Merge branch 'master' into fix/metis-clang-7.3

CHANGELOG.md

 Changelog
 =========
 
+v4.3.1
+------
+**Library**:
+- Add `THIRDPARTY_USE_SSL` option to disable use of SSL on systems where CMake
+  is not compiled with SSL support. (!602)
+- Fixed a number of documentation issues (!586, !593)
+- Fix Homogeneous transform when unshuffling is not used. (!599)
+- Fix namespace pollution in library header files. (!601)
+- Fix bug in modified Arnoldi algorithm causing convergence to be reported when
+  number of vectors is less than `nvec` (!608)
+
+**NekMesh**:
+- Fix incorrect link directory on CCMIO library.
+
 v4.3.0
 ------
 **Library:**

CMakeLists.txt

@@ -154,7 +154,13 @@ ENDIF()
 INCLUDE (NektarCommon)
 
 # Set various ThirdParty locations
-SET(TPURL   https://www.nektar.info/thirdparty)
+OPTION(THIRDPARTY_USE_SSL "Use secure HTTP connection to download third-party files." OFF)
+IF (THIRDPARTY_USE_SSL)
+    SET(TPURL https://www.nektar.info/thirdparty)
+ELSE()
+    SET(TPURL http://www.nektar.info/thirdparty)
+ENDIF()
+
 SET(TPSRC   ${CMAKE_SOURCE_DIR}/ThirdParty)
 SET(TPBUILD ${CMAKE_BINARY_DIR}/ThirdParty)
 SET(TPDIST  ${CMAKE_BINARY_DIR}/ThirdParty/dist)

cmake/ThirdPartyCCM.cmake

@@ -16,6 +16,8 @@ IF( NEKTAR_USE_CCM )
         MARK_AS_ADVANCED(CCMIO_LIBRARY)
         ADD_DEFINITIONS(-DNEKTAR_USE_CCM)
         FIND_PATH (CCMIO_INCLUDE_DIR ccmio.h)
+        GET_FILENAME_COMPONENT(CCMIO_LIBRARY_PATH ${CCMIO_LIBRARY} PATH)
+        LINK_DIRECTORIES(${CCMIO_LIBRARY_PATH})
      ELSE()
         MESSAGE(FATAL_ERROR "Cound not find ccmio library")
      ENDIF()

cmake/ThirdPartyTetGen.cmake

@@ -17,7 +17,7 @@ IF(NEKTAR_USE_MESHGEN)
         EXTERNALPROJECT_ADD(
             tetgen-1.5
             PREFIX ${TPSRC}
-            URL http://ae-nektar.ae.ic.ac.uk/~mt4313/tetgen.zip
+            URL ${TPURL}/tetgen.zip
             URL_MD5 6d62e63f9b1e7a8ce53d5bc87e6a0a09
             STAMP_DIR ${TPBUILD}/stamp
             DOWNLOAD_DIR ${TPSRC}

cmake/ThirdPartyTriangle.cmake

@@ -17,7 +17,7 @@ IF(NEKTAR_USE_MESHGEN)
         EXTERNALPROJECT_ADD(
             triangle-1.6
             PREFIX ${TPSRC}
-            URL http://ae-nektar.ae.ic.ac.uk/~mt4313/triangle.zip
+            URL ${TPURL}/triangle.zip
             URL_MD5 357cb7107f51f3f89940c47435d4fa49
             STAMP_DIR ${TPBUILD}/stamp
             DOWNLOAD_DIR ${TPSRC}

docs/developer-guide/library-design/library-design.tex

@@ -38,7 +38,7 @@ in the core sub-libraries, is depicted in the Figure~\ref{f:library:overview}.
 
 \begin{figure}
 \centering
-\includegraphics[width=0.6\textwidth]{img/architecture}
+\includegraphics[width=0.6\textwidth]{library-design/img/architecture}
 \caption{Structural overview of the Nektar++ libraries}
 \label{f:library:structure}
 \end{figure}

library/Collections/BwdTrans.cpp

@@ -37,6 +37,8 @@
 #include <Collections/Operator.h>
 #include <Collections/Collection.h>
 
+using namespace std;
+
 namespace Nektar {
 namespace Collections {
 

library/Collections/Collection.cpp

@@ -36,6 +36,8 @@
 #include <Collections/Collection.h>
 #include <sstream>
 
+using namespace std;
+
 namespace Nektar {
 namespace Collections {
 

library/Collections/Collection.h

@@ -36,6 +36,8 @@
 #ifndef NEKTAR_LIBRARY_COLLECTIONS_COLLECTION_H
 #define NEKTAR_LIBRARY_COLLECTIONS_COLLECTION_H
 
+#include <vector>
+
 #include <StdRegions/StdExpansion.h>
 #include <SpatialDomains/Geometry.h>
 #include <Collections/CollectionsDeclspec.h>
@@ -56,8 +58,8 @@ class Collection
     public:
 
         COLLECTIONS_EXPORT Collection(
-                vector<StdRegions::StdExpansionSharedPtr>     pCollExp,
-                OperatorImpMap                               &impTypes);
+                std::vector<StdRegions::StdExpansionSharedPtr>  pCollExp,
+                OperatorImpMap                                 &impTypes);
 
         inline void ApplyOperator(
                 const OperatorType                           &op,
@@ -81,7 +83,7 @@ class Collection
 
     protected:
         StdRegions::StdExpansionSharedPtr                     m_stdExp;
-        vector<SpatialDomains::GeometrySharedPtr>             m_geom;
+        std::vector<SpatialDomains::GeometrySharedPtr>        m_geom;
         boost::unordered_map<OperatorType, OperatorSharedPtr> m_ops;
         CoalescedGeomDataSharedPtr                            m_geomData;
 

library/Collections/CollectionOptimisation.cpp

@@ -36,6 +36,8 @@
 #include <Collections/CollectionOptimisation.h>
 #include <LibUtilities/BasicUtils/ParseUtils.hpp>
 
