rebase to master and cleanup

pyphare/pyphare/pharein/simulation.py

@@ -613,7 +613,7 @@ def check_hyper_resistivity(**kwargs):
 
 def check_clustering(**kwargs):
     valid_keys = ["berger", "tile"]
-    clustering = kwargs.get("clustering", "berger")
+    clustering = kwargs.get("clustering", "tile")
     if clustering not in valid_keys:
         raise ValueError(
             f"Error: clustering type is not supported, supported types are {valid_keys}"
@@ -906,7 +906,7 @@ class Simulation(object):
 
         * **max_nbr_levels** (``int``), default=1, max number of levels in the hierarchy. Used if no `refinement_boxes` are set
         * **tag_buffer** (``int``), default=1, value representing the number of cells by which tagged cells are buffered before clustering into boxes. The larger `tag_buffer`, the wider refined regions will be around tagged cells.
-        * **clustering** (``str``), {"berger" (default), "tile"}, type of clustering to use for AMR. `tile` results in wider patches, less artifacts and better scalability
+        * **clustering** (``str``), {"berger", "tile" (default)}, type of clustering to use for AMR. `tile` results in wider patches, less artifacts and better scalability
 
         **Expert parameters:**
 

src/amr/data/field/coarsening/default_field_coarsener.hpp

@@ -9,8 +9,8 @@
 #include "core/utilities/point/point.hpp"
 #include "core/data/grid/gridlayoutdefs.hpp"
 
-#include "amr/data/field/coarsening/field_coarsen_index_weight.hpp"
 #include "amr/resources_manager/amr_utils.hpp"
+#include "amr/data/field/coarsening/field_coarsen_index_weight.hpp"
 
 #include <SAMRAI/hier/Box.h>
 

src/amr/data/field/coarsening/field_coarsen_index_weight.hpp

@@ -1,18 +1,13 @@
 #ifndef PHARE_FIELD_COARSEN_HPP
 #define PHARE_FIELD_COARSEN_HPP
 
-
-#include "core/def/phare_mpi.hpp"
-
 #include "core/def.hpp"
-#include "coarsen_weighter.hpp"
+#include "core/def/phare_mpi.hpp" // IWYU pragma: keep
 #include "core/data/grid/gridlayoutdefs.hpp"
-#include "core/hybrid/hybrid_quantities.hpp"
-#include "core/data/field/field.hpp"
-#include "core/utilities/constants.hpp"
 
 #include "amr/resources_manager/amr_utils.hpp"
 
+#include "coarsen_weighter.hpp"
 
 #include <SAMRAI/hier/Box.h>
 

src/amr/data/field/coarsening/field_coarsen_operator.hpp

@@ -3,17 +3,17 @@
 
 #include "core/def/phare_mpi.hpp" // IWYU pragma: keep
 #include "core/utilities/constants.hpp"
-#include "core/utilities/point/point.hpp"
-#include "amr/data/tensorfield/tensor_field_data.hpp"
 
 #include "amr/data/field/field_data.hpp"
+#include "amr/utilities/box/amr_box.hpp"
 #include "amr/data/field/field_geometry.hpp"
+#include "amr/data/tensorfield/tensor_field_data.hpp"
 
 #include "default_field_coarsener.hpp"
 
 #include <SAMRAI/hier/Box.h>
-#include <SAMRAI/hier/CoarsenOperator.h>
 #include <SAMRAI/hier/IntVector.h>
+#include <SAMRAI/hier/CoarsenOperator.h>
 
 
 namespace PHARE::amr
@@ -23,74 +23,19 @@ namespace PHARE::amr
 template<typename Dst>
 void coarsen_field(Dst& destinationField, auto& sourceField, auto& intersectionBox, auto& coarsener)
 {
-    auto constexpr static dimension = Dst::dimension;
-
-    // now we can loop over the intersection box
-
-    core::Point<int, dimension> startIndex;
-    core::Point<int, dimension> endIndex;
-
-    startIndex[dirX] = intersectionBox.lower(dirX);
-    endIndex[dirX]   = intersectionBox.upper(dirX);
-
-    if constexpr (dimension > 1)
-    {
-        startIndex[dirY] = intersectionBox.lower(dirY);
-        endIndex[dirY]   = intersectionBox.upper(dirY);
-    }
-    if constexpr (dimension > 2)
-    {
-        startIndex[dirZ] = intersectionBox.lower(dirZ);
-        endIndex[dirZ]   = intersectionBox.upper(dirZ);
-    }
-
-    if constexpr (dimension == 1)
-    {
-        for (int ix = startIndex[dirX]; ix <= endIndex[dirX]; ++ix)
-        {
-            coarsener(sourceField, destinationField, {{ix}});
-        }
-    }
-
-
-    else if constexpr (dimension == 2)
-    {
-        for (int ix = startIndex[dirX]; ix <= endIndex[dirX]; ++ix)
-        {
-            for (int iy = startIndex[dirY]; iy <= endIndex[dirY]; ++iy)
-            {
-                coarsener(sourceField, destinationField, {{ix, iy}});
-            }
-        }
-    }
-
-
-    else if constexpr (dimension == 3)
-    {
-        for (int ix = startIndex[dirX]; ix <= endIndex[dirX]; ++ix)
-        {
-            for (int iy = startIndex[dirY]; iy <= endIndex[dirY]; ++iy)
-            {
-                for (int iz = startIndex[dirZ]; iz <= endIndex[dirZ]; ++iz)
-
-                {
-                    coarsener(sourceField, destinationField, {{ix, iy, iz}});
-                }
-            }
-        }
-    } // end 3D
+    for (auto const bix : phare_box_from<Dst::dimension>(intersectionBox))
+        coarsener(sourceField, destinationField, bix);
 }
 
