Debug ci fix (chaos-polymtl#1247)

Description
There were some asserts being thrown in debug mode. These asserts were all warrented.
They were cuased by the following:
1- std::shared_ptr cannot be created from a nullptr. Since the sharp edge in the tracer relies on this mechanism to assess if there is or not a shape, this was highly problematic. @oguevremont we will need to look more into this and refactor this more cleanly in the next month. I have made a solution using regular pointers which is fine, but relying on nullptr is not very nice in my opinion
2- There was an std::vector that was not used correctly in the find cell around flat mechanism
3- In the restart for sharp edge, the order of the checks was not done in the right order which violated the size issue.

Solution
Fixed all of those bugs.

Testing
Debug tests should pass now.

Former-commit-id: b255a9e

Author: blaisb

include/solvers/multiphysics_interface.h

@@ -567,14 +567,16 @@ class MultiphysicsInterface
   /**
    * @brief Request immersed solid signed distance function
    */
-  std::shared_ptr<Function<dim>>
+  Function<dim> *
   get_immersed_solid_signed_distance_function();
 
   /**
    * @brief Share immersed solid signed distance function
+   *
+   * @param function The immersed solid signed distance function
    */
   void
-    set_immersed_solid_signed_distance_function(std::shared_ptr<Function<dim>>);
+  set_immersed_solid_signed_distance_function(Function<dim> *function);
 
   /**
    * @brief Request the previous solutions of a given physics
@@ -921,7 +923,7 @@ class MultiphysicsInterface
   GlobalVectorType *reynolds_stress_solutions;
 
   // Immersed solid signed distance function to be used by auxiliary physics
-  std::shared_ptr<Function<dim>> immersed_solid_signed_distance_function;
+  Function<dim> *immersed_solid_signed_distance_function;
 
   // past (minus 1) solution
   std::map<PhysicsID, GlobalVectorType *>      physics_solutions_m1;

include/solvers/tracer.h

@@ -432,9 +432,6 @@ class Tracer : public AuxiliaryPhysics<dim, GlobalVectorType>
   AffineConstraints<double>      zero_constraints;
   TrilinosWrappers::SparseMatrix system_matrix;
 
-  // Immersed solid signed distance function with immersed solid solver
-  std::shared_ptr<Function<dim>> immersed_solid_signed_distance_function;
-
   // Previous solutions vectors
   std::vector<GlobalVectorType> previous_solutions;
 

include/solvers/tracer_scratch_data.h

@@ -159,8 +159,16 @@ class TracerScratchData
     auto &fe_tracer   = this->fe_values_tracer.get_fe();
 
     source_function->value_list(quadrature_points, source);
+
     if (properties_manager.field_is_required(field::levelset))
-      levelset_function->value_list(quadrature_points, sdf_values);
+      {
+        Assert(
+          levelset_function != nullptr,
+          ExcMessage(
+            "Levelset function is required for tracer assembly, but the level set function is a nullptr"));
+
+        levelset_function->value_list(quadrature_points, sdf_values);
+      }
 
     if (dim == 2)
       this->cell_size =

source/core/lethe_grid_tools.cc

@@ -870,7 +870,6 @@ LetheGridTools::cell_cut_by_flat(
   if (condition_B2)
     {
       bool condition_C2 = false;
-      manifold_points.clear();
       for (const auto face : cell->face_indices())
         {
           auto face_iter = cell->face(face);

source/fem-dem/fluid_dynamics_sharp.cc

@@ -817,7 +817,7 @@ FluidDynamicsSharp<dim>::define_particles()
   combined_shapes =
     std::make_shared<CompositeShape<dim>>(all_shapes, Point<dim>(), Point<3>());
   this->multiphysics->set_immersed_solid_signed_distance_function(
-    combined_shapes);
+    &(*combined_shapes));
 }
 
 
@@ -4341,15 +4341,15 @@ FluidDynamicsSharp<dim>::read_checkpoint()
   std::map<std::string, std::vector<double>> restart_data;
   fill_vectors_from_file(restart_data, filename);
 
-  // Implement the data  in the particles.
+  // Implement the data in the particles.
   if constexpr (dim == 2)
     {
       unsigned int row = 0;
       for (unsigned int p_i = 0; p_i < particles.size(); ++p_i)
         {
           unsigned int j = 0;
-          while (restart_data["ID"][row] == p_i and
-                 row < restart_data["ID"].size())
+          while (row < restart_data["ID"].size() &&
+                 restart_data["ID"][row] == p_i)
             {
               if (j == 0)
                 {
@@ -4415,8 +4415,8 @@ FluidDynamicsSharp<dim>::read_checkpoint()
       for (unsigned int p_i = 0; p_i < particles.size(); ++p_i)
         {
           unsigned int j = 0;
-          while (restart_data["ID"][row] == p_i and
-                 row < restart_data["ID"].size())
+          while (row < restart_data["ID"].size() &&
+                 restart_data["ID"][row] == p_i)
             {
               if (j == 0)
                 {

source/solvers/multiphysics_interface.cc

@@ -217,20 +217,20 @@ MultiphysicsInterface<dim>::get_projected_phase_fraction_gradient_dof_handler()
 }
 
