Merge branch 'master' into feature/cardiac-electrogram

CMakeLists.txt

@@ -8,9 +8,13 @@ PROJECT(Nektar++)
 # Helps organize projects in IDEs.
 SET_PROPERTY(GLOBAL PROPERTY USE_FOLDERS ON)
 
-SET(NEKTAR_VERSION_MAJOR 3)
-SET(NEKTAR_VERSION_MINOR 2)
-SET(NEKTAR_VERSION_PATCH 0)
+# Extract the version number from the VERSION file and set in CMake
+# The format of this file must be X.X.X
+FILE(STRINGS "VERSION" NEKVER)
+STRING(REPLACE "." ";" NEKVERLIST ${NEKVER})
+LIST(GET NEKVERLIST 0 NEKTAR_VERSION_MAJOR)
+LIST(GET NEKVERLIST 1 NEKTAR_VERSION_MINOR)
+LIST(GET NEKVERLIST 2 NEKTAR_VERSION_PATCH)
 SET(NEKTAR_VERSION ${NEKTAR_VERSION_MAJOR}.${NEKTAR_VERSION_MINOR}.${NEKTAR_VERSION_PATCH})
 
 INCLUDE(CMakeExportBuildSettings)

cmake/FindFFTW.cmake

@@ -18,7 +18,7 @@ ENDIF (FFTW_LIB)
 
 IF (FFTW_FOUND)
   IF (NOT FFTW_LIB_FIND_QUIETLY)
-     MESSAGE(STATUS "Found FFTW")
+     MESSAGE(STATUS "Found FFTW: ${FFTW_LIB}")
      GET_FILENAME_COMPONENT(FFTW_PATH ${FFTW_LIB} PATH CACHE)
      SET(FFTW_INCLUDE_DIR ${FFTW_PATH}/../include CACHE FILEPATH "FFTW include directory.")
      MARK_AS_ADVANCED(FFTW_PATH)

cmake/NektarCommon.cmake

@@ -167,10 +167,10 @@ MACRO(ADD_NEKTAR_EXECUTABLE name component sources)
         ${Boost_FILESYSTEM_LIBRARY} 
         ${Boost_SYSTEM_LIBRARY}
         ${Boost_PROGRAM_OPTIONS_LIBRARY} 
-        ${Boost_ZLIB_LIBRARY} 
+        ${ZLIB_LIBRARY} 
         optimized ${TINYXML_LIB} debug ${TINYXML_LIB}
 	)
-    ADD_DEPENDENCIES(${name} boost tinyxml zlib)
+    ADD_DEPENDENCIES(${name} boost tinyxml zlib-1.2.7)
 
     IF( NEKTAR_USE_MPI )
         TARGET_LINK_LIBRARIES(${name} ${MPI_LIBRARY} ${MPI_EXTRA_LIBRARY})
@@ -221,7 +221,8 @@ MACRO(ADD_NEKTAR_LIBRARY name component type)
 
     # NIST Sparse BLAS only static, so link into Nektar libraries directly.
     TARGET_LINK_LIBRARIES( ${name} ${NIST_SPARSE_BLAS} ${METIS_LIB})
-    ADD_DEPENDENCIES(${name} spblastk0.9b modmetis-5.0.2 boost tinyxml zlib)
+    ADD_DEPENDENCIES(${name} spblastk0.9b modmetis-5.0.2 boost tinyxml
+        zlib-1.2.7)
     SET_PROPERTY(TARGET ${name} PROPERTY FOLDER ${component})
     IF (NEKTAR_USE_MPI)
         TARGET_LINK_LIBRARIES( ${name} ${GSMPI_LIBRARY} ${XXT_LIBRARY})

cmake/ThirdPartyBoost.cmake

@@ -40,10 +40,10 @@ IF (THIRDPARTY_BUILD_BOOST)
             INSTALL_COMMAND ""
             BUILD_IN_SOURCE 1
         )
-
+    
         # If building ThirdParty zlib, force zlib build before boost
         IF (THIRDPARTY_BUILD_ZLIB)
-            ADD_DEPENDENCIES(boost zlib)
+             ADD_DEPENDENCIES(boost zlib-1.2.7)
         ENDIF(THIRDPARTY_BUILD_ZLIB)
 
