Merge pull request #209 from lanl/Nathaniel2

Nathaniel2

single-node-refactor/src/common/mesh.h

@@ -111,15 +111,15 @@ void bubble_sort(size_t arr[], const size_t num)
     } // end for i
 } // end function
 
-struct zones_in_MaterialPoint_t
+struct zones_in_elem_t
 {
     private:
         size_t num_zones_in_elem_;
     public:
-        zones_in_MaterialPoint_t() {
+        zones_in_elem_t() {
         };
 
-        zones_in_MaterialPoint_t(const size_t num_zones_in_elem_inp) {
+        zones_in_elem_t(const size_t num_zones_in_elem_inp) {
             this->num_zones_in_elem_ = num_zones_in_elem_inp;
         };
 
@@ -138,15 +138,15 @@ struct zones_in_MaterialPoint_t
 };
 
 // if material points are defined strictly internal to the element.
-struct legendre_in_MaterialPoint_t
+struct legendre_in_elem_t
 {
     private:
         size_t num_leg_gauss_in_elem_;
     public:
-        legendre_in_MaterialPoint_t() {
+        legendre_in_elem_t() {
         };
 
-        legendre_in_MaterialPoint_t(const size_t num_leg_gauss_in_elem_inp) {
+        legendre_in_elem_t(const size_t num_leg_gauss_in_elem_inp) {
                 this->num_leg_gauss_in_elem_ = num_leg_gauss_in_elem_inp;
         };
 
@@ -165,15 +165,15 @@ struct legendre_in_MaterialPoint_t
 };
 
 /// if material points are defined at element interfaces
-struct lobatto_in_MaterialPoint_t
+struct lobatto_in_elem_t
 {
     private:
         size_t num_lob_gauss_in_elem_;
     public:
-        lobatto_in_MaterialPoint_t() {
+        lobatto_in_elem_t() {
         };
 
-        lobatto_in_MaterialPoint_t(const size_t num_lob_gauss_in_elem_inp) {
+        lobatto_in_elem_t(const size_t num_lob_gauss_in_elem_inp) {
                 this->num_lob_gauss_in_elem_ = num_lob_gauss_in_elem_inp;
         };
 
@@ -249,9 +249,9 @@ struct mesh_t
     CArrayKokkos<size_t> surfs_in_elem; ///< Surfaces on an element
 
     // CArrayKokkos <size_t> zones_in_elem; ///< Zones in an element
-    zones_in_MaterialPoint_t zones_in_elem; ///< Zones in an element
-    lobatto_in_MaterialPoint_t lobatto_in_elem; ///< Gauss Lobatto points in an element
-    legendre_in_MaterialPoint_t legendre_in_elem; ///< Gauss Legendre points in an element
+    zones_in_elem_t zones_in_elem; ///< Zones in an element
+    lobatto_in_elem_t lobatto_in_elem; ///< Gauss Lobatto points in an element
+    legendre_in_elem_t legendre_in_elem; ///< Gauss Legendre points in an element
 
     // ---- Node Data Definitions ---- //
     size_t num_nodes; ///< Number of nodes in the mesh
@@ -348,10 +348,10 @@ struct mesh_t
 
         nodes_in_elem    = DCArrayKokkos<size_t>(num_elems, num_nodes_in_elem, "mesh.nodes_in_elem");
         corners_in_elem  = CArrayKokkos<size_t>(num_elems, num_nodes_in_elem, "mesh.corners_in_elem");
-        zones_in_elem    = zones_in_MaterialPoint_t(num_zones_in_elem);
+        zones_in_elem    = zones_in_elem_t(num_zones_in_elem);
         surfs_in_elem    = CArrayKokkos<size_t>(num_elems, num_surfs_in_elem, "mesh.surfs_in_zone");
         nodes_in_zone    = CArrayKokkos<size_t>(num_zones, num_nodes_in_zone, "mesh.nodes_in_zone");
-        legendre_in_elem = legendre_in_MaterialPoint_t(num_leg_gauss_in_elem);
+        legendre_in_elem = legendre_in_elem_t(num_leg_gauss_in_elem);
 
