Merge branch 'master' into develop-v1906

src/OpenFOAM/primitives/functions/Function1/CSV/CSV.C

@@ -6,7 +6,7 @@
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
     Copyright (C) 2011-2017 OpenFOAM Foundation
-    Copyright (C) 2016-2017 OpenCFD Ltd.
+    Copyright (C) 2016-2019 OpenCFD Ltd.
 -------------------------------------------------------------------------------
 License
     This file is part of OpenFOAM.
@@ -28,7 +28,6 @@ License
 
 #include "CSV.H"
 #include "DynamicList.H"
-//#include "IFstream.H"
 
 // * * * * * * * * * * * * * Private Member Functions  * * * * * * * * * * * //
 
@@ -36,7 +35,7 @@ template<>
 Foam::label Foam::Function1Types::CSV<Foam::label>::readValue
 (
     const List<string>& splitted
-)
+) const
 {
     if (componentColumns_[0] >= splitted.size())
     {
@@ -54,7 +53,7 @@ template<>
 Foam::scalar Foam::Function1Types::CSV<Foam::scalar>::readValue
 (
     const List<string>& splitted
-)
+) const
 {
     if (componentColumns_[0] >= splitted.size())
     {
@@ -69,7 +68,10 @@ Foam::scalar Foam::Function1Types::CSV<Foam::scalar>::readValue
 
 
 template<class Type>
-Type Foam::Function1Types::CSV<Type>::readValue(const List<string>& splitted)
+Type Foam::Function1Types::CSV<Type>::readValue
+(
+    const List<string>& splitted
+) const
 {
     Type result;
 
@@ -94,7 +96,6 @@ template<class Type>
 void Foam::Function1Types::CSV<Type>::read()
 {
     fileName expandedFile(fName_);
-    //IFstream is(expandedFile.expand());
     autoPtr<ISstream> isPtr(fileHandler().NewIFstream(expandedFile.expand()));
     ISstream& is = isPtr();
 
@@ -214,17 +215,24 @@ Foam::Function1Types::CSV<Type>::CSV
     TableBase<Type>(entryName, dict),
     nHeaderLine_(dict.get<label>("nHeaderLine")),
     refColumn_(dict.get<label>("refColumn")),
-    componentColumns_(dict.lookup("componentColumns")),
+    componentColumns_(),
-    separator_(dict.lookupOrDefault<string>("separator", ",")[0]),
+    separator_(dict.getOrDefault<string>("separator", ",")[0]),
     mergeSeparators_(dict.get<bool>("mergeSeparators")),
     fName_(fName.empty() ? dict.get<fileName>("file") : fName)
 {
+    // Writing of "componentColumns" was forced to be ASCII,
+    // do the same when reading
+    ITstream& is = dict.lookup("componentColumns");
+    is.format(IOstream::ASCII);
+    is >> componentColumns_;
+    dict.checkITstream(is, "componentColumns");
+
     if (componentColumns_.size() != pTraits<Type>::nComponents)
     {
-        FatalErrorInFunction
+        FatalIOErrorInFunction(dict)
             << componentColumns_ << " does not have the expected length of "
-            << pTraits<Type>::nComponents << endl
+            << pTraits<Type>::nComponents << nl
-            << exit(FatalError);
+            << exit(FatalIOError);
     }
 
     read();
@@ -246,13 +254,6 @@ Foam::Function1Types::CSV<Type>::CSV(const CSV<Type>& csv)
 {}
 
 
-// * * * * * * * * * * * * * * * * Destructor  * * * * * * * * * * * * * * * //
-
-template<class Type>
-Foam::Function1Types::CSV<Type>::~CSV()
-{}
-
-
 // * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
 
 template<class Type>

src/OpenFOAM/primitives/functions/Function1/CSV/CSV.H

@@ -6,7 +6,7 @@
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
     Copyright (C) 2011-2017 OpenFOAM Foundation
-    Copyright (C) 2017 OpenCFD Ltd.
+    Copyright (C) 2017-2019 OpenCFD Ltd.
 -------------------------------------------------------------------------------
 License
     This file is part of OpenFOAM.
@@ -105,7 +105,7 @@ class CSV
         void read();
 
         //- Read the next value from the splitted string
-        Type readValue(const List<string>&);
+        Type readValue(const List<string>& splitted) const;
 