         # Set up CMake variables
@@ -86,8 +86,7 @@ IF (THIRDPARTY_BUILD_BOOST)
         )
     ENDIF ()
 ELSE (THIRDPARTY_BUILD_BOOST)
-    SET(Boost_DEBUG 1)
-    SET(Boost_ADDITIONAL_VERSIONS "1.51" "1.51.0" "1.50" "1.50.0" "1.49" "1.49.0" "1.48" "1.48.0" "1.47.0" "1.47" "1.46" "1.46. 1" "1.40" "1.40.0" "1.35.0" "1.35")
+    SET(Boost_DEBUG 0)
     SET(Boost_NO_BOOST_CMAKE ON)
 
     #If the user has not set BOOST_ROOT, look in a couple common places first.
@@ -96,19 +95,40 @@ ELSE (THIRDPARTY_BUILD_BOOST)
         IF (DEFINED TEST_ENV)
             SET(Boost_NO_SYSTEM_PATHS ON)
             SET(BOOST_ROOT $ENV{BOOST_HOME})
-            FIND_PACKAGE( Boost COMPONENTS thread iostreams zlib date_time
+            FIND_PACKAGE( Boost QUIET COMPONENTS thread iostreams date_time
                 filesystem system program_options regex )
         ELSE ()
             SET(BOOST_ROOT ${CMAKE_SOURCE_DIR}/ThirdParty/boost)
-            FIND_PACKAGE( Boost COMPONENTS thread iostreams zlib date_time filesystem system program_options regex)
+            FIND_PACKAGE( Boost QUIET COMPONENTS thread iostreams date_time filesystem system program_options regex)
             SET(BOOST_ROOT ${CMAKE_SOURCE_DIR}/../ThirdParty/boost)
-            FIND_PACKAGE( Boost COMPONENTS thread iostreams zlib date_time filesystem system program_options regex)
+            FIND_PACKAGE( Boost QUIET COMPONENTS thread iostreams date_time filesystem system program_options regex)
             SET(BOOST_ROOT ${CMAKE_SOURCE_DIR}/ThirdParty/dist)
-            FIND_PACKAGE( Boost COMPONENTS thread iostreams zlib date_time filesystem system program_options regex)
+            FIND_PACKAGE( Boost QUIET COMPONENTS thread iostreams date_time filesystem system program_options regex)
         ENDIF()
     ELSE()
         FIND_PACKAGE( Boost COMPONENTS thread iostreams zlib date_time filesystem system program_options regex)
     ENDIF()
+    IF (Boost_IOSTREAMS_FOUND)
+        MESSAGE(STATUS "Found Boost iostreams library: ${Boost_IOSTREAMS_LIBRARY}")
+    ENDIF ()
+    IF (Boost_THREAD_FOUND)
+        MESSAGE(STATUS "Found Boost thread library: ${Boost_THREAD_LIBRARY}")
+    ENDIF ()
+    IF (Boost_DATE_TIME_FOUND)
+        MESSAGE(STATUS "Found Boost date_time library: ${Boost_DATE_TIME_LIBRARY}")
+    ENDIF ()
+    IF (Boost_FILESYSTEM_FOUND)
+        MESSAGE(STATUS "Found Boost filesystem library: ${Boost_FILESYSTEM_LIBRARY}")
+    ENDIF ()
+    IF (Boost_SYSTEM_FOUND)
+        MESSAGE(STATUS "Found Boost system library: ${Boost_SYSTEM_LIBRARY}")
+    ENDIF ()
+    IF (Boost_PROGRAM_OPTIONS_FOUND)
+        MESSAGE(STATUS "Found Boost program_options library: ${Boost_PROGRAM_OPTIONS_LIBRARY}")
+    ENDIF ()
+    IF (Boost_REGEX_FOUND)
+        MESSAGE(STATUS "Found Boost regex library: ${Boost_REGEX_LIBRARY}")
+    ENDIF ()
 ENDIF (THIRDPARTY_BUILD_BOOST)
 
