Merge branch 'master' into fix/error-output

.gitmodules

@@ -3,8 +3,3 @@
     path = docs/tutorial
     url = git@gitlab.nektar.info:nektar/tutorial
     ignore = all
-[submodule "docs/developer-guide"]
-    branch = master
-	path = docs/developer-guide
-	url = git@gitlab.nektar.info:nektar/developer-guide
-    ignore = all

CHANGELOG.md

@@ -54,7 +54,7 @@ v5.0.0
 - Fix ability to have periodic boundary conditions that are aligned by a
   rotation rather than just a translation (!933)
 - Added a coupling interface to exchange data between solvers at run time
-  and a DummySolver to test the implementations (!853, !931 !973)
+  and a DummySolver to test the implementations (!853, !931, !950, !973)
 - Fix compilation issue with newer Boost versions and clang (!940)
 - If only `NEKTAR_BUILD_LIBRARY` is enabled, only libraries up to and including
   `MultiRegions` will be built by default (!945)
@@ -69,6 +69,8 @@ v5.0.0
 - Add HDF5 geometry format (!977)
 - Combine and generalise demo code in StdRegions and LocalRegions (!993)
 - Fix for error output to allow for custom error streams (!944)
+- Fixed bug in ReOrientQuadFacePhysMap (!1003)
+- Add NekPy Python interface (!962, !990, !989, !1004)
 
 **NekMesh**:
 - Add feature to read basic 2D geo files as CAD (!731)
@@ -100,8 +102,10 @@ v5.0.0
 - Fix manifold face curvature nodes (!913)
 - Fix writing 1D surfaces (!930)
 - Fix surface string parsin in BL splitting (!937)
+- Enable use of distributed packages for triangle and TetGen (!953)
 - Fix issue with MLSC after Scotch conversion (!943)
 - Add support for Gmsh 4.0 mesh file format (!964)
+- Fix issue with extracting 1D curved surface from 2D file (!984)
 - Fix surface extraction, added regression test (!994)
 
 **FieldConvert**:
@@ -120,7 +124,9 @@ v5.0.0
 - Add module for evaluating the mean of variables on the domain (!894)
 - Add module for counting the total number of DOF (!948)
 - Fixed wss module for compressible flows (!958)
+- Made Sutherland's law non-dimensional (!972)
 - Add module for removing fields from .fld files (!978)
+- Fixed nparts option in FieldConvert and automated Info.xml generation (!995)
 - Added if statement to fix case of 1D/2D manifold interpolation in 1D/2D space,
   added check on dimensions for interpolation, fixed seg interp (!999)
 
@@ -139,6 +145,7 @@ v5.0.0
   seg, quad and hex elements (!771, !862)
 - Fix compressible solver with NUMMODES=1 (!868)
 - Introduce equations of state to account for real gas effects (!880)
+- Made Sutherland's law non-dimensional (!972)
 - Modified pressure outlet BCs to allow for the reference static pressure to be
   set from the VALUE fields (!981)
 

cmake/NektarCommon.cmake

@@ -279,8 +279,7 @@ MACRO(ADD_NEKPY_LIBRARY name)
     # Install __init__.py files.
     CONFIGURE_FILE(${CMAKE_SOURCE_DIR}/cmake/python/init.py.in
         ${CMAKE_BINARY_DIR}/NekPy/${name}/__init__.py)
-    SET_TARGET_PROPERTIES(_${name} PROPERTIES
-        LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/NekPy/${name})
+    INSTALL(TARGETS _${name} DESTINATION ${CMAKE_BINARY_DIR}/NekPy/${name})
 ENDMACRO()
 
 MACRO(ADD_NEKPY_EXECUTABLE name source)
@@ -288,4 +287,4 @@ MACRO(ADD_NEKPY_EXECUTABLE name source)
     INSTALL(FILES ${source} DESTINATION ${CMAKE_INSTALL_PREFIX}/bin)
     FILE(COPY ${source} DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
     ADD_CUSTOM_TARGET(${name} SOURCES ${source})
-ENDMACRO()
\ No newline at end of file
+ENDMACRO()

cmake/ThirdPartyTetGen.cmake

@@ -7,31 +7,50 @@
 ########################################################################
 