+
 } // namespace PHARE::amr
 
 
 namespace PHARE
 {
 namespace amr
 {
-    using core::dirX;
-    using core::dirY;
-    using core::dirZ;
+
     //
     template<typename GridLayoutT, typename FieldT, typename FieldCoarsenerPolicy,
              typename PhysicalQuantity = decltype(std::declval<FieldT>().physicalQuantity())>
@@ -152,7 +97,7 @@ namespace amr
          * get the Field and GridLayout encapsulated into the fieldData.
          * With the help of FieldGeometry, transform the coarseBox to the correct index.
          * After that we can now create FieldCoarsen with the indexAndWeight implementation
-         * selected. Finaly loop over the indexes in the box, and apply the coarsening defined
+         * selected. Finally loop over the indexes in the box, and apply the coarsening defined
          * in FieldCoarsen operator
          *
          */

src/amr/data/field/field_data.hpp

@@ -4,31 +4,21 @@
 #include "core/def/phare_mpi.hpp" // IWYU pragma: keep
 
 #include "core/logger.hpp"
-#include "core/data/grid/gridlayout.hpp"
-#include "core/data/grid/gridlayout_impl.hpp"
+#include "core/data/field/field_box.hpp"
+
 #include "amr/resources_manager/amr_utils.hpp"
 
 #include "field_geometry.hpp"
-#include "core/data/field/field_box.hpp"
-
 
 #include <SAMRAI/hier/PatchData.h>
 #include <SAMRAI/tbox/MemoryUtilities.h>
+
 #include <utility>
 
 namespace PHARE
 {
 namespace amr
 {
-    // We use another class here so that we can specialize specifics function: copy , pack , unpack
-    // on the dimension and we don't want to loose non specialized function related to SAMRAI
-    // interface
-    template<typename GridLayoutT, std::size_t dim, typename Grid_t,
-             typename PhysicalQuantity = decltype(std::declval<Grid_t>().physicalQuantity())>
-    class FieldDataInternals
-    {
-    };
-
 
     /**@brief FieldData is the specialization of SAMRAI::hier::PatchData to Field objects
      *

src/amr/data/field/field_data_factory.hpp

@@ -2,17 +2,17 @@
 #define PHARE_SRC_AMR_FIELD_FIELD_DATA_FACTORY_HPP
 
 
-#include "core/def/phare_mpi.hpp"
+#include "core/def/phare_mpi.hpp" // IWYU pragma: keep
 
-#include <SAMRAI/geom/CartesianPatchGeometry.h>
 #include <SAMRAI/hier/Patch.h>
-#include <SAMRAI/hier/PatchDataFactory.h>
 #include <SAMRAI/tbox/MemoryUtilities.h>
-
-#include <utility>
+#include <SAMRAI/hier/PatchDataFactory.h>
+#include <SAMRAI/geom/CartesianPatchGeometry.h>
 
 #include "field_data.hpp"
 
+#include <utility>
+
 namespace PHARE
 {
 namespace amr
@@ -35,7 +35,7 @@ namespace amr
         FieldDataFactory(bool fineBoundaryRepresentsVariable, bool dataLivesOnPatchBorder,
                          std::string const& name, PhysicalQuantity qty)
             : SAMRAI::hier::PatchDataFactory(
-                SAMRAI::hier::IntVector{SAMRAI::tbox::Dimension(dimension), n_ghosts})
+                  SAMRAI::hier::IntVector{SAMRAI::tbox::Dimension(dimension), n_ghosts})
             , fineBoundaryRepresentsVariable_{fineBoundaryRepresentsVariable}
             , dataLivesOnPatchBorder_{dataLivesOnPatchBorder}
             , quantity_{qty}
@@ -127,7 +127,7 @@ namespace amr
                 nbCell[iDim] = box.numberCells(iDim);
             }
 
-            const std::size_t baseField
+            std::size_t const baseField
                 = SAMRAI::tbox::MemoryUtilities::align(sizeof(FieldData<GridLayoutT, FieldImpl>));
 
