diff --git a/src/mesh/Connectivity1D.hpp b/src/mesh/Connectivity1D.hpp
index b78a8bf330eca6213ede9e20f1efd18d52bf50c2..21d89450c7ea14d0d9ac8f8467c5e929d98a057f 100644
--- a/src/mesh/Connectivity1D.hpp
+++ b/src/mesh/Connectivity1D.hpp
@@ -14,6 +14,9 @@ class Connectivity1D
{
public:
static constexpr size_t dimension = 1;
+
+ ConnectivityMatrix m_cell_to_node_matrix;
+
ConnectivityMatrix m_node_to_cell_matrix;
ConnectivityMatrixShort m_node_to_cell_local_node_matrix;
@@ -22,12 +25,12 @@ private:
const size_t m_number_of_cells;
- const Kokkos::View<const unsigned int**> m_cell_nodes;
- const Kokkos::View<const unsigned int**>& m_cell_faces = m_cell_nodes;
+ Kokkos::View<const unsigned int**> m_cell_nodes;
+ Kokkos::View<const unsigned int**>& m_cell_faces = m_cell_nodes;
- const Kokkos::View<const unsigned short*> m_cell_nb_nodes;
+ Kokkos::View<const unsigned short*> m_cell_nb_nodes;
Kokkos::View<double*> m_inv_cell_nb_nodes;
- const Kokkos::View<const unsigned short*>& m_cell_nb_faces = m_cell_nb_nodes;
+ Kokkos::View<const unsigned short*>& m_cell_nb_faces = m_cell_nb_nodes;
size_t m_max_nb_node_per_cell;
@@ -139,13 +142,30 @@ public:
m_node_to_cell_local_node_matrix);
}
- Connectivity1D(const Kokkos::View<const unsigned short*> cell_nb_nodes,
- const Kokkos::View<const unsigned int**> cell_nodes)
- : m_number_of_cells (cell_nb_nodes.extent(0)),
- m_cell_nodes (cell_nodes),
- m_cell_nb_nodes (cell_nb_nodes),
- m_inv_cell_nb_nodes ("inv_cell_nb_nodes", m_number_of_cells)
- {
+ Connectivity1D(const std::vector<std::vector<unsigned int>>& cell_by_node_vector)
+ : m_number_of_cells (cell_by_node_vector.size()),
+ m_inv_cell_nb_nodes ("inv_cell_nb_nodes", m_number_of_cells)
+ {
+ m_cell_to_node_matrix
+ = Kokkos::create_staticcrsgraph<ConnectivityMatrix>("cell_to_node_matrix",
+ cell_by_node_vector);
+ {
+ Kokkos::View<unsigned short*> cell_nb_nodes("cell_nb_nodes", cell_by_node_vector.size());
+ for (size_t j=0; j<cell_by_node_vector.size(); ++j) {
+ cell_nb_nodes[j] = cell_by_node_vector[j].size();
+ }
+ m_cell_nb_nodes = cell_nb_nodes;
+ }
+ {
+ Kokkos::View<unsigned int**> cell_nodes("cell_nodes", cell_by_node_vector.size(), 2);
+ for (size_t j=0; j<cell_by_node_vector.size(); ++j) {
+ for (size_t R=0; R<cell_by_node_vector[j].size(); ++R) {
+ cell_nodes(j,R) = cell_by_node_vector[j][R];
+ }
+ }
+ m_cell_nodes = cell_nodes;
+ }
+
Kokkos::parallel_for(m_number_of_cells, KOKKOS_LAMBDA(const size_t& j) {
m_inv_cell_nb_nodes[j] = 1./m_cell_nb_nodes[j];
});
diff --git a/src/mesh/Connectivity2D.hpp b/src/mesh/Connectivity2D.hpp
index 4eecf748545721b785106a18c516a66032b39a01..0bab4bf58d349575eb42f2baa920bce85f71c382 100644
--- a/src/mesh/Connectivity2D.hpp
+++ b/src/mesh/Connectivity2D.hpp
@@ -19,11 +19,14 @@ class Connectivity2D
public:
static constexpr size_t dimension = 2;
- ConnectivityMatrix m_node_to_cell_matrix;
- ConnectivityMatrixShort m_node_to_cell_local_node_matrix;
+ ConnectivityMatrix m_cell_to_node_matrix;
+
ConnectivityMatrix m_face_to_cell_matrix;
ConnectivityMatrix m_face_to_node_matrix;
+ ConnectivityMatrix m_node_to_cell_matrix;
+ ConnectivityMatrixShort m_node_to_cell_local_node_matrix;
+
private:
std::vector<RefFaceList> m_ref_face_list;
std::vector<RefNodeList> m_ref_node_list;
@@ -31,8 +34,8 @@ class Connectivity2D
const size_t m_number_of_cells;
size_t m_number_of_faces;
- const Kokkos::View<const unsigned short*> m_cell_nb_nodes;
- const Kokkos::View<const unsigned int**> m_cell_nodes;
+ Kokkos::View<const unsigned short*> m_cell_nb_nodes;
+ Kokkos::View<const unsigned int**> m_cell_nodes;
Kokkos::View<double*> m_inv_cell_nb_nodes;
Kokkos::View<const unsigned short*> m_cell_nb_faces;
@@ -260,12 +263,30 @@ class Connectivity2D
Connectivity2D(const Connectivity2D&) = delete;
- Connectivity2D(const Kokkos::View<const unsigned short*> cell_nb_nodes,
- const Kokkos::View<const unsigned int**> cell_nodes)
- : m_number_of_cells (cell_nodes.extent(0)),
- m_cell_nb_nodes(cell_nb_nodes),
- m_cell_nodes (cell_nodes)
+ Connectivity2D(std::vector<std::vector<unsigned int>> cell_by_node_vector)
+ : m_number_of_cells (cell_by_node_vector.size())
{
+ m_cell_to_node_matrix
+ = Kokkos::create_staticcrsgraph<ConnectivityMatrix>("cell_to_node_matrix",
+ cell_by_node_vector);
+
+ {
+ Kokkos::View<unsigned short*> cell_nb_nodes("cell_nb_nodes", cell_by_node_vector.size());
+ for (size_t j=0; j<cell_by_node_vector.size(); ++j) {
+ cell_nb_nodes[j] = cell_by_node_vector[j].size();
+ }
+ m_cell_nb_nodes = cell_nb_nodes;
+ }
+ {
+ Kokkos::View<unsigned int**> cell_nodes("cell_nodes", cell_by_node_vector.size(), 8);
+ for (size_t j=0; j<cell_by_node_vector.size(); ++j) {
+ for (size_t R=0; R<cell_by_node_vector[j].size(); ++R) {
+ cell_nodes(j,R) = cell_by_node_vector[j][R];
+ }
+ }
+ m_cell_nodes = cell_nodes;
+ }
+
{
Kokkos::View<double*> inv_cell_nb_nodes("inv_cell_nb_nodes", m_number_of_cells);
Kokkos::parallel_for(m_number_of_cells, KOKKOS_LAMBDA(const int&j){
diff --git a/src/mesh/Connectivity3D.hpp b/src/mesh/Connectivity3D.hpp
index c509e8e5bcdf029bfd00bd9932a9c91d794a462f..3a92bcfc9f3b88b17cdc6d550cf9677020380c1f 100644
--- a/src/mesh/Connectivity3D.hpp
+++ b/src/mesh/Connectivity3D.hpp
@@ -22,6 +22,8 @@ class Connectivity3D
public:
static constexpr size_t dimension = 3;
+ ConnectivityMatrix m_cell_to_node_matrix;
+
ConnectivityMatrix m_cell_to_face_matrix;
ConnectivityMatrixShort m_cell_to_face_is_reversed_matrix;
@@ -39,8 +41,8 @@ private:
const size_t m_number_of_cells;
size_t m_number_of_faces;
- const Kokkos::View<const unsigned short*> m_cell_nb_nodes;
- const Kokkos::View<const unsigned int**> m_cell_nodes;
+ Kokkos::View<const unsigned short*> m_cell_nb_nodes;
+ Kokkos::View<const unsigned int**> m_cell_nodes;
Kokkos::View<double*> m_inv_cell_nb_nodes;
Kokkos::View<const unsigned short*> m_node_nb_faces;
@@ -477,12 +479,28 @@ private:
Connectivity3D(const Connectivity3D&) = delete;
- Connectivity3D(const Kokkos::View<const unsigned short*> cell_nb_nodes,
- const Kokkos::View<const unsigned int**> cell_nodes)
- : m_number_of_cells (cell_nodes.extent(0)),
- m_cell_nb_nodes(cell_nb_nodes),
- m_cell_nodes (cell_nodes)
+ Connectivity3D(const std::vector<std::vector<unsigned int>>& cell_by_node_vector)
+ : m_number_of_cells (cell_by_node_vector.size())
{
+ m_cell_to_node_matrix
+ = Kokkos::create_staticcrsgraph<ConnectivityMatrix>("cell_to_node_matrix",
