CHANGELOG.md

 Changelog
 =========
 
+v4.3.2
+------
+**Library**:
+- Add small optimisation for DriverAdaptive (!618)
+- Updated FFTW build to use the compiler used for building Nektar++ (!629)
+- Fix numbering bug in periodic boundary conditions (!631)
+- Print error message for invalid equation also in release version (!634)
+- HistoryPoints filter now uses closest plane to requested z-coordinate and
+  output is produced in physical space (!621).
+- Fix minor performance issue with time integration schemes (!632)
+- Fix FilterCheckpoint filter to be consistent with `IO_CheckSteps` (!633)
+- Fix `IO_CheckSteps` to avoid missing first checkpoint (!639)
+- Fix bug in iterative solver where only root process would ASSERT when
+  exceeding the maximum number of iterations (!636)
+
+**FieldConvert**:
+- Fix appearence of duplicate messages when running in parallel (!626)
+- Fix issue with efficiency when using large number of 3DH1D planes (!627)
+- Add module for combining average fields (!620)
+- Fix wall shear stress processing module for parallel execution (!635)
+
+**Packaging**:
+- Fixes for DEB package dependencies (!630)
+
 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, !596)
+- Fix Homogeneous transform when unshuffling is not used. (!599)
+- Fix namespace pollution in library header files. (!601)
+- Fix issue with METIS compilation on clang 7.3 (!603)
+- Fix issue with heterogeneous quadrilaterals (!607)
+- Fix bug in modified Arnoldi algorithm causing convergence to be reported when
+  number of vectors is less than `nvec` (!608)
+- Fix uninitialised array bug in AssemblyMap (!598)
+- Fix issue with LAPACK call in eigenvalue calculation (!610)
+- Fix FieldConvert processing of partitions in serial (!612)
+- Fix use of multi-level static condensation in parallel with periodic
+  boundary conditions (!614)
+- Fix NaN detection to work in parallel (!605)
+- Add additional constructor to ContField3DHomogeneous1D for FieldConvert
+  extract module. (!590)
+
+**NekMesh**:
+- Fix incorrect link directory on CCMIO library.
+
+**FieldConvert**:
+- Fix to FLD input to update the field definitions always, not just when a range
+  is specified. (!611)
+
+**Tester**:
+- Remove requirement for executable to be specified in .tst file if it is
+  overridden on the command-line (!595)
+
+**Packaging**:
+- Fix dependency resolution on generation of DEB packages. (!616)
 
 v4.3.0
 ------

VERSION

-4.3.0
+4.3.2

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/ThirdPartyFFTW.cmake

@@ -38,7 +38,7 @@ IF (NEKTAR_USE_FFTW)
             BINARY_DIR ${TPBUILD}/fftw-3.2.2
             TMP_DIR ${TPBUILD}/fftw-3.2.2-tmp
             INSTALL_DIR ${TPDIST}
-            CONFIGURE_COMMAND ${TPSRC}/fftw-3.2.2/configure --prefix=${TPDIST} --quiet --enable-shared --disable-dependency-tracking
+            CONFIGURE_COMMAND CC=${CMAKE_C_COMPILER} ${TPSRC}/fftw-3.2.2/configure --prefix=${TPDIST} --quiet --enable-shared --disable-dependency-tracking
         )
 
         SET(FFTW_LIBRARY fftw3 CACHE FILEPATH

cmake/ThirdPartyMetis.cmake

@@ -27,7 +27,18 @@ EXTERNALPROJECT_ADD(
         -DCMAKE_C_FLAGS:STRING=-fPIC\ -w
         -DGKLIB_PATH:PATH=${TPSRC}/modmetis-5.1.0/GKlib
         ${TPSRC}/modmetis-5.1.0
-)
+    )
+
+IF (CMAKE_CXX_COMPILER_ID MATCHES "Clang")
+    # Clang 7.3 has a lovely bug that needs to be patched in order for it to
+    # compile.
+    IF (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER "7.3")
+        EXTERNALPROJECT_ADD_STEP(modmetis-5.1.0 patch-install-path
+            COMMAND sed -i ".bak" "s|#define MAX_JBUFS 128|#define MAX_JBUFS 24|" ${TPSRC}/modmetis-5.1.0/GKlib/error.c
+            DEPENDERS build
+            DEPENDEES download)
+    ENDIF()
+ENDIF()
 
 SET(METIS_LIB metis CACHE FILEPATH "METIS library" FORCE)
 MARK_AS_ADVANCED(METIS_LIB)

