Merge branch 'master' into feature/varP-3D

CHANGELOG.md

 Changelog
 =========
 
+v4.4.0
+------
+**IncNavierStokesSolver:**
+- Add ability to simulate additional scalar fields (!624)
+
+**NekMesh:**
+- Modify curve module to allow for spline input (!628)
+
+**FieldConvert:**
+- Add module to stretch homogeneous direction (!609)
+
+v4.3.3
+------
+**Library**:
+- Minor fix to suppress Xxt output unless `--verbose` is specified (!642)
+- Fix of DirectFull solver in case where only Neumann boundary conditions 
+  are imposed. (!655)
+
+**FieldConvert**:
+- Fix to avoid repeated import of field file (!649)
+- Fix issue with C^0 projection (!644)
+
+**CompressibleFlowSolver**:
+- Fix issue with residual output (!647)
+
+**Packaging**:
+- Fix NekMesh dependencies for DEB package (!650)
+
+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
 ------
 **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/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}

tutorial @ a20044f2

-Subproject commit 244b5128da8a9c9baedf71230db81344c790b03b
+Subproject commit a20044f232e15e3fe2754a90215f8646db241147

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/solvers/adr.tex

@@ -34,7 +34,7 @@ $\epsilon \nabla^2 u + \mathbf{V}\nabla u = f$ &
     \inltt{SteadyAdvectionDiffusion} & 2D only & Continuous/Discontinuous \\
 $\epsilon \nabla^2 u +  \lambda u = f$ & 
     \inltt{SteadyDiffusionReaction} & 2D only &  Continuous/Discontinuous \\
-$\epsilon \nabla^2 u  \mathbf{V}\nabla u + \lambda u = f$ & 
+$\epsilon \nabla^2 u + \mathbf{V}\nabla u + \lambda u = f$ & 
     \inltt{SteadyAdvectionDiffusionReaction} & 2D only & 
     Continuous/Discontinuous \\
 $ \dfrac{\partial u}{\partial t} + \mathbf{V}\nabla u = f$ &

docs/user-guide/solvers/incompressible-ns.tex

@@ -592,11 +592,15 @@ the advection term using the pressure inverse mass matrix. It can be used just i
 
 
 \item \inltt{SpectralVanishingViscosity}: activates a stabilization technique
-which increases the viscosity on the highest Fourier frequencies of a Quasi-3D approach.
+which increases the viscosity on the modes with the highest frequencies.
 \begin{lstlisting}[style=XMLStyle]
 <I PROPERTY="SpectralVanishingViscosity" VALUE="True"/>
 \end{lstlisting}
 
+In a Quasi-3D simulation, this will affect both the Fourier and the spectral/hp expansions.
+To activate them independently, use \inltt{SpectralVanishingViscositySpectralHP} 
+and \inltt{SpectralVanishingViscosityHomo1D}.
+
 \item \inltt{DEALIASING}: activates the 3/2 padding rule on the advection term
 of a Quasi-3D simulation.
 \begin{lstlisting}[style=XMLStyle]
@@ -1103,6 +1107,61 @@ element is taken as the average of the function in the quadrature
 points of the element. If these functions are defined, the values set
 for the tolerances in the \texttt{PARAMETERS} section are ignored.
 
+\section{Advecting extra passive scalar fields}
+
+In some cases, it might be useful to advect passive scalar fields with the velocity obtained from the
+solution of the Navier-Stokes equation. For example, in study of mass transfer or heat transfer problems
+where getting analytical expression for advection velocity is not possible, the transport (advection-diffusion)
+equation needs to be solved along with the Navier-Stokes equation to get the scalar concentration or
+temperature distribution in the flow field.
+
+In the input file, the extra field variables that are being advected need to be defined after the variables
+representing the velocity components. The pressure needs to be at the end of the list. For example, for
+a 2D simulation the expansions and variables would be defined as
+
+\begin{lstlisting}[style=XMLStyle]
+<EXPANSIONS>
+    <E COMPOSITE="C[0]" NUMMODES="5" FIELDS="u,v,c1,c2,p" TYPE="MODIFIED" />
+</EXPANSIONS>
+
+<VARIABLES>
+    <V ID="0"> u  </V>
+    <V ID="1"> v  </V>
+    <V ID="2"> c1 </V>
+    <V ID="3"> c2 </V>
+    <V ID="4"> p  </V>
+</VARIABLES>
+\end{lstlisting}
+where u, v are the velocity components, c1 and c2 are extra fields that are being advected and p is the pressure.
+
+In addition, diffusion coefficients for each extra variable can be specified by adding a function
+\inltt{DiffusionCoefficient}
+\begin{lstlisting}[style=XMLStyle]
+<FUNCTION NAME="DiffusionCoefficient">
+    <E VAR="c1" VALUE="0.1" />
+    <E VAR="c2" VALUE="0.01" />
+</FUNCTION>
+\end{lstlisting}
+
+Boundary conditions for the extra fields are set up in the same way as the velocity and pressure
+\begin{lstlisting}[style=XMLStyle]
+<BOUNDARYCONDITIONS>
+  <REGION REF="0">
+    <D VAR="u"  VALUE="0" />
+    <D VAR="v"  VALUE="0" />
+    <D VAR="c1" VALUE="1" />
+    <D VAR="c2" VALUE="0" />
+    <N VAR="p"  USERDEFINEDTYPE="H" VALUE="0" />
+  </REGION>
+</BOUNDARYCONDITIONS>
+\end{lstlisting}
+
+It should be noted that if the diffusion coefficient is too small, the transport equation becomes advection dominated.
+This leads to small grid spacing required to resolve all physical scales associated with the transport equation
+(the ratio of resolution required for transport to Navier Stokes equation scales with $Sc^{3/4}$, where $Sc$ is the
+Schmidt number = kinematic viscosity/diffusion coefficient). Hence, small diffusion coefficient might lead to spurious
+oscillations if the mesh spacing is not small enough.
+
 \section{Examples}
 
