Merge branch 'pyramid13'

Whew, had to fix a number of merge conflicts caused by the whitespace
changes by hand in order to merge this old branch.  If anyone else is
facing the same issue, please let me know and I can try and help you
out.

Conflicts:
	include/enums/enum_elem_type.h
	include/libmesh/Makefile.am
	src/fe/fe_abstract.C
	src/fe/fe_interface.C
	src/fe/fe_l2_lagrange.C
	src/fe/fe_lagrange.C
	src/fe/fe_lagrange_shape_3D.C
	src/fe/fe_monomial.C
	src/fe/fe_xyz.C
	src/geom/elem.C
	src/mesh/exodusII_io_helper.C
	src/mesh/mesh_generation.C
	src/utils/string_to_enum.C

include/Makefile.in

@@ -600,6 +600,7 @@ include_HEADERS = \
         geom/cell_prism18.h \
         geom/cell_prism6.h \
         geom/cell_pyramid.h \
+        geom/cell_pyramid13.h \
         geom/cell_pyramid14.h \
         geom/cell_pyramid5.h \
         geom/cell_tet.h \

include/enums/enum_elem_type.h

@@ -50,25 +50,26 @@ enum ElemType {EDGE2=0,    // 0
                PRISM18,    // 15
 
                PYRAMID5,   // 16
-               PYRAMID14,  // 17
+               PYRAMID13,  // 17
+               PYRAMID14,  // 18
 
-               INFEDGE2,   // 18
+               INFEDGE2,   // 19
 
-               INFQUAD4,   // 19
-               INFQUAD6,   // 20
+               INFQUAD4,   // 20
+               INFQUAD6,   // 21
 
-               INFHEX8,    // 21
-               INFHEX16,   // 22
-               INFHEX18,   // 23
+               INFHEX8,    // 22
+               INFHEX16,   // 23
+               INFHEX18,   // 24
 
-               INFPRISM6,  // 24
-               INFPRISM12, // 25
+               INFPRISM6,  // 25
+               INFPRISM12, // 26
 
-               NODEELEM,   // 26
+               NODEELEM,   // 27
 
-               REMOTEELEM,   // 27
+               REMOTEELEM,   // 28
 
-               INVALID_ELEM};  // 28 - should always be last
+               INVALID_ELEM};  // 29 - should always be last
 }
 