             GridLayoutT gridLayout{dl, nbCell, origin};

src/amr/data/field/field_geometry.hpp

@@ -2,17 +2,14 @@
 #define PHARE_SRC_AMR_FIELD_FIELD_GEOMETRY_HPP
 
 
-#include "core/def/phare_mpi.hpp"
-
-
-#include "SAMRAI/hier/IntVector.h"
-#include "core/data/grid/gridlayoutdefs.hpp"
-#include "core/data/grid/gridlayout.hpp"
 #include "core/utilities/types.hpp"
+#include "core/data/grid/gridlayout.hpp"
+#include "core/data/grid/gridlayoutdefs.hpp"
 
 #include "field_overlap.hpp"
 
 #include <SAMRAI/hier/Box.h>
+#include "SAMRAI/hier/IntVector.h"
 #include <SAMRAI/hier/BoxGeometry.h>
 
 #include <cassert>

src/amr/data/field/field_overlap.hpp

@@ -2,10 +2,10 @@
 #define PHARE_SRC_AMR_FIELD_FIELD_OVERLAP_HPP
 
 
-#include "core/def/phare_mpi.hpp"
+#include "core/def/phare_mpi.hpp" // IWYU pragma: keep
 
-#include <SAMRAI/hier/BoxContainer.h>
 #include <SAMRAI/hier/BoxOverlap.h>
+#include <SAMRAI/hier/BoxContainer.h>
 #include <SAMRAI/hier/Transformation.h>
 
 namespace PHARE

src/amr/data/field/field_variable.hpp

@@ -2,7 +2,7 @@
 #define PHARE_SRC_AMR_FIELD_FIELD_VARIABLE_HPP
 
 
-#include "core/def/phare_mpi.hpp"
+#include "core/def/phare_mpi.hpp" // IWYU pragma: keep
 
 #include <SAMRAI/hier/Variable.h>
 

src/amr/data/field/field_variable_fill_pattern.hpp

@@ -1,20 +1,19 @@
 #ifndef PHARE_SRC_AMR_FIELD_FIELD_VARIABLE_FILL_PATTERN_HPP
 #define PHARE_SRC_AMR_FIELD_FIELD_VARIABLE_FILL_PATTERN_HPP
 
-#include "amr/data/tensorfield/tensor_field_overlap.hpp"
 #include "core/logger.hpp"
 #include "core/def/phare_mpi.hpp"
-
+#include "core/utilities/types.hpp"
 #include <core/hybrid/hybrid_quantities.hpp>
-
 #include "core/data/tensorfield/tensorfield.hpp"
+
 #include <amr/utilities/box/amr_box.hpp>
 #include "amr/data/field/field_geometry.hpp"
+#include "amr/data/tensorfield/tensor_field_overlap.hpp"
 #include "amr/data/tensorfield/tensor_field_geometry.hpp"
 
 #include <SAMRAI/pdat/CellOverlap.h>
 #include "SAMRAI/xfer/VariableFillPattern.h"
-#include "core/utilities/types.hpp"
 
 #include <cassert>
 #include <cstddef>

src/amr/data/field/refine/electric_field_refiner.hpp

@@ -2,14 +2,15 @@
 #define PHARE_ELECTRIC_FIELD_REFINER_HPP
 
 
-#include "core/def/phare_mpi.hpp"
+#include "core/def/phare_mpi.hpp" // IWYU pragma: keep
 
-#include <SAMRAI/hier/Box.h>
-
-#include "amr/resources_manager/amr_utils.hpp"
 #include "core/utilities/constants.hpp"
-#include "core/data/grid/gridlayoutdefs.hpp"
 #include "core/utilities/point/point.hpp"
+#include "core/data/grid/gridlayoutdefs.hpp"
+
+#include "amr/resources_manager/amr_utils.hpp"
+
+#include <SAMRAI/hier/Box.h>
 
 #include <cstddef>
 

src/amr/data/field/refine/field_linear_refine.hpp

@@ -2,22 +2,19 @@
 #define PHARE_FIELD_LINEAR_REFINE_HPP
 
 
-#include "core/def/phare_mpi.hpp"
-
-
 #include "core/def.hpp"
-#include "core/data/grid/gridlayoutdefs.hpp"
-#include "core/data/field/field.hpp"
-#include "linear_weighter.hpp"
+#include "core/def/phare_mpi.hpp" // IWYU pragma: keep
 #include "core/utilities/constants.hpp"
 #include "core/utilities/point/point.hpp"
+#include "core/data/grid/gridlayoutdefs.hpp"
+
+#include "linear_weighter.hpp"
 
 #include <SAMRAI/hier/Box.h>
 #include <SAMRAI/hier/IntVector.h>
 
 #include <array>
 #include <utility>
-#include <vector>
 
 
 namespace PHARE