++

Author: PhilipDeegan

src/core/utilities/algorithm.hpp

@@ -7,7 +7,7 @@
 #include "core/utilities/span.hpp"
 #include "core/utilities/types.hpp"
 #include "core/data/field/field.hpp"
-
+#include "core/utilities/box/box.hpp"
 #include "core/data/grid/gridlayoutdefs.hpp"
 #include "core/data/ndarray/ndarray_vector.hpp"
 #include "core/data/tensorfield/tensorfield.hpp"
@@ -100,7 +100,7 @@ auto convert_to_primal(        //
 }
 
 template<std::size_t dim, typename... Ts>
-auto& _convert_to_fortran_primal( // DOES NOT WORK ON GHOST BOX!
+auto& convert_to_fortran_primal(  // DOES NOT WORK ON GHOST BOX!
     Field<dim, Ts...>& dst,       //
     Field<dim, Ts...> const& src, //
     auto const& layout            //
@@ -135,21 +135,17 @@ auto& _convert_to_fortran_primal( // DOES NOT WORK ON GHOST BOX!
 }
 
 template<typename Field_t, typename PQ, std::size_t rank>
-auto& _convert_to_fortran_primal(              //
+auto& convert_to_fortran_primal(               //
     TensorField<Field_t, PQ, rank>& dst,       //
     TensorField<Field_t, PQ, rank> const& src, //
     auto const& layout                         //
 )
 {
     for (std::size_t ci = 0; ci < src.size(); ++ci)
-        _convert_to_fortran_primal(dst[ci], src[ci], layout);
+        convert_to_fortran_primal(dst[ci], src[ci], layout);
     return dst;
 }
 
-auto& convert_to_fortran_primal(auto& dst, auto const& src, auto const& layout)
-{
-    return _convert_to_fortran_primal(dst, src, layout);
-}
 
 
 } // namespace PHARE::core

src/diagnostic/detail/vtkh5_type_writer.hpp

@@ -2,18 +2,17 @@
 #define PHARE_DIAGNOSTIC_DETAIL_VTK_H5_TYPE_WRITER_HPP
 
 
+#include "core/utilities/types.hpp"
 #include "core/utilities/box/box.hpp"
 #include "core/utilities/algorithm.hpp"
 #include "core/utilities/mpi_utils.hpp"
 #include "core/data/tensorfield/tensorfield.hpp"
 
-#include "core/utilities/types.hpp"
 #include "diagnostic/diagnostic_writer.hpp"
 
 #include "hdf5/detail/h5/h5_file.hpp"
 
 #include <string>
-#include <stdexcept>
 #include <unordered_map>
 
 
@@ -35,12 +34,13 @@ using namespace hdf5::h5;
 template<typename Writer>
 class H5TypeWriter : public PHARE::diagnostic::TypeWriter
 {
-    using FloatType                      = float; // Writer::FloatType;
+    using FloatType                      = float;
     std::string static inline base       = "/VTKHDF/";
     std::string static inline level_base = base + "Level";
     std::string static inline step_level = base + "Steps/Level";
     using physical_quantity_type         = Writer::ModelView::Field::physical_quantity_type;
 
+
 public:
     static constexpr auto dimension = Writer::dimension;
     using GridLayout                = Writer::GridLayout;
@@ -49,11 +49,14 @@ class H5TypeWriter : public PHARE::diagnostic::TypeWriter
     H5TypeWriter(Writer& h5Writer)
         : h5Writer_{h5Writer}
     {
-        if constexpr (dimension < 2)
-            throw std::runtime_error("VTK Diagnostics do not support 1D");
     }
 
 protected:
+    // data is duplicated in lower dimensions to fit a 3d view
+    //  so 2d data is * 2
+    //  and 1d data is * 4
+    constexpr static auto X_TIMES = std::array{4, 2, /* 3d noop */ 1}[dimension - 1];
+
     auto static flatten_boxes(auto const& boxes)
     {
         std::vector<std::array<int, dimension * 2>> data(boxes.size());
@@ -77,13 +80,6 @@ class H5TypeWriter : public PHARE::diagnostic::TypeWriter
     // Mostly gridlayout and box info
     struct VTKFileFieldInfo;
 
-    // Writes fields to HDF5 in VTK format
-    struct VTKFileFieldWriter;
-
-    // Writes tensor fields to HDF5 in VTK format
-    template<std::size_t rank>
-    struct VTKFileTensorFieldWriter;
-
     auto& getOrCreateH5File(DiagnosticProperties const& diagnostic)
     {
         if (!fileData_.count(diagnostic.quantity))
@@ -103,112 +99,17 @@ struct H5TypeWriter<Writer>::VTKFileFieldInfo
 {
     auto static constexpr primal_qty = physical_quantity_type::rho;
 