 IF(NEKTAR_USE_MESHGEN)
-    INCLUDE(ExternalProject)
-    EXTERNALPROJECT_ADD(
-        tetgen-1.5
-        PREFIX ${TPSRC}
-        URL ${TPURL}/tetgen.zip
-        URL_MD5 6d62e63f9b1e7a8ce53d5bc87e6a0a09
-        STAMP_DIR ${TPBUILD}/stamp
-        DOWNLOAD_DIR ${TPSRC}
-        SOURCE_DIR ${TPSRC}/tetgen-1.5
-        BINARY_DIR ${TPBUILD}/tetgen-1.5
-        TMP_DIR ${TPBUILD}/tetgen-1.5-tmp
-        INSTALL_DIR ${TPDIST}
-        CONFIGURE_COMMAND ${CMAKE_COMMAND}
+    # Search for system-installed Triangle installation
+    FIND_LIBRARY(TETGEN_LIBRARY NAMES tet)
+    FIND_PATH(TETGEN_INCLUDE_DIR tetgen.h)
+
+    IF(TETGEN_LIBRARY AND TETGEN_INCLUDE_DIR)
+        SET(BUILD_TETGEN OFF)
+    ELSE()
+        SET(BUILD_TETGEN ON)
+    ENDIF()
+
+    OPTION(THIRDPARTY_BUILD_TETGEN
+        "Build TetGen library from ThirdParty." ${BUILD_TETGEN})
+
+    IF (THIRDPARTY_BUILD_TETGEN)
+        INCLUDE(ExternalProject)
+        EXTERNALPROJECT_ADD(
+            tetgen-1.5
+            PREFIX ${TPSRC}
+            URL ${TPURL}/tetgen.zip
+            URL_MD5 6d62e63f9b1e7a8ce53d5bc87e6a0a09
+            STAMP_DIR ${TPBUILD}/stamp
+            DOWNLOAD_DIR ${TPSRC}
+            SOURCE_DIR ${TPSRC}/tetgen-1.5
+            BINARY_DIR ${TPBUILD}/tetgen-1.5
+            TMP_DIR ${TPBUILD}/tetgen-1.5-tmp
+            INSTALL_DIR ${TPDIST}
+            CONFIGURE_COMMAND ${CMAKE_COMMAND}
             -G ${CMAKE_GENERATOR}
             -DCMAKE_C_COMPILER:FILEPATH=${CMAKE_C_COMPILER}
             -DCMAKE_CXX_COMPILER:FILEPATH=${CMAKE_CXX_COMPILER}
             -DCMAKE_INSTALL_PREFIX:PATH=${TPDIST}
             ${TPSRC}/tetgen-1.5
-        )
-    THIRDPARTY_LIBRARY(TETGEN_LIBRARY STATIC tetgen
-        DESCRIPTION "Tetgen library")
-    SET(TETGEN_INCLUDE_DIR ${TPDIST}/include CACHE FILEPATH
-        "TetGen include" FORCE)
-    MESSAGE(STATUS "Build TetGen: ${TETGEN_LIBRARY}")
-    SET(TETGEN_CONFIG_INCLUDE_DIR ${TPINC})
+            )
+        THIRDPARTY_LIBRARY(TETGEN_LIBRARY STATIC tetgen
+            DESCRIPTION "Tetgen library")
+        SET(TETGEN_INCLUDE_DIR ${TPDIST}/include CACHE FILEPATH
+            "TetGen include" FORCE)
+        MESSAGE(STATUS "Build TetGen: ${TETGEN_LIBRARY}")
+        SET(TETGEN_CONFIG_INCLUDE_DIR ${TPINC})
+    ELSE()
+        ADD_CUSTOM_TARGET(tetgen-1.5 ALL)
+        MESSAGE(STATUS "Found TetGen: ${TETGEN_LIBRARY}")
+        SET(TETGEN_CONFIG_INCLUDE_DIR ${TETGEN_INCLUDE_DIR})
+    ENDIF()
 
