file clean up, broke something in gmsh and one nek test

library/MeshUtils/MeshElements/Composite.h

@@ -38,7 +38,7 @@
 
 namespace Nektar
 {
-namespace Utilities
+namespace MeshUtils
 {
     /**
      * @brief A composite is a collection of elements.

library/MeshUtils/MeshElements/Edge.h

@@ -38,7 +38,7 @@
 
 namespace Nektar
 {
-namespace Utilities
+namespace MeshUtils
 {
     /**
      * @brief Represents an edge which joins two points.

library/MeshUtils/MeshElements/Element.h

@@ -38,7 +38,7 @@
 
 namespace Nektar
 {
-namespace Utilities
+namespace MeshUtils
 {
     /**
      * @brief Basic information about an element.

library/MeshUtils/MeshElements/Face.h

@@ -38,7 +38,7 @@
 
 namespace Nektar
 {
-namespace Utilities
+namespace MeshUtils
 {
     /**
      * @brief Represents a face comprised of three or more edges.

library/MeshUtils/MeshElements/Hexahedron.h

@@ -38,7 +38,7 @@
 
 namespace Nektar
 {
-namespace Utilities
+namespace MeshUtils
 {
     /**
      * @brief A 3-dimensional six-faced element.

library/MeshUtils/MeshElements/Line.h

@@ -38,7 +38,7 @@
 
 namespace Nektar
 {
-namespace Utilities
+namespace MeshUtils
 {
     /**
      * @brief A 1-dimensional line between two vertex nodes.

library/MeshUtils/MeshElements/Mesh.h

@@ -38,7 +38,7 @@
 
 namespace Nektar
 {
-namespace Utilities
+namespace MeshUtils
 {
     /**
      * Enumeration of condition types (Dirichlet, Neumann, etc).

library/MeshUtils/MeshElements/MeshElements.cpp

@@ -33,8 +33,6 @@
 //
 ////////////////////////////////////////////////////////////////////////////////
 
-#include <iostream>
-#include <vector>
 #include <loki/Singleton.h>
 
 #include <StdRegions/StdNodalTriExp.h>
@@ -55,7 +53,7 @@ using namespace std;
 
 namespace Nektar
 {
-    namespace Utilities
+    namespace MeshUtils
     {
         ElementFactory& GetElementFactory()
         {

library/MeshUtils/MeshElements/Node.h

@@ -38,7 +38,7 @@
 
 namespace Nektar
 {
-namespace Utilities
+namespace MeshUtils
 {
     // Forwards declaration for Element class.
     class Element;

library/MeshUtils/MeshElements/Point.h

@@ -38,7 +38,7 @@
 
 namespace Nektar
 {
-namespace Utilities
+namespace MeshUtils
 {
     /**
      * @brief A 0-dimensional vertex.

library/MeshUtils/MeshElements/Prism.h

@@ -38,7 +38,7 @@
 
 namespace Nektar
 {
-namespace Utilities
+namespace MeshUtils
 {
     /**
      * @brief A 3-dimensional five-faced element (2 triangles, 3

library/MeshUtils/MeshElements/Pyramid.h

@@ -38,7 +38,7 @@
 
 namespace Nektar
 {
-namespace Utilities
+namespace MeshUtils
 {
     /**
      * @brief A 3-dimensional square-based pyramidic element

library/MeshUtils/MeshElements/Quadrilateral.h

@@ -38,7 +38,7 @@
 
 namespace Nektar
 {
-namespace Utilities
+namespace MeshUtils
 {
     /**
      * @brief A 2-dimensional four-sided element.

library/MeshUtils/MeshElements/Tetrahedron.h

@@ -38,7 +38,7 @@
 
 namespace Nektar
 {
-namespace Utilities
+namespace MeshUtils
 {
     /**
      * @brief A 3-dimensional four-faced element.

