done. to test

Xiangyu-Hu · Aug 3, 2024 · 773ab1d · 773ab1d
1 parent ddd064d
commit 773ab1d
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Showing 7 changed files with 50 additions and 45 deletions.
diff --git a/src/for_2D_build/meshes/base_mesh_2d.cpp b/src/for_2D_build/meshes/base_mesh_2d.cpp
@@ -3,19 +3,19 @@
 namespace SPH
 {
 //=============================================================================================//
-Arrayi BaseMesh::transfer1DtoMeshIndex(const Arrayi &mesh_size, size_t i)
+Arrayi Mesh::transfer1DtoMeshIndex(const Arrayi &mesh_size, size_t i)
 {
     size_t row_size = mesh_size[1];
     size_t column = i / row_size;
     return Arrayi(column, i - column * row_size);
 }
 //=============================================================================================//
-size_t BaseMesh::transferMeshIndexTo1D(const Arrayi &mesh_size, const Arrayi &mesh_index)
+size_t Mesh::transferMeshIndexTo1D(const Arrayi &mesh_size, const Arrayi &mesh_index)
 {
     return mesh_index[0] * mesh_size[1] + mesh_index[1];
 }
 //=============================================================================================//
-size_t BaseMesh::transferMeshIndexToMortonOrder(const Arrayi &mesh_index)
+size_t Mesh::transferMeshIndexToMortonOrder(const Arrayi &mesh_index)
 {
     return MortonCode(mesh_index[0]) | (MortonCode(mesh_index[1]) << 1);
 }

diff --git a/src/for_2D_build/particle_generator/particle_generator_lattice_2d.cpp b/src/for_2D_build/particle_generator/particle_generator_lattice_2d.cpp
@@ -11,9 +11,9 @@ namespace SPH
 //=================================================================================================//
 void ParticleGenerator<BaseParticles, Lattice>::prepareGeometricData()
 {
-    BaseMesh mesh(domain_bounds_, lattice_spacing_, 0);
+    Mesh mesh(domain_bounds_, lattice_spacing_, 0);
     Real particle_volume = lattice_spacing_ * lattice_spacing_;
-    Arrayi number_of_lattices = mesh.AllCellsFromAllGridPoints(mesh.AllGridPoints());
+    Arrayi number_of_lattices = mesh.AllCells();
     for (int i = 0; i < number_of_lattices[0]; ++i)
         for (int j = 0; j < number_of_lattices[1]; ++j)
         {
@@ -32,12 +32,12 @@ void ParticleGenerator<SurfaceParticles, Lattice>::prepareGeometricData()
 {
     // Calculate the total volume and
     // count the number of cells inside the body volume, where we might put particles.
-    std::unique_ptr<BaseMesh> mesh(new BaseMesh(domain_bounds_, lattice_spacing_, 0));
-    Arrayi number_of_lattices = mesh->AllCellsFromAllGridPoints(mesh->AllGridPoints());
+    Mesh mesh(domain_bounds_, lattice_spacing_, 0);
+    Arrayi number_of_lattices = mesh.AllCells();
     for (int i = 0; i < number_of_lattices[0]; ++i)
         for (int j = 0; j < number_of_lattices[1]; ++j)
         {
-            Vecd particle_position = mesh->CellPositionFromIndex(Arrayi(i, j));
+            Vecd particle_position = mesh.CellPositionFromIndex(Arrayi(i, j));
             if (initial_shape_.checkNotFar(particle_position, lattice_spacing_))
             {
                 if (initial_shape_.checkContain(particle_position))
@@ -63,7 +63,7 @@ void ParticleGenerator<SurfaceParticles, Lattice>::prepareGeometricData()
     for (int i = 0; i < number_of_lattices[0]; ++i)
         for (int j = 0; j < number_of_lattices[1]; ++j)
         {
-            Vecd particle_position = mesh->CellPositionFromIndex(Arrayi(i, j));
+            Vecd particle_position = mesh.CellPositionFromIndex(Arrayi(i, j));
             if (initial_shape_.checkNotFar(particle_position, lattice_spacing_))
             {
                 if (initial_shape_.checkContain(particle_position))

