Move includes after #define in DEM (chaos-polymtl#1223)

Description
Quick refactor as done in PR chaos-polymtl#1170 that moves header includes after the #define.
Some @brief has been added here and there at the same time.

include/dem/adaptive_sparse_contacts.h

@@ -187,7 +187,7 @@ class AdaptiveSparseContacts
    * fraction.
    * @param[in] advect_particles The flag for the advection of particles.
    */
-  void
+  inline void
   set_parameters(const double granular_temperature,
                  const double solid_fraction,
                  const double advect_particles)

include/dem/boundary_cells_info_struct.h

@@ -12,23 +12,22 @@
  * the top level of the Lethe distribution.
  *
  * ---------------------------------------------------------------------
- *
  */
+
+#ifndef lethe_boundary_cells_info_struct_h
+#define lethe_boundary_cells_info_struct_h
+
 #include <deal.II/base/point.h>
 #include <deal.II/base/tensor.h>
 
 #include <deal.II/distributed/tria.h>
 
-#ifndef boundary_cells_info_struct_h
-#  define boundary_cells_info_struct_h
+using namespace dealii;
 
 /**
- * This struct handles the information related to the boundary cells which will
- * be used for particle-wall contact detection
+ * @brief Handle the information related to the boundary cells
+ * which will be used for particle-wall contact detection.
  */
-
-using namespace dealii;
-
 template <int dim>
 struct boundary_cells_info_struct
 {
@@ -48,6 +47,10 @@ struct boundary_cells_info_struct
   Point<dim> point_on_face;
 };
 
+/**
+ * @brief Handle the information related to the periodic boundary cells
+ * which will be used for particle-wall contact detection.
+ */
 template <int dim>
 struct periodic_boundaries_cells_info_struct
 {
@@ -73,5 +76,4 @@ struct periodic_boundaries_cells_info_struct
   Point<dim> point_on_periodic_face;
 };
 
-
-#endif /* boundary_cells_info_struct_h */
+#endif

include/dem/contact_type.h

@@ -12,17 +12,14 @@
  * the top level of the Lethe distribution.
  *
  * ---------------------------------------------------------------------
- *
  */
 
 #ifndef lethe_contact_type_h
 #define lethe_contact_type_h
 
 /**
  * @brief Label for particle-object contact type.
- *
  */
-
 enum ContactType
 {
   local_particle_particle,
@@ -37,4 +34,4 @@ enum ContactType
   particle_line
 };
 
-#endif // lethe_contact_type_h
+#endif

include/dem/data_containers.h

@@ -12,9 +12,11 @@
  * the top level of the Lethe distribution.
  *
  * ---------------------------------------------------------------------
- *
  */
 
+#ifndef lethe_data_containers_h
+#define lethe_data_containers_h
+
 #include <dem/boundary_cells_info_struct.h>
 #include <dem/particle_particle_contact_info.h>
 #include <dem/particle_point_line_contact_info_struct.h>
@@ -28,35 +30,31 @@
 
 #include <boost/range/adaptor/map.hpp>
 
-#pragma GCC diagnostic push
-#pragma GCC diagnostic ignored "-Wmissing-braces"
-#include <ankerl/unordered_dense.h>
-#pragma GCC diagnostic pop
-
 #include <iostream>
 #include <unordered_map>
 #include <vector>
 
-#ifndef lethe_data_containers_h
-#  define lethe_data_containers_h
+#pragma GCC diagnostic push
+#pragma GCC diagnostic ignored "-Wmissing-braces"
+#include <ankerl/unordered_dense.h>
+#pragma GCC diagnostic pop
 
 /**
- * This namespace defines all the data containers and required operations on
+ * @brief This namespace defines all the data containers and required operations on
  * these containers for the DEM solver. At the moment, only overloaded operators
  * are here, but eventually all the data containers of the DEM solver will be
  * moved here
  */
 namespace DEM
 {
   /**
-   * Defined global face id as a type to ensure that we know what the
+   * @brief Defined global face id as a type to ensure that we know what the
    * structures use as index. This is more verbose than unsigned int
    */
   typedef unsigned int global_face_id;
 
-
   /**
-   * Operator overloading to enable using triangulation cells as map keys.
+   * @brief Operator overloading to enable using triangulation cells as map keys.
    */
   using namespace dealii;
 
@@ -74,7 +72,7 @@ namespace DEM
   };
 
   /**
-   * Operator overloading to enable using particle iterators as map keys.
+   * @brief Operator overloading to enable using particle iterators as map keys.
    */
 
   template <int dim>
@@ -89,7 +87,7 @@ namespace DEM
   };
 
   /**
-   * Operator overloading to enable using triangulation cells as map keys.
+   * @brief Operator overloading to enable using triangulation cells as map keys.
    */
   using namespace dealii;
 
@@ -107,12 +105,14 @@ namespace DEM
     }
   };
 
-  // DEM data structure containers
-  // To improve readability of containers, there's a simple description above
-  // all declarations which follow these representation :
-  // <> : map or unordered map
-  // () : tuple or pair
-  // [] : vector
+  /**
+   * @brief DEM data structure containers
+   * To improve readability of containers, there's a simple description above
+   * all declarations which follow these representation :
+   * <> : map or unordered map
+   * () : tuple or pair
+   * [] : vector
+   */
   template <int dim>
   struct dem_data_structures
   {

include/dem/dem.h

@@ -12,7 +12,6 @@
  * the top level of the Lethe distribution.
  *
  * ---------------------------------------------------------------------
- *
  */
 
