Run new FieldUtils library through clang-format

.clang-format

@@ -14,4 +14,3 @@ IndentCaseLabels: true
 Standard: Cpp03
 AccessModifierOffset: -4
 BinPackParameters: false
-BinPackArguments: false

library/FieldUtils/FieldUtilsDeclspec.h

@@ -34,16 +34,15 @@
 #define NEKTAR_FIELD_UTILS_DECLSPEC_H
 
 #if defined(_MSC_VER)
-    #ifdef FIELD_UTILS_EXPORTS
-        #define FIELD_UTILS_EXPORT _declspec(dllexport)
-    #else
-        #define FIELD_UTILS_EXPORT _declspec(dllimport)
-    #endif
+#ifdef FIELD_UTILS_EXPORTS
+#define FIELD_UTILS_EXPORT _declspec(dllexport)
 #else
-    #define FIELD_UTILS_EXPORT
+#define FIELD_UTILS_EXPORT _declspec(dllimport)
+#endif
+#else
+#define FIELD_UTILS_EXPORT
 #endif
 
 #define LOKI_CLASS_LEVEL_THREADING
 
-#endif //NEKTAR_FIELD_UTILS_DECLSPEC_H
-
+#endif // NEKTAR_FIELD_UTILS_DECLSPEC_H

library/FieldUtils/InputModules/InputDat.cpp

@@ -33,12 +33,12 @@
 //
 ////////////////////////////////////////////////////////////////////////////////
 
-#include <string>
 #include <iostream>
+#include <string>
 using namespace std;
 
-#include <LibUtilities/BasicUtils/PtsIO.h>
 #include <LibUtilities/BasicUtils/PtsField.h>
+#include <LibUtilities/BasicUtils/PtsIO.h>
 
 #include <tinyxml.h>
 
@@ -51,9 +51,9 @@ namespace FieldUtils
 
 ModuleKey InputDat::m_className[1] = {
     GetModuleFactory().RegisterCreatorFunction(
-            ModuleKey(eInputModule, "dat"),
-            InputDat::create,
-            "Reads Tecplot dat file for FE block triangular format."),
+        ModuleKey(eInputModule, "dat"),
+        InputDat::create,
+        "Reads Tecplot dat file for FE block triangular format."),
 };
 
 /**
@@ -65,7 +65,6 @@ InputDat::InputDat(FieldSharedPtr f) : InputModule(f)
     m_allowedFiles.insert("dat");
 }
 
-
 /**
  *
  */
@@ -73,29 +72,27 @@ InputDat::~InputDat()
 {
 }
 
-
 /**
  *
  */
 void InputDat::Process(po::variables_map &vm)
 {
 
-    if(m_f->m_verbose)
+    if (m_f->m_verbose)
     {
-        if(m_f->m_comm->TreatAsRankZero())
+        if (m_f->m_comm->TreatAsRankZero())
         {
             cout << "Processing input dat file" << endl;
         }
     }
 
-    string      line, word, tag;
+    string line, word, tag;
     std::ifstream datFile;
     stringstream s;
 
     // Open the file stream.
     string fname = m_f->m_inputfiles["dat"][0];
 
-
     datFile.open(fname.c_str());
     if (!datFile.good())
     {
@@ -111,17 +108,18 @@ void InputDat::Process(po::variables_map &vm)
     {
         getline(datFile, line);
 
-        if(line.find("VARIABLES") != string::npos)
+        if (line.find("VARIABLES") != string::npos)
         {
-            std::size_t  pos = line.find('=');
+            std::size_t pos = line.find('=');
             pos++;
 
             // note this expects a comma separated list but
             // does not work for white space separated lists!
             bool valid = ParseUtils::GenerateOrderedStringVector(
-                                line.substr(pos).c_str(), fieldNames);
-            ASSERTL0(valid,"Unable to process list of field variable in "
-                     " VARIABLES list:  "+ line.substr(pos));
+                line.substr(pos).c_str(), fieldNames);
+            ASSERTL0(valid, "Unable to process list of field variable in "
+                            " VARIABLES list:  " +
+                                line.substr(pos));
 
