{"action":"created","comment":{"url":"https://api.github.com/repos/dealii/dealii/pulls/comments/57583766","id":57583766,"diff_hunk":"@@ -0,0 +1,1308 @@\n+// ---------------------------------------------------------------------\n+//\n+// Copyright (C) 2000 - 2015 by the deal.II authors\n+//\n+// This file is part of the deal.II library.\n+//\n+// The deal.II library is free software; you can use it, redistribute\n+// it, and/or modify it under the terms of the GNU Lesser General\n+// Public License as published by the Free Software Foundation; either\n+// version 2.1 of the License, or (at your option) any later version.\n+// The full text of the license can be found in the file LICENSE at\n+// the top level of the deal.II distribution.\n+//\n+// ---------------------------------------------------------------------\n+\n+\n+#include <deal.II/base/derivative_form.h>\n+#include <deal.II/base/quadrature.h>\n+#include <deal.II/base/qprojector.h>\n+#include <deal.II/base/quadrature_lib.h>\n+#include <deal.II/base/tensor_product_polynomials.h>\n+#include <deal.II/base/memory_consumption.h>\n+#include <deal.II/base/std_cxx11/array.h>\n+#include <deal.II/base/std_cxx11/unique_ptr.h>\n+#include <deal.II/lac/full_matrix.h>\n+#include <deal.II/grid/tria.h>\n+#include <deal.II/grid/tria_iterator.h>\n+#include <deal.II/grid/tria_boundary.h>\n+#include <deal.II/dofs/dof_accessor.h>\n+#include <deal.II/grid/manifold.h>\n+#include <deal.II/fe/fe_tools.h>\n+#include <deal.II/fe/fe.h>\n+#include <deal.II/fe/fe_values.h>\n+#include <deal.II/fe/mapping_manifold.h>\n+#include <deal.II/fe/mapping_q1.h>\n+\n+#include <cmath>\n+#include <algorithm>\n+#include <numeric>\n+\n+\n+DEAL_II_NAMESPACE_OPEN\n+\n+template<int dim, int spacedim>\n+MappingManifold<dim,spacedim>::InternalData::InternalData ()\n+{}\n+\n+\n+template<int dim, int spacedim>\n+std::size_t\n+MappingManifold<dim,spacedim>::InternalData::memory_consumption () const\n+{\n+  return (Mapping<dim,spacedim>::InternalDataBase::memory_consumption() +\n+          MemoryConsumption::memory_consumption (covariant) +\n+          MemoryConsumption::memory_consumption (contravariant) +\n+          MemoryConsumption::memory_consumption (unit_tangentials) +\n+          MemoryConsumption::memory_consumption (aux) +\n+          MemoryConsumption::memory_consumption (volume_elements));\n+}\n+\n+\n+template <int dim, int spacedim>\n+void\n+MappingManifold<dim,spacedim>::InternalData::\n+initialize (const UpdateFlags      update_flags,\n+            const Quadrature<dim> &q,\n+            const unsigned int     n_original_q_points)\n+{\n+  // store the flags in the internal data object so we can access them\n+  // in fill_fe_*_values()\n+  this->update_each = update_flags;\n+\n+  // Store the quadrature\n+  this->quad = q;\n+  const unsigned int n_q_points = q.size();\n+\n+\n+  // see if we need the (transformation) shape function values\n+  // and/or gradients and resize the necessary arrays\n+  if (this->update_each & (update_quadrature_points | update_contravariant_transformation) )\n+    compute_manifold_quadrature_weights(q);\n+\n+  if (this->update_each & update_covariant_transformation)\n+    covariant.resize(n_original_q_points);\n+\n+  if (this->update_each & update_contravariant_transformation)\n+    contravariant.resize(n_original_q_points);\n+\n+  if (this->update_each & update_volume_elements)\n+    volume_elements.resize(n_original_q_points);\n+}\n+\n+\n+template <int dim, int spacedim>\n+void\n+MappingManifold<dim,spacedim>::InternalData::\n+initialize_face (const UpdateFlags      update_flags,\n+                 const Quadrature<dim> &q,\n+                 const unsigned int     n_original_q_points)\n+{\n+  initialize (update_flags, q, n_original_q_points);\n+\n+  if (dim > 1)\n+    {\n+      if (this->update_each & update_boundary_forms)\n+        {\n+          aux.resize (dim-1, std::vector<Tensor<1,spacedim> > (n_original_q_points));\n+\n+          // Compute tangentials to the\n+          // unit cell.