Addressed remaining comments in review.

library/MultiRegions/ExpList.cpp

@@ -2033,7 +2033,12 @@ namespace Nektar
                 {
                     for(int i = 0; i < NumHomoStrip; ++i)
                     {
-                        LibUtilities::FieldDefinitionsSharedPtr fdef  = MemoryManager<LibUtilities::FieldDefinitions>::AllocateSharedPtr(shape, elementIDs, basis, UniOrder, numModes,fields, NumHomoDir, HomoLen, HomoZIDs, HomoYIDs);
+                        LibUtilities::FieldDefinitionsSharedPtr fdef  =
+                            MemoryManager<LibUtilities::FieldDefinitions>::
+                                AllocateSharedPtr(shape, elementIDs, basis,
+                                                  UniOrder, numModes,fields,
+                                                  NumHomoDir, HomoLen, HomoZIDs,
+                                                  HomoYIDs);
                         fielddef.push_back(fdef);
                     }
                 }

library/MultiRegions/ExpList.h

@@ -64,13 +64,13 @@ namespace Nektar
         class GlobalMatrix;
 
         enum Direction
-    {
-        eX,
-        eY,
-        eZ,
-        eS,
-        eN
-    };
+        {
+            eX,
+            eY,
+            eZ,
+            eS,
+            eN
+        };
 
         enum ExpansionType
         {
@@ -84,11 +84,11 @@ namespace Nektar
         };       
         
         MultiRegions::Direction const DirCartesianMap[] =
-            {
-                eX,
-                eY,
-                eZ
-            }; 
+        {
+            eX,
+            eY,
+            eZ
+        }; 
     
         /// A map between global matrix keys and their associated block
         /// matrices.

library/MultiRegions/ExpList2D.cpp

@@ -1168,10 +1168,10 @@ namespace Nektar
         }
 
         void ExpList2D::v_WriteVtkPieceHeader(
-            std::ostream &outfile, 
-            int expansion, 
-	    int istrip)
-		{
+            std::ostream &outfile,
+            int expansion,
+            int istrip)
+        {
             int i,j;
             int nquad0 = (*m_exp)[expansion]->GetNumPoints(0);
             int nquad1 = (*m_exp)[expansion]->GetNumPoints(1);

library/SpatialDomains/PrismGeom.cpp

@@ -310,7 +310,7 @@ namespace Nektar
                 Lcoords[2] = 2.0*delta - 1.0;
 
                 // Set ptdist to distance to nearest vertex 
-                for(int i = 0; i < 5; ++i)
+                for(int i = 0; i < 6; ++i)
                 {
                     ptdist = min(ptdist,r.dist(*m_verts[i]));
                 }

utilities/FieldConvert/InputModules/InputFld.cpp

@@ -29,7 +29,7 @@
 //  FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
 //  DEALINGS IN THE SOFTWARE.
 //
-//  Description: GMSH converter.
+//  Description: Reads a Nektar++ FLD file.
 //
 ////////////////////////////////////////////////////////////////////////////////
 
@@ -216,8 +216,7 @@ void InputFld::Process(po::variables_map &vm)
                     {
                         m_f->m_exp[s*nfields+i] =
                             m_f->AppendExpList(
-                                m_f->m_fielddef[0]->m_numHomogeneousDir
-                            );
+                                m_f->m_fielddef[0]->m_numHomogeneousDir);
                     }
                 }
             }

utilities/FieldConvert/Module.h

@@ -61,7 +61,8 @@ namespace Nektar
          * Denotes different types of mesh converter modules: so far only
          * input, output and process modules are defined.
          */
-        enum ModuleType {
+        enum ModuleType
+        {
             eInputModule,
             eProcessModule,
             eOutputModule,
@@ -87,12 +88,12 @@ namespace Nektar
              * @param defValue  Default value of the option.
              * @param desc      Description of the option.
              */
-        ConfigOption(bool isBool, string defValue, string desc) :
-            m_isBool(isBool), m_beenSet(false), m_value(),
-                m_defValue(defValue), m_desc(desc) {}
-        ConfigOption() :
-            m_isBool(false), m_beenSet(false), m_value(),
-                m_defValue(), m_desc() {}
+            ConfigOption(bool isBool, string defValue, string desc) :
+                m_isBool(isBool), m_beenSet(false), m_value(),
+                    m_defValue(defValue), m_desc(desc) {}
+            ConfigOption() :
+                m_isBool(false), m_beenSet(false), m_value(),
+                    m_defValue(), m_desc() {}
 