 #endif // LIBMESH_ENUM_ELEM_TYPE_H

include/geom/cell_pyramid13.h

@@ -0,0 +1,214 @@
+// The libMesh Finite Element Library.
+// Copyright (C) 2002-2012 Benjamin S. Kirk, John W. Peterson, Roy H. Stogner
+
+// This library is free software; you can 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.
+
+// This library is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+// Lesser General Public License for more details.
+
+// You should have received a copy of the GNU Lesser General Public
+// License along with this library; if not, write to the Free Software
+// Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+
+
+
+#ifndef LIBMESH_CELL_PYRAMID13_H
+#define LIBMESH_CELL_PYRAMID13_H
+
+// Local includes
+#include "libmesh/cell_pyramid.h"
+
+// C++ includes
+#include <cstddef>
+
+namespace libMesh
+{
+
+
+
+
+/**
+ * The \p Pyramid13 is an element in 3D composed of 13 nodes, designed
+ * to interface with a QUAD8 element on the base and a TRI6 element on
+ * each of the triangular faces.  Cubit will generate hybrid meshes
+ * with linear pyramids, but as of version 14 will not export
+ * quadratic pyramids.  Paraview should support 13-node pyramids...
+ *
+ * The node numbering for the pyramid13 is given below:
+   \verbatim
+   PYRAMID13:
+                       o 4
+                     //|\
+                    // | \
+                   //  |  \
+                  //   |   \
+              12 o/    |    o 11
+                //     |     \
+               /o 9    o 10   \
+              //       |       \
+             //        |        \
+          3 o/.......o.|........o 2
+           ./       7  |       /
+          ./           |      /
+         ./            |     /
+        ./             |    /
+     8 o/              |   o 6
+      ./               |  /
+     ./                | /
+    ./                 |/
+    o--------o---------o
+    0        5         1
+
+   \endverbatim
+ */
+
+// ------------------------------------------------------------
+// Pyramid class definition
+class Pyramid13 : public Pyramid
+{
+public:
+
+  /**
+   * Constructor.  By default this element has no parent.
+   */
+  explicit
+  Pyramid13  (Elem* p=NULL);
+
+  /**
+   * @returns 13.
+   */
+  virtual unsigned int n_nodes() const { return 13; }
+
+  /**
+   * @returns \p PRYAMID13
+   */
+  ElemType type () const { return PYRAMID13; }
+
+  /**
+   * FIXME: we don't yet have a refinement pattern for pyramids...
+   * @returns 1
+   */
+  unsigned int n_sub_elem() const { return 1; }
+
+  /**
+   * @returns true iff the specified (local) node number is a vertex.
+   */
+  virtual bool is_vertex(const unsigned int i) const;
+
+  /**
+   * @returns true iff the specified (local) node number is an edge.
+   */
+  virtual bool is_edge(const unsigned int i) const;
+
+  /**
+   * @returns true iff the specified (local) node number is a face.
+   */
+  virtual bool is_face(const unsigned int i) const;
+
+  /*
+   * @returns true iff the specified (local) node number is on the
+   * specified side
+   */
+  virtual bool is_node_on_side(const unsigned int n,
+                               const unsigned int s) const;
+
+  /*
+   * @returns true iff the specified (local) node number is on the
+   * specified edge
+   */
+  virtual bool is_node_on_edge(const unsigned int n,
+                               const unsigned int e) const;
+
+  /*
+   * @returns true iff the element map is definitely affine within
+   * numerical tolerances
+   */
+  virtual bool has_affine_map () const;
+
+  /**
+   * @returns SECOND
+   */
+  Order default_order() const { return SECOND; }
+
+  /**
+   * Builds a \p QUAD8 or \p TRI6 coincident with face i.
+   * The \p AutoPtr<Elem> handles the memory aspect.
+   */
+  AutoPtr<Elem> build_side (const unsigned int i,
+                            bool proxy) const;
+
+  /**
+   * Builds a \p EDGE3 coincident with edge i.
+   * The \p AutoPtr<Elem> handles the memory aspect.
+   */
+  AutoPtr<Elem> build_edge (const unsigned int i) const;
+
+  virtual void connectivity(const unsigned int sc,
+                            const IOPackage iop,
+                            std::vector<dof_id_type>& conn) const;
+
+  /**
+   * @returns 2 for all edge nodes
+   */
+  virtual unsigned int n_second_order_adjacent_vertices (const unsigned int n) const;
+
+  /**
+   * @returns the element-local number of the  \f$ v^{th} \f$ vertex
+   * that defines the \f$ n^{th} \f$ second-order node.
+   */
+  virtual unsigned short int second_order_adjacent_vertex (const unsigned int n,
+                                                           const unsigned int v) const;
+
+  /**
+   * This maps the \f$ j^{th} \f$ node of the \f$ i^{th} \f$ side to
+   * element node numbers.
+   */
+  static const unsigned int side_nodes_map[5][8];
+
+  /**
+   * This maps the \f$ j^{th} \f$ node of the \f$ i^{th} \f$ edge to
+   * element node numbers.
+   */
+  static const unsigned int edge_nodes_map[8][3];
+
+protected:
+
+  /**
+   * Data for links to nodes
+   */
+  Node* _nodelinks_data[13];
+
+
+
+#ifdef LIBMESH_ENABLE_AMR
+
+  /**
+   * Matrix used to create the elements children.
+   */
+  float embedding_matrix (const unsigned int,
+                          const unsigned int,
+                          const unsigned int) const
+  { libmesh_error(); return 0.; }
+
+#endif
+};
+
+
+
+// ------------------------------------------------------------
+// Pyramid13 class member functions
+inline
+Pyramid13::Pyramid13(Elem* p) :
+  Pyramid(Pyramid13::n_nodes(), p, _nodelinks_data)
+{
+}
+
+} // namespace libMesh
+
+
+#endif // LIBMESH_CELL_PYRAMID13_H

include/include_HEADERS

@@ -111,6 +111,7 @@ include_HEADERS =  \
         geom/cell_prism18.h \
         geom/cell_prism6.h \
         geom/cell_pyramid.h \
+        geom/cell_pyramid13.h \
         geom/cell_pyramid14.h \
         geom/cell_pyramid5.h \
         geom/cell_tet.h \