Remove all clang tidy warnings from the core library of Lethe (#1243)

Description
Since I have deployed the new CI action, we are able to identify many more alerts using clang sanitizer. This PR aims at removing the alerts from the core library of Lethe. We still have warnings when we compile with clang, but this will need an additional CI instance check.

Testing
All units tests and application tests should pass before this is merged.

include/core/bdf.h

@@ -50,7 +50,7 @@ using namespace dealii;
 Vector<double>
 calculate_bdf_coefficients(
   const Parameters::SimulationControl::TimeSteppingMethod method,
-  const std::vector<double>                               time_steps);
+  const std::vector<double>                              &time_steps);
 
 
 /**
@@ -78,10 +78,10 @@ calculate_bdf_coefficients(
  * calculation of BDF coefficients.
  */
 Vector<double>
-delta(const unsigned int   order,
-      const unsigned int   n,
-      const unsigned int   j,
-      const Vector<double> times);
+delta(const unsigned int    order,
+      const unsigned int    n,
+      const unsigned int    j,
+      const Vector<double> &times);
 
 
 

include/core/manifolds.h

@@ -186,19 +186,19 @@ attach_manifolds_to_triangulation(
  */
 void
 attach_cad_to_manifold(parallel::DistributedTriangulationBase<2> &triangulation,
-                       std::string                                cad_name,
-                       unsigned int                               manifold_id);
+                       const std::string                         &cad_name,
+                       const unsigned int                         manifold_id);
 
 void
 attach_cad_to_manifold(
   parallel::DistributedTriangulationBase<2, 3> &triangulation,
-  std::string                                   cad_name,
-  unsigned int                                  manifold_id);
+  const std::string                            &cad_name,
+  const unsigned int                            manifold_id);
 
 void
 attach_cad_to_manifold(parallel::DistributedTriangulationBase<3> &triangulation,
-                       std::string                                cad_name,
-                       unsigned int                               manifold_id);
+                       const std::string                         &cad_name,
+                       const unsigned int                         manifold_id);
 
 
 

include/core/parameters.h

@@ -384,12 +384,12 @@ namespace Parameters
     {}
 
     void
-    declare_parameters(ParameterHandler &prm,
-                       std::string       material_prefix,
-                       unsigned int      id);
+    declare_parameters(ParameterHandler  &prm,
+                       const std::string &material_prefix,
+                       unsigned int       id);
     void
     parse_parameters(ParameterHandler    &prm,
-                     std::string          material_prefix,
+                     const std::string   &material_prefix,
                      const unsigned int   id,
                      const Dimensionality dimensions);
 
@@ -815,8 +815,8 @@ namespace Parameters
     // z =2) value of the beam_orientation parameter
     unsigned int beam_orientation_coordinate;
 
-    // beam_direction shows the direction of laser beam (either in positive (1)
-    // or negative (0) direction
+    // beam_direction shows the direction of laser beam (either in positive
+    // (true) or negative (false) direction
     bool beam_direction;
 
     // Based on the laser beam orientation, the integer values of a

include/core/parsed_function_custom.h

@@ -81,9 +81,9 @@ class ParsedFunctionCustom
    * @param[in] constants_list Constants used by the expressions
    */
   void
-  initialize(const std::string vnames,
-             const std::string expression,
-             const std::string constants_list);
+  initialize(const std::string &vnames,
+             const std::string &expression,
+             const std::string &constants_list);
 
   /**
    * @brief Evaluate all components at the evaluation point

include/core/pvd_handler.h

@@ -35,18 +35,18 @@ class PVDHandler
    * @param filename Name of the file to which the PVDHandler content is save
    */
   void
-  save(std::string filename);
+  save(const std::string &filename);
 
   /**
    * @brief read Reads the content of a pvd times_and_names checpoint
    *
    * @param filename Name of the file frin which the PVDHandler content is read
    */
   void
-  read(std::string filename);
+  read(const std::string &filename);
 
   void
-  append(double time, std::string pvtu_filename)
+  append(double time, const std::string &pvtu_filename)
   {
     times_and_names.push_back(
       std::pair<double, std::string>(time, pvtu_filename));

include/core/serial_solid.h

@@ -201,7 +201,8 @@ class SerialSolid
    * @param simulation_control The simulation control object
    */
   void
-  write_output_results(std::shared_ptr<SimulationControl> simulation_control);
+  write_output_results(
+    const std::shared_ptr<SimulationControl> &simulation_control);
 
