Rename GrainSet class to Grain

include/grains/FloodFiller.h

@@ -16,7 +16,7 @@
  * vertices in that grain.
  */
 template <int dim>
-class GrainSet
+class Grain
 {
 public:
   /**
@@ -111,7 +111,7 @@ class FloodFiller
 
   /**
    * The primary external interface. This method takes in information about the
-   * mesh/field and outputs a vector of GrainSet objects.
+   * mesh/field and outputs a vector of Grain objects.
    */
   void
   calcGrainSets(dealii::FESystem<dim>                              &finite_element,
@@ -121,7 +121,7 @@ class FloodFiller
                 double                                              threshold_upper,
                 int                                                 min_id,
                 unsigned int                                        order_parameter_index,
-                std::vector<GrainSet<dim>>                         &grain_sets);
+                std::vector<Grain<dim>>                            &grain_sets);
 
 protected:
   /**
@@ -136,21 +136,21 @@ class FloodFiller
                      double                                              threshold_upper,
                      int                                                 min_id,
                      unsigned int                                       &grain_index,
-                     std::vector<GrainSet<dim>>                         &grain_sets,
+                     std::vector<Grain<dim>>                            &grain_sets,
                      bool                                               &grain_assigned);
 
   /**
    * The method to merge the grain sets from all the processors.
    */
   void
-  createGlobalGrainSetList(std::vector<GrainSet<dim>> &grain_sets) const;
+  createGlobalGrainSetList(std::vector<Grain<dim>> &grain_sets) const;
 
   /**
    * Checks to see if grains found on different processors are parts of a larger
    * grain. If so, it merges the grain_sets entries.
    */
   void
-  mergeSplitGrains(std::vector<GrainSet<dim>> &grain_sets) const;
+  mergeSplitGrains(std::vector<Grain<dim>> &grain_sets) const;
 
   /**
    * The quadrature used to calculate the element-wise value of the solution

include/grains/SimplifiedGrainRepresentation.h

@@ -16,11 +16,11 @@ class SimplifiedGrainRepresentation
 public:
   /**
    * Constructor. Creates the simplified representation of a grain from its
-   * GrainSet. This sets all of the internal data members and is the only way
+   * Grain. This sets all of the internal data members and is the only way
    * to set the radius and center of the grain. The members order_parameter_id
    * and old_order_parameter_id are initialized to the same value.
    */
-  SimplifiedGrainRepresentation(const GrainSet<dim> &grain_set);
+  SimplifiedGrainRepresentation(const Grain<dim> &grain);
 
   /**
    * Getter for the grain center/centroid.

src/core/initial_conditions/initialConditions.cc

@@ -125,12 +125,12 @@ MatrixFreePDE<dim, degree>::applyInitialConditions()
       FloodFiller<dim, degree> flood_filler(*FESet.at(scalar_field_index), quadrature2);
 
       pcout << "Locating the grains...\n";
-      std::vector<GrainSet<dim>> grain_sets;
+      std::vector<Grain<dim>> grain_sets;
       for (unsigned int id = min_id; id < max_id + 1; id++)
         {
           pcout << "Locating grain " << id << "...\n";
 
-          std::vector<GrainSet<dim>> grain_sets_single_id;
+          std::vector<Grain<dim>> grain_sets_single_id;
 
           flood_filler.calcGrainSets(*FESet.at(scalar_field_index),
                                      *dofHandlersSet_nonconst.at(scalar_field_index),

src/grains/FloodFiller.cc

@@ -10,7 +10,7 @@ FloodFiller<dim, degree>::calcGrainSets(
   double                                              threshold_upper,
   int                                                 min_id,
   unsigned int                                        order_parameter_index,
-  std::vector<GrainSet<dim>>                         &grain_sets)
+  std::vector<Grain<dim>>                            &grain_sets)
 {
   unsigned int grain_index = 0;
 
@@ -23,8 +23,8 @@ FloodFiller<dim, degree>::calcGrainSets(
       ++cell;
     }
 
-  GrainSet<dim> grain_set;
-  grain_sets.push_back(grain_set);
+  Grain<dim> grain;
+  grain_sets.push_back(grain);
   grain_sets.back().setOrderParameterIndex(order_parameter_index);
 
   // The flood fill loop
@@ -49,9 +49,9 @@ FloodFiller<dim, degree>::calcGrainSets(
             {
               // Get the grain set initialized for the next grain to be found
               grain_index++;
-              GrainSet<dim> new_grain_set;
-              new_grain_set.setOrderParameterIndex(order_parameter_index);
-              grain_sets.push_back(new_grain_set);
+              Grain<dim> new_grain;
+              new_grain.setOrderParameterIndex(order_parameter_index);
+              grain_sets.push_back(new_grain);
             }
         }
 