-    VTKFileFieldInfo(auto const& lyout)
-        : lvl{std::to_string(lyout.levelNumber())}
-        , layout{lyout}
+    VTKFileFieldInfo(auto const& layout)
+        : lvl{std::to_string(layout.levelNumber())}
         , ghost_box{layout.AMRGhostBoxFor(primal_qty)}
         , local_box{layout.AMRToLocal(core::grow(ghost_box, -1 * layout.nbrGhosts()))}
     {
     }
 
-
     std::string lvl;
-    GridLayout const& layout;
     Box_t const ghost_box;
     core::Box<std::uint32_t, dimension> const local_box;
-    std::uint32_t const primal_row_len = local_box.shape(dimension - 1);
-    std::string const path             = level_base + lvl + "/PointData/data";
-};
-
-
-
-template<typename Writer>
-struct H5TypeWriter<Writer>::VTKFileFieldWriter
-{
-    void write2D(auto const& field)
-    {
-        auto ds            = fw->h5file.getDataSet(finfo.path);
-        auto const lcl_box = finfo.local_box;
-        auto const size    = lcl_box.size();
-        auto const write   = [&]() {
-            ds.select({data_offset, 0}, {size, 1}).write_raw(field.data());
-            data_offset += size;
-        };
-        write();
-        write();
-    }
-
-
-    void write3D(auto const& field)
-    {
-        auto ds            = fw->h5file.getDataSet(finfo.path);
-        auto const lcl_box = finfo.local_box;
-        auto const size    = lcl_box.size();
-        ds.select({data_offset, 0}, {size, 1}).write_raw(field.data());
-        data_offset += size;
-    }
-
-
-    void operator()(auto const& field)
-    {
-        auto& tmp         = fw->typewriter->h5Writer_.modelView().tmpField();
-        auto const frimal = core::convert_to_fortran_primal(tmp, field, finfo.layout);
-        if constexpr (dimension == 2)
-            write2D(frimal);
-        if constexpr (dimension == 3)
-            write3D(frimal);
-    }
-
-    VTKFileWriter* fw;
-    VTKFileFieldInfo finfo;
-    std::size_t& data_offset = fw->data_offset; // NOT OWNED HERE
-};
-
-template<typename Writer>
-template<std::size_t rank>
-struct H5TypeWriter<Writer>::VTKFileTensorFieldWriter
-{
-    auto static constexpr N = core::detail::tensor_field_dim_from_rank<rank>();
-
-    void write2D(auto const& tf)
-    {
-        auto ds            = fw->h5file.getDataSet(finfo.path);
-        auto const lcl_box = finfo.local_box;
-        auto const size    = lcl_box.size();
-        auto const write   = [&]() {
-            for (std::uint32_t c = 0; c < N; ++c)
-                ds.select({data_offset, c}, {size, 1}).write_raw(tf[c].data());
-            data_offset += size;
-        };
-        write();
-        write();
-    }
-
-
-    void write3D(auto const& tf)
-    {
-        auto ds            = fw->h5file.getDataSet(finfo.path);
-        auto const lcl_box = finfo.local_box;
-        auto const size    = lcl_box.size();
-        for (std::uint32_t c = 0; c < N; ++c)
-            ds.select({data_offset, c}, {size, 1}).write_raw(tf[c].data());
-        data_offset += size;
-    }
-
-
-    void operator()(auto const& tf)
-    {
-        auto& tmp         = fw->typewriter->h5Writer_.modelView().template tmpTensorField<rank>();
-        auto const frimal = core::convert_to_fortran_primal(tmp, tf, finfo.layout);
-        if constexpr (dimension == 2)
-            write2D(frimal);
-        if constexpr (dimension == 3)
-            write3D(frimal);
-    }
-
-    VTKFileWriter* fw;
-    VTKFileFieldInfo finfo;
-    std::size_t& data_offset = fw->data_offset; // NOT OWNED HERE
+    std::string const path = level_base + lvl + "/PointData/data";
 };
 
 
@@ -223,6 +124,7 @@ struct H5TypeWriter<Writer>::VTKFileWriter
         , typewriter{tw}
         , h5file{tw->getOrCreateH5File(prop)}
     {
+        // set global per file attributes and datasets
         {
             initDSDefault(base + "/Steps/Values");
             auto steps_group = h5file.file().getGroup(base + "/Steps");
@@ -267,13 +169,34 @@ struct H5TypeWriter<Writer>::VTKFileWriter
 