diff --git a/src/for_3D_build/meshes/base_mesh_3d.cpp b/src/for_3D_build/meshes/base_mesh_3d.cpp
@@ -3,7 +3,7 @@
 namespace SPH
 {
 //=================================================================================================//
-Arrayi BaseMesh::transfer1DtoMeshIndex(const Arrayi &mesh_size, size_t i)
+Arrayi Mesh::transfer1DtoMeshIndex(const Arrayi &mesh_size, size_t i)
 {
     size_t row_times_column_size = mesh_size[1] * mesh_size[2];
     size_t page = i / row_times_column_size;
@@ -13,14 +13,14 @@ Arrayi BaseMesh::transfer1DtoMeshIndex(const Arrayi &mesh_size, size_t i)
     return Arrayi(page, column, left_over - column * row_size);
 }
 //=================================================================================================//
-size_t BaseMesh::transferMeshIndexTo1D(const Arrayi &mesh_size, const Arrayi &mesh_index)
+size_t Mesh::transferMeshIndexTo1D(const Arrayi &mesh_size, const Arrayi &mesh_index)
 {
     return mesh_index[0] * mesh_size[1] * mesh_size[2] +
            mesh_index[1] * mesh_size[2] +
            mesh_index[2];
 }
 //=================================================================================================//
-size_t BaseMesh::transferMeshIndexToMortonOrder(const Arrayi &mesh_index)
+size_t Mesh::transferMeshIndexToMortonOrder(const Arrayi &mesh_index)
 {
     return MortonCode(mesh_index[0]) | (MortonCode(mesh_index[1]) << 1) | (MortonCode(mesh_index[2]) << 2);
 }

diff --git a/src/for_3D_build/particle_generator/particle_generator_lattice_3d.cpp b/src/for_3D_build/particle_generator/particle_generator_lattice_3d.cpp
@@ -11,9 +11,9 @@ namespace SPH
 //=================================================================================================//
 void ParticleGenerator<BaseParticles, Lattice>::prepareGeometricData()
 {
-    BaseMesh mesh(domain_bounds_, lattice_spacing_, 0);
+    Mesh mesh(domain_bounds_, lattice_spacing_, 0);
     Real particle_volume = lattice_spacing_ * lattice_spacing_ * lattice_spacing_;
-    Arrayi number_of_lattices = mesh.AllCellsFromAllGridPoints(mesh.AllGridPoints());
+    Arrayi number_of_lattices = mesh.AllCells();
     for (int i = 0; i < number_of_lattices[0]; ++i)
         for (int j = 0; j < number_of_lattices[1]; ++j)
             for (int k = 0; k < number_of_lattices[2]; ++k)
@@ -33,13 +33,13 @@ void ParticleGenerator<SurfaceParticles, Lattice>::prepareGeometricData()
 {
     // Calculate the total volume and
     // count the number of cells inside the body volume, where we might put particles.
-    std::unique_ptr<BaseMesh> mesh(new BaseMesh(domain_bounds_, lattice_spacing_, 0));
-    Arrayi number_of_lattices = mesh->AllCellsFromAllGridPoints(mesh->AllGridPoints());
+    Mesh mesh(domain_bounds_, lattice_spacing_, 0);
+    Arrayi number_of_lattices = mesh.AllCells();
     for (int i = 0; i < number_of_lattices[0]; ++i)
         for (int j = 0; j < number_of_lattices[1]; ++j)
             for (int k = 0; k < number_of_lattices[2]; ++k)
             {
-                Vecd particle_position = mesh->CellPositionFromIndex(Arrayi(i, j, k));
+                Vecd particle_position = mesh.CellPositionFromIndex(Arrayi(i, j, k));
                 if (initial_shape_.checkNotFar(particle_position, lattice_spacing_))
                 {
                     if (initial_shape_.checkContain(particle_position))
@@ -66,7 +66,7 @@ void ParticleGenerator<SurfaceParticles, Lattice>::prepareGeometricData()
         for (int j = 0; j < number_of_lattices[1]; ++j)
             for (int k = 0; k < number_of_lattices[2]; ++k)
             {
-                Vecd particle_position = mesh->CellPositionFromIndex(Arrayi(i, j, k));
+                Vecd particle_position = mesh.CellPositionFromIndex(Arrayi(i, j, k));
                 if (initial_shape_.checkNotFar(particle_position, lattice_spacing_))
                 {
                     if (initial_shape_.checkContain(particle_position))