     MARK_AS_ADVANCED(TETGEN_LIBRARY)
     MARK_AS_ADVANCED(TETGEN_INCLUDE_DIR)

cmake/ThirdPartyTriangle.cmake

@@ -7,7 +7,15 @@
 ########################################################################
 
 IF(NEKTAR_USE_MESHGEN)
-    SET(BUILD_TRIANGLE ON)
+    # Search for system-installed Triangle installation
+    FIND_LIBRARY(TRIANGLE_LIBRARY NAMES triangle)
+    FIND_PATH(TRIANGLE_INCLUDE_DIR triangle.h)
+
+    IF(TRIANGLE_LIBRARY AND TRIANGLE_INCLUDE_DIR)
+        SET(BUILD_TRIANGLE OFF)
+    ELSE()
+        SET(BUILD_TRIANGLE ON)
+    ENDIF()
 
     OPTION(THIRDPARTY_BUILD_TRIANGLE
     "Build Triangle library from ThirdParty." ${BUILD_TRIANGLE})

developer-guide @ 0724faa5

-Subproject commit 0724faa50ed893acb7ca256b1582d288396bb5d4

tutorial @ 8f8ed6f9

-Subproject commit 7c88d86e78a8908720b971d71ce8b5aafdd5eb92
+Subproject commit 8f8ed6f96bad562bedd8c242a4dc247e605ca20d

docs/user-guide/utilities/fieldconvert.tex

@@ -1153,63 +1153,13 @@ process each parallel partition in serial, for example when interpolating a
 solution field from one mesh to another or creating an output file for
 visualization.
 
-\subsection{Using the \textit{nparts} options}
-
-One option is to use the \inltt{nparts}  command line
-option. For example, the following command will create a
-\inltt{.vtu} file using 10 partitions of \inltt{file1.xml}:
-\begin{lstlisting}[style=BashInputStyle]
-FieldConvert --nparts 10  file1.xml file1.fld file1.vtu
-\end{lstlisting}
-Note this will create a parallel vtu file as it processes each partition. 
-
-
-Another example is to interpolate \inltt{file1.fld} from one mesh
-\inltt{file1.xml} to another \inltt{file2.xml}. If the mesh files are
-large we can do this by partitioning \inltt{file2.xml} into 10 (or more)
-partitions and interpolating each partition one by one using the
-command:
-\begin{lstlisting}[style=BashInputStyle]
-  FieldConvert --nparts 10 -m interpfield:fromxml=file1.xml:fromfld=file1.fld \
-  file2.xml file2.fld
-\end{lstlisting}
-Note that internally the routine uses the range option so that it
-only has to load the part of \inltt{file1.xml} that overlaps with each
-partition of \inltt{file2.xml}.
-The resulting output will lie in a directory called \inltt{file2.fld}, with each
-of the different parallel partitions in files with names \inltt{P0000000.fld},
-\inltt{P0000001.fld}, \dots, \inltt{P0000009.fld}. This is nearly a complete
-parallel field file. However, when the output file is in the .fld format,
-the \inltt{Info.xml} file, which contains the information about which elements
-lie in each partition, is not correct since it will only contain the information for one of the partitions. The correct \inltt{Info.xml} file  can be generated by using the command
-\begin{lstlisting}[style=BashInputStyle]
-FieldConvert file2.xml file2.fld/Info.xml:info:nparts=10
-\end{lstlisting}
-Note the \inltt{:info} extension on the last argument is necessary to tell
-FieldConvert that you wish to generate an info file, but with the extension
-\inltt{.xml}. This syntax allows the routine not to get confused with the
-input/output XML files.
-
-\subsection{Running in parallel with the \textit{ nparts} option}
-
-The examples above will process each partition serially which may now
-take a while for many partitions. You can however run this option in
-parallel using a smaller number of cores than the nparts.
-
-For the example of creating a vtu file above you can use 4 processor concurrently wiht the command line:
-\begin{lstlisting}[style=BashInputStyle]
-mpirun -n 4 FieldConvert --nparts 10   file1.xml file1.fld file1.vtu
-\end{lstlisting}
-
-Obviously the executable will have to have been compiled with the MPI option for this to work. 
 
