Flatten data structures in geometry

cpp/dolfinx/geometry/BoundingBoxTree.cpp

@@ -1,5 +1,5 @@
-// Copyright (C) 2013-2021 Chris N. Richardson, Anders Logg, Garth N. Wells and
-// Jørgen S. Dokken
+// Copyright (C) 2013-2022 Chris N. Richardson, Anders Logg, Garth N. Wells,
+// Jørgen S. Dokken, Sarah Roggendorf
 //
 // This file is part of DOLFINx (https://www.fenicsproject.org)
 //
@@ -16,6 +16,7 @@
 
 using namespace dolfinx;
 using namespace dolfinx::geometry;
+namespace stdex = std::experimental;
 
 namespace
 {
@@ -34,8 +35,8 @@ std::vector<std::int32_t> range(const mesh::Mesh& mesh, int tdim)
 }
 //-----------------------------------------------------------------------------
 // Compute bounding box of mesh entity
-std::array<std::array<double, 3>, 2>
-compute_bbox_of_entity(const mesh::Mesh& mesh, int dim, std::int32_t index)
+std::array<double, 6> compute_bbox_of_entity(const mesh::Mesh& mesh, int dim,
+                                             std::int32_t index)
 {
   // Get the geometrical indices for the mesh entity
   std::span<const double> xg = mesh.geometry().x();
@@ -45,78 +46,74 @@ compute_bbox_of_entity(const mesh::Mesh& mesh, int dim, std::int32_t index)
   const std::vector<std::int32_t> vertex_indices
       = mesh::entities_to_geometry(mesh, dim, entity, false);
 
-  std::array<std::array<double, 3>, 2> b;
-  b[0] = {xg[3 * vertex_indices.front()], xg[3 * vertex_indices.front() + 1],
-          xg[3 * vertex_indices.front() + 2]};
-  b[1] = b[0];
-
+  std::array<double, 6> b;
+  common::impl::copy_N<3>(std::next(xg.begin(), 3 * vertex_indices.front()),
+                          b.begin());
+  common::impl::copy_N<3>(std::next(xg.begin(), 3 * vertex_indices.front()),
+                          std::next(b.begin(), 3));
+  AB_span<2, 3> bsp(b.data());
   // Compute min and max over vertices
   for (int local_vertex : vertex_indices)
   {
     for (int j = 0; j < 3; ++j)
     {
-      b[0][j] = std::min(b[0][j], xg[3 * local_vertex + j]);
-      b[1][j] = std::max(b[1][j], xg[3 * local_vertex + j]);
+      bsp(0, j) = std::min(bsp(0, j), xg[3 * local_vertex + j]);
+      bsp(1, j) = std::max(bsp(1, j), xg[3 * local_vertex + j]);
     }
   }
 
   return b;
 }
 //-----------------------------------------------------------------------------
 // Compute bounding box of bounding boxes
-std::array<std::array<double, 3>, 2> compute_bbox_of_bboxes(
-    const std::span<const std::pair<std::array<std::array<double, 3>, 2>,
-                                    std::int32_t>>& leaf_bboxes)
+std::array<double, 6> compute_bbox_of_bboxes(
+    const std::span<const std::pair<std::array<double, 6>, std::int32_t>>&
+        leaf_bboxes)
 {
   // Compute min and max over remaining boxes
-  std::array<std::array<double, 3>, 2> b;
-  b[0] = leaf_bboxes[0].first[0];
-  b[1] = leaf_bboxes[0].first[1];
+  std::array<double, 6> b = leaf_bboxes[0].first;
+
   for (auto& box : leaf_bboxes)
   {
-    std::transform(box.first[0].begin(), box.first[0].end(), b[0].begin(),
-                   b[0].begin(),
+    std::transform(box.first.begin(), std::next(box.first.begin(), 3),
+                   b.begin(), b.begin(),
                    [](double a, double b) { return std::min(a, b); });
-    std::transform(box.first[1].begin(), box.first[1].end(), b[1].begin(),
-                   b[1].begin(),
+    std::transform(std::next(box.first.begin(), 3), box.first.end(),
+                   std::next(b.begin(), 3), std::next(b.begin(), 3),
                    [](double a, double b) { return std::max(a, b); });
   }
 
   return b;
 }
 //------------------------------------------------------------------------------
 int _build_from_leaf(
-    std::span<std::pair<std::array<std::array<double, 3>, 2>, std::int32_t>>
-        leaf_bboxes,
-    std::vector<std::array<int, 2>>& bboxes,
-    std::vector<double>& bbox_coordinates)
+    std::span<std::pair<std::array<double, 6>, std::int32_t>> leaf_bboxes,
+    std::vector<int>& bboxes, std::vector<double>& bbox_coordinates)
 {
   if (leaf_bboxes.size() == 1)
   {
     // Reached leaf
 