 INCLUDE_DIRECTORIES(SYSTEM ${Boost_INCLUDE_DIRS})

cmake/ThirdPartyFFTW.cmake

@@ -21,6 +21,7 @@ IF( NEKTAR_USE_FFTW )
         SET(FFTW_LIB fftw3)
         MARK_AS_ADVANCED(FFTW_LIB)
         INCLUDE_DIRECTORIES(${TPSRC}/dist/include)
+        MESSAGE(STATUS "Build FFTW: ${TPSRC}/dist/lib/lib${FFTW_LIB}.so")
     ELSE ()
         INCLUDE (FindFFTW)
         INCLUDE_DIRECTORIES(${FFTW_INCLUDE_DIR})

cmake/ThirdPartyMPI.cmake

@@ -31,6 +31,8 @@ IF( NEKTAR_USE_MPI )
         SET(XXT_LIBRARY xxt CACHE FILEPATH
             "XXT path" FORCE)
         MARK_AS_ADVANCED(XXT_LIBRARY)
+        MESSAGE(STATUS "Build GSMPI: ${TPSRC}/dist/lib/lib${GSMPI_LIBRARY}.a")
+        MESSAGE(STATUS "Build XXT: ${TPSRC}/dist/lib/lib${XXT_LIBRARY}.a")
     ELSE (THIRDPARTY_BUILD_GSMPI)
         INCLUDE (FindGSMPI)
         INCLUDE (FindXXT)

cmake/ThirdPartyMetis.cmake

@@ -16,6 +16,7 @@ IF (THIRDPARTY_BUILD_METIS)
     MARK_AS_ADVANCED(METIS_LIB)
     LINK_DIRECTORIES(${TPSRC}/dist/lib)
     INCLUDE_DIRECTORIES(${TPSRC}/dist/include)
+    MESSAGE(STATUS "Build Metis: ${TPSRC}/dist/lib/lib${METIS_LIB}.a")
 ELSE (THIRDPARTY_BUILD_METIS)
     INCLUDE (FindMetis)
 ENDIF (THIRDPARTY_BUILD_METIS)

cmake/ThirdPartyQT4.cmake

@@ -6,4 +6,7 @@ IF( NEKTAR_USE_QT4 )
     FIND_PACKAGE(Qt4 COMPONENTS QtCore QtGui REQUIRED)
     INCLUDE(${QT_USE_FILE})
     ADD_DEFINITIONS(${QT_DEFINITIONS})
+    IF (QT4_FOUND)
+        MESSAGE(STATUS "Found QT4: ${QT_INCLUDE_DIR}")
+    ENDIF(QT4_FOUND)
 ENDIF( NEKTAR_USE_QT4 )

cmake/ThirdPartySpblastk.cmake

@@ -15,6 +15,7 @@ IF (THIRDPARTY_BUILD_NIST_SPBLASTK)
         "Path to NIST Sparse BLAS." FORCE)
     MARK_AS_ADVANCED(NIST_SPARSE_BLAS)
     LINK_DIRECTORIES(${TPSRC}/dist/lib)
+    MESSAGE(STATUS "Build NIST Sparse BLAS: ${TPSRC}/dist/lib/lib${NIST_SPARSE_BLAS}.a")
 ELSE (THIRDPARTY_BUILD_NIST_SPBLASTK)
     INCLUDE(FindNistSparseBlas)
 ENDIF (THIRDPARTY_BUILD_NIST_SPBLASTK)

cmake/ThirdPartyVTK.cmake

@@ -25,9 +25,11 @@ IF( NEKTAR_USE_VTK )
         INCLUDE (${VTK_DIR}/VTKConfig.cmake)
     ELSE()
         INCLUDE (FindVTK)
-        IF (NOT VTK_FOUND)
+        IF (VTK_FOUND)
+            MESSAGE(STATUS "Found VTK: ${VTK_USE_FILE}")
+        ELSE (VTK_FOUND)
             MESSAGE(FATAL_ERROR "VTK not found")
-        ENDIF (NOT VTK_FOUND)
+        ENDIF (VTK_FOUND)
     ENDIF()
     
