From: Wolfgang Bangerth <bangerth@math.tamu.edu>
Date: Wed, 25 Nov 2015 15:14:22 +0000 (-0600)
Subject: Allow setting manifold ids on interior edges and faces.
X-Git-Tag: v8.4.0-rc2~192^2
X-Git-Url: https://gitweb.dealii.org/cgi-bin/gitweb.cgi?a=commitdiff_plain;h=refs%2Fpull%2F1912%2Fhead;p=dealii.git

Allow setting manifold ids on interior edges and faces.
---

diff --git a/doc/news/changes.h b/doc/news/changes.h
index ba93a5e553..436249b091 100644
--- a/doc/news/changes.h
+++ b/doc/news/changes.h
@@ -444,6 +444,20 @@ inconvenience this causes.
   (Martin Kronbichler, 2015/11/26)
   </li>
 
+  <li> New: In 3d, GridGenerator::extract_boundary_mesh() now copies the
+  manifold ids of edges of the volume mesh to the manifold ids of the edges
+  of the extracted surface mesh.
+  <br>
+  (Wolfgang Bangerth, 2015/11/25)
+  </li>
+
+  <li> New: Triangulation::create_triangulation() now accepts subcell-data
+  objects that may include information about interior edges and faces, to
+  facilitate setting manifold indicators on interior edges and faces.
+  <br>
+  (Wolfgang Bangerth, 2015/11/25)
+  </li>
+
   <li> Fixed: GridGenerator::extract_boundary_mesh() in 3d could generate
   surface cells that did not uniformly had a right- or left-handed coordinate
   system associated with them when viewed from one side of the surface. This
diff --git a/include/deal.II/grid/tria.h b/include/deal.II/grid/tria.h
index abe2993c30..115af08038 100644
--- a/include/deal.II/grid/tria.h
+++ b/include/deal.II/grid/tria.h
@@ -160,9 +160,15 @@ struct CellData
  * a common number describing the boundary condition to hold on this part of
  * the boundary. The triangulation creation function gives lines not in this
  * list either the boundary indicator zero (if on the boundary) or
- * numbers::internal_face_boundary_id (if in the interior). Explicitly giving
- * a line the indicator numbers::internal_face_boundary_id will result in an
- * error, as well as giving an interior line a boundary indicator.
+ * numbers::internal_face_boundary_id (if in the interior).
+ *
+ * You will get an error if you try to set the boundary indicator of
+ * an interior edge or face, i.e., an edge or face that is not at the
+ * boundary of the mesh. However, one may sometimes want to set the
+ * manifold indicator to an interior object. In this case, set its
+ * boundary indicator to numbers::internal_face_boundary_id, to
+ * indicate that you understand that it is an interior object, but set
+ * its manifold id to the value you want.
  *
  * @ingroup grid
  */
diff --git a/source/grid/grid_generator.cc b/source/grid/grid_generator.cc
index 57a4480fc1..d6d7768b91 100644
--- a/source/grid/grid_generator.cc
+++ b/source/grid/grid_generator.cc
@@ -4209,7 +4209,8 @@ namespace GridGenerator
 
     std::vector< bool > touched (get_tria(volume_mesh).n_vertices(), false);
     std::vector< CellData< boundary_dim > > cells;
-    std::vector< Point<spacedim> >      vertices;
+    SubCellData                             subcell_data;
+    std::vector< Point<spacedim> >          vertices;
 
     std::map<unsigned int,unsigned int> map_vert_index; //volume vertex indices to surf ones
 
@@ -4258,6 +4259,57 @@ namespace GridGenerator
                 if (i % 2 == 1)
                   std::swap (c_data.vertices[1], c_data.vertices[2]);
 
