From eff0922be7f4ef7f84038ab12f45eeeea37a0cb9 Mon Sep 17 00:00:00 2001
From: landinjm <landinjm@umich.edu>
Date: Thu, 10 Oct 2024 10:26:15 -0400
Subject: [PATCH] comments and renaming makeTriangulation function

---
 .../CHiMaD_benchmark1c/customPDE.h            |  4 +--
 .../CHiMaD_benchmark6b/customPDE.h            |  4 +--
 include/core/matrixFreePDE.h                  | 33 ++++++++++++-------
 src/core/init.cc                              |  4 +--
 4 files changed, 27 insertions(+), 18 deletions(-)

diff --git a/applications/CHiMaD_benchmarks/CHiMaD_benchmark1c/customPDE.h b/applications/CHiMaD_benchmarks/CHiMaD_benchmark1c/customPDE.h
index 78bd368e1..57392ceb8 100644
--- a/applications/CHiMaD_benchmarks/CHiMaD_benchmark1c/customPDE.h
+++ b/applications/CHiMaD_benchmarks/CHiMaD_benchmark1c/customPDE.h
@@ -85,7 +85,7 @@ class customPDE : public MatrixFreePDE<dim, degree>
   // ================================================================
 
   void
-  makeTriangulation(parallel::distributed::Triangulation<dim> &) const override;
+  create_triangulation(parallel::distributed::Triangulation<dim> &tria) const override;
 
   // ================================================================
   // Model constants specific to this subclass
@@ -104,7 +104,7 @@ class customPDE : public MatrixFreePDE<dim, degree>
 
 template <int dim, int degree>
 void
-customPDE<dim, degree>::makeTriangulation(
+customPDE<dim, degree>::create_triangulation(
   parallel::distributed::Triangulation<dim> &tria) const
 {
   parallel::distributed::Triangulation<dim> tria_horizontal_box(MPI_COMM_WORLD);
diff --git a/applications/CHiMaD_benchmarks/CHiMaD_benchmark6b/customPDE.h b/applications/CHiMaD_benchmarks/CHiMaD_benchmark6b/customPDE.h
index 1e9c70510..176c83294 100644
--- a/applications/CHiMaD_benchmarks/CHiMaD_benchmark6b/customPDE.h
+++ b/applications/CHiMaD_benchmarks/CHiMaD_benchmark6b/customPDE.h
@@ -87,7 +87,7 @@ class customPDE : public MatrixFreePDE<dim, degree>
 
   // Virtual method in MatrixFreePDE
   void
-  makeTriangulation(parallel::distributed::Triangulation<dim> &) const override;
+  create_triangulation(parallel::distributed::Triangulation<dim> &tria) const override;
 
   // ================================================================
   // Model constants specific to this subclass
@@ -108,7 +108,7 @@ class customPDE : public MatrixFreePDE<dim, degree>
 
 template <int dim, int degree>
 void
-customPDE<dim, degree>::makeTriangulation(
+customPDE<dim, degree>::create_triangulation(
   parallel::distributed::Triangulation<dim> &tria) const
 {
   parallel::distributed::Triangulation<dim> tria_box(MPI_COMM_WORLD);
diff --git a/include/core/matrixFreePDE.h b/include/core/matrixFreePDE.h
index 3ab03fc90..4a8fbb6ef 100644
--- a/include/core/matrixFreePDE.h
+++ b/include/core/matrixFreePDE.h
@@ -52,36 +52,45 @@ using vectorType = LinearAlgebra::distributed::Vector<double>;
 // macro for constants
 #define constV(a) make_vectorized_array(a)
 
-//
-// base class for matrix free PDE's
-//
 /**
- * This is the abstract base class for the matrix free implementation of
- * Parabolic and Elliptic BVP's, and supports MPI, Threads and Vectorization
- * (Hybrid Parallel). This class contains the parallel data structures, mesh
- * (referred to as triangulation), parallel degrees of freedom distribution,
- * constraints,  and general utility methods.
+ * \brief This is the abstract base class for the matrix free implementation of parabolic
+ * and elliptic BVP's, and supports MPI, threads and vectorization (Hybrid Parallel). This
+ * class contains the parallel data structures, mesh (referred to as triangulation),
+ * parallel degrees of freedom distribution, constraints, and general utility methods.
  *
  * All the physical models in this package inherit this base class.
+ *
+ * \tparam dim The number of dimensions in the problem.
+ * \tparam degree The polynomial degree of the shape functions.
  */
 template <int dim, int degree>
 class MatrixFreePDE : public Subscriptor
 {
 public:
   /**
-   * Class contructor
+   * \brief Class contructor.
    */
   MatrixFreePDE(userInputParameters<dim>);
-  ~MatrixFreePDE();
+
+  /**
+   * \brief Class destructor.
+   */
+  ~MatrixFreePDE() override;
+
   /**
-   * Initializes the mesh, degrees of freedom, constraints and data structures
+   * \brief Initializes the mesh, degrees of freedom, constraints and data structures
    * using the user provided inputs in the application parameters file.
    */
   virtual void
   init();
 
+  /**
+   * \brief Create the mesh with the user provided domain sizes.
+   *
+   * \param tria Triangulation object. It must be empty prior to calling this function.
+   */
   virtual void
-  makeTriangulation(parallel::distributed::Triangulation<dim> &) const;
+  create_triangulation(parallel::distributed::Triangulation<dim> &tria) const;
 
   /**
    * Initializes the data structures for enabling unit tests.
diff --git a/src/core/init.cc b/src/core/init.cc
index a4fb0a29b..9e3e6473e 100644
--- a/src/core/init.cc
+++ b/src/core/init.cc
@@ -16,7 +16,7 @@ MatrixFreePDE<dim, degree>::init()
 
   pcout << "creating problem mesh...\n";
   // Create the coarse mesh and mark the boundaries
-  makeTriangulation(triangulation);
+  create_triangulation(triangulation);
 
   // Set which (if any) faces of the triangulation are periodic
   setPeriodicity();
@@ -376,7 +376,7 @@ MatrixFreePDE<dim, degree>::init()
 
 template <int dim, int degree>
 void
-MatrixFreePDE<dim, degree>::makeTriangulation(
+MatrixFreePDE<dim, degree>::create_triangulation(
   parallel::distributed::Triangulation<dim> &tria) const
 {
   if (dim == 3)