     INCLUDE (${VTK_USE_FILE})

cmake/ThirdPartyZlib.cmake

-OPTION(THIRDPARTY_BUILD_ZLIB "Build ZLib library" OFF)
+########################################################################
+#
+# ThirdParty configuration for Nektar++
+#
+# ZLib
+#
+########################################################################
 
+# Attempt to identify Macports libraries, if they exist. This prevents
+# cmake warnings later on.
+SET(ZLIB_ROOT /opt/local/)
+
+
+# Find a system ZLIB library
+# If not found enable the THIRDPARTY_BUILD_ZLIB option
+FIND_PACKAGE( ZLIB )
+IF (ZLIB_FOUND AND NOT ZLIB_VERSION_PATCH LESS 7 )
+    SET(ZLIB_LIBRARY ${ZLIB_LIBRARIES})
+    SET(ZLIB_LIBRARY_DEBUG ${ZLIB_LIBRARIES})
+    SET(ZLIB_LIBRARY_RELEASE ${ZLIB_LIBRARIES})
+    MESSAGE(STATUS "Found Zlib library: ${ZLIB_LIBRARY}")
+    OPTION(THIRDPARTY_BUILD_ZLIB "Build ZLib library" OFF)
+ELSE ()
+    OPTION(THIRDPARTY_BUILD_ZLIB "Build ZLib library" ON)
+ENDIF()
+
+
+# If we or the user
 IF (THIRDPARTY_BUILD_ZLIB)
+    MESSAGE(STATUS "Will build Zlib 1.2.7")
     # Build the Zlib library separately
     EXTERNALPROJECT_ADD(
-        zlib
+        zlib-1.2.7
         PREFIX ${TPSRC}
-        URL ${TPURL}/zlib-1.2.3.tar.bz2
-        URL_MD5 "dee233bf288ee795ac96a98cc2e369b6"
+        URL ${TPURL}/zlib-1.2.7.tar.gz
+        URL_MD5 "4a162e0f643232e7e278d59a0603ceb0"
         DOWNLOAD_DIR ${TPSRC}
-        CONFIGURE_COMMAND ./configure --shared --prefix=${TPSRC}/dist
-        BUILD_IN_SOURCE 1
+        CONFIGURE_COMMAND ${CMAKE_COMMAND} -DCMAKE_INSTALL_PREFIX:PATH=${TPSRC}/dist -DCMAKE_C_FLAGS:STRING=-fPIC ${TPSRC}/src/zlib-1.2.7
     )
-    SET(Boost_ZLIB_LIBRARY z)
-    SET(Boost_ZLIB_LIBRARY_DEBUG z)
-    SET(Boost_ZLIB_LIBRARY_RELEASE z)
-ELSE (THIRDPARTY_BUILD_ZLIB)
-  # Attempt to identify Macports libraries, if they exist. This prevents
-  # cmake warnings later on.
-  IF (APPLE)
-    FIND_LIBRARY(ZLIB_LIBRARY z PATHS /opt/local/lib NO_DEFAULT_PATH)
-  ENDIF()
-  
-  # Find a system ZLIB library and use that instead
-  IF (ZLIB_LIBRARY-NOTFOUND OR NOT APPLE) 
-    FIND_PACKAGE( ZLIB )
-    IF (ZLIB_FOUND)
-      SET(ZLIB_LIBRARY ${ZLIB_LIBRARIES})
-    ENDIF()
-  ENDIF()
-  
-  IF (ZLIB_LIBRARY)
-    SET(Boost_ZLIB_LIBRARY ${ZLIB_LIBRARY})
-    SET(Boost_ZLIB_LIBRARY_RELEASE ${ZLIB_LIBRARY})
-    SET(Boost_ZLIB_LIBRARY_DEBUG ${ZLIB_LIBRARY})
-  ENDIF()
+    IF (WIN32)
+        SET(ZLIB_LIBRARY zlib)
+        SET(ZLIB_LIBRARY_DEBUG zlib)
+        SET(ZLIB_LIBRARY_RELEASE zlib)
+    ELSE (WIN32)
+        SET(ZLIB_LIBRARY z)
+        SET(ZLIB_LIBRARY_DEBUG z)
+        SET(ZLIB_LIBRARY_RELEASE z)
+    ENDIF (WIN32)
 ENDIF (THIRDPARTY_BUILD_ZLIB)
 