             /**
              * @brief Re-interpret the value stored in #value as some type using
@@ -246,9 +247,11 @@ namespace Nektar
             virtual ~FieldConvertComm() {}
             void v_SplitComm(int pRows, int pColumns)
             {
-            // Compute row and column in grid.
-                m_commRow    = boost::shared_ptr<FieldConvertComm>(new FieldConvertComm(pColumns,m_rank));
-                m_commColumn = boost::shared_ptr<FieldConvertComm>(new FieldConvertComm(pRows,0));
+                // Compute row and column in grid.
+                m_commRow    = boost::shared_ptr<FieldConvertComm>(
+                                    new FieldConvertComm(pColumns,m_rank));
+                m_commColumn = boost::shared_ptr<FieldConvertComm>(
+                                    new FieldConvertComm(pRows,0));
             }
 
         protected:

utilities/FieldConvert/OutputModules/OutputInfo.cpp

@@ -29,7 +29,7 @@
 //  FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
 //  DEALINGS IN THE SOFTWARE.
 //
-//  Description: FLD file format output.
+//  Description: Generates a Nektar++ info XML file.
 //
 ////////////////////////////////////////////////////////////////////////////////
 

utilities/FieldConvert/OutputModules/OutputXml.cpp

@@ -41,39 +41,41 @@ using namespace std;
 
 namespace Nektar
 {
-    namespace Utilities
-    {
-        ModuleKey OutputXml::m_className =
-            GetModuleFactory().RegisterCreatorFunction(
-                ModuleKey(eOutputModule, "xml"), OutputXml::create,
-                "Writes an XML file.");
+namespace Utilities
+{
 
-        OutputXml::OutputXml(FieldSharedPtr f) : OutputModule(f)
-        {
+ModuleKey OutputXml::m_className =
+    GetModuleFactory().RegisterCreatorFunction(
+        ModuleKey(eOutputModule, "xml"), OutputXml::create,
+        "Writes an XML file.");
 
-        }
+OutputXml::OutputXml(FieldSharedPtr f) : OutputModule(f)
+{
 
-        OutputXml::~OutputXml()
-        {
-        }
-        
-        void OutputXml::Process(po::variables_map &vm)
-        {
-            if(!m_f->m_exp.size()) // do nothing if no expansion defined
-            {
-                return; 
-            }
+}
 
-            if (m_f->m_verbose)
-            {
-                cout << "OutputXml: Writing file..." << endl;
-            }
+OutputXml::~OutputXml()
+{
+}
 
-            // Extract the output filename and extension
-            string filename = m_config["outfile"].as<string>();
+void OutputXml::Process(po::variables_map &vm)
+{
+    if(!m_f->m_exp.size()) // do nothing if no expansion defined
+    {
+        return;
+    }
 
-            m_f->m_graph->WriteGeometry(filename);
-            cout << "Written file: " << filename << endl;
-        }        
+    if (m_f->m_verbose)
+    {
+        cout << "OutputXml: Writing file..." << endl;
     }
+
+    // Extract the output filename and extension
+    string filename = m_config["outfile"].as<string>();
+
+    m_f->m_graph->WriteGeometry(filename);
+    cout << "Written file: " << filename << endl;
+}
+
+}
 }

utilities/FieldConvert/OutputModules/OutputXml.h

@@ -41,25 +41,25 @@
 
 namespace Nektar
 {
-    namespace Utilities
-    {
-        /// Converter from fld to vtk.
-        class OutputXml : public OutputModule
-        {
-        public:
-            /// Creates an instance of this class
-            static boost::shared_ptr<Module> create(FieldSharedPtr f) {
-                return MemoryManager<OutputXml>::AllocateSharedPtr(f);
-            }
-            static ModuleKey m_className;
-            
-            OutputXml(FieldSharedPtr f);
-            virtual ~OutputXml();
-            
-            /// Write fld to output file.
-            virtual void Process(po::variables_map &vm);
-        };
+namespace Utilities
+{
+/// Converter from fld to vtk.
+class OutputXml : public OutputModule
+{
+public:
+    /// Creates an instance of this class
+    static boost::shared_ptr<Module> create(FieldSharedPtr f) {
+        return MemoryManager<OutputXml>::AllocateSharedPtr(f);
     }
+    static ModuleKey m_className;
+
+    OutputXml(FieldSharedPtr f);
+    virtual ~OutputXml();
+
+    /// Write fld to output file.
+    virtual void Process(po::variables_map &vm);
+};
+}
 }
 