+ cell_by_node_vector);
+ {
+ Kokkos::View<unsigned short*> cell_nb_nodes("cell_nb_nodes", cell_by_node_vector.size());
+ for (size_t j=0; j<cell_by_node_vector.size(); ++j) {
+ cell_nb_nodes[j] = cell_by_node_vector[j].size();
+ }
+ m_cell_nb_nodes = cell_nb_nodes;
+ }
+ {
+ Kokkos::View<unsigned int**> cell_nodes("cell_nodes", cell_by_node_vector.size(), 8);
+ for (size_t j=0; j<cell_by_node_vector.size(); ++j) {
+ for (size_t R=0; R<cell_by_node_vector[j].size(); ++R) {
+ cell_nodes(j,R) = cell_by_node_vector[j][R];
+ }
+ }
+ m_cell_nodes = cell_nodes;
+ }
{
Kokkos::View<double*> inv_cell_nb_nodes("inv_cell_nb_nodes", m_number_of_cells);
Kokkos::parallel_for(m_number_of_cells, KOKKOS_LAMBDA(const int& j){
diff --git a/src/mesh/GmshReader.cpp b/src/mesh/GmshReader.cpp
index c8c2e09e7a28bf484cac0840b41d964f87fc994a..11516ed001bf8bf182ca55c4f00218f183770a31 100644
--- a/src/mesh/GmshReader.cpp
+++ b/src/mesh/GmshReader.cpp
@@ -799,29 +799,25 @@ GmshReader::__proceedData()
if (elementNumber[4] > 0) {
max_nb_node_per_cell = 8;
}
- const Kokkos::View<unsigned int**> cell_nodes("cell_nodes", nb_cells, max_nb_node_per_cell);
+
+ std::vector<std::vector<unsigned int>> cell_by_node_vector(nb_cells);
const size_t nb_tetrahedra = __tetrahedra.extent(0);
for (size_t j=0; j<nb_tetrahedra; ++j) {
+ cell_by_node_vector[j].resize(4);
for (int r=0; r<4; ++r) {
- cell_nodes(j,r) = __tetrahedra[j][r];
+ cell_by_node_vector[j][r] = __tetrahedra[j][r];
}
}
const size_t nb_hexahedra = __hexahedra.extent(0);
for (size_t j=0; j<nb_hexahedra; ++j) {
- const size_t jh = j+nb_tetrahedra;
+ const size_t jh = nb_tetrahedra+j;
+ cell_by_node_vector[jh].resize(8);
for (int r=0; r<8; ++r) {
- cell_nodes(jh,r) = __hexahedra[j][r];
+ cell_by_node_vector[jh][r] = __hexahedra[j][r];
}
}
- const Kokkos::View<unsigned short*> cell_nb_nodes("cell_nb_nodes", nb_cells);
- for (size_t j=0; j<nb_tetrahedra; ++j) {
- cell_nb_nodes[j] = 4;
- }
- for (size_t j=nb_tetrahedra; j<nb_tetrahedra+nb_hexahedra; ++j) {
- cell_nb_nodes[j] = 8;
- }
- std::shared_ptr<Connectivity3D> p_connectivity(new Connectivity3D(cell_nb_nodes, cell_nodes));
+ std::shared_ptr<Connectivity3D> p_connectivity(new Connectivity3D(cell_by_node_vector));
Connectivity3D& connectivity = *p_connectivity;
std::map<unsigned int, std::vector<unsigned int>> ref_faces_map;
@@ -847,16 +843,6 @@ GmshReader::__proceedData()
connectivity.addRefFaceList(RefFaceList(physical_ref_id.refId(), face_list));
}
- // for (size_t j=0; j<nb_cells; ++j) {
- // std::cout << std::setw(5) << j << ": ";
- // for (size_t r=0; r<cell_nb_nodes[j]; ++r) {
- // std::cout << ' ' << cell_nodes(j,r);
- // }
- // std::cout << '\n';
- // }
-
- // std::cerr << "*** using a 3d mesh (NIY)\n";
- // std::exit(0);
typedef Mesh<Connectivity3D> MeshType;
typedef TinyVector<3, double> Rd;
@@ -874,30 +860,49 @@ GmshReader::__proceedData()
if (elementNumber[2] > 0) {
max_nb_node_per_cell = 4;
}
- const Kokkos::View<unsigned int**> cell_nodes("cell_nodes", nb_cells, max_nb_node_per_cell);
+
+ std::vector<std::vector<unsigned int>> cell_by_node_vector(nb_cells);
const size_t nb_triangles = __triangles.extent(0);