         //- No copy assignment
         void operator=(const CSV<Type>&) = delete;
@@ -138,7 +138,7 @@ public:
 
 
     //- Destructor
-    virtual ~CSV();
+    virtual ~CSV() = default;
 
 
     // Member Functions
@@ -151,11 +151,12 @@ public:
 };
 
 
+// Template specialisations
 template<>
-label CSV<label>::readValue(const List<string>& splitted);
+label CSV<label>::readValue(const List<string>& splitted) const;
 
 template<>
-Foam::scalar CSV<scalar>::readValue(const List<string>& splitted);
+Foam::scalar CSV<scalar>::readValue(const List<string>& splitted) const;
 
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //

src/fileFormats/ensight/read/ensightReadFile.C

@@ -5,7 +5,7 @@
     \\  /    A nd           | www.openfoam.com
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
-    Copyright (C) 2016 OpenCFD Ltd.
+    Copyright (C) 2016-2019 OpenCFD Ltd.
 -------------------------------------------------------------------------------
 License
     This file is part of OpenFOAM.
@@ -56,25 +56,37 @@ Foam::Istream& Foam::ensightReadFile::read(string& value)
 {
     if (format() == IOstream::BINARY)
     {
-        char buf[80];
+        auto& iss = stdStream();
 
-        read(reinterpret_cast<char*>(buf), sizeof(buf));
+        // Binary string is *exactly* 80 characters
+        value.resize(80, '\0');
+        iss.read(&value[0], 80);
 
-        string strBuf(value);
+        if (!iss)
-
-        const size_t iEnd = strBuf.find('\0', 0);
-        if (iEnd == string::npos)
         {
-            value = buf;
+            // Truncated - could also exit here, but no real advantage
+            value.erase(iss.gcount());
         }
-        else
+
+        // Truncate at the first embedded '\0'
+        auto endp = value.find('\0');
+
+        if (endp != std::string::npos)
         {
-            value = strBuf.substr(0, iEnd - 1);
+            value.erase(endp);
+        }
+
+        // May have been padded with trailing spaces - remove those
+        endp = value.find_last_not_of(" \t\f\v\n\r");
+
+        if (endp != std::string::npos)
+        {
+            value.erase(endp + 1);
         }
     }
     else
     {
-        value = "";
+        value.clear();
         while (value.empty() && !eof())
         {
             getLine(value);

src/optimisation/adjointOptimisation/adjoint/adjointBoundaryConditions/adjointWallVelocityLowRe/adjointWallVelocityLowReFvPatchVectorField.C

@@ -41,7 +41,7 @@ adjointWallVelocityLowReFvPatchVectorField
 )
 :
     fixedValueFvPatchVectorField(p, iF),
-    adjointBoundaryCondition(p, iF, "Ua")
+    adjointBoundaryCondition(p, iF, word::null)
 {}
 
 
@@ -55,7 +55,7 @@ adjointWallVelocityLowReFvPatchVectorField
 )
 :
     fixedValueFvPatchVectorField(ptf, p, iF, mapper),
-    adjointBoundaryCondition(p, iF, "Ua")
+    adjointBoundaryCondition(p, iF, ptf.adjointSolverName_)
 {}
 
 
@@ -68,7 +68,7 @@ adjointWallVelocityLowReFvPatchVectorField
 )
 :
     fixedValueFvPatchVectorField(p, iF),
-    adjointBoundaryCondition(p, iF, "Ua")
+    adjointBoundaryCondition(p, iF, dict.get<word>("solverName"))
 {
     fvPatchField<vector>::operator=
     (

src/optimisation/adjointOptimisation/adjoint/turbulenceModels/turbulenceModelVariables/RAS/SpalartAllmaras/SpalartAllmaras.C

@@ -28,6 +28,7 @@ License
 \*---------------------------------------------------------------------------*/
 