 \subsection{Using the \textit{ part-only} and \textit{ part-only-overlapping} options}
 
-The options above will all load in the full \inltt{file1.xml}, partition
-it into \inltt{nparts} files in a director called \inltt{file1\_xml}.
-This can be expensive if the \inltt{file1.xml} is already large. So instead you can
-pre-partition the file using the using the  \inltt{--part-only}
-option. So the command
+Loading full \inltt{file1.xml} can be expensive if the
+\inltt{file1.xml} is already large. So instead you can pre-partition
+the file using the using the \inltt{--part-only} option. So the
+command
 \begin{lstlisting}[style=BashInputStyle]
 FieldConvert --part-only 10 file.xml file.fld
 \end{lstlisting}
@@ -1218,13 +1168,6 @@ directory called \inltt{file\_xml}. If you enter this directory you will find
 partitioned XML files \inltt{P0000000.xml}, \inltt{P0000001.xml}, \dots,
 \inltt{P0000009.xml} which can then be processed individually as outlined above.
 
-If you have a partitioned directory either from a parallel run or using the \inltt{--part-only} option  you can now run the \inltt{FieldConvert} option using the command
-\begin{lstlisting}[style=BashInputStyle]
-mpirun -n 4 FieldConvert --nparts 10  file1\_xml:xml file1.fld file1.vtu
-\end{lstlisting}
-
-Note the form \inltt{file1\_xml:xml} option tells the code it is a parallel partition which should be treated as an \inltt{xml} type file. 
-
 There is also a \inltt{--part-only-overlapping} option, which can be run in the
 same fashion.
 \begin{lstlisting}[style=BashInputStyle]
@@ -1241,6 +1184,58 @@ within a partition. using the \inltt{--part-only-overlapping} option will still
 yield a shrinking isocontour, but the overlapping partitions help to overlap the
 partiiton boundaries.
 
+\subsection{Using the \textit{nparts} options}
+
+If you have a partitioned directory either from a parallel run or
+using the \inltt{--part-only} option you can now run the
+\inltt{FieldConvert} option using the \inltt{nparts}  command line
+option, that is
+\begin{lstlisting}[style=BashInputStyle]
+FieldConvert --nparts 10  file1\_xml:xml file1.fld file1.vtu
+\end{lstlisting}
+
+Note the form \inltt{file1\_xml:xml} option tells the code it is a
+parallel partition which should be treated as an \inltt{xml} type
+file. the argument of \inltt{nparts} should correpsond to the number
+of partitions used in generating the file1\_xml directory. This will
+create a parallel vtu file as it processes each partition.
+
+
+Another example is to interpolate \inltt{file1.fld} from one mesh
+\inltt{file1.xml} to another \inltt{file2.xml}. If the mesh files are
+large we can do this by partitioning \inltt{file2.xml} into 10 (or
+more) partitions to generate the \inltt{file\_xml} directory and
+interpolating each partition one by one using the command:
+\begin{lstlisting}[style=BashInputStyle]
+  FieldConvert --nparts 10 -m interpfield:fromxml=file1.xml:fromfld=file1.fld \
+  file2_xml:xml file2.fld
+\end{lstlisting}
+Note that internally the routine uses the range option so that it only
+has to load the part of \inltt{file1.xml} that overlaps with each
+partition of \inltt{file2.xml}.  The resulting output will lie in a
+directory called \inltt{file2.fld}, with each of the different
+parallel partitions in files with names \inltt{P0000000.fld},
+\inltt{P0000001.fld}, \dots, \inltt{P0000009.fld}. In previous
+versions of FieldConvert it was necessary to generate an updated
+\inltt{Info.xml} file but in the current version it should
+automatically be updating this file.
+
+\subsection{Running in parallel with the \textit{ nparts} option}
+
+The examples above will process each partition serially which may now
+take a while for many partitions. You can however run this option in
+parallel using a smaller number of cores than the nparts.
+
+For the example of creating a vtu file above you can use 4 processor
+concurrently wiht the command line:
+\begin{lstlisting}[style=BashInputStyle]
+mpirun -n 4 FieldConvert --nparts 10   file1\_xml:xml file1.fld file1.vtu
+\end{lstlisting}
+
+Obviously the executable will have to have been compiled with the MPI
+option for this to work.
+
+
 %%% Local Variables:
 %%% mode: latex
 %%% TeX-master: "../user-guide"