             // remove coordinates from fieldNames
             fieldNames.erase(fieldNames.begin(), fieldNames.begin() + dim);
@@ -141,9 +139,9 @@ void InputDat::Process(po::variables_map &vm)
     {
         getline(datFile, line);
 
-        if((line.find("ZONE") != string::npos)||
-           (line.find("Zone") != string::npos)||
-           (line.find("zone") != string::npos))
+        if ((line.find("ZONE") != string::npos) ||
+            (line.find("Zone") != string::npos) ||
+            (line.find("zone") != string::npos))
         {
             ReadTecplotFEBlockZone(datFile, line, pts, ptsConn);
         }
@@ -151,88 +149,81 @@ void InputDat::Process(po::variables_map &vm)
 
     datFile.close();
 
-    m_f->m_fieldPts =
-        MemoryManager<LibUtilities::PtsField>::AllocateSharedPtr(
-            dim, fieldNames, pts);
+    m_f->m_fieldPts = MemoryManager<LibUtilities::PtsField>::AllocateSharedPtr(
+        dim, fieldNames, pts);
     m_f->m_fieldPts->SetPtsType(LibUtilities::ePtsTriBlock);
     m_f->m_fieldPts->SetConnectivity(ptsConn);
 }
 
-
 /**
  *
  */
-void InputDat::ReadTecplotFEBlockZone(
-    std::ifstream   &datFile,
-    string          &line,
-    Array<OneD, Array<OneD, NekDouble> > &pts,
-    vector<Array<OneD, int> > &ptsConn)
+void InputDat::ReadTecplotFEBlockZone(std::ifstream &datFile,
+                                      string &line,
+                                      Array<OneD, Array<OneD, NekDouble> > &pts,
+                                      vector<Array<OneD, int> > &ptsConn)
 {
     ASSERTL0(line.find("FEBlock") != string::npos,
              "Routine only set up for FEBLock format");
-    ASSERTL0(line.find("ET") != string::npos,
-             "Routine only set up TRIANLES");
+    ASSERTL0(line.find("ET") != string::npos, "Routine only set up TRIANLES");
 
     // read the number of nodes
 
     stringstream s;
     string tag;
-    int start,end;
+    int start, end;
 
     s.clear();
     s.str(line);
     tag = s.str();
 
     // read the number of vertices
-    start = tag.find("N=");
-    end   = tag.find_first_of(',',start);
-    int nvert = atoi(tag.substr(start+2,end).c_str());
+    start     = tag.find("N=");
+    end       = tag.find_first_of(',', start);
+    int nvert = atoi(tag.substr(start + 2, end).c_str());
 
     // read the number of elements
-    start = tag.find("E=");
-    end   = tag.find_first_of(',',start);
-    int nelmt = atoi(tag.substr(start+2,end).c_str());
+    start     = tag.find("E=");
+    end       = tag.find_first_of(',', start);
+    int nelmt = atoi(tag.substr(start + 2, end).c_str());
 
     // set-up or extend m_pts array;
     int norigpts  = pts[0].num_elements();
     int totfields = pts.num_elements();
     Array<OneD, Array<OneD, NekDouble> > origpts(totfields);
-    for(int i = 0; i < totfields; ++i)
+    for (int i = 0; i < totfields; ++i)
     {
         origpts[i] = pts[i];
-        pts[i] = Array<OneD, NekDouble>(norigpts + nvert);
+        pts[i]     = Array<OneD, NekDouble>(norigpts + nvert);
     }
 
     NekDouble value;
-    for(int n = 0; n < totfields; ++n)
+    for (int n = 0; n < totfields; ++n)
     {
 
-        for(int i = 0; i < norigpts; ++i)
+        for (int i = 0; i < norigpts; ++i)
         {
             pts[n][i] = origpts[n][i];
         }
-        for(int i = 0; i < nvert; ++i)
+        for (int i = 0; i < nvert; ++i)
         {
             datFile >> value;
-            pts[n][norigpts+i] = value;
+            pts[n][norigpts + i] = value;
         }
     }
 