 #include "SpalartAllmaras.H"
+#include "wallDist.H"
 #include "addToRunTimeSelectionTable.H"
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
@@ -77,7 +78,7 @@ SpalartAllmaras::SpalartAllmaras
     nutPtr_ = mesh_.getObjectPtr<volScalarField>("nut");
 
     hasDist_ = true;
-    dPtr_ = mesh_.getObjectPtr<volScalarField>("yWall");
+    dPtr_ = &(const_cast<volScalarField&>(wallDist::New(mesh_).y()));
 
     allocateInitValues();
     allocateMeanFields();

src/sampling/sampledSet/array/arraySet.C

@@ -69,7 +69,7 @@ void Foam::arraySet::calcSamples
             for (label i=1; i<=pointsDensity_.x(); ++i)
             {
                 // Local Cartesian
-                point pt(i*dx*i , j*dy, k*dz);
+                point pt(i*dx, j*dy, k*dz);
 
                 // Global Cartesian
                 pt = csys_.globalPosition(pt);

src/sampling/sampledSurface/readers/ensight/ensightSurfaceReader.C

@@ -5,7 +5,7 @@
     \\  /    A nd           | www.openfoam.com
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
-    Copyright (C) 2015-2016 OpenCFD Ltd.
+    Copyright (C) 2015-2019 OpenCFD Ltd.
 -------------------------------------------------------------------------------
 License
     This file is part of OpenFOAM.
@@ -101,23 +101,23 @@ void Foam::ensightSurfaceReader::readGeometryHeader(ensightReadFile& is) const
 
     // Ensight Geometry File
     is.read(buffer);
-    DebugInfo<< "buffer: " << buffer << nl;
+    DebugInfo<< "buffer [" << buffer.length() << "] " << buffer << nl;
 
     // Description - 1
     is.read(buffer);
-    DebugInfo<< "buffer: " << buffer << nl;
+    DebugInfo<< "buffer [" << buffer.length() << "] " << buffer << nl;
 
     // Node info
     is.read(buffer);
-    DebugInfo<< "buffer: " << buffer << nl;
+    DebugInfo<< "buffer [" << buffer.length() << "] " << buffer << nl;
 
     // Element info
     is.read(buffer);
-    DebugInfo<< "buffer: " << buffer << nl;
+    DebugInfo<< "buffer [" << buffer.length() << "] " << buffer << nl;
 
     // Part
     is.read(buffer);
-    DebugInfo<< "buffer: " << buffer << nl;
+    DebugInfo<< "buffer [" << buffer.length() << "] " << buffer << nl;
 
     // Part number
     label ibuffer;
@@ -126,11 +126,11 @@ void Foam::ensightSurfaceReader::readGeometryHeader(ensightReadFile& is) const
 
     // Description - 2
     is.read(buffer);
-    DebugInfo<< "buffer: " << buffer << nl;
+    DebugInfo<< "buffer [" << buffer.length() << "] " << buffer << nl;
 
     // Coordinates
     is.read(buffer);
-    DebugInfo<< "buffer: " << buffer << nl;
+    DebugInfo<< "buffer [" << buffer.length() << "] " << buffer << nl;
 }
 
 
@@ -280,29 +280,30 @@ const Foam::meshedSurface& Foam::ensightSurfaceReader::geometry()
 
         streamFormat_ = IOstream::BINARY;
         {
-            istream& is = isBinary.stdStream();
+            istream& iss = isBinary.stdStream();
 
-            char buffer[80];
+            // Binary string is *exactly* 80 characters
-            is.read(buffer, 80);
+            string buf(size_t(80), '\0');
+            iss.read(&buf[0], 80);
 
-            char test[80];
+            if (!iss)
-            label nChar = 0;
-            for (label i = 0; i < 80; ++i)
             {
-                if (buffer[i] == '\0')
+                // Truncated?
-                {
+                buf.erase(iss.gcount());
-                    break;
-                }
-                test[i] = buffer[i];
-                nChar++;
             }
 
-            string testStr(test, nChar);
+            // Truncate at the first embedded '\0'
+            const auto endp = buf.find('\0');
+            if (endp != std::string::npos)
+            {
+                buf.erase(endp);
+            }
 
+            // Contains "C Binary" ?
             if
             (
-                (testStr.find("binary", 0) == string::npos)
+                (buf.find("binary") == std::string::npos)
-             && (testStr.find("Binary", 0) == string::npos)
+             && (buf.find("Binary") == std::string::npos)
             )
             {
                 streamFormat_ = IOstream::ASCII;
@@ -354,8 +355,7 @@ const Foam::meshedSurface& Foam::ensightSurfaceReader::geometry()
         // Read faces - may be a mix of tris, quads and polys
         DynamicList<face> faces(ceil(nPoints/3));
         DynamicList<Tuple2<string, label>> schema(faces.size());
-        string faceType = "";
+        string faceType;
-        label nFace = 0;
         while (is.good()) // (is.peek() != EOF)
         {
             is.read(faceType);
@@ -365,20 +365,22 @@ const Foam::meshedSurface& Foam::ensightSurfaceReader::geometry()
                 break;
             }
 