library/FieldUtils/InputModules/InputXml.cpp

@@ -220,6 +220,15 @@ void InputXml::Process(po::variables_map &vm)
     m_f->m_session = LibUtilities::SessionReader::CreateInstance(
         argc, (char **)argv, files, m_f->m_comm);
 
+    if (vm.count("nparts"))
+    {
+        // make sure have pre-partitioned mesh for nparts option
+        ASSERTL0(boost::icontains(files[0],"_xml"),
+                 "Expect the mesh to have been pre-partitioned when "
+                 " using the\"--nparts\" option. Please use \"--part-only\" "
+                 "option to prepartition xml file.");
+    }
+
     // Free up memory.
     delete[] argv;
 

library/FieldUtils/Module.h

@@ -317,6 +317,11 @@ protected:
         return true;
     }
 
+    bool v_IsSerial(void)
+    {
+        return true;
+    }
+
     bool v_RemoveExistingFiles(void)
     {
         return false;

library/FieldUtils/OutputModules/OutputFileBase.cpp

@@ -218,6 +218,9 @@ void OutputFileBase::Process(po::variables_map &vm)
                         PrintErrorFromExp();
                     }
                 }
+
+                // put outfile back to filename in case of nparts option
+                RegisterConfig("outfile", filename);
             }
             // Restore m_exp
             exp.swap(m_f->m_exp);

library/FieldUtils/OutputModules/OutputFld.cpp

@@ -107,7 +107,8 @@ void OutputFld::OutputFromExp(po::variables_map &vm)
                 }
             }
         }
-        fld->Write(filename, FieldDef, FieldData, m_f->m_fieldMetaDataMap);
+        fld->Write(filename, FieldDef, FieldData, m_f->m_fieldMetaDataMap,
+                   false);
     }
     else
     {

library/FieldUtils/OutputModules/OutputInfo.cpp

@@ -68,75 +68,58 @@ void OutputInfo::Process(po::variables_map &vm)
 {
     // Extract the output filename and extension
     string filename = m_config["outfile"].as<string>();
-    int i = 0;
 
     // partition mesh
     ASSERTL0(m_config["nparts"].as<string>().compare("NotSet") != 0,
              "Need to specify nparts for info output");
-    const int nparts = m_config["nparts"].as<int>();
+    int nparts = m_config["nparts"].as<int>();
 
-    std::vector<std::string> files;
-    // load .xml ending
-    for (auto &x : m_f->m_inputfiles["xml"]) {
-        files.push_back(x);
-    }
-
-    // load any .xml.gz endings
-    for (auto &x: m_f->m_inputfiles["xml.gz"])
-    {
-        files.push_back(x);
-    }
-
-    ASSERTL0(m_f->m_comm->GetSize() == 1,
-             "OutputInfo module should be run in serial.");
-
-    // Default partitioner to use is Scotch. Override default with
-    // command-line flags if they are set.
-    string vPartitionerName = "Scotch";
-    if (m_f->m_session->DefinesCmdLineArgument("use-metis"))
-    {
-        vPartitionerName = "Metis";
-    }
-    if (m_f->m_session->DefinesCmdLineArgument("use-scotch"))
-    {
-        vPartitionerName = "Scotch";
-    }
-
-    // Construct mesh partitioning.
-    SpatialDomains::MeshPartitionSharedPtr meshPartition =
-        SpatialDomains::GetMeshPartitionFactory().CreateInstance(
-            vPartitionerName, m_f->m_session, m_f->m_graph->GetMeshDimension(),
-            m_f->m_graph->CreateMeshEntities(),
-            m_f->m_graph->CreateCompositeDescriptor());
-
-    meshPartition->PartitionMesh(nparts, true);
-
-    // get hold of local partition ids
-    std::vector<std::vector<unsigned int> > ElementIDs(nparts);
-
-    // Populate the list of element ID lists from all processes
-    for (i = 0; i < nparts; ++i)
-    {
-        std::vector<unsigned int> tmp;
-        meshPartition->GetElementIDs(i, tmp);
-        ElementIDs[i] = tmp;
-    }
+    // Input/output file
+    LibUtilities::CommSharedPtr c = m_f->m_comm;
+    std::shared_ptr<LibUtilities::FieldIOXml> fldXml =
+        std::static_pointer_cast<LibUtilities::FieldIOXml>(
+            LibUtilities::GetFieldIOFactory().CreateInstance("Xml", c, true));
 