     // Get bounding box coordinates for leaf
-    const std::int32_t entity_index = leaf_bboxes[0].second;
-    const std::array<double, 3> b0 = leaf_bboxes[0].first[0];
-    const std::array<double, 3> b1 = leaf_bboxes[0].first[1];
+    const auto [b, entity_index] = leaf_bboxes[0];
 
     // Store bounding box data
-    bboxes.push_back({entity_index, entity_index});
-    bbox_coordinates.insert(bbox_coordinates.end(), b0.begin(), b0.end());
-    bbox_coordinates.insert(bbox_coordinates.end(), b1.begin(), b1.end());
-    return bboxes.size() - 1;
+    bboxes.push_back(entity_index);
+    bboxes.push_back(entity_index);
+    bbox_coordinates.insert(bbox_coordinates.end(), b.begin(),
+                            std::next(b.begin(), 3));
+    bbox_coordinates.insert(bbox_coordinates.end(), std::next(b.begin(), 3),
+                            b.end());
+    return bboxes.size() / 2 - 1;
   }
   else
   {
     // Compute bounding box of all bounding boxes
-    std::array<std::array<double, 3>, 2> b
-        = compute_bbox_of_bboxes(leaf_bboxes);
-    std::array<double, 3> b0 = b[0];
-    std::array<double, 3> b1 = b[1];
+    std::array<double, 6> b = compute_bbox_of_bboxes(leaf_bboxes);
 
     // Sort bounding boxes along longest axis
     std::array<double, 3> b_diff;
-    std::transform(b1.begin(), b1.end(), b0.begin(), b_diff.begin(),
+    std::transform(std::next(b.begin(), 3), b.end(), b.begin(), b_diff.begin(),
                    std::minus<double>());
     const std::size_t axis = std::distance(
         b_diff.begin(), std::max_element(b_diff.begin(), b_diff.end()));
@@ -125,49 +122,44 @@ int _build_from_leaf(
     std::nth_element(leaf_bboxes.begin(), middle, leaf_bboxes.end(),
                      [axis](auto& p0, auto& p1) -> bool
                      {
-                       double x0 = p0.first[0][axis] + p0.first[1][axis];
-                       double x1 = p1.first[0][axis] + p1.first[1][axis];
+                       AB_span<2, 3> p0sp(p0.first.data());
+                       AB_span<2, 3> p1sp(p1.first.data());
+                       double x0 = p0sp(0, axis) + p0sp(1, axis);
+                       double x1 = p1sp(0, axis) + p1sp(1, axis);
                        return x0 < x1;
                      });
 
     // Split bounding boxes into two groups and call recursively
     assert(!leaf_bboxes.empty());
     std::size_t part = leaf_bboxes.size() / 2;
-    std::array bbox{
-        _build_from_leaf(leaf_bboxes.first(part), bboxes, bbox_coordinates),
-        _build_from_leaf(leaf_bboxes.last(leaf_bboxes.size() - part), bboxes,
-                         bbox_coordinates)};
+    int bbox0
+        = _build_from_leaf(leaf_bboxes.first(part), bboxes, bbox_coordinates);
+    int bbox1 = _build_from_leaf(leaf_bboxes.last(leaf_bboxes.size() - part),
+                                 bboxes, bbox_coordinates);
 