     void writeField(auto const& field, auto const& layout)
     {
-        VTKFileFieldWriter{this, {layout}}(field);
+        VTKFileFieldInfo const finfo{layout};
+        auto const frimal = core::convert_to_fortran_primal(
+            typewriter->h5Writer_.modelView().tmpField(), field, layout);
+        auto ds         = h5file.getDataSet(finfo.path);
+        auto const size = finfo.local_box.size();
+        for (std::uint16_t i = 0; i < X_TIMES; ++i)
+        {
+            ds.select({data_offset, 0}, {size, 1}).write_raw(frimal.data());
+            data_offset += size;
+        }
     }
 
     template<std::size_t rank = 2>
     void writeTensorField(auto const& tf, auto const& layout)
     {
-        VTKFileTensorFieldWriter<rank>{this, {layout}}(tf);
+        auto static constexpr N = core::detail::tensor_field_dim_from_rank<rank>();
+
+        VTKFileFieldInfo const finfo{layout};
+        auto const frimal = core::convert_to_fortran_primal(
+            typewriter->h5Writer_.modelView().template tmpTensorField<rank>(), tf, layout);
+        auto ds         = h5file.getDataSet(finfo.path);
+        auto const size = finfo.local_box.size();
+        for (std::uint16_t i = 0; i < X_TIMES; ++i)
+        {
+            for (std::uint32_t c = 0; c < N; ++c)
+                ds.select({data_offset, c}, {size, 1}).write_raw(frimal[c].data());
+            data_offset += size;
+        }
     }
 
     template<typename T = FloatType>
@@ -327,36 +250,28 @@ struct H5TypeWriter<Writer>::VTKFileWriter
         }
     }
 
-    void initFieldFileLevel(int const level, auto& boxes)
+    template<std::size_t N = 1>
+    void initAnyFieldLevel(int const level, auto& boxes)
     {
         auto const path = level_base + std::to_string(level) + "/PointData/data";
-        h5file.template create_chunked_data_set<FloatType>(
-            path, std::vector<hsize_t>{detail::CHUNK_SIZE, 1},
-            HighFive::DataSpace({0, 1}, {HighFive::DataSpace::UNLIMITED, 1}));
-        resize(level, boxes);
-    }
-
-    template<std::size_t rank = 2>
-    void initTensorFieldFileLevel(auto const level, auto& boxes)
-    {
-        auto constexpr N = core::detail::tensor_field_dim_from_rank<rank>();
-        auto const path  = level_base + std::to_string(level) + "/PointData/data";
         h5file.template create_chunked_data_set<FloatType>(
             path, std::vector<hsize_t>{detail::CHUNK_SIZE, N},
             HighFive::DataSpace({0, N}, {HighFive::DataSpace::UNLIMITED, N}));
         resize<N>(level, boxes);
     }
 
+    void initFieldFileLevel(int const level, auto& boxes) { initAnyFieldLevel(level, boxes); }
+
+    template<std::size_t rank = 2>
+    void initTensorFieldFileLevel(int const level, auto& boxes)
+    {
+        initAnyFieldLevel<core::detail::tensor_field_dim_from_rank<rank>()>(level, boxes);
+    }
 
 
     template<std::size_t N = 1>
     void resize_data(auto const ilvl, auto const& boxes)
     {
-        // data is per face of a cube (cell)
-        //  so 2d data is * 2
-        //  and 1d data is * 4
-        constexpr static auto X_TIMES = std::array{4, 2, /* 3d noop */ 1}[dimension - 1];
-
         auto const lvl       = std::to_string(ilvl);
         auto const data_path = level_base + lvl + "/PointData/data";
         auto point_data_ds   = h5file.getDataSet(data_path);
@@ -392,8 +307,8 @@ struct H5TypeWriter<Writer>::VTKFileWriter
             ds.select({old_size}, {1}).write(total_boxes);
         }
 
-        auto amrbox_ds = h5file.getDataSet(level_base + lvl + "/AMRBox");
-        box_offset     = amrbox_ds.getDimensions()[0];
+        auto amrbox_ds  = h5file.getDataSet(level_base + lvl + "/AMRBox");
+        auto box_offset = amrbox_ds.getDimensions()[0];
 
         {
             auto ds             = h5file.getDataSet(step_level + lvl + "/AMRBoxOffset");
@@ -410,6 +325,7 @@ struct H5TypeWriter<Writer>::VTKFileWriter
         amrbox_ds.select({box_offset, 0}, {boxes.size(), dimension * 2}).write(vtk_boxes);
     }
 
+
     template<std::size_t N = 1>
     void resize(auto const ilvl, auto& boxes)
     {
@@ -423,7 +339,7 @@ struct H5TypeWriter<Writer>::VTKFileWriter
     DiagnosticProperties& diagnostic;
     H5TypeWriter<Writer>* typewriter;
     HighFiveFile& h5file;
-    std::size_t box_offset = 0, data_offset = 0;
+    std::size_t data_offset = 0;
 };