Correct some warnings in doxygen compilation

include/core/grids.h

@@ -32,8 +32,6 @@ using namespace dealii;
  * @param triangulation The triangulation to which a grid is attached
  *
  * @param mesh_parameters The mesh parameters used to decide what type of mesh or primitive is  used
- *
- * @param boundary_conditions The information about the boundary conditions id. This is used to set-up the periodicity of the domain
  */
 template <int dim, int spacedim = dim>
 void

include/core/manifolds.h

@@ -165,7 +165,7 @@ class BoundaryPostprocessor : public DataPostprocessorScalar<dim>
  *
  * @param triangulation The triangulation to manifolds are attached
  *
- * @param manifolds_parameters The information about the type of manifolds attached to the faces
+ * @param manifolds The information about the type of manifolds attached to the faces
  */
 template <int dim, int spacedim = dim>
 void
@@ -180,7 +180,7 @@ attach_manifolds_to_triangulation(
  *
  * @param triangulation The triangulation to manifolds are attached
  *
- * @param std::string Filename of the cad file
+ * @param cad_name Filename of the cad file
  *
  * @param manifold_id Identifier of the manifold
  */

include/core/parameters_multiphysics.h

@@ -47,7 +47,8 @@ namespace Parameters
   /** @brief Class to account for different phase fraction filtering types:
    * - none: no filter wil be applied on the calculated phase fraction
    * - tanh: the tanh filter function will be applied to the phase fraction,
-   * a $$\beta$$ parameter influencing the interface definition must be defined
+   * a \f$\beta\f$ parameter influencing the interface definition must be
+   * defined
    */
   enum class FilterType
   {

include/core/phase_change.h

@@ -26,6 +26,7 @@ using namespace dealii;
  * a temperature T
  *
  * @param T temperature at which to calculate the liquid fraction
+ * @param phase_change_parameters
  * @return value of the liquid_fraction
  *
  */
@@ -46,8 +47,8 @@ calculate_liquid_fraction(
  * a temperature T
  *
  * @param T temperature at which to calculate the liquid fraction
- * @param solidus temperature
- * @param liquidus temperature
+ * @param T_solidus temperature
+ * @param T_liquidus temperature
  * @return value of the liquid_fraction
  *
  */

include/core/shape.h

@@ -1586,9 +1586,9 @@ class Plane : public Shape<dim>
 
 
 /**
- * @class This class defines superquadric shapes. Their signed distance
- * function is: \left|\frac{x}{a}\right|^r + \left|\frac{y}{b}\right|^s +
- * \left|\frac{z}{c}\right|^t - 1 = 0
+ * @brief This class defines superquadric shapes. Their signed distance
+ * function is: \f$\left|\frac{x}{a}\right|^r + \left|\frac{y}{b}\right|^s +
+ * \left|\frac{z}{c}\right|^t - 1 = 0\f$
  * @tparam dim Dimension of the shape
  */
 template <int dim>
@@ -2121,7 +2121,7 @@ class DeathStar : public Shape<dim>
 };
 
 /**
- * @class This class was designed so that specific composite shapes could be
+ * @brief This class was designed so that specific composite shapes could be
  * defined through the parameter file. Boolean operations such as union,
  * difference, and intersection are allowed.
  * @tparam dim Dimension of the shape
@@ -2635,7 +2635,7 @@ class OpenCascadeShape : public Shape<dim>
 
 /**
  * @tparam dim Dimension of the shape
- * @class RBF Shapes express the signed distance function as a linear
+ * @brief RBF Shapes express the signed distance function as a linear
  * combination of Radial Basis Functions (RBF), which have a defined support
  * radius and basis function. A collection of nodes and weights compose the
  * object. Outside of the domain covered by the nodes, the distance is

include/core/tensors_and_points_dimension_manipulation.h

@@ -54,8 +54,8 @@ tensor_nd_to_3d(const Tensor<1, dim> &tensor)
  * If the vector is tensor given is two-dimensional, do nothing and return the
  * tensor.
  *
- * @param point_2d Two-dimensional input point
- * @return point_3d Three-dimensional output point
+ * @param tensor Three-dimensional input tensor
+ * @return tensor_2d Three-dimensional output tensor
  *
  */
 template <int dim>
@@ -73,7 +73,7 @@ tensor_nd_to_2d(const Tensor<1, dim> &tensor)
  * element of the three-dimensional point (in z direction) is set to zero.
  * If the point given is already 3d, do nothing and return the point.
  *
- * @param point_2d Two-dimensional input point
+ * @param point Two-dimensional input point
  * @return point_3d Three-dimensional output point
  *
  */
@@ -98,8 +98,8 @@ point_nd_to_3d(const Point<dim> &point)
  * If the point given is already two dimensional, do nothing and return the
  * point.
  *
- * @param point_2d Two-dimensional input point
- * @return point_3d Three-dimensional output point
+ * @param point Three-dimensional input point
+ * @return point_2d Two-dimensional output point
  *
  */
 template <int dim>

include/core/utilities.h

@@ -190,7 +190,7 @@ make_table_scalars_tensors(
  *
  * @tparam dim Integer that denotes the number of spatial dimensions.
  *
- * @param[in] independent_values Vector of Tensor<1,dim> that serves as the
+ * @param[in] independent_vector Vector of Tensor<1,dim> that serves as the
  * independent variable (e.g., position).
  *
  * @param[in] independent_column_names Vector of strings representing labels of
@@ -228,17 +228,20 @@ make_table_tensors_tensors(
  *
  * @tparam dim Integer that denotes the number of spatial dimensions.
  *
- * @param[in] independent_values Vector of Tensor<1,dim> that serves as the
+ * @param[in] independent_vector Vector of Tensor<1,dim> that serves as the
  * independent variable (e.g., position).
  *
  * @param[in] independent_column_names Vector of strings representing labels of
  * the independent tensor.
  *
- * @param[in] dependent_vector Vector of scalar that serves as the dependent
- * variable (e.g., energy).
+ * @param[in] dependent_values Vector of of doubles containing
+ * dependent variables values (e.g., force).
  *
  * @param[in] dependent_column_name Label of the dependent variable.
  *
+ * @param[in] display_precision Integer indicating the precision at which the
+ * table is written.
+ *
  * @param[in] display_scientific_notation Boolean indicating if the values
  * should be displayed in scientific notation (true) or not (false).
  *
@@ -305,10 +308,11 @@ sgn(T val)
 