   /**
    * @brief read solid base triangulation checkpoint and replaces the
@@ -211,15 +212,15 @@ class SerialSolid
    *
    */
   void
-  read_checkpoint(std::string prefix_name);
+  read_checkpoint(const std::string &prefix_name);
 
   /**
    * @brief write solid base triangulation checkpoint
    *
    * @param prefix_name The prefix of the checkpoint of the simulation
    */
   void
-  write_checkpoint(std::string prefix_name);
+  write_checkpoint(const std::string &prefix_name);
 
 
 private:

include/core/shape.h

@@ -2680,7 +2680,7 @@ class RBFShape : public Shape<dim>
    * @param orientation the orientation of the shape with respect to each main
    * axis
    */
-  RBFShape(const std::string   shape_arguments_str,
+  RBFShape(const std::string  &shape_arguments_str,
            const Point<dim>   &position,
            const Tensor<1, 3> &orientation);
 

include/core/shape_parsing.h

@@ -33,8 +33,8 @@ namespace ShapeGenerator
    */
   template <int dim>
   std::shared_ptr<Shape<dim>>
-  initialize_shape(const std::string   type,
-                   const std::string   shape_arguments_str,
+  initialize_shape(const std::string  &type,
+                   const std::string  &shape_arguments_str,
                    const Point<dim>   &position,
                    const Tensor<1, 3> &orientation);
 
@@ -47,10 +47,10 @@ namespace ShapeGenerator
    */
   template <int dim>
   std::shared_ptr<Shape<dim>>
-  initialize_shape_from_vector(const std::string         type,
-                               const std::vector<double> shape_arguments,
-                               const Point<dim>         &position,
-                               const Tensor<1, 3>       &orientation);
+  initialize_shape_from_vector(const std::string         &type,
+                               const std::vector<double> &shape_arguments,
+                               const Point<dim>          &position,
+                               const Tensor<1, 3>        &orientation);
 
   /**
    * Initializes the shape from its type and a text file that contains the real
@@ -62,8 +62,8 @@ namespace ShapeGenerator
    */
   template <int dim>
   std::shared_ptr<Shape<dim>>
-  initialize_shape_from_file(const std::string   type,
-                             const std::string   file_name,
+  initialize_shape_from_file(const std::string  &type,
+                             const std::string  &file_name,
                              const Point<dim>   &position,
                              const Tensor<1, 3> &orientation);
 } // namespace ShapeGenerator

include/core/simulation_control.h

@@ -165,7 +165,7 @@ class SimulationControl
    *
    **/
 
-  SimulationControl(const Parameters::SimulationControl param);
+  SimulationControl(const Parameters::SimulationControl &param);
 
   /**
    * @brief Pure virtual function to control the progression of the simulation.
@@ -472,23 +472,31 @@ class SimulationControl
     return bdf_coefs;
   }
 
-
+  /**
+   * @brief Save the simulation control information from the checkpoint file and updates the time step vector, the CFL value, the time and the iteration number.
+   *
+   * @param prefix The prefix of the checkpoint of the simulation
+   */
   void
-  save(std::string filename);
+  save(const std::string &prefix);
 
   /**
    * @brief Reads the simulation control information from the checkpoint file and updates the time step vector, the CFL value, the time and the iteration number.
+   *
+   * @param prefix The prefix of the checkpoint of the simulation
    */
   void
-  read(std::string filename);
+  read(const std::string &prefix);
 
   /**
    * @brief Reads and returns the simulation control information from the checkpoint file filename without updating the simulation control information.
    *
+   * @param prefix The prefix of the checkpoint of the simulation
+   *
    * @return A vector containing the last checkpointed file and time step.
    */
   std::vector<double>
-  get_checkpointed_simulation_control_info(std::string filename);
+  get_checkpointed_simulation_control_info(const std::string &prefix);
 };
 
 
@@ -518,7 +526,7 @@ class SimulationControlTransient : public SimulationControl
 
 
 public:
-  SimulationControlTransient(Parameters::SimulationControl param);
+  SimulationControlTransient(const Parameters::SimulationControl &param);
 
   virtual void
   print_progression(const ConditionalOStream &pcout) override;
@@ -543,7 +551,7 @@ class SimulationControlTransient : public SimulationControl
 class SimulationControlTransientDEM : public SimulationControlTransient
 {
 public:
-  SimulationControlTransientDEM(Parameters::SimulationControl param);
+  SimulationControlTransientDEM(const Parameters::SimulationControl &param);
 
   virtual void
   print_progression(const ConditionalOStream &pcout) override;
@@ -571,7 +579,8 @@ class SimulationControlTransientDynamicOutput
   calculate_time_step() override;
 
 public:
-  SimulationControlTransientDynamicOutput(Parameters::SimulationControl param);
+  SimulationControlTransientDynamicOutput(
+    const Parameters::SimulationControl &param);
 