-

library/Demos/LibUtilities/CMakeLists.txt

@@ -28,9 +28,8 @@ SET(NodalTetElecSources
 
 SET(TimeIntegrationDemoSources
 	TimeIntegrationDemo.cpp)
-   
 
-   		
+
 #ADD_NEKTAR_EXECUTABLE(Graph demos GraphSources )
 #SET_LAPACK_LINK_LIBRARIES(Graph)
 
@@ -58,3 +57,4 @@ SET_LAPACK_LINK_LIBRARIES(NodalTetElecDemo)
 
 ADD_NEKTAR_EXECUTABLE(TimeIntegrationDemo demos TimeIntegrationDemoSources)
 SET_LAPACK_LINK_LIBRARIES(TimeIntegrationDemo)
+

library/Demos/LocalRegions/CMakeLists.txt

@@ -5,7 +5,7 @@ SET(LinkLibraries
     optimized LibUtilities debug LibUtilities-g
     optimized ${Boost_THREAD_LIBRARY_RELEASE} debug ${Boost_THREAD_LIBRARY_DEBUG}
     optimized ${Boost_IOSTREAMS_LIBRARY_RELEASE} debug ${Boost_IOSTREAMS_LIBRARY_DEBUG}
-    optimized ${Boost_ZLIB_LIBRARY_RELEASE} debug ${Boost_ZLIB_LIBRARY_DEBUG}
+    optimized ${ZLIB_LIBRARY_RELEASE} debug ${ZLIB_LIBRARY_DEBUG}
     optimized ${TINYXML_LIB} debug ${TINYXML_LIB}
 )
 

library/Demos/MultiRegions/CMakeLists.txt

@@ -6,7 +6,7 @@ SET(LinkLibraries
     optimized LibUtilities debug LibUtilities-g
     optimized ${Boost_THREAD_LIBRARY_RELEASE} debug ${Boost_THREAD_LIBRARY_DEBUG}
     optimized ${Boost_IOSTREAMS_LIBRARY_RELEASE} debug ${Boost_IOSTREAMS_LIBRARY_DEBUG}
-    optimized ${Boost_ZLIB_LIBRARY_RELEASE} debug ${Boost_ZLIB_LIBRARY_DEBUG}
+    optimized ${ZLIB_LIBRARY_RELEASE} debug ${ZLIB_LIBRARY_DEBUG}
     optimized ${TINYXML_LIB} debug ${TINYXML_LIB}
     optimized sbtk    debug sbtk
 )

library/Demos/MultiRegions/ExtraDemos/CMakeLists.txt

@@ -6,7 +6,7 @@ SET(LinkLibraries
     optimized LibUtilities debug LibUtilities-g
     optimized ${Boost_THREAD_LIBRARY_RELEASE} debug ${Boost_THREAD_LIBRARY_DEBUG}
     optimized ${Boost_IOSTREAMS_LIBRARY_RELEASE} debug ${Boost_IOSTREAMS_LIBRARY_DEBUG}
-    optimized ${Boost_ZLIB_LIBRARY_RELEASE} debug ${Boost_ZLIB_LIBRARY_DEBUG}
+    optimized ${ZLIB_LIBRARY_RELEASE} debug ${ZLIB_LIBRARY_DEBUG}
     optimized ${TINYXML_LIB} debug ${TINYXML_LIB}
     optimized sbtk    debug sbtk
 )