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}

docs/user-guide/installation/doc.tex

+\section{Compiling Documentation}
+Documentation for Nektar++ is provided in a number of forms:
+\begin{itemize}
+\item User Guide (LaTeX, compiled to pdf or html)
+\item Source code documentation (Doxygen compiled to html)
+\end{itemize}
+
+\subsection{Dependencies}
+To build the LaTeX documents (user guide or tutorials), the following
+dependencies are required:
+\begin{itemize}
+\item texlive-base
+\item texlive-latex-extra
+\item texlive-science
+\item imagemagick
+\end{itemize}
+
+To build the Doxygen documentation, the following dependencies are required:
+\begin{itemize}
+\item doxygen
+\item graphviz
+\end{itemize}
+
+\subsection{Compiling the User Guide}
+To compile the User Guide:
+\begin{enumerate}
+\item Configure the Nektar++ build tree as normal.
+\item Run
+    \begin{lstlisting}[style=BashInputStyle]
+make user-guide-pdf
+\end{lstlisting}
+to make the PDF version, or run
+\begin{lstlisting}[style=BashInputStyle]
+make user-guide-html
+\end{lstlisting}
+to make the HTML version.
+\end{enumerate}
+
+\subsection{Compiling the code documentation}
+To compile the code documentation enable the \inltt{NEKTAR\_BUILD\_DOC} option
+in the \inlsh{ccmake} configuration tool.
+
+You can then compile the HTML code documentation using:
+\begin{lstlisting}[style=BashInputStyle]
+make doc
+\end{lstlisting}
+
+
+\section{Compiling Tutorials}
+If you are using a clone of the \nekpp git repository, you can also download
+the source for the \nekpp tutorials which is available as a \emph{git submodule}.
+
+\begin{enumerate}
+\item From a \nekpp working directory (e.g. \inlsh{\$NEKPP}):
+\begin{lstlisting}[style=BashInputStyle]
+git submodule init
+git submodule update --remote
+\end{lstlisting}
+\item From your build directory (e.g. \inlsh{\$NEKPP/build}), re-run \inlsh{cmake} to update the build system to include the tutorials
+\begin{lstlisting}[style=BashInputStyle]
+cmake ../
+\end{lstlisting}
+\item Compile each required tutorial, for example
+\begin{lstlisting}[style=BashInputStyle]
+make flow-stability-channel
+\end{lstlisting}
+\end{enumerate}

docs/user-guide/installation/installation.tex

@@ -9,4 +9,4 @@ solvers for simulation and do not need to perform additional code development.
 
 \input{source}
 
-
+\input{doc}

docs/user-guide/utilities/fieldconvert.tex

@@ -96,6 +96,8 @@ Specifically, FieldConvert has these additional functionalities
 \item \inltt{C0Projection}: Computes the C0 projection of a given output file;
 \item \inltt{QCriterion}: Computes the Q-Criterion for a given output file;
 \item \inltt{addFld}: Sum two .fld files;
+\item \inltt{combineAvg}: Combine two \nekpp binary output (.chk or .fld) field file containing averages of fields (and
+possibly also Reynolds stresses) into single file;
 \item \inltt{concatenate}: Concatenate a \nekpp binary output (.chk or .fld) field file into single file;
 \item \inltt{equispacedoutput}: Write data as equi-spaced output using simplices to represent the data for connecting points;
 \item \inltt{extract}: Extract a boundary field;
@@ -202,6 +204,21 @@ the result either in Tecplot, Paraview or VisIt.
 %
 %
 %
+\subsection{Combine two .fld files containing time averages: \textit{combineAvg} module}
+To combine two .fld files obtained through the AverageFields or ReynoldsStresses filters,
+use the \inltt{combineAvg} module of FieldConvert
+%
+\begin{lstlisting}[style=BashInputStyle]
+  FieldConvert -m combineAvg:fromfld=file1.fld file1.xml file2.fld \
+  file3.fld
+\end{lstlisting}
+%
+\inltt{file3.fld} can be processed in a similar way as described 
+in section \ref{s:utilities:fieldconvert:sub:convert} to visualise 
+the result either in Tecplot, Paraview or VisIt.
+%
+%
+%
 \subsection{Concatenate two files: \textit{concatenate} module}
 To concatenate \inltt{file1.fld} and \inltt{file2.fld} into \inltt{file-conc.fld}
 one can run the following command

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