 template <int dim>
-std::shared_ptr<Function<dim>>
+Function<dim> *
 MultiphysicsInterface<dim>::get_immersed_solid_signed_distance_function()
 {
   // This pointer is also used to check if an immersed boundary solid method is
   // being used, depending on whether the pointer is assigned.
-  return this->immersed_solid_signed_distance_function;
+  return immersed_solid_signed_distance_function;
 }
 
 template <int dim>
 void
 MultiphysicsInterface<dim>::set_immersed_solid_signed_distance_function(
-  std::shared_ptr<Function<dim>> function)
+  Function<dim> *function)
 {
-  this->immersed_solid_signed_distance_function = function;
+  immersed_solid_signed_distance_function = function;
 }
 
 template <int dim>

source/solvers/tracer.cc

@@ -51,10 +51,9 @@ Tracer<dim>::assemble_system_matrix()
   this->system_matrix = 0;
   setup_assemblers();
 
-  // We get the immersed function, which is null when no immersed solids are
-  // involved.
-  immersed_solid_signed_distance_function =
-    this->multiphysics->get_immersed_solid_signed_distance_function();
+  // Update the source term time
+  simulation_parameters.source_term.tracer_source->set_time(
+    simulation_control->get_current_time());
 
   const DoFHandler<dim> *dof_handler_fluid =
     multiphysics->get_dof_handler(PhysicsID::fluid_dynamics);
@@ -89,14 +88,13 @@ Tracer<dim>::assemble_local_system_matrix(
   if (!cell->is_locally_owned())
     return;
 
-  auto source_term = simulation_parameters.source_term.tracer_source;
-  source_term->set_time(simulation_control->get_current_time());
 
-  scratch_data.reinit(cell,
-                      this->evaluation_point,
-                      this->previous_solutions,
-                      &(*source_term),
-                      &(*immersed_solid_signed_distance_function));
+  scratch_data.reinit(
+    cell,
+    this->evaluation_point,
+    this->previous_solutions,
+    &(*simulation_parameters.source_term.tracer_source),
+    &(*this->multiphysics->get_immersed_solid_signed_distance_function()));
 
   const DoFHandler<dim> *dof_handler_fluid =
     multiphysics->get_dof_handler(PhysicsID::fluid_dynamics);
@@ -193,10 +191,9 @@ Tracer<dim>::assemble_system_rhs()
   this->system_rhs = 0;
   setup_assemblers();
 
-  // We get the immersed function, which is null when no immersed solids are
-  // involved
-  immersed_solid_signed_distance_function =
-    this->multiphysics->get_immersed_solid_signed_distance_function();
+  // Update the source term time
+  simulation_parameters.source_term.tracer_source->set_time(
+    simulation_control->get_current_time());
 
   const DoFHandler<dim> *dof_handler_fluid =
     multiphysics->get_dof_handler(PhysicsID::fluid_dynamics);
@@ -234,11 +231,12 @@ Tracer<dim>::assemble_local_system_rhs(
   auto source_term = simulation_parameters.source_term.tracer_source;
   source_term->set_time(simulation_control->get_current_time());
 
-  scratch_data.reinit(cell,
-                      this->evaluation_point,
-                      this->previous_solutions,
-                      &(*source_term),
-                      &(*immersed_solid_signed_distance_function));
+  scratch_data.reinit(
+    cell,
+    this->evaluation_point,
+    this->previous_solutions,
+    &(*source_term),
+    (this->multiphysics->get_immersed_solid_signed_distance_function()));
 
   const DoFHandler<dim> *dof_handler_fluid =
     multiphysics->get_dof_handler(PhysicsID::fluid_dynamics);
@@ -650,11 +648,9 @@ Tracer<dim>::postprocess_tracer_flow_rate(const VectorType &current_solution_fd)
                                                               n_q_points_face));
                       face_quadrature_points =
                         fe_face_values_tracer.get_quadrature_points();
-                      immersed_solid_signed_distance_function =
-                        this->multiphysics
-                          ->get_immersed_solid_signed_distance_function();
-                      this->immersed_solid_signed_distance_function->value_list(
-                        face_quadrature_points, levelset_values);
+                      this->multiphysics
+                        ->get_immersed_solid_signed_distance_function()
+                        ->value_list(face_quadrature_points, levelset_values);
                       set_field_vector(field::levelset,
                                        levelset_values,
                                        fields);

tests/core/lethe_grid_tool_mesh_cut_by_flat_2.cc

@@ -111,15 +111,10 @@ test()
               << std::endl;
     }
 
-    // Printing the final position for all the vertices
-
-#if (DEAL_II_VERSION_MAJOR < 10 && DEAL_II_VERSION_MINOR < 4)
-  Legacy::DataOut<2>                   data_out;
-  Legacy::DataOut<1, DoFHandler<1, 2>> flat_data_out;
-#else
+  // Printing the final position for all the vertices
   DataOut<2>    data_out;
   DataOut<1, 2> flat_data_out;
-#endif
+
   data_out.attach_dof_handler(dof_handler);
   data_out.add_data_vector(subdomain, "subdomain");
   data_out.build_patches();

tests/tests.h

@@ -20,7 +20,6 @@
 
 #include <deal.II/base/config.h>
 
-#include <deal.II/base/cuda.h>
 #include <deal.II/base/exceptions.h>
 #include <deal.II/base/job_identifier.h>
 #include <deal.II/base/logstream.h>