library/LibUtilities/BasicUtils/MeshPartition.cpp

@@ -217,15 +217,28 @@ namespace Nektar
                     MeshCurved c;
                     ASSERTL0(x->Attribute("ID", &c.id),
                              "Failed to get attribute ID");
-                    ASSERTL0(x->Attribute("EDGEID", &c.edgeid),
-                             "Failed to get attribute EDGEID");
                     c.type = std::string(x->Attribute("TYPE"));
                     ASSERTL0(!c.type.empty(),
                              "Failed to get attribute TYPE");
                     ASSERTL0(x->Attribute("NUMPOINTS", &c.npoints),
                              "Failed to get attribute NUMPOINTS");
                     c.data = x->FirstChild()->ToText()->Value();
-                    m_meshCurved[c.id] = c;
+                    c.entitytype = x->Value()[0];
+                    if (c.entitytype == "E")
+                    {
+                        ASSERTL0(x->Attribute("EDGEID", &c.entityid),
+                             "Failed to get attribute EDGEID");
+                    }
+                    else if (c.entitytype == "F")
+                    {
+                        ASSERTL0(x->Attribute("FACEID", &c.entityid),
+                             "Failed to get attribute FACEID");
+                    }
+                    else
+                    {
+                        ASSERTL0(false, "Unknown curve type.");
+                    }
+                    m_meshCurved[std::make_pair(c.entitytype, c.id)] = c;
                     x = x->NextSiblingElement();
                 }
             }
@@ -572,15 +585,26 @@ namespace Nektar
 
             if (m_dim >= 2)
             {
-                std::map<int, MeshCurved>::const_iterator vItCurve;
-                for (vItCurve = m_meshCurved.begin(); vItCurve != m_meshCurved.end(); ++vItCurve)
+                std::map<MeshCurvedKey, MeshCurved>::const_iterator vItCurve;
+                for (vItCurve  = m_meshCurved.begin(); 
+                     vItCurve != m_meshCurved.end(); 
+                     ++vItCurve)
                 {
                     MeshCurved c = vItCurve->second;
-                    if (vEdges.find(c.edgeid) != vEdges.end())
+                    
+                    if (vEdges.find(c.entityid) != vEdges.end() || 
+                        vFaces.find(c.entityid) != vFaces.end())
                     {
-                        x = new TiXmlElement("E");
+                        x = new TiXmlElement(c.entitytype);
                         x->SetAttribute("ID", c.id);
-                        x->SetAttribute("EDGEID", c.edgeid);
+                        if (c.entitytype == "E")
+                        {
+                            x->SetAttribute("EDGEID", c.entityid);
+                        }
+                        else
+                        {
+                            x->SetAttribute("FACEID", c.entityid);
+                        }
                         x->SetAttribute("TYPE", c.type);
                         x->SetAttribute("NUMPOINTS", c.npoints);
                         y = new TiXmlText(c.data);

library/LibUtilities/BasicUtils/MeshPartition.h

@@ -99,12 +99,14 @@ namespace Nektar
             struct MeshCurved
             {
                 int id;
-                int edgeid;
+                std::string entitytype;
+                int entityid;
                 std::string type;
                 int npoints;
                 std::string data;
             };
-
+            typedef std::pair<std::string, int> MeshCurvedKey;
+            
             struct MeshComposite
             {
                 int id;
@@ -160,20 +162,20 @@ namespace Nektar
                         BoostGraph
                     >::adjacency_iterator BoostAdjacencyIterator;
 
-            int                        m_dim;
+            int                                 m_dim;
 