+using namespace std;
+
 namespace Nektar
 {
 namespace Collections

library/Collections/CollectionOptimisation.h

@@ -142,7 +142,7 @@ class CollectionOptimisation
 
         // Get Map by doing autotuning testing.
         COLLECTIONS_EXPORT OperatorImpMap SetWithTimings(
-                vector<StdRegions::StdExpansionSharedPtr> pGeom,
+                std::vector<StdRegions::StdExpansionSharedPtr> pGeom,
                 OperatorImpMap &impTypes,
                 bool verbose = true);
 
@@ -152,10 +152,10 @@ class CollectionOptimisation
         }
 
     private:
-        typedef pair<LibUtilities::ShapeType, int> ElmtOrder;
+        typedef std::pair<LibUtilities::ShapeType, int> ElmtOrder;
 
-        static map<OpImpTimingKey,OperatorImpMap> m_opImpMap;
-        map<OperatorType, map<ElmtOrder, ImplementationType> > m_global;
+        static std::map<OpImpTimingKey,OperatorImpMap> m_opImpMap;
+        std::map<OperatorType, std::map<ElmtOrder, ImplementationType> > m_global;
         bool m_setByXml;
         bool m_autotune;
         ImplementationType m_defaultType;

library/Collections/IProduct.cpp

@@ -36,6 +36,8 @@
 #include <Collections/Collection.h>
 #include <Collections/IProduct.h>
 
+using namespace std;
+
 namespace Nektar
 {
 namespace Collections

library/Collections/IProductWRTBase.cpp

@@ -38,6 +38,8 @@
 #include <Collections/Collection.h>
 #include <Collections/IProduct.h>
 
+using namespace std;
+
 namespace Nektar {
 namespace Collections {
 

library/Collections/IProductWRTDerivBase.cpp

@@ -38,6 +38,8 @@
 #include <Collections/Collection.h>
 #include <Collections/IProduct.h>
 
+using namespace std;
+
 namespace Nektar {
 namespace Collections {
 

library/Collections/Operator.h

@@ -46,7 +46,7 @@
     static OperatorKey m_typeArr[];                             \
     friend class MemoryManager<cname>;                          \
     static OperatorSharedPtr create(                            \
-        vector<StdRegions::StdExpansionSharedPtr> pCollExp,     \
+        std::vector<StdRegions::StdExpansionSharedPtr> pCollExp,\
         boost::shared_ptr<CoalescedGeomData> GeomData)          \
     {                                                           \
         return MemoryManager<cname>                             \
@@ -99,7 +99,7 @@ const char* const ImplementationTypeMap[] =
 
 typedef bool ExpansionIsNodal;
 
-typedef map<OperatorType, ImplementationType> OperatorImpMap;
+typedef std::map<OperatorType, ImplementationType> OperatorImpMap;
 
 /// simple Operator Implementation Map generator
 OperatorImpMap SetFixedImpType(ImplementationType defaultType);
@@ -110,7 +110,7 @@ class Operator
     public:
         /// Constructor
         Operator(
-                vector<StdRegions::StdExpansionSharedPtr> pCollExp,
+                std::vector<StdRegions::StdExpansionSharedPtr> pCollExp,
                 boost::shared_ptr<CoalescedGeomData> GeomData)
             : m_stdExp(pCollExp[0]->GetStdExp()),
               m_numElmt(pCollExp.size()),
@@ -161,7 +161,7 @@ std::ostream &operator<<(std::ostream &os, OperatorKey const &p);
 typedef Nektar::LibUtilities::NekFactory<
     OperatorKey,
     Operator,
-    vector<StdRegions::StdExpansionSharedPtr>,
+    std::vector<StdRegions::StdExpansionSharedPtr>,
     CoalescedGeomDataSharedPtr> OperatorFactory;
 
 /// Returns the singleton Operator factory object

library/Collections/PhysDeriv.cpp

@@ -37,6 +37,8 @@
 #include <Collections/Operator.h>
 #include <Collections/Collection.h>
 
+using namespace std;
+
 namespace Nektar {
 namespace Collections {
 

library/Demos/Collections/CollectionTiming.cpp

@@ -46,6 +46,7 @@
 #include <Collections/Collection.h>
 #include <SpatialDomains/MeshGraph.h>
 
+using namespace std;
 using namespace Nektar;
 
 using boost::timer::cpu_timer;

library/Demos/LibUtilities/NodalTriFeketeDemo.cpp

@@ -11,8 +11,8 @@ using namespace std;
 #include <LibUtilities/Foundations/Foundations.hpp>
 #include <LibUtilities/Foundations/Points.h>
 
-using namespace Nektar;
 using namespace boost;
+using namespace Nektar;
 using namespace Nektar::LibUtilities;
 
 int main(int argc, char *argv[])

library/Demos/LocalRegions/LocProject1D.cpp

@@ -3,6 +3,7 @@
 #include <LocalRegions/SegExp.h>
 #include <SpatialDomains/SegGeom.h>
 
+using namespace std;
 using namespace Nektar;
 
 static double solutionpoly(double x, int order);

library/Demos/LocalRegions/LocProject2D.cpp

@@ -8,6 +8,7 @@
 
 #include <LibUtilities/Foundations/Foundations.hpp>
 
+using namespace std;
 using namespace Nektar;
 
 NekDouble Tri_sol(NekDouble x, NekDouble y, int order1, int order2);