\n+          const unsigned int nfaces = GeometryInfo<dim>::faces_per_cell;\n+          unit_tangentials.resize (nfaces*(dim-1),\n+                                   std::vector<Tensor<1,dim> > (n_original_q_points));\n+          if (dim==2)\n+            {\n+              // ensure a counterclockwise\n+              // orientation of tangentials\n+              static const int tangential_orientation[4]= {-1,1,1,-1};\n+              for (unsigned int i=0; i<nfaces; ++i)\n+                {\n+                  Tensor<1,dim> tang;\n+                  tang[1-i/2]=tangential_orientation[i];\n+                  std::fill (unit_tangentials[i].begin(),\n+                             unit_tangentials[i].end(), tang);\n+                }\n+            }\n+          else if (dim==3)\n+            {\n+              for (unsigned int i=0; i<nfaces; ++i)\n+                {\n+                  Tensor<1,dim> tang1, tang2;\n+\n+                  const unsigned int nd=\n+                    GeometryInfo<dim>::unit_normal_direction[i];\n+\n+                  // first tangential\n+                  // vector in direction\n+                  // of the (nd+1)%3 axis\n+                  // and inverted in case\n+                  // of unit inward normal\n+                  tang1[(nd+1)%dim]=GeometryInfo<dim>::unit_normal_orientation[i];\n+                  // second tangential\n+                  // vector in direction\n+                  // of the (nd+2)%3 axis\n+                  tang2[(nd+2)%dim]=1.;\n+\n+                  // same unit tangents\n+                  // for all quadrature\n+                  // points on this face\n+                  std::fill (unit_tangentials[i].begin(),\n+                             unit_tangentials[i].end(), tang1);\n+                  std::fill (unit_tangentials[nfaces+i].begin(),\n+                             unit_tangentials[nfaces+i].end(), tang2);\n+                }\n+            }\n+        }\n+    }\n+}\n+\n+\n+template<int dim, int spacedim>\n+MappingManifold<dim,spacedim>::MappingManifold ()\n+{}\n+\n+\n+\n+template<int dim, int spacedim>\n+MappingManifold<dim,spacedim>::MappingManifold (const MappingManifold<dim,spacedim> &mapping)\n+{}\n+\n+\n+\n+\n+template<int dim, int spacedim>\n+Mapping<dim,spacedim> *\n+MappingManifold<dim,spacedim>::clone () const\n+{\n+  return new MappingManifold<dim,spacedim>(*this);\n+}\n+\n+\n+template<int dim, int spacedim>\n+Point<dim>\n+MappingManifold<dim,spacedim>::\n+transform_real_to_unit_cell (const typename Triangulation<dim,spacedim>::cell_iterator &cell,\n+                             const Point<spacedim> &p) const\n+{\n+  Assert(false, ExcNotImplemented());\n+  return Point<dim>();\n+}\n+\n+template<int dim, int spacedim>\n+Point<spacedim>\n+MappingManifold<dim,spacedim>::\n+transform_unit_to_real_cell (const typename Triangulation<dim,spacedim>::cell_iterator &cell,\n+                             const Point<dim> &p) const\n+{\n+  std::vector<Point<spacedim> > vertices;\n+  std::vector<double> weights;\n+  for (unsigned int v=0; v<GeometryInfo<dim>::vertices_per_cell; ++v)\n+    {\n+      vertices.push_back(cell->vertex(v));\n+      weights.push_back(GeometryInfo<dim>::d_linear_shape_function(p,v));\n+    }\n+  return cell->get_manifold().get_new_point(Quadrature<spacedim>(vertices, weights));\n+}\n+\n+\n+// In the code below, GCC tries to instantiate MappingManifold<3,4> when\n+// seeing which of the overloaded versions of\n+// do_transform_real_to_unit_cell_internal() to call. This leads to bad\n+// error messages and, generally, nothing very good. Avoid this by ensuring\n+// that this class exists, but does not have an inner InternalData\n+// type, thereby ruling out the codim-1 version of the function\n+// below when doing overload resolution.