 
 /**
- * @brief Clip a properties between a lower and a higher value
+ * @brief Clip a property between a lower and a higher value
  * @tparam T argument's type
  * @param[in,out] lower Lower admissible value
  * @param[in,out] upper Upper admissible value
+ * @param[in,out] n
  * @return Clipped variable that is not below the lower limit and not above the upper limit
  *
  */
@@ -323,7 +327,7 @@ clip(const T &n, const T &lower, const T &upper)
  * @brief Calculate the equivalent properties for a given phase. Method called
  * in quadrature points loops in Cahn-Hilliard simulations.
  *
- * @param phase Phase value for the given quadrature point
+ * @param phase_cahn_hilliard Phase value for the given quadrature point
  *
  * @param property0 Property value for the fluid with index 0 (fluid for phase = -1)
  *
@@ -352,11 +356,11 @@ calculate_point_property_cahn_hilliard(const double phase_cahn_hilliard,
 
 /**
  * @brief Reads a file that was built by writing a deal.II TableHandler class, and refills a TableHandler with the data in the file.
- * * @param table The table to be filled. Warning ! if the table is empty, it's content will be erased.
+ * @param table The table to be filled. Warning ! if the table is empty, it's content will be erased.
  *
- *    @param file The path the file that will be use to fill up the table.
+ * @param file_name The path the file that will be use to fill up the table.
  *
- *   @param delimiter The delimiter used to read the table.
+ * @param delimiter The delimiter used to read the table.
  */
 void
 fill_table_from_file(TableHandler     &table,
@@ -367,11 +371,11 @@ fill_table_from_file(TableHandler     &table,
  * @brief function that read a file that was build from a dealii table and fill 2 vectors.
  * The first vector contains all the columns names and the second one contained
  * all the column data.
- * * @param map A map used to contain the data based on the columns name.
+ * @param map A map used to contain the data based on the columns name.
  *
- *   @param file The path the file that will be use to fill up the table.
+ * @param file_name The path the file that will be use to fill up the table.
  *
- *   @param delimiter The delimiter used to read the table.
+ * @param delimiter The delimiter used to read the table.
  */
 void
 fill_vectors_from_file(std::map<std::string, std::vector<double>> &map,
@@ -380,11 +384,11 @@ fill_vectors_from_file(std::map<std::string, std::vector<double>> &map,
 
 /**
  * @brief Function that read a file that was build from a dealii table and create a map with the key being the column name and the variable the vectors of data.
- * * @param map Container to be filled with the information in the dealii table.
+ * @param map Container to be filled with the information in the dealii table.
  *
- *   @param file The path the file that will be use to fill up the table.
+ * @param file_name The path the file that will be use to fill up the table.
  *
- *   @param delimiter The delimiter used to read the table.
+ * @param delimiter The delimiter used to read the table.
  */
 void
 fill_string_vectors_from_file(
@@ -394,7 +398,7 @@ fill_string_vectors_from_file(
 
 /**
  * @brief Creates the simulation output folder
- * * @param dirname Output directory name
+ * @param dirname Output directory name
  */
 void
 create_output_folder(const std::string &dirname);

include/solvers/vof.h

@@ -518,10 +518,10 @@ class VolumeOfFluid : public AuxiliaryPhysics<dim, GlobalVectorType>
   /**
    * @brief Assemble the system for interface sharpening
    *  * This function assembles the weak form of:
-   *  $$ \Phi = c ^ (1 - \alpha) * (\phi ^ \alpha)  if 0 <=
-   * \phi <= c $$
-   *  $$ \Phi = 1 - (1 - c) ^ (1 - \alpha) * (1 - \phi) ^ \alpha  if c <
-   * \phi <= 1 $$
+   * \f$ \Phi = c ^ {(1 - \alpha)} * (\phi ^ \alpha)\f$  if \f$ 0 <=
+   * \phi <= c  \ \f$
+   * \f$ \Phi = 1 - (1 - c) ^ {(1 - \alpha)} * (1 - \phi) ^ \alpha \f$ if \f$c <
+   * \phi <= 1 \f$
    * Reference for sharpening method
    * https://www.sciencedirect.com/science/article/pii/S0045782500002000
    *
@@ -666,9 +666,9 @@ class VolumeOfFluid : public AuxiliaryPhysics<dim, GlobalVectorType>
    * @brief Assembles the matrix and rhs for calculation of the curvature.
    *
    * Solves:
-   * $$ v * k + \eta * \nabla v . \nabla k = \nabla v . (\psi / |\psi|) $$
-   * where $$v$$, $$psi$$, $$eta$$, and $$k$$ are test function, fpg, filter
-   * value, and curvature.
+   * \f$v * k + \eta * \nabla v . \nabla k = \nabla v . (\psi / |\psi|)\f$
+   * where \f$v\f$, \f$\psi\f$, \f$\eta\f$, and \f$k\f$ are test function, fpg,
+   * filter value, and curvature.
    *
    * @param present_projected_phase_fraction_gradient_solution
    */