-    // Set up output names
+    // open file and setup meta data.
+    fs::path pinfilename(filename);
     std::vector<std::string> filenames;
-    for (int i = 0; i < nparts; ++i)
+    std::vector<std::vector<unsigned int> > ElementIDs;
+
+    for (int p = 0; p < nparts; ++p)
     {
-        boost::format pad("P%1$07d.fld");
-        pad % i;
+        boost::format pad("P%1$07d.%2$s");
+        pad % p % "fld";
+
+        fs::path fullpath              = pinfilename / pad.str();
+        string fname                   = LibUtilities::PortablePath(fullpath);
+        LibUtilities::DataSourceSharedPtr dataSource =
+            LibUtilities::XmlDataSource::create(fname);
+
+        std::vector<LibUtilities::FieldDefinitionsSharedPtr> fielddefs;
+        std::vector<unsigned int>              PartElmtIDs;
+
+        // read in header of partition if it exists
+        fldXml->ImportFieldDefs(dataSource,fielddefs,false);
+
+        // create ElmenetIDs list then use
+        for(int i = 0; i < fielddefs.size(); ++i)
+        {
+            for(int j = 0; j < fielddefs[i]->m_elementIDs.size(); ++j)
+            {
+                PartElmtIDs.push_back(fielddefs[i]->m_elementIDs[j]);
+            }
+        }
+
+        ElementIDs.push_back(PartElmtIDs);
         filenames.push_back(pad.str());
     }
 
-    // Write the output file
-    LibUtilities::CommSharedPtr c = m_f->m_comm;
-    std::shared_ptr<LibUtilities::FieldIOXml> fldXml =
-        std::static_pointer_cast<LibUtilities::FieldIOXml>(
-            LibUtilities::GetFieldIOFactory().CreateInstance("Xml", c, true));
-    fldXml->WriteMultiFldFileIDs(filename, filenames, ElementIDs);
+    // Write the Info.xml file
+    string infofile =
+        LibUtilities::PortablePath(pinfilename / fs::path("Info.xml"));
+
+    fldXml->WriteMultiFldFileIDs(infofile,filenames, ElementIDs);
 }
+
 }
 }

library/FieldUtils/OutputModules/OutputTecplot.cpp

@@ -75,6 +75,10 @@ OutputTecplot::OutputTecplot(FieldSharedPtr f) : OutputFileBase(f),
                                                  m_oneOutputFile(false)
 {
     m_requireEquiSpaced = true;
+    m_config["double"] =
+        ConfigOption(true, "0", "Write double-precision (binary) or scientific "
+                                "format data: more accurate but more disk space"
+                                " required");
 }
 
 OutputTecplot::~OutputTecplot()
@@ -92,7 +96,7 @@ void OutputTecplot::Process(po::variables_map &vm)
     {
         m_oneOutputFile = (m_f->m_comm->GetSize()> 1);
     }
-    
+
     OutputFileBase::Process(vm);
 }
 