\n+template <>\n+class MappingManifold<3,4>\n+{};\n+\n+\n+template<int dim, int spacedim>\n+UpdateFlags\n+MappingManifold<dim,spacedim>::requires_update_flags (const UpdateFlags in) const\n+{\n+  // add flags if the respective quantities are necessary to compute\n+  // what we need. note that some flags appear in both the conditions\n+  // and in subsequent set operations. this leads to some circular\n+  // logic. the only way to treat this is to iterate. since there are\n+  // 5 if-clauses in the loop, it will take at most 5 iterations to\n+  // converge. do them:\n+  UpdateFlags out = in;\n+  for (unsigned int i=0; i<5; ++i)\n+    {\n+      // The following is a little incorrect:\n+      // If not applied on a face,\n+      // update_boundary_forms does not\n+      // make sense. On the other hand,\n+      // it is necessary on a\n+      // face. Currently,\n+      // update_boundary_forms is simply\n+      // ignored for the interior of a\n+      // cell.\n+      if (out & (update_JxW_values\n+                 | update_normal_vectors))\n+        out |= update_boundary_forms;\n+\n+      if (out & (update_covariant_transformation\n+                 | update_JxW_values\n+                 | update_jacobians\n+                 | update_jacobian_grads\n+                 | update_boundary_forms\n+                 | update_normal_vectors))\n+        out |= update_contravariant_transformation;\n+\n+      if (out & (update_inverse_jacobians\n+                 | update_jacobian_pushed_forward_grads\n+                 | update_jacobian_pushed_forward_2nd_derivatives\n+                 | update_jacobian_pushed_forward_3rd_derivatives) )\n+        out |= update_covariant_transformation;\n+\n+      // The contravariant transformation used in the Piola\n+      // transformation, which requires the determinant of the Jacobi\n+      // matrix of the transformation.  Because we have no way of\n+      // knowing here whether the finite elements wants to use the\n+      // contravariant of the Piola transforms, we add the JxW values\n+      // to the list of flags to be updated for each cell.\n+      if (out & update_contravariant_transformation)\n+        out |= update_JxW_values;\n+\n+      if (out & update_normal_vectors)\n+        out |= update_JxW_values;\n+    }\n+\n+  // Now throw an exception if we stumble upon something that was not\n+  // implemented yet\n+  Assert(!(out & (\n+             update_jacobian_grads |\n+             update_jacobian_pushed_forward_grads |\n+             update_jacobian_pushed_forward_2nd_derivatives |\n+             update_jacobian_pushed_forward_3rd_derivatives\n+           )), ExcNotImplemented());\n+\n+  return out;\n+}\n+\n+\n+\n+template<int dim, int spacedim>\n+typename MappingManifold<dim,spacedim>::InternalData *\n+MappingManifold<dim,spacedim>::get_data (const UpdateFlags update_flags,\n+                                         const Quadrature<dim> &q) const\n+{\n+  InternalData *data = new InternalData();\n+  data->initialize (this->requires_update_flags(update_flags), q, q.size());\n+\n+  return data;\n+}\n+\n+\n+\n+template<int dim, int spacedim>\n+typename MappingManifold<dim,spacedim>::InternalData *\n+MappingManifold<dim,spacedim>::get_face_data (const UpdateFlags        update_flags,\n+                                              const Quadrature<dim-1> &quadrature) const\n+{\n+  InternalData *data = new InternalData();\n+  data->initialize_face (this->requires_update_flags(update_flags),\n+                         QProjector<dim>::project_to_all_faces(quadrature),\n+                         quadrature.size());\n+\n+  return data;\n+}\n+\n+\n+\n+template<int dim, int spacedim>\n+typename MappingManifold<dim,spacedim>::InternalData *\n+MappingManifold<dim,spacedim>::get_subface_data (const UpdateFlags update_flags,\n+                                                 const Quadrature<dim-1>& quadrature) const\n+{\n+  InternalData *data = new InternalData();\n+  data->initialize_face (this->requires_update_flags(update_flags),\n+                         QProjector<dim>::project_to_all_subfaces(quadrature),\n+                         quadrature.size());\n+\n+  return data;\n+}\n+\n+\n+\n+namespace internal\n+{\n+  namespace\n+  {\n+    /**\n+     * Some specialization for face Manifolds. In one dimension, there\n+     * are no Manifolds associated to faces. The mapping argument is\n+     * only used to help the compiler infer dim and spacedim.