-            DebugInfo
+            label nFace = 0;
-                << "faceType: " << faceType << endl;
 
             if (faceType == "tria3")
             {
                 is.read(nFace);
 
-                const label np = 3;
+                DebugInfo
-                for (label faceI = 0; faceI < nFace; ++faceI)
+                    << "faceType <" << faceType.c_str() << "> count: "
+                    << nFace << nl;
+
+                face f(3);
+                for (label facei = 0; facei < nFace; ++facei)
                 {
-                    face f(np);
+                    for (label& fp : f)
-                    for (label fpI = 0; fpI < np; fpI++)
                     {
-                        is.read(f[fpI]);
+                        is.read(fp);
                     }
 
                     faces.append(f);
@@ -388,13 +390,16 @@ const Foam::meshedSurface& Foam::ensightSurfaceReader::geometry()
             {
                 is.read(nFace);
 
-                const label np = 4;
+                DebugInfo
-                for (label faceI = 0; faceI < nFace; ++faceI)
+                    << "faceType <" << faceType.c_str() << "> count: "
+                    << nFace << nl;
+
+                face f(4);
+                for (label facei = 0; facei < nFace; ++facei)
                 {
-                    face f(np);
+                    for (label& fp : f)
-                    for (label fpI = 0; fpI < np; fpI++)
                     {
-                        is.read(f[fpI]);
+                        is.read(fp);
                     }
 
                     faces.append(f);
@@ -404,17 +409,21 @@ const Foam::meshedSurface& Foam::ensightSurfaceReader::geometry()
             {
                 is.read(nFace);
 
+                DebugInfo
+                    << "faceType <" << faceType.c_str() << "> count: "
+                    << nFace << nl;
+
                 labelList np(nFace);
-                for (label faceI = 0; faceI < nFace; ++faceI)
+                for (label facei = 0; facei < nFace; ++facei)
                 {
-                    is.read(np[faceI]);
+                    is.read(np[facei]);
                 }
-                for (label faceI = 0; faceI < nFace; ++faceI)
+                for (label facei = 0; facei < nFace; ++facei)
                 {
-                    face f(np[faceI]);
+                    face f(np[facei]);
-                    for (label fpI = 0; fpI < f.size(); ++fpI)
+                    for (label& fp : f)
                     {
-                        is.read(f[fpI]);
+                        is.read(fp);
                     }
 
                     faces.append(f);
@@ -425,11 +434,10 @@ const Foam::meshedSurface& Foam::ensightSurfaceReader::geometry()
                 if (debug)
                 {
                     WarningInFunction
-                        << "Unknown face type: " << faceType
+                        << "Unknown face type: <" << faceType.c_str()
-                        << ".  Aborting read and continuing with current "
+                        << ">. Stopping read and continuing with current "
                         << "elements only" << endl;
                 }
-
                 break;
             }
             schema.append(Tuple2<string, label>(faceType, nFace));

src/sampling/sampledSurface/readers/ensight/ensightSurfaceReaderTemplates.C

@@ -113,10 +113,11 @@ Foam::tmp<Foam::Field<Type>> Foam::ensightSurfaceReader::readField
 
     if (primitiveType != pTraits<Type>::typeName)
     {
-        FatalIOErrorInFunction(is)
+        IOWarningInFunction(is)
-            << "Expected " << pTraits<Type>::typeName << "values "
+            << "Expected '" << pTraits<Type>::typeName
-            << "but found type " << primitiveType
+            << "' values but found type " << primitiveType << nl
-            << exit(FatalIOError);
+            << "    This may be okay, but could also indicate an error"
+            << nl << nl;
     }
 
     scalar value;

tutorials/combustion/reactingFoam/RAS/chokedNozzle/system/controlDict

@@ -33,7 +33,7 @@ writeInterval   0.02;
 
 purgeWrite      0;
 
-writeFormat     ascii;
+writeFormat     binary;
 
 writePrecision  10;