library/MeshUtils/MeshElements/Triangle.h

@@ -38,7 +38,7 @@
 
 namespace Nektar
 {
-namespace Utilities
+namespace MeshUtils
 {
     /**
      * @brief A lightweight struct for dealing with high-order triangle

utilities/MeshConvert/CMakeLists.txt

@@ -7,7 +7,7 @@ SET(MeshConvertHeaders
     InputModules/InputSwan.h
     InputModules/InputStarTec.h
     Module.h
-    OutputModules/OutputGmsh.h
+#    OutputModules/OutputGmsh.h
     OutputModules/OutputNekpp.h
     ProcessModules/ProcessBL.h
     ProcessModules/ProcessCyl.h
@@ -31,7 +31,7 @@ SET(MeshConvertSources
     InputModules/InputStarTec.cpp
     MeshConvert.cpp
     Module.cpp
-    OutputModules/OutputGmsh.cpp
+#    OutputModules/OutputGmsh.cpp
     OutputModules/OutputNekpp.cpp
     ProcessModules/ProcessBL.cpp
     ProcessModules/ProcessCyl.cpp

utilities/MeshConvert/InputModules/InputCAD.cpp

@@ -33,9 +33,7 @@
 //
 ////////////////////////////////////////////////////////////////////////////////
 
-#include <string>
-
-
+#include <MeshUtils/MeshElements/MeshElements.h>
 
 #include <MeshUtils/CADSystem/CADSystem.h>
 #include <MeshUtils/Octree/Octree.h>
@@ -45,12 +43,15 @@
 
 #include <LibUtilities/BasicUtils/SharedArray.hpp>
 
-#include <MeshUtils/MeshElements/MeshElements.h>
 #include "InputCAD.h"
 
 using namespace std;
-namespace Nektar{
-namespace Utilities{
+using namespace Nektar::MeshUtils;
+
+namespace Nektar
+{
+namespace Utilities
+{
 
 ModuleKey InputCAD::className =
 GetModuleFactory().RegisterCreatorFunction(

utilities/MeshConvert/InputModules/InputCAD.h

@@ -40,23 +40,25 @@
 
 namespace Nektar
 {
-    namespace Utilities
-    {
-        class InputCAD : public InputModule
-        {
-        public:
-            InputCAD(MeshSharedPtr m);
-            virtual ~InputCAD();
-            virtual void Process();
+namespace Utilities
+{
+
+class InputCAD : public InputModule
+{
+public:
+    InputCAD(MeshSharedPtr m);
+    virtual ~InputCAD();
+    virtual void Process();
 
-            /// Creates an instance of this class
-            static ModuleSharedPtr create(MeshSharedPtr m) {
-                return MemoryManager<InputCAD>::AllocateSharedPtr(m);
-            }
-            /// %ModuleKey for class.
-            static ModuleKey className;
-        };
+    /// Creates an instance of this class
+    static ModuleSharedPtr create(MeshSharedPtr m) {
+        return MemoryManager<InputCAD>::AllocateSharedPtr(m);
     }
+    /// %ModuleKey for class.
+    static ModuleKey className;
+};
+
+}
 }
 
 #endif

utilities/MeshConvert/InputModules/InputGmsh.h

@@ -33,48 +33,50 @@
 //
 ////////////////////////////////////////////////////////////////////////////////
 
-#ifndef UTILITIES_PREPROCESSING_MESHCONVERT_INPUTGMSH
-#define UTILITIES_PREPROCESSING_MESHCONVERT_INPUTGMSH
+#ifndef UTILITIES_MESHCONVERT_INPUTGMSH
+#define UTILITIES_MESHCONVERT_INPUTGMSH
 
 #include "../Module.h"
 
 namespace Nektar
 {
-    namespace Utilities
-    {
-        /**
-         * Converter for Gmsh files.
-         */
-        class InputGmsh : public InputModule
-        {
-        public:
-            InputGmsh(MeshSharedPtr m);
-            virtual ~InputGmsh();
-            virtual void Process();
+namespace Utilities
+{
 
-            /// Creates an instance of this class
-            static ModuleSharedPtr create(MeshSharedPtr m) {
-                return MemoryManager<InputGmsh>::AllocateSharedPtr(m);
-            }
-            /// %ModuleKey for class.
-            static ModuleKey className;
-            static std::map<unsigned int, ElmtConfig> GenElmMap();
-            
-            /**
-             * Element map; takes a msh id to an %ElmtConfig object.
-             */
-            static std::map<unsigned int, ElmtConfig> elmMap;
+/**
+ * Converter for Gmsh files.
+ */
+class InputGmsh : public InputModule
+{
+public:
+    InputGmsh(MeshSharedPtr m);
+    virtual ~InputGmsh();
+    virtual void Process();
 