\n+     */\n+    template<int spacedim>\n+    const dealii::Manifold<1, spacedim> &\n+    get_face_manifold(const MappingManifold<1,spacedim> &,\n+                      const typename dealii::Triangulation<1,spacedim>::cell_iterator &cell,\n+                      const unsigned int &)\n+    {\n+      return cell->get_manifold();\n+    }\n+\n+    /**\n+     * Some specialization for face Manifolds. The mapping argument is\n+     * only used to help the compiler infer dim and spacedim.\n+     */\n+    template<int dim, int spacedim>\n+    const dealii::Manifold<dim,spacedim> &\n+    get_face_manifold(const MappingManifold<dim,spacedim> &,\n+                      const typename dealii::Triangulation<dim,spacedim>::cell_iterator &cell,\n+                      const unsigned int face_no)\n+    {\n+      return cell->face(face_no)->get_manifold();\n+    }\n+\n+    /**\n+     * Compute the locations of quadrature points on the object described by\n+     * the first argument (and the cell for which the mapping support points\n+     * have already been set), but only if the update_flags of the @p data\n+     * argument indicate so.\n+     */\n+    template <int dim, int spacedim>\n+    void\n+    maybe_compute_q_points (const typename QProjector<dim>::DataSetDescriptor                 data_set,\n+                            const typename dealii::MappingManifold<dim,spacedim>::InternalData      &data,\n+                            std::vector<Point<spacedim> >                                     &quadrature_points)\n+    {\n+      const UpdateFlags update_flags = data.update_each;\n+\n+      AssertDimension(data.vertices.size(), GeometryInfo<dim>::vertices_per_cell);\n+\n+      if (update_flags & update_quadrature_points)\n+        {\n+          for (unsigned int point=0; point<quadrature_points.size(); ++point)\n+            {\n+              quadrature_points[point] = data.manifold->\n+                                         get_new_point(Quadrature<spacedim>(data.vertices,\n+                                                       data.cell_manifold_quadrature_weights[point+data_set]));\n+            }\n+        }\n+    }\n+\n+\n+    /**\n+     * Update the co- and contravariant matrices as well as their determinant, for the cell\n+     * described stored in the data object, but only if the update_flags of the @p data\n+     * argument indicate so.\n+     */\n+    template <int dim, int spacedim>\n+    void\n+    maybe_update_Jacobians (const typename dealii::QProjector<dim>::DataSetDescriptor          data_set,\n+                            const typename dealii::MappingManifold<dim,spacedim>::InternalData      &data)\n+    {\n+      const UpdateFlags update_flags = data.update_each;\n+\n+      if (update_flags & update_contravariant_transformation)\n+        {\n+          const unsigned int n_q_points = data.contravariant.size();\n+\n+          std::fill(data.contravariant.begin(), data.contravariant.end(),\n+                    DerivativeForm<1,dim,spacedim>());\n+\n+          // Cache of weights used to compute points on the reference cell\n+          std::vector<double> weights(GeometryInfo<dim>::vertices_per_cell);\n+\n+          AssertDimension(GeometryInfo<dim>::vertices_per_cell,\n+                          data.vertices.size());\n+          for (unsigned int point=0; point<n_q_points; ++point)\n+            {\n+              // Start by figuring out how to compute the direction in\n+              // the reference space:\n+              const Point<dim> &p = data.quad.point(point+data_set);\n+\n+              // And get its image on the manifold:\n+              const Point<spacedim> P = data.manifold->\n+                                        get_new_point(Quadrature<spacedim>(data.vertices,\n+                                                      data.cell_manifold_quadrature_weights[point+data_set]));\n+\n+              // Always get the maximum length from the point to the\n+              // boundary of the reference element, to compute the\n+              // tangent vectors from the Manifold object\n+              for (unsigned int i=0; i<dim; ++i)\n+                {\n+                  Point<dim> ei = Point<dim>::unit_vector(i);\n+                  double ai = ei*p;","path":"source/fe/mapping_manifold.cc","position":431,"original_position":431,"commit_id":"d009d5b9b3d19435ac523c42baf79e58f90b369e","original_commit_id":"d009d5b9b3d19435ac523c42baf79e58f90b369e","user":{"login":"bangerth","id":7504421,"avatar_url":"https://avatars.githubusercontent.com/u/7504421?v=3","gravatar_id":"","url":"https://api.github.com/users/bangerth","html_url":"https://github.com/bangerth","followers_url":"https://api.github.com/users/bangerth/followers","following_url":"https://api.github.com/users/bangerth/following{/other_user}","gists_url":"https://api.github.com/users/bangerth/gists{/gist_id}","starred_url":"https://api.github.com/users/bangerth/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bangerth/subscriptions","organizations_url":"https://api.github.com/users/bangerth/orgs","repos_url":"https://api.github.com/users/bangerth/repos","events_url":"https://api.github.com/users/bangerth/events{/privacy}","received_events_url":"https://api.github.com/users/bangerth/received_events","type":"User","site_admin":false},"body":"make it `const`.","created_at":"2016-03-28T15:25:21Z","updated_at":"2016-03-28T15:25:21Z","html_url":"https://github.com/dealii/dealii/pull/2272#discussion_r57583766","pull_request_url":"https://api.github.com/repos/dealii/dealii/pulls/2272","_links":{"self":{"href":"https://api.github.com/repos/dealii/dealii/pulls/comments/57583766"},"html":{"href":"https://github.com/dealii/dealii/pull/2272#discussion_r57583766"},"pull_request":{"href":"https://api.github.com/repos/dealii/dealii/pulls/2272"}}},"pull_request":{"url":"https://api.github.com/repos/dealii/dealii/pulls/2272","id":61098914,"html_url":"https://github.com/dealii/dealii/pull/2272","diff_url":"https://github.com/dealii/dealii/pull/2272.diff","patch_url":"https://github.com/dealii/dealii/pull/2272.patch","issue_url":"https://api.github.com/repos/dealii/dealii/issues/2272","number":2272,"state":"open","locked":false,"title":"First working version of MappingManifold","user":{"login":"luca-heltai","id":2919756,"avatar_url":"https://avatars.githubusercontent.com/u/2919756?v=3","gravatar_id":"","url":"https://api.github.com/users/luca-heltai","html_url":"https://github.com/luca-heltai","followers_url":"https://api.github.com/users/luca-heltai/followers","following_url":"https://api.github.com/users/luca-heltai/following{/other_user}","gists_url":"https://api.github.com/users/luca-heltai/gists{/gist_id}","starred_url":"https://api.github.com/users/luca-heltai/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/luca-heltai/subscriptions","organizations_url":"https://api.github.com/users/luca-heltai/orgs","repos_url":"https://api.github.com/users/luca-heltai/repos","events_url":"https://api.github.com/users/luca-heltai/events{/privacy}","received_events_url":"https://api.github.com/users/luca-heltai/received_events","type":"User","site_admin":false},"body":"Working PR on `MappingManifold`. \r\n\r\n- [x] Unit to real\r\n- [x] Quadrature points\r\n- [x] Jacobians\r\n- [x] Compute fill\r\n- [x] fill_fe_face_values\r\n- [x] Use face manifold when computing face fills\r\n- [x] JxW values (check with some tests)\r\n- [x] Simple example program, using MappingManifold 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