 
   /**
@@ -585,7 +594,7 @@ class SimulationControlTransientDynamicOutput
 class SimulationControlSteady : public SimulationControl
 {
 public:
-  SimulationControlSteady(Parameters::SimulationControl param);
+  SimulationControlSteady(const Parameters::SimulationControl &param);
 
   virtual void
   print_progression(const ConditionalOStream &pcout) override;
@@ -606,7 +615,7 @@ class SimulationControlSteady : public SimulationControl
 class SimulationControlAdjointSteady : public SimulationControlTransient
 {
 public:
-  SimulationControlAdjointSteady(Parameters::SimulationControl param);
+  SimulationControlAdjointSteady(const Parameters::SimulationControl &param);
 
   virtual void
   print_progression(const ConditionalOStream &pcout) override;

include/core/solid_base.h

@@ -101,14 +101,14 @@ class SolidBase
    * @brief Loads a solid triangulation from a restart file
    */
   void
-  load_triangulation(const std::string filename_tria);
+  load_triangulation(const std::string &filename_tria);
 
   /**
    * @brief Loads a particle handler in the fluid triangulation domain that holds the particles of the solid
    * according to a specific quadrature, and sets up dofs
    */
   void
-  load_particles(const std::string filename_part);
+  load_particles(const std::string &filename_part);
 
   /**
    * @return the reference to the std::shared_ptr of a Particles::ParticleHandler<spacedim> that contains the solid particle handler
@@ -220,13 +220,13 @@ class SolidBase
    * @brief read solid base triangulation checkpoint
    */
   void
-  read_checkpoint(std::string prefix_name);
+  read_checkpoint(const std::string &prefix_name);
 
   /**
    * @brief write solid base triangulation checkpoint
    */
   void
-  write_checkpoint(std::string prefix_name);
+  write_checkpoint(const std::string &prefix_name);
 
 
 private:

include/core/solutions_output.h

@@ -55,8 +55,8 @@ template <int dim, int spacedim = dim>
 void
 write_vtu_and_pvd(PVDHandler                            &pvd_handler,
                   const DataOutInterface<dim, spacedim> &data_out,
-                  const std::string                      folder,
-                  const std::string                      file_prefix,
+                  const std::string                     &folder,
+                  const std::string                     &file_prefix,
                   const double                           time,
                   const unsigned int                     iter,
                   const unsigned int                     group_files,
@@ -80,10 +80,10 @@ write_vtu_and_pvd(PVDHandler                            &pvd_handler,
 template <int dim>
 void
 write_boundaries_vtu(const DataOutFaces<dim> &data_out,
-                     const std::string        folder,
+                     const std::string       &folder,
                      const double             time,
                      const unsigned int       iter,
                      const MPI_Comm          &mpi_communicator,
-                     const std::string  file_prefix = std::string("boundaries"),
+                     const std::string &file_prefix = std::string("boundaries"),
                      const unsigned int digits      = 5);
 #endif

include/core/utilities.h

@@ -363,9 +363,9 @@ calculate_point_property_cahn_hilliard(const double phase_cahn_hilliard,
  * @param delimiter The delimiter used to read the table.
  */
 void
-fill_table_from_file(TableHandler     &table,
-                     const std::string file_name,
-                     const std::string delimiter = " ");
+fill_table_from_file(TableHandler      &table,
+                     const std::string &file_name,
+                     const std::string &delimiter = " ");
 
 /**
  * @brief function that read a file that was build from a dealii table and fill 2 vectors.
@@ -379,8 +379,8 @@ fill_table_from_file(TableHandler     &table,
  */
 void
 fill_vectors_from_file(std::map<std::string, std::vector<double>> &map,
-                       const std::string                           file_name,
-                       const std::string delimiter = " ");
+                       const std::string                          &file_name,
+                       const std::string &delimiter = " ");
 
 /**
  * @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.
@@ -393,8 +393,8 @@ fill_vectors_from_file(std::map<std::string, std::vector<double>> &map,
 void
 fill_string_vectors_from_file(
   std::map<std::string, std::vector<std::string>> &map,
-  const std::string                                file_name,
-  const std::string                                delimiter = " ");
+  const std::string                               &file_name,
+  const std::string                               &delimiter = " ");
 
 /**
  * @brief Creates the simulation output folder