-            std::map<int, MeshVertex>  m_meshVertices;
-            std::map<int, MeshEntity>  m_meshEdges;
-            std::map<int, MeshEntity>  m_meshFaces;
-            std::map<int, MeshEntity>  m_meshElements;
-            std::map<int, MeshCurved>  m_meshCurved;
-            std::map<int, MeshEntity>  m_meshComposites;
-            std::vector<unsigned int>  m_domain;
+            std::map<int, MeshVertex>           m_meshVertices;
+            std::map<int, MeshEntity>           m_meshEdges;
+            std::map<int, MeshEntity>           m_meshFaces;
+            std::map<int, MeshEntity>           m_meshElements;
+            std::map<MeshCurvedKey, MeshCurved> m_meshCurved;
+            std::map<int, MeshEntity>           m_meshComposites;
+            std::vector<unsigned int>           m_domain;
 
-            BoostSubGraph              m_mesh;
-            BoostSubGraph              m_localPartition;
+            BoostSubGraph                       m_mesh;
+            BoostSubGraph                       m_localPartition;
 
-            CommSharedPtr              m_comm;
+            CommSharedPtr                       m_comm;
 
             void ReadMesh(const SessionReaderSharedPtr& pSession);
             void CreateGraph(BoostSubGraph& pGraph);

library/LibUtilities/BasicUtils/SessionReader.cpp

@@ -1434,6 +1434,11 @@ namespace Nektar
         {
             m_geometricInfo.clear();
 
+            if (!geometry)
+            {
+                return;
+            }
+
             TiXmlElement *geometricInfoElement = 
                 geometry->FirstChildElement("GEOMINFO");
 

library/LibUtilities/BasicUtils/Vmath.cpp

 ///////////////////////////////////////////////////////////////////////////////
 //
-// File Vmath.hpp
+// File: Vmath.hpp
 //
 // For more information, please see: http://www.nektar.info
 //
@@ -463,8 +463,9 @@ namespace Vmath
              const int incx, const Nektar::NekDouble *y, const int incy,
              Nektar::NekDouble *z, const int incz);
 
+
     /// \brief  svtvp (scalar times vector plus vector): z = alpha*x + y
-    template<class T> void Svtvp(int n, const T alpha, const T *x,
+    template<class T> LIB_UTILITIES_EXPORT void Svtvp(int n, const T alpha, const T *x,
                  const int incx, const T *y, const int incy,
                  T *z, const int incz)
     {
@@ -492,8 +493,9 @@ namespace Vmath
     }
 
     template LIB_UTILITIES_EXPORT void Svtvp(int n, const Nektar::NekDouble alpha, const Nektar::NekDouble *x,
-             const int incx, const Nektar::NekDouble *y, const int incy,
-             Nektar::NekDouble *z, const int incz);
+                 const int incx, const Nektar::NekDouble *y, const int incy,
+                 Nektar::NekDouble *z, const int incz);
+
 
     /// \brief  svtvp (scalar times vector plus vector): z = alpha*x - y
     template<class T> void Svtvm(int n, const T alpha, const T *x,

library/LibUtilities/BasicUtils/Vmath.hpp

 ///////////////////////////////////////////////////////////////////////////////
 //
-// File Vmath.hpp
+// File: Vmath.hpp
 //
 // For more information, please see: http://www.nektar.info
 //

library/LibUtilities/CMakeLists.txt

@@ -4,111 +4,6 @@ SET(BasicConstHeaders
 	./BasicConst/NektarUnivTypeDefs.hpp
 )
 