 #endif

utilities/FieldConvert/ProcessModules/ProcessAddFld.cpp

@@ -128,14 +128,13 @@ void ProcessAddFld::Process(po::variables_map &vm)
 
     if(samelength == true)
     {
-
         for(int i = 0; i < m_f->m_data.size(); ++i)
         {
             int datalen = m_f->m_data[i].size();
 
-            Vmath::Vadd(datalen, &(m_f->m_data[i][0]),         1,
+            Vmath::Vadd(datalen, &(m_f->m_data[i][0]),       1,
                                  &(fromField->m_data[i][0]), 1,
-                                 &(m_f->m_data[i][0]),         1);
+                                 &(m_f->m_data[i][0]),       1);
         }
     }
     else

utilities/FieldConvert/ProcessModules/ProcessAddFld.h

@@ -29,7 +29,7 @@
 //  FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
 //  DEALINGS IN THE SOFTWARE.
 //
-//  Description: Computes C0 projection.
+//  Description: Add a field to the input field.
 //
 ////////////////////////////////////////////////////////////////////////////////
 

utilities/FieldConvert/ProcessModules/ProcessDeform.cpp

@@ -29,7 +29,7 @@
 //  FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
 //  DEALINGS IN THE SOFTWARE.
 //
-//  Description: Computes Q Criterion field.
+//  Description: Deforms grid.
 //
 ////////////////////////////////////////////////////////////////////////////////
 
@@ -39,11 +39,7 @@ using namespace std;
 
 #include "ProcessDeform.h"
 
-#include <StdRegions/StdSegExp.h>
-#include <StdRegions/StdQuadExp.h>
-#include <StdRegions/StdTriExp.h>
-#include <LibUtilities/BasicUtils/SharedArray.hpp>
-#include <LibUtilities/BasicUtils/ParseUtils.hpp>
+#include <MultiRegions/ExpList.h>
 #include <SolverUtils/Core/Deform.h>
 
 namespace Nektar

utilities/FieldConvert/ProcessModules/ProcessDeform.h

@@ -29,39 +29,37 @@
 //  FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
 //  DEALINGS IN THE SOFTWARE.
 //
-//  Description: Computes Q Criterion field.
+//  Description: Deforms grid
 //
 ////////////////////////////////////////////////////////////////////////////////
 
-#ifndef UTILITIES_PREPROCESSING_FIELDCONVERT_PROCESSQCRITERION
-#define UTILITIES_PREPROCESSING_FIELDCONVERT_PROCESSQCRITERION
+#ifndef UTILITIES_FIELDCONVERT_PROCESSDEFORM
+#define UTILITIES_FIELDCONVERT_PROCESSDEFORM
 
 #include "../Module.h"
 
 namespace Nektar
 {
-    namespace Utilities
-    {
-        /**
-         * @brief This processing module calculates the Q Criterion and adds it
-         * as an extra-field to the output file.
-         */
-        class ProcessDeform : public ProcessModule
-        {
-        public:
-            /// Creates an instance of this class
-            static boost::shared_ptr<Module> create(FieldSharedPtr f) {
-                return MemoryManager<ProcessDeform>::AllocateSharedPtr(f);
-            }
-            static ModuleKey className;
-            
-            ProcessDeform(FieldSharedPtr f);
-            virtual ~ProcessDeform();
-            
-            /// Write mesh to output file.
-            virtual void Process(po::variables_map &vm);
-        };
+namespace Utilities
+{
+
+class ProcessDeform : public ProcessModule
+{
+public:
+    /// Creates an instance of this class
+    static boost::shared_ptr<Module> create(FieldSharedPtr f) {
+        return MemoryManager<ProcessDeform>::AllocateSharedPtr(f);
     }
+    static ModuleKey className;
+
+    ProcessDeform(FieldSharedPtr f);
+    virtual ~ProcessDeform();
+
+    /// Write mesh to output file.
+    virtual void Process(po::variables_map &vm);
+};
+
+}
 }
 