     // read connectivity and add to list
     int intvalue;
-    Array<OneD, int> conn(3*nelmt);
-    for(int i = 0; i < 3*nelmt; ++i)
+    Array<OneD, int> conn(3 * nelmt);
+    for (int i = 0; i < 3 * nelmt; ++i)
     {
         datFile >> intvalue;
-        intvalue -=1; // decrement intvalue by 1 for c array convention
+        intvalue -= 1; // decrement intvalue by 1 for c array convention
         conn[i] = norigpts + intvalue;
     }
     ptsConn.push_back(conn);
 
     getline(datFile, line);
 }
-
-
 }
 }
-

library/FieldUtils/InputModules/InputDat.h

@@ -46,30 +46,30 @@ namespace FieldUtils
 /// Input module for Xml files.
 class InputDat : public InputModule
 {
-    public:
-        InputDat(FieldSharedPtr f);
-        virtual ~InputDat();
-        virtual void Process(po::variables_map &vm);
+public:
+    InputDat(FieldSharedPtr f);
+    virtual ~InputDat();
+    virtual void Process(po::variables_map &vm);
 
-        /// Creates an instance of this class
-        static ModuleSharedPtr create(FieldSharedPtr f)
-        {
-            return MemoryManager<InputDat>::AllocateSharedPtr(f);
-        }
-        /// %ModuleKey for class.
-        static ModuleKey m_className[];
+    /// Creates an instance of this class
+    static ModuleSharedPtr create(FieldSharedPtr f)
+    {
+        return MemoryManager<InputDat>::AllocateSharedPtr(f);
+    }
+    /// %ModuleKey for class.
+    static ModuleKey m_className[];
 
-        virtual std::string GetModuleName()
-        {
-            return "InputDat";
-        }
+    virtual std::string GetModuleName()
+    {
+        return "InputDat";
+    }
 
-    private:
-        void ReadTecplotFEBlockZone(std::ifstream &datFile, string &line,
-                                    Array<OneD, Array<OneD, NekDouble> > &pts,
-                                    vector<Array<OneD, int> > &ptsConn);
+private:
+    void ReadTecplotFEBlockZone(std::ifstream &datFile,
+                                string &line,
+                                Array<OneD, Array<OneD, NekDouble> > &pts,
+                                vector<Array<OneD, int> > &ptsConn);
 };
-
 }
 }
 #endif

library/FieldUtils/InputModules/InputFld.h

@@ -48,27 +48,26 @@ namespace FieldUtils
  */
 class InputFld : public InputModule
 {
-    public:
-        InputFld(FieldSharedPtr f);
-        virtual ~InputFld();
-        virtual void Process(po::variables_map &vm);
+public:
+    InputFld(FieldSharedPtr f);
+    virtual ~InputFld();
+    virtual void Process(po::variables_map &vm);
 
-        /// Creates an instance of this class
-        static ModuleSharedPtr create(FieldSharedPtr f)
-        {
-            return MemoryManager<InputFld>::AllocateSharedPtr(f);
-        }
-        /// %ModuleKey for class.
-        static ModuleKey m_className[];
+    /// Creates an instance of this class
+    static ModuleSharedPtr create(FieldSharedPtr f)
+    {
+        return MemoryManager<InputFld>::AllocateSharedPtr(f);
+    }
+    /// %ModuleKey for class.
+    static ModuleKey m_className[];
 
-        virtual std::string GetModuleName()
-        {
-            return "InputFld";
-        }
+    virtual std::string GetModuleName()
+    {
+        return "InputFld";
+    }
 
-    private:
+private:
 };
-
 }
 }
 

library/FieldUtils/InputModules/InputPts.cpp

@@ -33,12 +33,12 @@
 //
 ////////////////////////////////////////////////////////////////////////////////
 
-#include <string>
 #include <iostream>
+#include <string>
 using namespace std;
 
-#include <LibUtilities/BasicUtils/PtsIO.h>
 #include <LibUtilities/BasicUtils/PtsField.h>
+#include <LibUtilities/BasicUtils/PtsIO.h>
 
 #include <tinyxml.h>
 
@@ -56,7 +56,6 @@ ModuleKey InputPts::m_className[5] = {
         ModuleKey(eInputModule, "pts.gz"), InputPts::create, "Reads Pts file."),
 };
 