-        private:
-            int GetNnodes(unsigned int InputGmshEntity);
-            vector<int> CreateReordering(unsigned int InputGmshEntity);
-            vector<int> TriReordering(ElmtConfig conf);
-            vector<int> QuadReordering(ElmtConfig conf);
-            vector<int> HexReordering(ElmtConfig conf);
-            vector<int> PrismReordering(ElmtConfig conf);
-            vector<int> TetReordering(ElmtConfig conf);
-        };
+    /// Creates an instance of this class
+    static ModuleSharedPtr create(MeshSharedPtr m) {
+        return MemoryManager<InputGmsh>::AllocateSharedPtr(m);
     }
+    /// %ModuleKey for class.
+    static ModuleKey className;
+    static std::map<unsigned int, ElmtConfig> GenElmMap();
+
+    /**
+     * Element map; takes a msh id to an %ElmtConfig object.
+     */
+    static std::map<unsigned int, ElmtConfig> elmMap;
+
+private:
+    int GetNnodes(unsigned int InputGmshEntity);
+    vector<int> CreateReordering(unsigned int InputGmshEntity);
+    vector<int> TriReordering(ElmtConfig conf);
+    vector<int> QuadReordering(ElmtConfig conf);
+    vector<int> HexReordering(ElmtConfig conf);
+    vector<int> PrismReordering(ElmtConfig conf);
+    vector<int> TetReordering(ElmtConfig conf);
+};
+
+}
 }
 
 #endif

utilities/MeshConvert/InputModules/InputNek.h

@@ -33,87 +33,89 @@
 //
 ////////////////////////////////////////////////////////////////////////////////
 
-#ifndef UTILITIES_PREPROCESSING_MESHCONVERT_INPUTNEK
-#define UTILITIES_PREPROCESSING_MESHCONVERT_INPUTNEK
+#ifndef UTILITIES_MESHCONVERT_INPUTNEK
+#define UTILITIES_MESHCONVERT_INPUTNEK
 
 #include "../Module.h"
 
 namespace Nektar
 {
-    namespace Utilities
+namespace Utilities
+{
+
+enum NekCurve
+{
+    eFile,
+    eRecon
+};
+
+typedef HOTriangle<NodeSharedPtr> HOSurf;
+typedef boost::shared_ptr<HOSurf> HOSurfSharedPtr;
+
+/**
+ * Hash class for high-order surfaces.
+ */
+struct HOSurfHash : std::unary_function<HOSurfSharedPtr, std::size_t>
+{
+    /**
+     * Calculate hash of a given high-order surface p by taking
+     * successive hashes of the vertex IDs.
+     */
+    std::size_t operator()(HOSurfSharedPtr const& p) const
     {
-        enum NekCurve
+        std::size_t seed = 0;
+        std::vector<int> ids = p->vertId;
+        std::sort(ids.begin(), ids.end());
+        for (int i = 0; i < ids.size(); ++i)
         {
-            eFile,
-            eRecon
-        };
+            boost::hash_combine(seed, ids[i]);
+        }
+        return seed;
+    }
+};
 
-        typedef HOTriangle<NodeSharedPtr> HOSurf;
-        typedef boost::shared_ptr<HOSurf> HOSurfSharedPtr;
+bool operator==(HOSurfSharedPtr const &p1, HOSurfSharedPtr const &p2);
 