 #endif

utilities/FieldConvert/ProcessModules/ProcessDisplacement.cpp

@@ -29,7 +29,7 @@
 //  FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
 //  DEALINGS IN THE SOFTWARE.
 //
-//  Description: Computes Q Criterion field.
+//  Description: Deforms a mesh given input field defining displacement.
 //
 ////////////////////////////////////////////////////////////////////////////////
 

utilities/FieldConvert/ProcessModules/ProcessDisplacement.h

@@ -29,12 +29,12 @@
 //  FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
 //  DEALINGS IN THE SOFTWARE.
 //
-//  Description: Computes Q Criterion field.
+//  Description: Deforms a mesh given input field defining displacement.
 //
 ////////////////////////////////////////////////////////////////////////////////
 
-#ifndef UTILITIES_PREPROCESSING_FIELDCONVERT_PROCESSDISPLACEMENT
-#define UTILITIES_PREPROCESSING_FIELDCONVERT_PROCESSDISPLACEMENT
+#ifndef UTILITIES_FIELDCONVERT_PROCESSDISPLACEMENT
+#define UTILITIES_FIELDCONVERT_PROCESSDISPLACEMENT
 
 #include "../Module.h"
 
@@ -42,25 +42,23 @@ namespace Nektar
 {
 namespace Utilities
 {
-    /**
-     * @brief This processing module calculates the Q Criterion and adds it
-     * as an extra-field to the output file.
-     */
-    class ProcessDisplacement : public ProcessModule
-    {
-    public:
-        /// Creates an instance of this class
-        static boost::shared_ptr<Module> create(FieldSharedPtr f) {
-            return MemoryManager<ProcessDisplacement>::AllocateSharedPtr(f);
-        }
-        static ModuleKey className;
-        
-        ProcessDisplacement(FieldSharedPtr f);
-        virtual ~ProcessDisplacement();
-        
-        /// Write mesh to output file.
-        virtual void Process(po::variables_map &vm);
-    };
+
+class ProcessDisplacement : public ProcessModule
+{
+public:
+    /// Creates an instance of this class
+    static boost::shared_ptr<Module> create(FieldSharedPtr f) {
+        return MemoryManager<ProcessDisplacement>::AllocateSharedPtr(f);
+    }
+    static ModuleKey className;
+
+    ProcessDisplacement(FieldSharedPtr f);
+    virtual ~ProcessDisplacement();
+
+    /// Write mesh to output file.
+    virtual void Process(po::variables_map &vm);
+};
+
 }
 }
 

utilities/FieldConvert/ProcessModules/ProcessEquiSpacedOutput.cpp

@@ -209,7 +209,7 @@ void ProcessEquiSpacedOutput::SetupEquiSpacedField(void)
                 int np0 = e->GetBasis(0)->GetNumPoints();
                 int np1 = e->GetBasis(1)->GetNumPoints();
                 int np = max(np0,np1);
-                newpoints     = LibUtilities::StdTriData::
+                newpoints = LibUtilities::StdTriData::
                                     getNumberOfCoefficients(np,np);
             }
             break;
@@ -219,7 +219,7 @@ void ProcessEquiSpacedOutput::SetupEquiSpacedField(void)
                 int np1 = e->GetBasis(1)->GetNumPoints();
                 int np = max(np0,np1);
 
-                newpoints  = LibUtilities::StdQuadData::
+                newpoints = LibUtilities::StdQuadData::
                                     getNumberOfCoefficients(np,np);
             }
             break;
@@ -230,7 +230,7 @@ void ProcessEquiSpacedOutput::SetupEquiSpacedField(void)
                 int np2 = e->GetBasis(2)->GetNumPoints();
                 int np = max(np0,max(np1,np2));
 
-                newpoints  = LibUtilities::StdTetData::
+                newpoints = LibUtilities::StdTetData::
                                     getNumberOfCoefficients(np,np,np);
             }
             break;
@@ -241,7 +241,7 @@ void ProcessEquiSpacedOutput::SetupEquiSpacedField(void)
                 int np2 = e->GetBasis(2)->GetNumPoints();
                 int np = max(np0,max(np1,np2));
 
-                newpoints  = LibUtilities::StdPrismData::
+                newpoints = LibUtilities::StdPrismData::
                                     getNumberOfCoefficients(np,np,np);
             }
             break;
@@ -252,7 +252,7 @@ void ProcessEquiSpacedOutput::SetupEquiSpacedField(void)
                 int np2 = e->GetBasis(2)->GetNumPoints();
                 int np = max(np0,max(np1,np2));
 