-SET(LinearAlgebraHeaders
-    ./LinearAlgebra/Arpack.hpp
-    ./LinearAlgebra/Blas.hpp
-    ./LinearAlgebra/BlasOverrideUtil.hpp
-    ./LinearAlgebra/SparseBlas.hpp
-    ./LinearAlgebra/BlasArray.hpp
-    ./LinearAlgebra/BlockMatrix.hpp
-    ./LinearAlgebra/CanGetRawPtr.hpp
-    ./LinearAlgebra/DgemmOverride.hpp
-    ./LinearAlgebra/DgemvOverride.hpp
-    ./LinearAlgebra/ExplicitInstantiation.h
-    ./LinearAlgebra/Lapack.hpp
-    ./LinearAlgebra/MatrixBase.hpp
-    ./LinearAlgebra/MatrixFuncs.h
-    ./LinearAlgebra/MatrixOperationsDeclarations.hpp
-    ./LinearAlgebra/MatrixOperations.cpp
-    ./LinearAlgebra/MatrixOperations.hpp
-    ./LinearAlgebra/MatrixSize.hpp
-    ./LinearAlgebra/MatrixStorageType.h
-    ./LinearAlgebra/MatrixType.h
-    ./LinearAlgebra/MatrixVectorMultiplication.hpp
-    ./LinearAlgebra/NekLinAlgAlgorithms.hpp
-    ./LinearAlgebra/NekLinSys.hpp
-    ./LinearAlgebra/NekMatrix.hpp
-    ./LinearAlgebra/NekMatrixFwd.hpp
-    ./LinearAlgebra/NekMatrixMetadata.hpp
-    ./LinearAlgebra/NekPoint.hpp
-    ./LinearAlgebra/NekTypeDefs.hpp
-    ./LinearAlgebra/NekVector.hpp
-    ./LinearAlgebra/NekVectorCommon.hpp
-    ./LinearAlgebra/NekVectorConstantSized.hpp
-    ./LinearAlgebra/NekVectorFwd.hpp
-    ./LinearAlgebra/NekVectorMetadata.hpp
-    ./LinearAlgebra/NekVectorTypeTraits.hpp
-    ./LinearAlgebra/NekVectorVariableSized.hpp
-    ./LinearAlgebra/PointerWrapper.h
-    ./LinearAlgebra/ScaledMatrix.hpp
-    ./LinearAlgebra/Space.h
-    ./LinearAlgebra/StandardMatrix.hpp
-    ./LinearAlgebra/TransF77.hpp
-    ./LinearAlgebra/SparseStandardMatrix.hpp
-)
-
-SET(FoundationHeaders
-    ./Foundations/Graph.h
-    ./Foundations/Basis.h
-    ./Foundations/BasisType.h
-    ./Foundations/Foundations.hpp
-    ./Foundations/FourierPoints.h
-    ./Foundations/FourierSingleModePoints.h
-    ./Foundations/BLPoints.h
-    ./Foundations/GaussPoints.h
-    ./Foundations/Interp.h
-    ./Foundations/InterpCoeff.h
-    ./Foundations/ManagerAccess.h
-    ./Foundations/NodalTetElec.h
-    ./Foundations/NodalTriElec.h
-    ./Foundations/NodalTriFekete.h
-    ./Foundations/Points.h
-    ./Foundations/PointsType.h
-    ./Foundations/PolyEPoints.h
-    ./Foundations/NodalUtil.h
-    ./Foundations/NodalTriEvenlySpaced.h
-    ./Foundations/NodalTetEvenlySpaced.h
-    ./Foundations/NodalPrismEvenlySpaced.h
-    ./Foundations/PhysGalerkinProject.h
-)
-
-SET(InterpreterHeaders
-	  ./Interpreter/AnalyticExpressionEvaluator.hpp   
-#	  ./Interpreter/ExpressionEvaluator.h
-)       
-
-SET(PolyLibHeaders
-	./Polylib/Polylib.h
-)	
-
-SET(CommunicationHeaders
-    ./Communication/Comm.h
-    ./Communication/CommSerial.h
-    ./Communication/GsLib.hpp
-    ./Communication/Transposition.h
-    ./Communication/Xxt.hpp
-)
-
-SET(ExpressionTemplates
-    ../ExpressionTemplates/AssociativeTraits.hpp
-    ../ExpressionTemplates/AssociativeTransform.hpp
-    ../ExpressionTemplates/BackwardInverseTransform.hpp
-    ../ExpressionTemplates/CommutativeTraits.hpp
-    ../ExpressionTemplates/CommutativeTransform.hpp
-    ../ExpressionTemplates/CreateFromTree.hpp
-    ../ExpressionTemplates/ExpressionEvaluator.hpp
-    ../ExpressionTemplates/ExpressionTemplates.hpp
-    ../ExpressionTemplates/ForwardInverseTransform.hpp