-        /**
-         * Hash class for high-order surfaces.
-         */
-        struct HOSurfHash : std::unary_function<HOSurfSharedPtr, std::size_t>
-        {
-            /** 
-             * Calculate hash of a given high-order surface p by taking
-             * successive hashes of the vertex IDs.
-             */
-            std::size_t operator()(HOSurfSharedPtr const& p) const
-            {
-                std::size_t seed = 0;
-                std::vector<int> ids = p->vertId;
-                std::sort(ids.begin(), ids.end());
-                for (int i = 0; i < ids.size(); ++i)
-                {
-                    boost::hash_combine(seed, ids[i]);
-                }
-                return seed;
-            }
-        };
-
-        bool operator==(HOSurfSharedPtr const &p1, HOSurfSharedPtr const &p2);
-        
-        typedef boost::unordered_set<HOSurfSharedPtr, HOSurfHash> HOSurfSet;
-
-        /**
-         * Converter class for Nektar session files.
-         */
-        class InputNek : public InputModule
-        {
-        public:
-            InputNek(MeshSharedPtr p_m);
-            virtual ~InputNek();
-            virtual void Process();
-            
-            /// Creates an instance of this class.
-            static ModuleSharedPtr create(MeshSharedPtr m) {
-                return MemoryManager<InputNek>::AllocateSharedPtr(m);
-            }
-            /// %ModuleKey for class.
-            static ModuleKey className;
-            
-        private:
-            void LoadHOSurfaces();
-            int  GetNnodes     (LibUtilities::ShapeType elType);
-
-            /**
-             * Maps a curve tag to a filename containing surface information.
-             */
-            std::map<string, pair<NekCurve, string> > curveTags;
-
-            /**
-             * Maps a curve tag to the high-order surface data for that tag.
-             */
-            std::map<string, HOSurfSet> hoData;
-
-            /**
-             * Maps ordering of hsf standard element to Nektar++ ordering.
-             */
-            std::map<int, int> hoMap;
-        };
+typedef boost::unordered_set<HOSurfSharedPtr, HOSurfHash> HOSurfSet;
+
+/**
+ * Converter class for Nektar session files.
+ */
+class InputNek : public InputModule
+{
+public:
+    InputNek(MeshSharedPtr p_m);
+    virtual ~InputNek();
+    virtual void Process();
+
+    /// Creates an instance of this class.
+    static ModuleSharedPtr create(MeshSharedPtr m) {
+        return MemoryManager<InputNek>::AllocateSharedPtr(m);
     }
+    /// %ModuleKey for class.
+    static ModuleKey className;
+
+private:
+    void LoadHOSurfaces();
+    int  GetNnodes     (LibUtilities::ShapeType elType);
+
+    /**
+     * Maps a curve tag to a filename containing surface information.
+     */
+    std::map<string, pair<NekCurve, string> > curveTags;
+
+    /**
+     * Maps a curve tag to the high-order surface data for that tag.
+     */
+    std::map<string, HOSurfSet> hoData;
+
+    /**
+     * Maps ordering of hsf standard element to Nektar++ ordering.
+     */
+    std::map<int, int> hoMap;
+};
+
+}
 }
 
 #endif

utilities/MeshConvert/InputModules/InputStar.h

@@ -37,7 +37,7 @@
 #define UTILITIES_PREPROCESSING_MESHCONVERT_INPUTSTAR
 
 #include "../Module.h"
-#include <MeshUtils/MeshElements/MeshElements.h>
+
 #include "ccmio.h"
 
 

utilities/MeshConvert/InputModules/InputStarTec.h

@@ -37,7 +37,6 @@
 #define UTILITIES_PREPROCESSING_MESHCONVERT_INPUTTEC
 
 #include "../Module.h"
-#include <MeshUtils/MeshElements/MeshElements.h>
 
 namespace Nektar
 {

utilities/MeshConvert/Module.h

@@ -36,13 +36,20 @@
 #ifndef UTILITIES_PREPROCESSING_MESHCONVERT_MODULE
 #define UTILITIES_PREPROCESSING_MESHCONVERT_MODULE
 
+#include <map>
+#include <vector>
+#include <sstream>
 #include <string>
 #include <iostream>
-#include <LibUtilities/BasicUtils/NekFactory.hpp>
+#include <fstream>
+#include <set>
 
+#include <LibUtilities/BasicUtils/NekFactory.hpp>
 
 #include <MeshUtils/MeshElements/MeshElements.h>
 
+using namespace Nektar::MeshUtils;
+
 namespace Nektar
 {
     namespace Utilities