-                newpoints     = LibUtilities::StdPyrData::
+                newpoints = LibUtilities::StdPyrData::
                                     getNumberOfCoefficients(np,np,np);
             }
             break;
@@ -263,7 +263,7 @@ void ProcessEquiSpacedOutput::SetupEquiSpacedField(void)
                 int np2 = e->GetBasis(2)->GetNumPoints();
                 int np = max(np0,max(np1,np2));
 
-                newpoints     = LibUtilities::StdPyrData::
+                newpoints = LibUtilities::StdPyrData::
                                     getNumberOfCoefficients(np,np,np);
             }
             break;
@@ -372,7 +372,6 @@ void ProcessEquiSpacedOutput::SetupEquiSpacedField(void)
 
             if(m_config["modalenergy"].m_beenSet)
             {
-
                 Array<OneD, const NekDouble> phys = m_f->m_exp[n]->GetPhys();
                 for(int i = 0; i < nel; ++i)
                 {
@@ -412,16 +411,17 @@ void ProcessEquiSpacedOutput::SetupEquiSpacedField(void)
 }
 
 
-    void ProcessEquiSpacedOutput::GenOrthoModes(int n,
-                                                const Array<OneD,const NekDouble> &phys,
-                                                Array<OneD, NekDouble> &coeffs)
+    void ProcessEquiSpacedOutput::GenOrthoModes(
+            int n,
+            const Array<OneD,const NekDouble> &phys,
+                  Array<OneD, NekDouble> &coeffs)
     {
         LocalRegions::ExpansionSharedPtr e;
         e = m_f->m_exp[0]->GetExp(n);
 
-                switch(e->DetShapeType())
+        switch(e->DetShapeType())
         {
-        case LibUtilities::eTriangle:
+            case LibUtilities::eTriangle:
             {
                 int np0 = e->GetBasis(0)->GetNumPoints();
                 int np1 = e->GetBasis(1)->GetNumPoints();
@@ -443,9 +443,9 @@ void ProcessEquiSpacedOutput::SetupEquiSpacedField(void)
                                        phys,Ba,Bb,tophys);
 
                 OrthoExp.FwdTrans(tophys,coeffs);
+                break;
             }
-            break;
-        case LibUtilities::eQuadrilateral:
+            case LibUtilities::eQuadrilateral:
             {
                 int np0 = e->GetBasis(0)->GetNumPoints();
                 int np1 = e->GetBasis(1)->GetNumPoints();
@@ -465,12 +465,11 @@ void ProcessEquiSpacedOutput::SetupEquiSpacedField(void)
                                        phys,Ba,Bb,tophys);
 
                 OrthoExp.FwdTrans(phys,coeffs);
+                break;
             }
-            break;
-        default:
-            ASSERTL0(false,"Shape needs setting up");
-            break;
-
+            default:
+                ASSERTL0(false,"Shape needs setting up");
+                break;
         }
     }
 

utilities/FieldConvert/ProcessModules/ProcessEquiSpacedOutput.h

@@ -29,7 +29,7 @@
 //  FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
 //  DEALINGS IN THE SOFTWARE.
 //
-//  Description: Computes vorticity field.
+//  Description: Set up fields as interpolation to equispaced output.
 //
 ////////////////////////////////////////////////////////////////////////////////
 

utilities/FieldConvert/ProcessModules/ProcessGrad.cpp

@@ -69,13 +69,8 @@ void ProcessGrad::Process(po::variables_map &vm)
 
     int i, j;
     int expdim    = m_f->m_graph->GetMeshDimension();
-    int spacedim  = expdim;
-    if ((m_f->m_fielddef[0]->m_numHomogeneousDir) == 1 ||
-        (m_f->m_fielddef[0]->m_numHomogeneousDir) == 2)
-    {
-        spacedim = 3;
-    }
-    int nfields = m_f->m_fielddef[0]->m_fields.size();
+    int spacedim  = m_f->m_fielddef[0]->m_numHomogeneousDir + expdim;
+    int nfields   = m_f->m_fielddef[0]->m_fields.size();
     int addfields = nfields*spacedim;
 
     int npoints = m_f->m_exp[0]->GetNpoints();

utilities/FieldConvert/ProcessModules/ProcessInterpField.h

@@ -29,12 +29,12 @@
 //  FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
 //  DEALINGS IN THE SOFTWARE.
 //
-//  Description: Computes vorticity field.
+//  Description: Interpolate one field to another.
 //
 ////////////////////////////////////////////////////////////////////////////////
 
-#ifndef UTILITIES_PREPROCESSING_FIELDCONVERT_PROCESSFIELD