+              // in 3d, we also need to make sure we copy the manifold
+              // indicators from the edges of the volume mesh to the
+              // edges of the surface mesh
+              //
+              // one might think that we we can also prescribe
+              // boundary indicators for edges, but this is only
+              // possible for edges that aren't just on the boundary
+              // of the domain (all of the edges we consider are!) but
+              // that would actually end up at the boundary of the
+              // surface mesh. there is no easy way to check this, so
+              // we simply don't do it and instead set it to an
+              // invalid value that makes sure
+              // Triangulation::create_triangulation doesn't copy it
+              if (dim == 3)
+                for (unsigned int e=0; e<4; ++e)
+                  {
+                    // see if we already saw this edge from a
+                    // neighboring face, either in this or the reverse
+                    // orientation. if so, skip it.
+                    {
+                      bool edge_found = false;
+                      for (unsigned int i=0; i<subcell_data.boundary_lines.size(); ++i)
+                        if (((subcell_data.boundary_lines[i].vertices[0]
+                              == map_vert_index[face->line(e)->vertex_index(0)])
+                             &&
+                             (subcell_data.boundary_lines[i].vertices[1]
+                              == map_vert_index[face->line(e)->vertex_index(1)]))
+                            ||
+                            ((subcell_data.boundary_lines[i].vertices[0]
+                              == map_vert_index[face->line(e)->vertex_index(1)])
+                             &&
+                             (subcell_data.boundary_lines[i].vertices[1]
+                              == map_vert_index[face->line(e)->vertex_index(0)])))
+                          {
+                            edge_found = true;
+                            break;
+                          }
+                      if (edge_found == true)
+                        continue;   // try next edge of current face
+                    }
+
+                    CellData<1> edge;
+                    edge.vertices[0] = map_vert_index[face->line(e)->vertex_index(0)];
+                    edge.vertices[1] = map_vert_index[face->line(e)->vertex_index(1)];
+                    edge.boundary_id = numbers::internal_face_boundary_id;
+                    edge.manifold_id = face->line(e)->manifold_id();
+
+                    subcell_data.boundary_lines.push_back (edge);
+                  }
+
+
               cells.push_back(c_data);
               mapping.push_back(face);
             }
@@ -4266,7 +4318,7 @@ namespace GridGenerator
     // create level 0 surface triangulation
     Assert (cells.size() > 0, ExcMessage ("No boundary faces selected"));
     const_cast<Triangulation<dim-1,spacedim>&>(get_tria(surface_mesh))
-    .create_triangulation (vertices, cells, SubCellData());
+    .create_triangulation (vertices, cells, subcell_data);
 
     // Make the actual mapping
     for (typename Container<dim-1,spacedim>::active_cell_iterator
diff --git a/source/grid/tria.cc b/source/grid/tria.cc
index ec95159c5c..0dc87a5423 100644
--- a/source/grid/tria.cc
+++ b/source/grid/tria.cc
@@ -1884,8 +1884,7 @@ namespace internal
             line->set_manifold_id(numbers::flat_manifold_id);
           }
 
-        // set boundary indicators where
-        // given
+        // set boundary indicators where given
         std::vector<CellData<1> >::const_iterator boundary_line
           = subcelldata.boundary_lines.begin();
         std::vector<CellData<1> >::const_iterator end_boundary_line
@@ -1896,13 +1895,11 @@ namespace internal
             std::pair<int,int> line_vertices(std::make_pair(boundary_line->vertices[0],
                                                             boundary_line->vertices[1]));
             if (needed_lines.find(line_vertices) != needed_lines.end())
-              // line found in this
-              // direction
+              // line found in this direction
               line = needed_lines[line_vertices];
             else
               {
-                // look whether it exists
-                // in reverse direction
+                // look whether it exists in reverse direction
                 std::swap (line_vertices.first, line_vertices.second);
                 if (needed_lines.find(line_vertices) != needed_lines.end())
                   line = needed_lines[line_vertices];
@@ -1912,21 +1909,26 @@ namespace internal
                                                         line_vertices.second));
               }
 
-            // assert that we only set
-            // boundary info once
+            // assert that we only set boundary info once
             AssertThrow (! (line->boundary_id() != 0 &&
                             line->boundary_id() != numbers::internal_face_boundary_id),
                          ExcMultiplySetLineInfoOfLine(line_vertices.first,
                                                       line_vertices.second));
 
-            // Assert that only exterior lines
-            // are given a boundary indicator
-            AssertThrow (! (line->boundary_id() == numbers::internal_face_boundary_id),
-                         ExcInteriorLineCantBeBoundary(line->vertex_index(0),
-                                                       line->vertex_index(1),
-                                                       boundary_line->boundary_id));
+            // Assert that only exterior lines are given a boundary
+            // indicator; however, it is possible that someone may
+            // want to give an interior line a manifold id (and thus
+            // lists this line in the subcell_data structure), and we
+            // need to allow that
+            if (boundary_line->boundary_id != numbers::internal_face_boundary_id)
+              {
+                AssertThrow (! (line->boundary_id() == numbers::internal_face_boundary_id),
+                             ExcInteriorLineCantBeBoundary(line->vertex_index(0),
+                                                           line->vertex_index(1),
+                                                           boundary_line->boundary_id));
+                line->set_boundary_id (boundary_line->boundary_id);
+              }
 