-
 /**
  * @brief Set up InputPts object.
  *
@@ -66,7 +65,6 @@ InputPts::InputPts(FieldSharedPtr f) : InputModule(f)
     m_allowedFiles.insert("pts");
 }
 
-
 /**
  *
  */
@@ -74,7 +72,6 @@ InputPts::~InputPts()
 {
 }
 
-
 /**
  *
  */
@@ -82,7 +79,7 @@ void InputPts::Process(po::variables_map &vm)
 {
     if (m_f->m_verbose)
     {
-        if(m_f->m_comm->TreatAsRankZero())
+        if (m_f->m_comm->TreatAsRankZero())
         {
             cout << "Processing input pts file" << endl;
         }
@@ -90,21 +87,19 @@ void InputPts::Process(po::variables_map &vm)
 
     string inFile = (m_f->m_inputfiles["pts"][0]).c_str();
 
-    if(m_f->m_session)
+    if (m_f->m_session)
     {
-        m_f->m_ptsIO = MemoryManager<LibUtilities::PtsIO>::
-        AllocateSharedPtr(m_f->m_session->GetComm());
-
+        m_f->m_ptsIO = MemoryManager<LibUtilities::PtsIO>::AllocateSharedPtr(
+            m_f->m_session->GetComm());
     }
     else // serial communicator
     {
-        LibUtilities::CommSharedPtr c = LibUtilities::GetCommFactory().CreateInstance("Serial", 0, 0);
-        m_f->m_ptsIO = MemoryManager<LibUtilities::PtsIO>
-            ::AllocateSharedPtr(c);
+        LibUtilities::CommSharedPtr c =
+            LibUtilities::GetCommFactory().CreateInstance("Serial", 0, 0);
+        m_f->m_ptsIO = MemoryManager<LibUtilities::PtsIO>::AllocateSharedPtr(c);
     }
 
-    m_f->m_ptsIO->Import(inFile,  m_f->m_fieldPts);
+    m_f->m_ptsIO->Import(inFile, m_f->m_fieldPts);
 }
-
 }
 }

library/FieldUtils/InputModules/InputPts.h

@@ -43,33 +43,31 @@ namespace Nektar
 namespace FieldUtils
 {
 
-
 /**
  *  Input module for Xml files.
  */
 class InputPts : public InputModule
 {
-    public:
-        InputPts(FieldSharedPtr f);
-        virtual ~InputPts();
-        virtual void Process(po::variables_map &vm);
+public:
+    InputPts(FieldSharedPtr f);
+    virtual ~InputPts();
+    virtual void Process(po::variables_map &vm);
 
-        /// Creates an instance of this class
-        static ModuleSharedPtr create(FieldSharedPtr f)
-        {
-            return MemoryManager<InputPts>::AllocateSharedPtr(f);
-        }
-        /// %ModuleKey for class.
-        static ModuleKey m_className[];
+    /// Creates an instance of this class
+    static ModuleSharedPtr create(FieldSharedPtr f)
+    {
+        return MemoryManager<InputPts>::AllocateSharedPtr(f);
+    }
+    /// %ModuleKey for class.
+    static ModuleKey m_className[];
 
-        virtual std::string GetModuleName()
-        {
-            return "InputPts";
-        }
+    virtual std::string GetModuleName()
+    {
+        return "InputPts";
+    }
 
-    private:
+private:
 };
-
 }
 }
 

library/FieldUtils/InputModules/InputXml.h

@@ -48,27 +48,26 @@ namespace FieldUtils
  */
 class InputXml : public InputModule
 {
-    public:
-        InputXml(FieldSharedPtr f);
-        virtual ~InputXml();
-        virtual void Process(po::variables_map &vm);
+public:
+    InputXml(FieldSharedPtr f);
+    virtual ~InputXml();
+    virtual void Process(po::variables_map &vm);
 
-        /// Creates an instance of this class
-        static ModuleSharedPtr create(FieldSharedPtr f)
-        {
-            return MemoryManager<InputXml>::AllocateSharedPtr(f);
-        }
-        /// %ModuleKey for class.
-        static ModuleKey m_className[];
+    /// Creates an instance of this class
+    static ModuleSharedPtr create(FieldSharedPtr f)
+    {
+        return MemoryManager<InputXml>::AllocateSharedPtr(f);
+    }
+    /// %ModuleKey for class.
+    static ModuleKey m_className[];
 