         return;
     }; // end method

single-node-refactor/src/common/mesh_inputs.h

@@ -80,7 +80,7 @@ struct mesh_input_t
     int num_dims = 3;   ///< Number of dimensions for the mesh
     mesh_input::source source = mesh_input::none;   ///< Source of mesh, file or generate
     std::string file_path     = ""; ///< Absolute path of mesh file
-    mesh_input::type type;  ///< Type of mesh to generate if
+    mesh_input::type type;          ///< Type of mesh to generate if
 
     double origin[3] = {0.0, 0.0, 0.0}; ///< Mesh origin for generating a mesh
     double length[3] = {0.0, 0.0, 0.0}; ///< x,y,z length of generated mesh

single-node-refactor/src/common/region.h

@@ -44,15 +44,18 @@ ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 // ==============================================================================
 namespace region
 {
-    // for tagging boundary faces
+    // for tagging volumes to paint material onto the mesh
     enum vol_tag
     {
         no_volume = 0,
         global = 1,         // tag every elements in the mesh
         box = 2,            // tag all elements inside a box
         cylinder = 3,       // tag all elements inside a cylinder
         sphere = 4,         // tag all elements inside a sphere
-        readVoxelFile = 5,  // tag all elements in a voxel mesh input WARING: Currently unimplemented
+        readVoxelFile = 5,  // tag all elements in a voxel mesh (structured VTK)
+        readPolycrystalFile = 6, // tag all elements in a polycrystallince voxel mesh (structured VTK)
+        readSTLFile = 7,    // read a STL file and voxelize it
+        readVTKFile = 8,    // tag all elements in a VTK mesh (unstructured mesh)
     };
 } // end of namespace
 
@@ -62,7 +65,7 @@ static std::map<std::string, region::vol_tag> region_type_map
     { "box", region::box },
     { "sphere", region::sphere },
     { "cylinder", region::cylinder },
-    { "readVoxelFile", region::readVoxelFile }
+    { "voxel_file", region::readVoxelFile }
 };
 
 /////////////////////////////////////////////////////////////////////////////
@@ -109,12 +112,31 @@ struct reg_fill_t
     double origin[3] = {0.0, 0.0, 0.0}; ///< Origin for region
 };
 
+
+/////////////////////////////////////////////////////////////////////////////
+///
+/// \struct reg_fill_host_t
+///
+/// \brief Geometry data, on the cpu only, for regions of materials/states 
+///
+/////////////////////////////////////////////////////////////////////////////
+struct reg_fill_host_t
+{
+    std::string file_path; ///< path of mesh file
+
+    // scale parameters for input mesh files
+    double scale_x = 1.0;
+    double scale_y = 1.0;
+    double scale_z = 1.0;
+};
+
 // ----------------------------------
 // valid inputs for a material fill
 // ----------------------------------
 static std::vector<std::string> str_region_inps
 {
     "type",
+    "file_path",
     "material_id",
     "x1",
     "x2",
@@ -124,6 +146,9 @@ static std::vector<std::string> str_region_inps
     "z2",
     "radius1",
     "radius2",
+    "scale_x",
+    "scale_y",
+    "scale_z",
     "velocity",
     "u",
     "v",

single-node-refactor/src/common/simulation_parameters.h

@@ -62,7 +62,9 @@ struct SimulationParameters_t
 
     std::vector<solver_input_t> solver_inputs;  ///< Solvers to use during the simulation
 
-    DCArrayKokkos<reg_fill_t> region_fills;  ///< Region data for simulation mesh, set the initial conditions
+    CArrayKokkos<reg_fill_t> region_fills;  ///< Region data for simulation mesh, set the initial conditions
+
+    CArray<reg_fill_host_t> region_fills_host;  ///< Region data on CPU, set the initial conditions
 
 }; // simulation_parameters_t