     // Store bounding box data. Note that root box will be added last.
-    bboxes.push_back(bbox);
-    bbox_coordinates.insert(bbox_coordinates.end(), b0.begin(), b0.end());
-    bbox_coordinates.insert(bbox_coordinates.end(), b1.begin(), b1.end());
-    return bboxes.size() - 1;
+    bboxes.push_back(bbox0);
+    bboxes.push_back(bbox1);
+    bbox_coordinates.insert(bbox_coordinates.end(), b.begin(),
+                            std::next(b.begin(), 3));
+    bbox_coordinates.insert(bbox_coordinates.end(), std::next(b.begin(), 3),
+                            b.end());
+    return bboxes.size() / 2 - 1;
   }
 }
 //-----------------------------------------------------------------------------
 std::pair<std::vector<std::int32_t>, std::vector<double>> build_from_leaf(
-    std::vector<std::pair<std::array<std::array<double, 3>, 2>, std::int32_t>>
-        leaf_bboxes)
+    std::vector<std::pair<std::array<double, 6>, std::int32_t>> leaf_bboxes)
 {
-  std::vector<std::array<std::int32_t, 2>> bboxes;
+  std::vector<std::int32_t> bboxes;
   std::vector<double> bbox_coordinates;
   _build_from_leaf(leaf_bboxes, bboxes, bbox_coordinates);
-
-  std::vector<std::int32_t> bbox_array(2 * bboxes.size());
-  for (std::size_t i = 0; i < bboxes.size(); ++i)
-  {
-    bbox_array[2 * i] = bboxes[i][0];
-    bbox_array[2 * i + 1] = bboxes[i][1];
-  }
-
-  return {std::move(bbox_array), std::move(bbox_coordinates)};
+  return {std::move(bboxes), std::move(bbox_coordinates)};
 }
 //-----------------------------------------------------------------------------
 int _build_from_point(
     std::span<std::pair<std::array<double, 3>, std::int32_t>> points,
-    std::vector<std::array<std::int32_t, 2>>& bboxes,
-    std::vector<double>& bbox_coordinates)
+    std::vector<std::int32_t>& bboxes, std::vector<double>& bbox_coordinates)
 {
   // Reached leaf
   if (points.size() == 1)
@@ -176,12 +168,13 @@ int _build_from_point(
 
     // Index of entity contained in leaf
     const std::int32_t c1 = points[0].second;
-    bboxes.push_back({c1, c1});
+    bboxes.push_back(c1);
+    bboxes.push_back(c1);
     bbox_coordinates.insert(bbox_coordinates.end(), points[0].first.begin(),
                             points[0].first.end());
     bbox_coordinates.insert(bbox_coordinates.end(), points[0].first.begin(),
                             points[0].first.end());
-    return bboxes.size() - 1;
+    return bboxes.size() / 2 - 1;
   }
 
   // Compute bounding box of all points
@@ -204,16 +197,17 @@ int _build_from_point(
   // Split bounding boxes into two groups and call recursively
   assert(!points.empty());
   std::size_t part = points.size() / 2;
-  std::array bbox{
-      _build_from_point(points.first(part), bboxes, bbox_coordinates),
-      _build_from_point(points.last(points.size() - part), bboxes,
-                        bbox_coordinates)};
+  std::int32_t bbox0
+      = _build_from_point(points.first(part), bboxes, bbox_coordinates);
+  std::int32_t bbox1 = _build_from_point(points.last(points.size() - part),
+                                          bboxes, bbox_coordinates);
 
   // Store bounding box data. Note that root box will be added last.
-  bboxes.push_back(bbox);
+  bboxes.push_back(bbox0);
+  bboxes.push_back(bbox1);
   bbox_coordinates.insert(bbox_coordinates.end(), b0.begin(), b0.end());
   bbox_coordinates.insert(bbox_coordinates.end(), b1.begin(), b1.end());
-  return bboxes.size() - 1;
+  return bboxes.size() / 2 - 1;
 }
 //-----------------------------------------------------------------------------
 } // namespace
@@ -242,16 +236,14 @@ BoundingBoxTree::BoundingBoxTree(const mesh::Mesh& mesh, int tdim,
   mesh.topology_mutable().create_connectivity(tdim, mesh.topology().dim());
 
