Make is_prepared() more fine-grained

examples/eigenproblems/eigenproblems_ex3/eigenproblems_ex3.C

@@ -170,6 +170,8 @@ int main (int argc, char ** argv)
       if (elem->neighbor_ptr (side) == nullptr)
         mesh.get_boundary_info().add_side(elem, side, BOUNDARY_ID);
 
+  mesh.get_boundary_info().regenerate_id_sets();
+
   // Print information about the mesh to the screen.
   mesh.print_info();
 

examples/fem_system/fem_system_ex3/fem_system_ex3.C

@@ -173,6 +173,10 @@ int main (int argc, char ** argv)
             mesh.get_boundary_info().add_edge(elem, e, edge_boundary_id);
     }
 
+  // We're all done adding to the boundary_info; let's make sure its
+  // caches know about it.
+  mesh.get_boundary_info().regenerate_id_sets();
+
   // Create an equation systems object.
   EquationSystems equation_systems (mesh);
 

examples/fem_system/fem_system_ex4/fem_system_ex4.C

@@ -157,6 +157,9 @@ int main (int argc, char ** argv)
     if (elem->dim() < dim)
       elem->subdomain_id() = 1;
 
+  // Make sure the mesh knows we added new subdomains.
+  mesh.cache_elem_data();
+
   mesh_refinement.uniformly_refine(coarserefinements);
 
   // Print information about the mesh to the screen.

examples/fem_system/fem_system_ex5/fem_system_ex5.C

@@ -225,6 +225,9 @@ int main (int argc, char ** argv)
         }
     }
 
+  // We're done modifying the BoundaryInfo; get its caches up to date.
+  mesh.get_boundary_info().regenerate_id_sets();
+
   // Create an equation systems object.
   EquationSystems equation_systems (mesh);
 

examples/miscellaneous/miscellaneous_ex9/augment_sparsity_on_interface.h

@@ -56,6 +56,13 @@ class AugmentSparsityOnInterface : public GhostingFunctor
                              boundary_id_type crack_boundary_lower,
                              boundary_id_type crack_boundary_upper);
 
+
+  virtual std::unique_ptr<GhostingFunctor> clone () const override
+  {
+    return std::make_unique<AugmentSparsityOnInterface>
+      (_mesh, _crack_boundary_lower, _crack_boundary_upper);
+  }
+
   /**
    * @return a const reference to the lower-to-upper element ID map.
    */

examples/subdomains/subdomains_ex1/subdomains_ex1.C

@@ -243,6 +243,9 @@ int main (int argc, char ** argv)
         elem->subdomain_id() = 1;
     }
 
+  // Make sure the mesh knows we added new subdomains.
+  mesh.cache_elem_data();
+
   // Create an equation systems object.
   EquationSystems equation_systems (mesh);
 

examples/subdomains/subdomains_ex2/subdomains_ex2.C

@@ -195,6 +195,9 @@ int main (int argc, char ** argv)
         elem->subdomain_id() = 1;
     }
 
+  // Make sure the mesh knows we added new subdomains.
+  mesh.cache_elem_data();
+
   // Print information about the mesh to the screen.
   mesh.print_info();
 

examples/systems_of_equations/systems_of_equations_ex6/systems_of_equations_ex6.C

@@ -507,6 +507,10 @@ int main (int argc, char ** argv)
             mesh.get_boundary_info().add_edge(elem, e, EDGE_BOUNDARY_ID);
     }
 
+  // We're all done adding to the boundary_info; let's make sure its
+  // caches know about it.
+  mesh.get_boundary_info().regenerate_id_sets();
+
   // Create an equation systems object.
   EquationSystems equation_systems (mesh);
 

include/base/libmesh_common.h

@@ -271,7 +271,7 @@ extern bool warned_about_auto_ptr;
   } while (0)
 
 // The libmesh_dbg_var() macro indicates that an argument to a function
-// is used only in debug mode (i.e., when NDEBUG is not defined).
+// is used only in debug and devel modes (i.e., when NDEBUG is not defined).
 #ifndef NDEBUG
 #define libmesh_dbg_var(var) var
 #else

include/geom/elem.h

@@ -290,13 +290,19 @@ class Elem : public ReferenceCountedObject<Elem>,
   virtual dof_id_type key () const;
 
