.stdout + proc.stderr).decode().strip()