@@ -453,6 +457,13 @@ void OutputTecplotBinary::WriteTecplotHeader(std::ofstream &outfile,
  */
 void OutputTecplot::WriteTecplotZone(std::ofstream &outfile)
 {
+    bool useDoubles = m_config["double"].as<bool>();
+
+    if (useDoubles)
+    {
+        outfile << std::scientific;
+    }
+
     // Write either points or finite element block
     if (m_zoneType != eOrdered)
     {

library/FieldUtils/OutputModules/OutputTecplot.h

@@ -148,9 +148,6 @@ public:
     OutputTecplotBinary(FieldSharedPtr f) : OutputTecplot(f)
     {
         m_binary = true;
-        m_config["double"] =
-            ConfigOption(true, "0", "Write double-precision data: more "
-                                    "accurate but more disk space required");
     }
 
     virtual ~OutputTecplotBinary()

library/FieldUtils/ProcessModules/ProcessWSS.cpp

@@ -70,19 +70,6 @@ void ProcessWSS::Process(po::variables_map &vm)
     int expdim  = m_f->m_graph->GetSpaceDimension();
     m_spacedim  = expdim + m_f->m_numHomogeneousDir;
 
-    if (m_spacedim == 2)
-    {
-        m_f->m_variables.push_back("Shear_x");
-        m_f->m_variables.push_back("Shear_y");
-        m_f->m_variables.push_back("Shear_mag");
-    }
-    else
-    {
-        m_f->m_variables.push_back("Shear_x");
-        m_f->m_variables.push_back("Shear_y");
-        m_f->m_variables.push_back("Shear_z");
-        m_f->m_variables.push_back("Shear_mag");
-    }
 
     if (m_f->m_exp[0]->GetNumElmts() == 0)
     {
@@ -108,11 +95,14 @@ void ProcessWSS::Process(po::variables_map &vm)
     Array<OneD, MultiRegions::ExpListSharedPtr> BndExp(nshear);
     Array<OneD, MultiRegions::ExpListSharedPtr> BndElmtExp(nfields);
 
-    // Resize m_exp
-    m_f->m_exp.resize(nfields + nshear);
-    for (i = 0; i < nshear; ++i)
+    // will resuse nfields expansions to write shear components.
+    if(nshear > nfields)
     {
-        m_f->m_exp[nfields + i] = m_f->AppendExpList(m_f->m_numHomogeneousDir);
+        m_f->m_exp.resize(nshear);
+        for (i = nfields; i < nshear; ++i)
+        {
+            m_f->m_exp[nfields + i] = m_f->AppendExpList(m_f->m_numHomogeneousDir);
+        }
     }
 
     // Create map of boundary ids for partitioned domains
@@ -137,8 +127,7 @@ void ProcessWSS::Process(po::variables_map &vm)
             // bnd
             for (i = 0; i < nshear; i++)
             {
-                BndExp[i] =
-                    m_f->m_exp[nfields + i]->UpdateBndCondExpansion(bnd);
+                BndExp[i] = m_f->m_exp[i]->UpdateBndCondExpansion(bnd);
             }
             for (i = 0; i < nfields; i++)
             {
@@ -294,6 +283,20 @@ void ProcessWSS::Process(po::variables_map &vm)
                                          BndExp[nshear - 1]->UpdateCoeffs());
         }
     }
+
+    if (m_spacedim == 2)
+    {
+        m_f->m_variables[0] = "Shear_x";
+        m_f->m_variables[1] = "Shear_y";
+        m_f->m_variables[2] = "Shear_mag";
+    }
+    else
+    {
+        m_f->m_variables[0] = "Shear_x";
+        m_f->m_variables[1] = "Shear_y";
+        m_f->m_variables[2] = "Shear_z";
+        m_f->m_variables[3] = "Shear_mag";
+    }
 }
 
 void ProcessWSS::GetViscosity(
@@ -369,14 +372,19 @@ void ProcessWSS::GetViscosity(
             Vmath::Smul(npoints, cv_inv, energy, 1, temperature, 1 );
 
             // Variable viscosity through the Sutherland's law
+            //
+            // WARNING, if this routine is modified the same must be done in the
+            // CompressibleFlowSolver function in VariableConverter.cpp
+            // (this class should be restructured).
+
+            const NekDouble C = .38175;
             NekDouble mu_star = m_mu;
             NekDouble T_star  = m_pInf / (m_rhoInf * m_gasConstant);
             NekDouble ratio;
             for (int i = 0; i < npoints; ++i)
             {
                 ratio = temperature[i] / T_star;