@@ -86,7 +86,7 @@ FloodFiller<dim, degree>::recursiveFloodFill(
   double                                              threshold_upper,
   int                                                 min_id,
   unsigned int                                       &grain_index,
-  std::vector<GrainSet<dim>>                         &grain_sets,
+  std::vector<Grain<dim>>                            &grain_sets,
   bool                                               &grain_assigned)
 {
   if (cell == cell_end)
@@ -189,7 +189,7 @@ FloodFiller<dim, degree>::recursiveFloodFill(
 template <int dim, int degree>
 void
 FloodFiller<dim, degree>::createGlobalGrainSetList(
-  std::vector<GrainSet<dim>> &grain_sets) const
+  std::vector<Grain<dim>> &grain_sets) const
 {
   unsigned int numProcs = dealii::Utilities::MPI::n_mpi_processes(MPI_COMM_WORLD);
 
@@ -308,12 +308,12 @@ FloodFiller<dim, degree>::createGlobalGrainSetList(
                  MPI_DOUBLE,
                  MPI_COMM_WORLD);
 
-  // Put the GrainSet objects back together
+  // Put the Grain objects back together
   grain_sets.clear();
 
   for (int g = 0; g < num_grains_global; g++)
     {
-      GrainSet<dim> new_grain_set;
+      Grain<dim> new_grain;
       for (unsigned int c = 0; c < num_elements_global.at(g); c++)
         {
           std::vector<dealii::Point<dim>> verts;
@@ -329,10 +329,10 @@ FloodFiller<dim, degree>::createGlobalGrainSetList(
               dealii::Point<dim>     vert(tensor_coords);
               verts.push_back(vert);
             }
-          new_grain_set.addVertexList(verts);
+          new_grain.addVertexList(verts);
         }
-      new_grain_set.setOrderParameterIndex(order_parameters_global.at(g));
-      grain_sets.push_back(new_grain_set);
+      new_grain.setOrderParameterIndex(order_parameters_global.at(g));
+      grain_sets.push_back(new_grain);
     }
 }
 
@@ -342,7 +342,7 @@ FloodFiller<dim, degree>::createGlobalGrainSetList(
 
 template <int dim, int degree>
 void
-FloodFiller<dim, degree>::mergeSplitGrains(std::vector<GrainSet<dim>> &grain_sets) const
+FloodFiller<dim, degree>::mergeSplitGrains(std::vector<Grain<dim>> &grain_sets) const
 {
   // Loop though each vertex in the base grain "g"
   for (unsigned int g = 0; g < grain_sets.size(); g++)

src/grains/SimplifiedGrainRepresentation.cc

@@ -5,16 +5,15 @@
 // ============================================================================
 
 template <int dim>
-SimplifiedGrainRepresentation<dim>::SimplifiedGrainRepresentation(
-  const GrainSet<dim> &grain_set)
-  : grain_id(grain_set.getGrainIndex())
-  , order_parameter_id(grain_set.getOrderParameterIndex())
+SimplifiedGrainRepresentation<dim>::SimplifiedGrainRepresentation(const Grain<dim> &grain)
+  : grain_id(grain.getGrainIndex())
+  , order_parameter_id(grain.getOrderParameterIndex())
   , old_order_parameter_id(order_parameter_id)
   , distance_to_neighbor_sharing_op(0.0)
 {
   // Calculate the centroid assuming that the elements are rectangular and with
   // no weighting based on the actual value of the field
-  std::vector<std::vector<dealii::Point<dim>>> vertex_list = grain_set.getVertexList();
+  std::vector<std::vector<dealii::Point<dim>>> vertex_list = grain.getVertexList();
 
   double                 grain_volume = 0.0;
   dealii::Tensor<1, dim> centroid;

src/grains/reassignGrains.cc

@@ -29,7 +29,7 @@ MatrixFreePDE<dim, degree>::reassignGrains()
   QGaussLobatto<dim>       quadrature2(degree + 1);
   FloodFiller<dim, degree> flood_filler(*FESet.at(scalar_field_index), quadrature2);
 
-  std::vector<GrainSet<dim>> grain_sets;
+  std::vector<Grain<dim>> grain_sets;
 
   unsigned int op_list_index = 0;
   for (unsigned int fieldIndex = 0; fieldIndex < fields.size(); fieldIndex++)
@@ -40,7 +40,7 @@ MatrixFreePDE<dim, degree>::reassignGrains()
             {
               op_list_index++;
 
-              std::vector<GrainSet<dim>> single_OP_grain_sets;
+              std::vector<Grain<dim>> single_OP_grain_sets;
               flood_filler.calcGrainSets(*FESet.at(scalar_field_index),
                                          *dofHandlersSet_nonconst.at(scalar_field_index),
                                          solutionSet.at(fieldIndex),