 \subsection{Kovasznay Flow 2D}

docs/user-guide/utilities/fieldconvert.tex

@@ -96,10 +96,13 @@ 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;
 \item \inltt{homplane}: Extract a plane from 3DH1D expansions;
+\item \inltt{homstretch}: Stretch a 3DH1D expansion by an integer factor;
 \item \inltt{innerproduct}: take the inner product between one or a series of fields with another field (or series of fields). 
 \item \inltt{interpfield}: Interpolates one field to another, requires fromxml, fromfld to be defined;
 \item \inltt{interppointdatatofld}: Interpolates given discrete data using a finite difference approximation to a fld file given an xml file;
@@ -202,6 +205,21 @@ 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
@@ -310,6 +328,21 @@ The output file \inltt{file-plane.fld} can be processed in a similar
 way as described in section \ref{s:utilities:fieldconvert:sub:convert}
 to visualise it either in Tecplot or in Paraview.
 
+\subsection{Stretch a 3DH1D expansion: \textit{homstretch} module}
+
+To stretch a 3DH1D expansion in the z-direction, use the command:
+\begin{lstlisting}[style=BashInputStyle] 
+FieldConvert -m homstretch:factor=value file.xml file.fld file-stretch.fld
+\end{lstlisting}
+The number of modes in the resulting field can be chosen using the command-line
+parameter \inltt{output-points-hom-z}. Note that the output for
+this module should always be a \inltt{.fld} file and this should not
+be used in combination with other modules using a single command.
+
+The output file \inltt{file-stretch.fld} can be processed in a similar 
+way as described in section \ref{s:utilities:fieldconvert:sub:convert}
+to visualise it either in Tecplot or in Paraview.
+
 
 \subsection{Inner Product of a single or series of fields with respect to a single or series of fields: \textit{innerproduct} module}
 You can take the inner product of one field with another field using

docs/user-guide/utilities/nekmesh.tex

@@ -32,7 +32,7 @@ mesh-generator \gmsh to the XML file format.
   converted into base64. This is identified for each section by the attribute
   \inltt{COMPRESSED="B64Z-LittleEndian''}.  To output
   in ascii format add the module option ``:xml:uncompress'' to the .xml file,
-  i.e. \\ \inltt{ MeshConvert file.msh newfile.xml:xml:uncompress}
+  i.e. \\ \inltt{ \mc file.msh newfile.xml:xml:uncompress}
 \end{notebox}
 
 \section{Exporting a mesh from \gmsh}
@@ -290,7 +290,7 @@ converted into base64. If you wish to see an ascii output you need to
 specify the output module option \inltt{uncompress} by executing:
 
 \begin{lstlisting}[style=BashInputStyle]
-MeshConvert Mesh.msh output.xml:xml:uncompress
+NekMesh Mesh.msh output.xml:xml:uncompress
 \end{lstlisting}
 
 In the rest of these subsections, we discuss the various processing modules
@@ -302,13 +302,13 @@ To extract composite surfaces 2 and 3  from a mesh use the module \inltt{extract
 module:
 %
 \begin{lstlisting}[style=BashInputStyle]
-MeshConvert -m extract:surf=2,3 Mesh.xml output.xml
+NekMesh -m extract:surf=2,3 Mesh.xml output.xml
 \end{lstlisting}
 %
 If you also wish to have the boundaries of the extracted surface detected add the \inltt{detectbnd} option
 %
 \begin{lstlisting}[style=BashInputStyle]
-MeshConvert -m extract:surf=2,3:detectbnd Mesh.xml output.xml
+NekMesh -m extract:surf=2,3:detectbnd Mesh.xml output.xml
 \end{lstlisting}
 
 \subsection{Negative Jacobian detection}

docs/user-guide/xml/xml-geometry.tex

@@ -48,7 +48,7 @@ The description below explains how the \inltt{GEOMETRY} section is laid out in
 uncompressed ascii format. From Jan 2016 the distribution uses the compressed
 format for each of the above sections. To convert a compressed xml file into
 ascii format use \\
-  \inltt{ MeshConvert file.msh newfile.xml:xml:uncompress}
+  \inltt{ NekMesh file.msh newfile.xml:xml:uncompress}
 \end{notebox}
 
 

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