-        virtual std::string GetModuleName()
-        {
-            return "InputXml";
-        }
+    virtual std::string GetModuleName()
+    {
+        return "InputXml";
+    }
 
-    private:
+private:
 };
-
 }
 }
 

library/FieldUtils/Interpolator.cpp

@@ -333,8 +333,8 @@ void Interpolator::Interpolate(
         }
 
         // Obtain Element and LocalCoordinate to interpolate
-        int elmtid = m_expInField[0]->GetExpIndex(
-            Scoords, Lcoords, NekConstants::kNekZeroTol);
+        int elmtid = m_expInField[0]->GetExpIndex(Scoords, Lcoords,
+                                                  NekConstants::kNekZeroTol);
 
         if (elmtid >= 0)
         {
@@ -410,8 +410,8 @@ void Interpolator::Interpolate(
         }
 
         // Obtain Element and LocalCoordinate to interpolate
-        int elmtid = m_expInField[0]->GetExpIndex(
-            coords, Lcoords, NekConstants::kNekZeroTol);
+        int elmtid = m_expInField[0]->GetExpIndex(coords, Lcoords,
+                                                  NekConstants::kNekZeroTol);
 
         if (elmtid >= 0)
         {
@@ -430,8 +430,8 @@ void Interpolator::Interpolate(
                 }
                 else
                 {
-                    m_ptsOutField->SetPointVal(
-                        m_ptsOutField->GetDim() + f, i, value);
+                    m_ptsOutField->SetPointVal(m_ptsOutField->GetDim() + f, i,
+                                               value);
                 }
             }
         }
@@ -600,7 +600,7 @@ void Interpolator::CalcW_Gauss(const PtsPoint &searchPt,
     m_weights[searchPt.idx] = Array<OneD, float>(numPts, 0.0);
 
     NekDouble wSum = 0.0;
-    NekDouble ts2 = 2 * sigmaNew * sigmaNew;
+    NekDouble ts2  = 2 * sigmaNew * sigmaNew;
     for (int i = 0; i < numPts; ++i)
     {
         m_weights[searchPt.idx][i] =
@@ -658,9 +658,9 @@ void Interpolator::CalcW_Linear(const PtsPoint &searchPt, int m_coordId)
             break;
         }
     }
-    ASSERTL0(i != npts - 1,
-             "Failed to find coordinate " + boost::lexical_cast<string>(coord) +
-                 " within provided input points");
+    ASSERTL0(i != npts - 1, "Failed to find coordinate " +
+                                boost::lexical_cast<string>(coord) +
+                                " within provided input points");
 };
 
 /**
@@ -704,7 +704,7 @@ void Interpolator::CalcW_Shepard(const PtsPoint &searchPt)
     // find nearest neighbours
     vector<PtsPoint> neighbourPts;
     int numPts = pow(double(2), m_ptsInField->GetDim());
-    numPts = min(numPts, int(m_ptsInField->GetNpoints() / 2));
+    numPts     = min(numPts, int(m_ptsInField->GetNpoints() / 2));
     FindNNeighbours(searchPt, neighbourPts, numPts);
 
     m_neighInds[searchPt.idx] = Array<OneD, unsigned int>(numPts);
@@ -824,9 +824,9 @@ void Interpolator::CalcW_Quadratic(const PtsPoint &searchPt, int m_coordId)
             break;
         }
     }
-    ASSERTL0(i != npts - 1,
-             "Failed to find coordinate " + boost::lexical_cast<string>(coord) +
-                 " within provided input points");
+    ASSERTL0(i != npts - 1, "Failed to find coordinate " +
+                                boost::lexical_cast<string>(coord) +
+                                " within provided input points");
 };
 
 void Interpolator::SetupTree()
@@ -847,8 +847,7 @@ void Interpolator::SetupTree()
 
     // remove duplicates from tree
     for (std::vector<PtsPointPair>::iterator it = inPoints.begin();
-         it != inPoints.end();
-         ++it)