diff --git a/src/shared/meshes/base_mesh.cpp b/src/shared/meshes/base_mesh.cpp
@@ -4,12 +4,20 @@ namespace SPH
 {
 //=================================================================================================//
 Mesh::Mesh(BoundingBox tentative_bounds, Real grid_spacing, size_t buffer_width)
-    : grid_spacing_(grid_spacing)
+    : grid_spacing_(grid_spacing), buffer_width_(buffer_width)
 {
     Vecd mesh_buffer = Real(buffer_width) * grid_spacing * Vecd::Ones();
     mesh_lower_bound_ = tentative_bounds.first_ - mesh_buffer;
     Vecd tentative_dimension = tentative_bounds.second_ + mesh_buffer - mesh_lower_bound_;
     all_grid_points_ = ceil(tentative_dimension.array() / grid_spacing).cast<int>() + Arrayi::Ones();
+    all_cells_ = all_grid_points_ - Arrayi::Ones();
+}
+//=================================================================================================//
+Mesh::Mesh(Vecd mesh_lower_bound, Real grid_spacing, Arrayi all_grid_points)
+    : mesh_lower_bound_{mesh_lower_bound}, grid_spacing_{grid_spacing},
+      buffer_width_(0), all_grid_points_{all_grid_points}
+{
+    all_cells_ = all_grid_points_ - Arrayi::Ones();
 }
 //=================================================================================================//
 Arrayi Mesh::CellIndexFromPosition(const Vecd &position)
@@ -20,14 +28,14 @@ Arrayi Mesh::CellIndexFromPosition(const Vecd &position)
         .min(all_grid_points_ - 2 * Arrayi::Ones());
 }
 //=================================================================================================//
-Vecd Mesh::CellLowerCorner(const Arrayi &cell_index)
+Vecd Mesh::CellLowerCornerPosition(const Arrayi &cell_index)
 {
     return mesh_lower_bound_ + cell_index.cast<Real>().matrix() * grid_spacing_;
 }
 //=================================================================================================//
 Vecd Mesh::CellPositionFromIndex(const Arrayi &cell_index)
 {
-    return CellLowerCorner(cell_index) + 0.5 * Vecd::Ones() * grid_spacing_;
+    return CellLowerCornerPosition(cell_index) + 0.5 * Vecd::Ones() * grid_spacing_;
 }
 //=================================================================================================//
 Vecd Mesh::GridPositionFromIndex(const Arrayi &grid_index)

diff --git a/src/shared/meshes/base_mesh.h b/src/shared/meshes/base_mesh.h
@@ -47,52 +47,50 @@ using namespace std::placeholders;
 namespace SPH
 {
 /**
- * @class BaseMesh
+ * @class Mesh
  * @brief Base class for all structured meshes which may be grid or cell based.
  * The basic properties of the mesh, such as lower bound, grid spacing
  * and number of grid points may be determined by the derived class.
  * Note that there is no mesh-based data defined here.
  */
 class Mesh
 {
-  protected:
-    Vecd mesh_lower_bound_;  /**< mesh lower bound as reference coordinate */
-    Real grid_spacing_;      /**< grid_spacing */
-    Arrayi all_grid_points_; /**< number of grid points by dimension */
   public:
     Mesh(BoundingBox tentative_bounds, Real grid_spacing, size_t buffer_width);
+    Mesh(Vecd mesh_lower_bound, Real grid_spacing, Arrayi all_grid_points);
     ~Mesh(){};
 