for (size_t j=0; j<nb_triangles; ++j) {
- cell_nodes(j,0) = __triangles[j][0];
- cell_nodes(j,1) = __triangles[j][1];
- cell_nodes(j,2) = __triangles[j][2];
+ cell_by_node_vector[j].resize(3);
+ for (int r=0; r<3; ++r) {
+ cell_by_node_vector[j][r] = __triangles[j][r];
+ }
}
const size_t nb_quadrangles = __quadrangles.extent(0);
for (size_t j=0; j<nb_quadrangles; ++j) {
const size_t jq = j+nb_triangles;
- cell_nodes(jq,0) = __quadrangles[j][0];
- cell_nodes(jq,1) = __quadrangles[j][1];
- cell_nodes(jq,2) = __quadrangles[j][2];
- cell_nodes(jq,3) = __quadrangles[j][3];
- }
- const Kokkos::View<unsigned short*> cell_nb_nodes("cell_nb_nodes", nb_cells);
- for (size_t j=0; j<nb_triangles; ++j) {
- cell_nb_nodes[j] = 3;
- }
- for (size_t j=nb_triangles; j<nb_triangles+nb_quadrangles; ++j) {
- cell_nb_nodes[j] = 4;
+ cell_by_node_vector[jq].resize(4);
+ for (int r=0; r<4; ++r) {
+ cell_by_node_vector[jq][r] = __quadrangles[j][r];
+ }
}
- std::shared_ptr<Connectivity2D> p_connectivity(new Connectivity2D(cell_nb_nodes, cell_nodes));
+
+ // const Kokkos::View<unsigned int**> cell_nodes("cell_nodes", nb_cells, max_nb_node_per_cell);
+
+ // for (size_t j=0; j<nb_triangles; ++j) {
+ // cell_nodes(j,0) = __triangles[j][0];
+ // cell_nodes(j,1) = __triangles[j][1];
+ // cell_nodes(j,2) = __triangles[j][2];
+ // }
+
+ // const size_t nb_quadrangles = __quadrangles.extent(0);
+ // for (size_t j=0; j<nb_quadrangles; ++j) {
+ // const size_t jq = j+nb_triangles;
+ // cell_nodes(jq,0) = __quadrangles[j][0];
+ // cell_nodes(jq,1) = __quadrangles[j][1];
+ // cell_nodes(jq,2) = __quadrangles[j][2];
+ // cell_nodes(jq,3) = __quadrangles[j][3];
+ // }
+ // const Kokkos::View<unsigned short*> cell_nb_nodes("cell_nb_nodes", nb_cells);
+ // for (size_t j=0; j<nb_triangles; ++j) {
+ // cell_nb_nodes[j] = 3;
+ // }
+ // for (size_t j=nb_triangles; j<nb_triangles+nb_quadrangles; ++j) {
+ // cell_nb_nodes[j] = 4;
+ // }
+ std::shared_ptr<Connectivity2D> p_connectivity(new Connectivity2D(cell_by_node_vector));
Connectivity2D& connectivity = *p_connectivity;
std::map<unsigned int, std::vector<unsigned int>> ref_faces_map;
@@ -945,20 +950,16 @@ GmshReader::__proceedData()
} else if ((dimension1_mask, elementNumber)>0) {
const size_t nb_cells = (dimension1_mask, elementNumber);
- const size_t max_nb_node_per_cell=2;
-
- const Kokkos::View<unsigned int**> cell_nodes("cell_nodes", nb_cells, max_nb_node_per_cell);
- for (size_t j=0; j<nb_cells; ++j) {
- cell_nodes(j,0) = __edges[j][0];
- cell_nodes(j,1) = __edges[j][1];
- }
- const Kokkos::View<unsigned short*> cell_nb_nodes("cell_nb_nodes", nb_cells);
+ std::vector<std::vector<unsigned int>> cell_by_node_vector(nb_cells);
for (size_t j=0; j<nb_cells; ++j) {
- cell_nb_nodes[j] = 2;
+ cell_by_node_vector[j].resize(2);
+ for (int r=0; r<2; ++r) {
+ cell_by_node_vector[j][r] = __edges[j][r];
+ }
}
- std::shared_ptr<Connectivity1D> p_connectivity(new Connectivity1D(cell_nb_nodes, cell_nodes));
+ std::shared_ptr<Connectivity1D> p_connectivity(new Connectivity1D(cell_by_node_vector));
Connectivity1D& connectivity = *p_connectivity;
std::map<unsigned int, std::vector<unsigned int>> ref_points_map;