 #ifndef lethe_dem_h

include/dem/dem_action_manager.h

@@ -1,6 +1,21 @@
-#ifndef dem_action_manager_h
-#define dem_action_manager_h
+/* ---------------------------------------------------------------------
+ *
+ * Copyright (C) 2019 - 2024 by the Lethe authors
+ *
+ * This file is part of the Lethe library
+ *
+ * The Lethe library is free software; you can use it, redistribute
+ * it, and/or modify it under the terms of the GNU Lesser General
+ * Public License as published by the Free Software Foundation; either
+ * version 2.1 of the License, or (at your option) any later version.
+ * The full text of the license can be found in the file LICENSE at
+ * the top level of the Lethe distribution.
+ *
+ * ---------------------------------------------------------------------
+ */
 
+#ifndef lethe_dem_action_manager_h
+#define lethe_dem_action_manager_h
 
 /**
  * @brief Manage the actions to be performed in the DEM solver and on the DEM

include/dem/dem_contact_manager.h

@@ -12,7 +12,6 @@
  * the top level of the Lethe distribution.
  *
  * ---------------------------------------------------------------------
- *
  */
 
 #ifndef lethe_dem_contact_manager_h

include/dem/post_processing.h → include/dem/dem_post_processing.h

@@ -12,19 +12,17 @@
  * the top level of the Lethe distribution.
  *
  * ---------------------------------------------------------------------
- *
  */
 
+#ifndef lethe_dem_post_processing_h
+#define lethe_dem_post_processing_h
+
 #include <core/utilities.h>
 
 #include <deal.II/particles/particle_handler.h>
 
-#ifndef dem_post_processing_h
-#  define dem_post_processing_h
-
 using namespace dealii;
 
-
 namespace DEM
 {
   /**
@@ -40,24 +38,26 @@ namespace DEM
   };
 
   /**
-   * @brief Calculate statistics on a DEM ParticleHandler. At the moment, the following statistics are supported:
+   * @brief Calculate statistics on a DEM ParticleHandler. At the moment, the
+   * following statistics are supported:
    * - Translational kinetic energy
    * - Rotational (angular) kinetic energy
    * - Translational velocity
    * - Rotational (angular) velocity
    *
    * @tparam dim Dimensionality of the problem (2D or 3D)
-   * @tparam dem_statistics_variable Enum variable used to identify which granular statistics is being calculated
+   * @tparam dem_statistics_variable Enum variable used to identify which
+   * granular statistics is being calculated
    *
-   * @param particle_handler A reference to the particle handler being used for DEM
+   * @param particle_handler A reference to the particle handler being used for
+   * DEM
    * @param mpi_communicator The MPI communicator
    */
   template <int dim, dem_statistic_variable var>
   statistics
   calculate_granular_statistics(
     const Particles::ParticleHandler<dim> &particle_handler,
     const MPI_Comm                        &mpi_communicator);
-
-
 } // namespace DEM
+
 #endif

include/dem/dem_solver_parameters.h

@@ -12,20 +12,19 @@
  * the top level of the Lethe distribution.
  *
  * ---------------------------------------------------------------------
- *
  */
+
+#ifndef lethe_dem_solver_parameters_h
+#define lethe_dem_solver_parameters_h
+
 #include <core/parameters.h>
 #include <core/parameters_lagrangian.h>
 #include <core/simulation_control.h>
 #include <core/solid_objects_parameters.h>
 
-#ifndef parameters_DEM_h
-#  define parameters_DEM_h
-
 /**
- * Handles all the parameters declared in the parameter handler file
+ * @brief Handles all the parameters declared in the parameter handler file.
  */
-
 template <int dim>
 class DEMSolverParameters
 {
@@ -93,4 +92,4 @@ class DEMSolverParameters
   }
 };
 
-#endif /* parameters_DEM_h */
+#endif

include/dem/distributions.h

@@ -12,18 +12,17 @@
  * the top level of the Lethe distribution.
  *
  * ---------------------------------------------------------------------
- *
  */
 
+#ifndef lethe_distributions_h
+#define lethe_distributions_h
+
 #include <cmath>
 #include <fstream>
 #include <iostream>
 #include <random>
 #include <string>
 
-#ifndef distributions_h
-#  define distributions_h
-
 class Distribution
 {
 public:
@@ -97,17 +96,17 @@ class NormalDistribution : public Distribution
 
 private:
   /**
-   * Average diameter of the normal distribution.
+   * @brief Average diameter of the normal distribution.
    */
   const double diameter_average;
 
   /**
-   * Standard deviation of distribution of the normal distribution.
+   * @brief Standard deviation of distribution of the normal distribution.
    */
   const double standard_deviation;
 
   /**
-   * Random number generator for the diameter selection.
+   * @brief Random number generator for the diameter selection.
    */
   std::mt19937 gen;
 };
@@ -150,7 +149,7 @@ class UniformDistribution : public Distribution
 
 private:
   /**
-   *  The diameter value of the distribution.
+   * @brief The diameter value of the distribution.
    */
   const double diameter_value;
 };
@@ -204,16 +203,16 @@ class CustomDistribution : public Distribution
   const std::vector<double> diameter_custom_values;
 
   /**
-   * Vector containing cumulative probabilities associated with de
+   * @brief Vector containing cumulative probabilities associated with de
    * diameter_custom_values vector. The probabilities are based on the volume
    * fraction, not the number of particles.
    */
-  std::vector<double> diameter_custom_cumu_prob;
+  std::vector<double> diameter_custom_cumul_prob;
 
   /**
-   * Random number generator for the diameter selection.
+   * @brief Random number generator for the diameter selection.
    */
   std::mt19937 gen;
 };
 
-#endif /* distributions_h */
+#endif