-            line->set_boundary_id (boundary_line->boundary_id);
             line->set_manifold_id (boundary_line->manifold_id);
           }
 
diff --git a/tests/codim_one/extract_boundary_mesh_10.cc b/tests/codim_one/extract_boundary_mesh_10.cc
new file mode 100644
index 0000000000..721fbc84b6
--- /dev/null
+++ b/tests/codim_one/extract_boundary_mesh_10.cc
@@ -0,0 +1,74 @@
+// ---------------------------------------------------------------------
+//
+// Copyright (C) 2010 - 2015 by the deal.II authors
+//
+// This file is part of the deal.II library.
+//
+// The deal.II 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 deal.II distribution.
+//
+// ---------------------------------------------------------------------
+
+
+// We can not copy boundary ids from edges of the volume mesh to edges
+// of the surface mesh in 3d because the boundary edges of the volume
+// mesh are not necessarily boundary edges of the surface mesh.
+//
+// if the original mesh's geometry was only defined via the boundary
+// indicators, this leads to a surface mesh with a geometry
+// description of edges that is not likely what was desired. there is
+// little one can do about it with only boundary_ids, and without
+// resorting to manifold_ids. this testcase in essence just ensures
+// that we continue to get this "undesirable" behavior until someone
+// comes up with a better idea
+
+#include "../tests.h"
+
+#include <deal.II/grid/tria.h>
+#include <deal.II/grid/grid_generator.h>
+#include <deal.II/grid/grid_out.h>
+#include <deal.II/grid/grid_tools.h>
+#include <deal.II/grid/tria_boundary_lib.h>
+
+
+
+void test()
+{
+  const int dim=3;
+
+  Triangulation<dim>   triangulation;
+  GridGenerator::cylinder(triangulation, 100, 200);
+
+  static const CylinderBoundary<dim> outer_cylinder (100,0);
+  triangulation.set_boundary(0,outer_cylinder);
+
+  // now extract the surface mesh
+  Triangulation<dim-1,dim> triangulation_surface;
+
+  static const CylinderBoundary<dim-1,dim> surface_cyl(100,0);
+  triangulation_surface.set_boundary(0,surface_cyl);
+
+  GridGenerator::extract_boundary_mesh(triangulation,triangulation_surface);
+
+  // refine the surface mesh to see the effect of boundary/manifold
+  // indicators
+  triangulation_surface.refine_global (1);
+  GridOut().write_gnuplot(triangulation_surface, deallog.get_file_stream());
+
+  deallog << triangulation_surface.n_used_vertices() << std::endl;
+  deallog << triangulation_surface.n_active_cells() << std::endl;
+}
+
+
+int main ()
+{
+  std::ofstream logfile("output");
+  deallog.attach(logfile);
+  deallog.depth_console(0);
+
+  test();
+}
diff --git a/tests/codim_one/extract_boundary_mesh_10.output b/tests/codim_one/extract_boundary_mesh_10.output
new file mode 100644
index 0000000000..65e6d91e62
--- /dev/null
+++ b/tests/codim_one/extract_boundary_mesh_10.output
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diff --git a/tests/codim_one/extract_boundary_mesh_11.cc b/tests/codim_one/extract_boundary_mesh_11.cc
new file mode 100644
index 0000000000..6e0acaf6ea
--- /dev/null
+++ b/tests/codim_one/extract_boundary_mesh_11.cc
@@ -0,0 +1,79 @@
+// ---------------------------------------------------------------------
+//
+// Copyright (C) 2010 - 2015 by the deal.II authors
+//
+// This file is part of the deal.II library.
+//
+// The deal.II 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 deal.II distribution.
+//
+// ---------------------------------------------------------------------
+
+
+// like _10, but this time try to use manifold ids that can be copied
+// from the volume to the surface mesh
+
+#include "../tests.h"
+
+#include <deal.II/grid/tria.h>
+#include <deal.II/grid/grid_generator.h>
+#include <deal.II/grid/grid_out.h>
+#include <deal.II/grid/grid_tools.h>
+#include <deal.II/grid/tria_boundary_lib.h>
+
+
+
+void test()
+{
+  const int dim=3;
+
+  Triangulation<dim>   triangulation;
+  GridGenerator::cylinder(triangulation, 100, 200);
+
+  // copy boundary indicators to manifold indicators for boundary
+  // faces. for boundary zero (the outer hull of the cylinder), we
+  // need to make sure that the adjacent edges are also all
+  // correct. for the other boundaries, don't bother with adjacent
+  // edges
+  for (Triangulation<dim>::active_cell_iterator cell=triangulation.begin_active();
+       cell != triangulation.end(); ++cell)
+    for (unsigned int f=0; f<GeometryInfo<dim>::faces_per_cell; ++f)