   /**
-   * \returns \p true if two elements are equivalent, false otherwise.
-   * This is true if the elements are connected to identical global
-   * nodes, regardless of how those nodes might be numbered local
-   * to the elements.
+   * \returns \p true if two elements are equivalent, \p false
+   * otherwise.  This is true if the elements are connected to
+   * identical global nodes, regardless of how those nodes might be
+   * numbered local to the elements.
    */
   bool operator == (const Elem & rhs) const;
 
+  /**
+   * \returns \p false if two elements are equivalent, \p true
+   * otherwise.
+   */
+  bool operator != (const Elem & rhs) const;
+
   /**
    * \returns \p true if two elements have equal topologies, false
    * otherwise.
@@ -1585,6 +1591,21 @@ class Elem : public ReferenceCountedObject<Elem>,
                             unsigned int side,
                             bool reset = true);
 
+  /**
+   * Same as the \p total_family_tree() member, but only adds elements
+   * which are next to \p side.
+   */
+  void total_family_tree_by_side (std::vector<const Elem *> & family,
+                                  unsigned int side,
+                                  bool reset = true) const;
+
+  /**
+   * Non-const version of function above; fills a vector of non-const pointers.
+   */
+  void total_family_tree_by_side (std::vector<Elem *> & family,
+                                  unsigned int side,
+                                  bool reset = true);
+
   /**
    * Same as the \p active_family_tree() member, but only adds elements
    * which are next to \p side.
@@ -2579,6 +2600,14 @@ subdomain_id_type & Elem::subdomain_id ()
 
 
 
+inline
+bool Elem::operator != (const Elem & rhs) const
+{
+  return !(*this == rhs);
+}
+
+
+
 inline
 const Elem * Elem::neighbor_ptr (unsigned int i) const
 {

include/geom/elem_internal.h

@@ -144,6 +144,35 @@ family_tree_by_side (T elem,
 
 
 
+template <class T>
+void
+total_family_tree_by_side (T elem,
+                           std::vector<T> & family,
+                           unsigned int s,
+                           bool reset)
+{
+  // Clear the vector if the flag reset tells us to.
+  if (reset)
+    family.clear();
+
+  libmesh_assert_less (s, elem->n_sides());
+
+  // Add this element to the family tree.
+  family.push_back(elem);
+
+  // Recurse into the elements children, if it has them.
+  // Do not clear the vector any more.
+  if (elem->has_children())
+    {
+      const unsigned int nc = elem->n_children();
+      for (unsigned int c = 0; c != nc; c++)
+        if (!elem->child_ptr(c)->is_remote() && elem->is_child_on_side(c, s))
+          ElemInternal::total_family_tree_by_side (elem->child_ptr(c), family, s, false);
+    }
+}
+
+
+
 template <class T>
 void
 active_family_tree_by_side (T elem,

include/ghosting/ghosting_functor.h

@@ -213,10 +213,12 @@ class GhostingFunctor : public ReferenceCountedObject<GhostingFunctor>
    * different meshes. The operations in  GhostingFunctor are mesh dependent.
    */
   virtual std::unique_ptr<GhostingFunctor> clone () const
-  // Let us return nullptr for backward compatibility.
-  // We will come back to mark this function as pure virtual
-  // once the API upgrade is done.
-  { return nullptr; }
+#ifndef LIBMESH_ENABLE_DEPRECATED
+  = 0;
+#else
+  // Return nullptr for backward compatibility.
+  { libmesh_deprecated(); return nullptr; }
+#endif
 
   /**
    * It should be called after cloning a ghosting functor.

include/mesh/distributed_mesh.h

@@ -111,7 +111,7 @@ class DistributedMesh : public UnstructuredMesh
    * Shim to allow operator == (&) to behave like a virtual function
    * without having to be one.
    */
-  virtual bool subclass_locally_equals (const MeshBase & other_mesh) const override;
+  virtual std::string_view subclass_first_difference_from (const MeshBase & other_mesh_base) const override;
 
   /**
    * Virtual copy-constructor, creates a copy of this mesh