   // Create bounding boxes for all mesh entities (leaves)
-  std::vector<std::pair<std::array<std::array<double, 3>, 2>, std::int32_t>>
-      leaf_bboxes;
+  std::vector<std::pair<std::array<double, 6>, std::int32_t>> leaf_bboxes;
   leaf_bboxes.reserve(entities.size());
   for (std::int32_t e : entities)
   {
-    std::array<std::array<double, 3>, 2> b
-        = compute_bbox_of_entity(mesh, tdim, e);
-    std::transform(b[0].begin(), b[0].end(), b[0].begin(),
+    std::array<double, 6> b = compute_bbox_of_entity(mesh, tdim, e);
+    std::transform(b.begin(), std::next(b.begin(), 3), b.begin(),
                    [padding](double x) { return x - padding; });
-    std::transform(b[1].begin(), b[1].end(), b[1].begin(),
+    std::transform(std::next(b.begin(), 3), b.end(), std::next(b.begin(), 3),
                    [padding](double& x) { return x + padding; });
     leaf_bboxes.emplace_back(b, e);
   }
@@ -269,16 +261,10 @@ BoundingBoxTree::BoundingBoxTree(
     : _tdim(0)
 {
   // Recursively build the bounding box tree from the leaves
-  std::vector<std::array<int, 2>> bboxes;
   if (!points.empty())
   {
-    _build_from_point(std::span(points), bboxes, _bbox_coordinates);
-    _bboxes.resize(2 * bboxes.size());
-    for (std::size_t i = 0; i < bboxes.size(); ++i)
-    {
-      _bboxes[2 * i] = bboxes[i][0];
-      _bboxes[2 * i + 1] = bboxes[i][1];
-    }
+    _bboxes.clear();
+    _build_from_point(std::span(points), _bboxes, _bbox_coordinates);
   }
 
   LOG(INFO) << "Computed bounding box tree with " << num_bboxes()
@@ -305,14 +291,14 @@ BoundingBoxTree BoundingBoxTree::create_global_tree(MPI_Comm comm) const
   MPI_Allgather(send_bbox.data(), 6, MPI_DOUBLE, recv_bbox.data(), 6,
                 MPI_DOUBLE, comm);
 
-  std::vector<std::pair<std::array<std::array<double, 3>, 2>, std::int32_t>>
-      _recv_bbox(mpi_size);
+  std::vector<std::pair<std::array<double, 6>, std::int32_t>> _recv_bbox(
+      mpi_size);
   for (std::size_t i = 0; i < _recv_bbox.size(); ++i)
   {
     common::impl::copy_N<3>(std::next(recv_bbox.begin(), 6 * i),
-                            _recv_bbox[i].first[0].begin());
+                            _recv_bbox[i].first.begin());
     common::impl::copy_N<3>(std::next(recv_bbox.begin(), 6 * i + 3),
-                            _recv_bbox[i].first[1].begin());
+                            std::next(_recv_bbox[i].first.begin(), 3));
     _recv_bbox[i].second = i;
   }
 
@@ -362,14 +348,13 @@ void BoundingBoxTree::tree_print(std::stringstream& s, int i) const
   }
 }
 //-----------------------------------------------------------------------------
-std::array<std::array<double, 3>, 2>
-BoundingBoxTree::get_bbox(std::size_t node) const
+std::array<double, 6> BoundingBoxTree::get_bbox(std::size_t node) const
 {
-  std::array<std::array<double, 3>, 2> x;
+  std::array<double, 6> x;
   common::impl::copy_N<3>(std::next(_bbox_coordinates.begin(), 6 * node),
-                          x[0].begin());
+                          x.begin());
   common::impl::copy_N<3>(std::next(_bbox_coordinates.begin(), 6 * node + 3),
-                          x[1].begin());
+                          std::next(x.begin(), 3));
   return x;
 }
 //-----------------------------------------------------------------------------

cpp/dolfinx/geometry/BoundingBoxTree.h

@@ -7,13 +7,17 @@
 #pragma once
 
 #include <array>
+#include <basix/mdspan.hpp>
 #include <cassert>
 #include <cstdint>
 #include <mpi.h>
 #include <span>
 #include <string>
 #include <vector>
+namespace stdex = std::experimental;
 
+template <std::size_t A, std::size_t B>
+using AB_span = stdex::mdspan<double, stdex::extents<std::size_t, A, B>>;
 namespace dolfinx::mesh
 {
 class Mesh;
@@ -70,9 +74,9 @@ class BoundingBoxTree
 
   /// Return bounding box coordinates for a given node in the tree
   /// @param[in] node The bounding box node index
-  /// @return The bounding box where [0] is the lower corner and [1] is
-  /// the upper corner
-  std::array<std::array<double, 3>, 2> get_bbox(std::size_t node) const;
+  /// @return The bounding box [:3] contains the lower corner and [3:] the upper
+  /// corner
+  std::array<double, 6> get_bbox(std::size_t node) const;
 
   /// Compute a global bounding tree (collective on comm)
   /// This can be used to find which process a point might have a