+      if (cell->face(f)->at_boundary())
+        if (cell->face(f)->boundary_id() == 0)
+          cell->face(f)->set_all_manifold_ids(0);
+        else
+          cell->face(f)->set_manifold_id(cell->face(f)->boundary_id());
+
+  static const CylinderBoundary<dim> outer_cylinder (100,0);
+  triangulation.set_manifold(0,outer_cylinder);
+
+  // now extract the surface mesh
+  Triangulation<dim-1,dim> triangulation_surface;
+
+  static const CylinderBoundary<dim-1,dim> surface_cyl(100,0);
+  triangulation_surface.set_manifold(0,surface_cyl);
+
+  GridGenerator::extract_boundary_mesh(triangulation,triangulation_surface);
+
+  // refine the surface mesh to see the effect of boundary/manifold
+  // indicators
+  triangulation_surface.refine_global (1);
+  GridOut().write_gnuplot(triangulation_surface, deallog.get_file_stream());
+
+  deallog << triangulation_surface.n_used_vertices() << std::endl;
+  deallog << triangulation_surface.n_active_cells() << std::endl;
+}
+
+
+int main ()
+{
+  std::ofstream logfile("output");
+  deallog.attach(logfile);
+  deallog.depth_console(0);
+
+  test();
+}
diff --git a/tests/codim_one/extract_boundary_mesh_11.output b/tests/codim_one/extract_boundary_mesh_11.output
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index 0000000000..cfab62ea4d
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+++ b/tests/codim_one/extract_boundary_mesh_11.output
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diff --git a/tests/codim_one/extract_boundary_mesh_13.cc b/tests/codim_one/extract_boundary_mesh_13.cc
new file mode 100644
index 0000000000..27223b23b3
--- /dev/null
+++ b/tests/codim_one/extract_boundary_mesh_13.cc
@@ -0,0 +1,80 @@
+// ---------------------------------------------------------------------
+//
+// Copyright (C) 2010 - 2015 by the deal.II authors
+//
+// This file is part of the deal.II library.
+//
+// The deal.II 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 deal.II distribution.
+//
+// ---------------------------------------------------------------------
+
+
+// like _11, but refine the volume mesh and not the surface mesh. this
+// should yield the same result
+
+#include "../tests.h"
+
+#include <deal.II/grid/tria.h>
+#include <deal.II/grid/grid_generator.h>
+#include <deal.II/grid/grid_out.h>
+#include <deal.II/grid/grid_tools.h>
+#include <deal.II/grid/tria_boundary_lib.h>
+
+
+
+void test()
+{
+  const int dim=3;
+
+  Triangulation<dim>   triangulation;
+  GridGenerator::cylinder(triangulation, 100, 200);
+
+  // copy boundary indicators to manifold indicators for boundary
+  // faces. for boundary zero (the outer hull of the cylinder), we
+  // need to make sure that the adjacent edges are also all
+  // correct. for the other boundaries, don't bother with adjacent
+  // edges
+  for (Triangulation<dim>::active_cell_iterator cell=triangulation.begin_active();
+       cell != triangulation.end(); ++cell)
+    for (unsigned int f=0; f<GeometryInfo<dim>::faces_per_cell; ++f)
+      if (cell->face(f)->at_boundary())
+        if (cell->face(f)->boundary_id() == 0)
+          cell->face(f)->set_all_manifold_ids(0);
+        else
+          cell->face(f)->set_manifold_id(cell->face(f)->boundary_id());
+
+  static const CylinderBoundary<dim> outer_cylinder (100,0);
+  triangulation.set_manifold(0,outer_cylinder);
+
+  // refine the surface mesh to see the effect of boundary/manifold
+  // indicators
+  triangulation.refine_global (1);
+
+  // now extract the surface mesh
+  Triangulation<dim-1,dim> triangulation_surface;
+
+  static const CylinderBoundary<dim-1,dim> surface_cyl(100,0);
+  triangulation_surface.set_manifold(0,surface_cyl);
+
+  GridGenerator::extract_boundary_mesh(triangulation,triangulation_surface);
+
+  GridOut().write_gnuplot(triangulation_surface, deallog.get_file_stream());
+
+  deallog << triangulation_surface.n_used_vertices() << std::endl;
+  deallog << triangulation_surface.n_active_cells() << std::endl;
+}
+
+
+int main ()
+{
+  std::ofstream logfile("output");
+  deallog.attach(logfile);
+  deallog.depth_console(0);
+
+  test();
+}
diff --git a/tests/codim_one/extract_boundary_mesh_13.output b/tests/codim_one/extract_boundary_mesh_13.output
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index 0000000000..cfab62ea4d
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+++ b/tests/codim_one/extract_boundary_mesh_13.output
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