     Vecd MeshLowerBound() { return mesh_lower_bound_; };
     Real GridSpacing() { return grid_spacing_; };
     Arrayi AllGridPoints() { return all_grid_points_; };
-    Arrayi AllCells() { return all_grid_points_ - Arrayi::Ones(); };
+    Arrayi AllCells() { return all_cells_; };
     size_t NumberOfGridPoints() { return transferMeshIndexTo1D(all_grid_points_, all_grid_points_); };
-    size_t NumberOfCells() { return transferMeshIndexTo1D(AllCells(), AllCells()); };
-    /** Given the grid point number, return the cell number. */
-    Arrayi AllCellsFromAllGridPoints(const Arrayi &all_grid_points) { return all_grid_points - Arrayi::Ones(); };
-    /** Given the cell position, return the grid position. */
-    Vecd GridPositionFromCellPosition(const Vecd &cell_position) { return cell_position - 0.5 * grid_spacing_ * Vecd::Ones(); };
-    /** Given the position, return the cell index. */
+    size_t NumberOfCells() { return transferMeshIndexTo1D(all_cells_, all_cells_); };
     Arrayi CellIndexFromPosition(const Vecd &position);
-    /** Given the cell index, return the cell position. */
     Vecd CellPositionFromIndex(const Arrayi &cell_index);
-    /** Given the cell index, return the position of its lower corner. */
-    Vecd CellLowerCorner(const Arrayi &cell_index);
-    /** Given the index, return the grid position. */
     Vecd GridPositionFromIndex(const Arrayi &grid_index);
-    /** Transfer 1D int to mesh index.  */
+    Vecd CellLowerCornerPosition(const Arrayi &cell_index);
+    //----------------------------------------------------------------------
+    // Transferring between 1D mesh indexes.
+    // Here, mesh size can be either AllGridPoints or AllCells.
+    //----------------------------------------------------------------------
     Arrayi transfer1DtoMeshIndex(const Arrayi &mesh_size, size_t i);
-    /** Transfer mesh index to 1D int.  */
     size_t transferMeshIndexTo1D(const Arrayi &mesh_size, const Arrayi &mesh_index);
     /** converts mesh index into a Morton order.
      * Interleave a 10 bit number in 32 bits, fill one bit and leave the other 2 as zeros
      * https://stackoverflow.com/questions/18529057/
      * produce-interleaving-bit-patterns-morton-keys-for-32-bit-64-bit-and-128bit
      */
-    size_t MortonCode(const size_t &i);
-    /** Converts mesh index into a Morton order. */
     size_t transferMeshIndexToMortonOrder(const Arrayi &mesh_index);
+
+  protected:
+    Vecd mesh_lower_bound_;  /**< mesh lower bound as reference coordinate */
+    Real grid_spacing_;      /**< grid_spacing */
+    size_t buffer_width_;    /**< buffer width to avoid bound check.*/
+    Arrayi all_grid_points_; /**< number of grid points by dimension */
+    Arrayi all_cells_;       /**< number of cells by dimension */
+
+    size_t MortonCode(const size_t &i);
 };
 
 /**

diff --git a/src/shared/meshes/mesh_with_data_packages.h b/src/shared/meshes/mesh_with_data_packages.h
@@ -118,8 +118,7 @@ class MeshWithGridDataPackages : public Mesh
   public:
     template <typename... Args>
     explicit MeshWithGridDataPackages(BoundingBox tentative_bounds, Real data_spacing, size_t buffer_size)
-        : Mesh(tentative_bounds, pkg_size * data_spacing, buffer_size),
-          data_spacing_(data_spacing),
+        : Mesh(tentative_bounds, pkg_size * data_spacing, buffer_size), data_spacing_(data_spacing),
           global_mesh_(mesh_lower_bound_ + 0.5 * data_spacing * Vecd::Ones(), data_spacing, all_cells_ * pkg_size)
     {
         allocateMetaDataMatrix();
@@ -137,7 +136,7 @@ class MeshWithGridDataPackages : public Mesh
     MeshVariableAssemble all_mesh_variables_;         /**< all mesh variables on this mesh. */
     static constexpr int pkg_size = PKG_SIZE;         /**< the size of the data package matrix*/
     const Real data_spacing_;                         /**< spacing of data in the data packages*/
-    BaseMesh global_mesh_;                            /**< the mesh for the locations of all possible data points. */
+    Mesh global_mesh_;                                /**< the mesh for the locations of all possible data points. */
     size_t num_grid_pkgs_ = 2;                        /**< the number of all distinct packages, initially only 2 singular packages. */
     using MetaData = std::pair<int, size_t>;          /**< stores the metadata for each cell: (int)singular0/inner1/core2, (size_t)package data index*/
     MeshDataMatrix<MetaData> meta_data_mesh_;         /**< metadata for all cells. */
@@ -235,7 +234,7 @@ class MeshWithGridDataPackages : public Mesh
     /** return the position of the lower bound data in a cell. */
     Vecd DataLowerBoundInCell(const Arrayi &cell_index)
     {
-        return CellLowerCorner(cell_index) + 0.5 * data_spacing_ * Vecd::Ones();
+        return CellLowerCornerPosition(cell_index) + 0.5 * data_spacing_ * Vecd::Ones();
     }
 
     /** return the grid index from its position and the index of the cell it belongs to. */