Merge branch 'master' of /home/hunt2/OpenFOAM/OpenFOAM-dev

applications/utilities/parallelProcessing/reconstructPar/fvFieldReconstructor.H

@@ -151,18 +151,20 @@ public:
             const IOobject& fieldIoObject
         );
 
-        //- Reconstruct and write all volume fields
+        //- Reconstruct and write all/selected volume fields
         template<class Type>
         void reconstructFvVolumeFields
         (
-            const IOobjectList& objects
+            const IOobjectList& objects,
+            const HashSet<word>& selectedFields
         );
 
-        //- Reconstruct and write all volume fields
+        //- Reconstruct and write all/selected volume fields
         template<class Type>
         void reconstructFvSurfaceFields
         (
-            const IOobjectList& objects
+            const IOobjectList& objects,
+            const HashSet<word>& selectedFields
         );
 };
 

applications/utilities/parallelProcessing/reconstructPar/fvFieldReconstructorReconstructFields.C

@@ -131,7 +131,7 @@ Foam::fvFieldReconstructor::reconstructFvVolumeField
                 forAll(cp, faceI)
                 {
                     // Subtract one to take into account offsets for
-                    // face direction.  
+                    // face direction.
                     reverseAddressing[faceI] = cp[faceI] - 1 - curPatchStart;
                 }
 
@@ -151,7 +151,7 @@ Foam::fvFieldReconstructor::reconstructFvVolumeField
                 forAll(cp, faceI)
                 {
                     // Subtract one to take into account offsets for
-                    // face direction.  
+                    // face direction.
                     label curF = cp[faceI] - 1;
 
                     // Is the face on the boundary?
@@ -282,7 +282,7 @@ Foam::fvFieldReconstructor::reconstructFvSurfaceField
 
         // It is necessary to create a copy of the addressing array to
         // take care of the face direction offset trick.
-        // 
+        //
         {
             labelList curAddr(faceProcAddressing_[procI]);
 
@@ -342,7 +342,7 @@ Foam::fvFieldReconstructor::reconstructFvSurfaceField
                 forAll(cp, faceI)
                 {
                     // Subtract one to take into account offsets for
-                    // face direction.  
+                    // face direction.
                     reverseAddressing[faceI] = cp[faceI] - 1 - curPatchStart;
                 }
 
@@ -452,11 +452,12 @@ Foam::fvFieldReconstructor::reconstructFvSurfaceField
 }
 
 
-// Reconstruct and write all volume fields
+// Reconstruct and write all/selected volume fields
 template<class Type>
 void Foam::fvFieldReconstructor::reconstructFvVolumeFields
 (
-    const IOobjectList& objects
+    const IOobjectList& objects,
+    const HashSet<word>& selectedFields
 )
 {
     const word& fieldClassName =
@@ -468,27 +469,29 @@ void Foam::fvFieldReconstructor::reconstructFvVolumeFields
     {
         Info<< "    Reconstructing " << fieldClassName << "s\n" << endl;
 
-        for
-        (
-            IOobjectList::const_iterator fieldIter = fields.begin();
-            fieldIter != fields.end();
-            ++fieldIter
-        )
+        forAllConstIter(IOobjectList, fields, fieldIter)
         {
-            Info<< "        " << fieldIter()->name() << endl;
+            if
+            (
+                !selectedFields.size()
+             || selectedFields.found(fieldIter()->name())
+            )
+            {
+                Info<< "        " << fieldIter()->name() << endl;
 
-            reconstructFvVolumeField<Type>(*fieldIter())().write();
+                reconstructFvVolumeField<Type>(*fieldIter())().write();
+            }
         }
-
         Info<< endl;
     }
 }
 
-// Reconstruct and write all surface fields
+// Reconstruct and write all/selected surface fields
 template<class Type>
 void Foam::fvFieldReconstructor::reconstructFvSurfaceFields
 (
-    const IOobjectList& objects
+    const IOobjectList& objects,
+    const HashSet<word>& selectedFields
 )
 {
     const word& fieldClassName =
@@ -500,18 +503,19 @@ void Foam::fvFieldReconstructor::reconstructFvSurfaceFields
     {
         Info<< "    Reconstructing " << fieldClassName << "s\n" << endl;
 
-        for
-        (
-            IOobjectList::const_iterator fieldIter = fields.begin();
-            fieldIter != fields.end();
-            ++fieldIter
-        )
+        forAllConstIter(IOobjectList, fields, fieldIter)
         {
-            Info<< "        " << fieldIter()->name() << endl;
+            if
+            (
+                !selectedFields.size()
+             || selectedFields.found(fieldIter()->name())
+            )
+            {
+                Info<< "        " << fieldIter()->name() << endl;
 
-            reconstructFvSurfaceField<Type>(*fieldIter())().write();
+                reconstructFvSurfaceField<Type>(*fieldIter())().write();
+            }
         }
-
         Info<< endl;
     }
 }

applications/utilities/parallelProcessing/reconstructPar/reconstructPar.C

@@ -48,9 +48,17 @@ int main(int argc, char *argv[])
     argList::noParallel();
     timeSelector::addOptions();
 #   include "addRegionOption.H"
+    argList::validOptions.insert("fields", "\"(list of fields)\"");
+
 #   include "setRootCase.H"
 #   include "createTime.H"
 
+    HashSet<word> selectedFields;
+    if (args.options().found("fields"))
+    {
+        IStringStream(args.options()["fields"])() >> selectedFields;
+    }
+
     // determine the processor count directly
     label nProcs = 0;
     while (dir(args.path()/(word("processor") + name(nProcs))))
@@ -184,13 +192,37 @@ int main(int argc, char *argv[])
                 procMeshes.boundaryProcAddressing()
             );
 
-            fvReconstructor.reconstructFvVolumeFields<scalar>(objects);
-            fvReconstructor.reconstructFvVolumeFields<vector>(objects);
-            fvReconstructor.reconstructFvVolumeFields<sphericalTensor>(objects);
-            fvReconstructor.reconstructFvVolumeFields<symmTensor>(objects);
-            fvReconstructor.reconstructFvVolumeFields<tensor>(objects);
+            fvReconstructor.reconstructFvVolumeFields<scalar>
+            (
+                objects,
+                selectedFields
+            );
+            fvReconstructor.reconstructFvVolumeFields<vector>
+            (
+                objects,
+                selectedFields
+            );
+            fvReconstructor.reconstructFvVolumeFields<sphericalTensor>
+            (
+                objects,
+                selectedFields
+            );
+            fvReconstructor.reconstructFvVolumeFields<symmTensor>
+            (
+                objects,
+                selectedFields
+            );
+            fvReconstructor.reconstructFvVolumeFields<tensor>
+            (
+                objects,
+                selectedFields
+            );
 
-            fvReconstructor.reconstructFvSurfaceFields<scalar>(objects);
+            fvReconstructor.reconstructFvSurfaceFields<scalar>
+            (
+                objects,
+                selectedFields
+            );
         }
         else
         {

applications/utilities/postProcessing/miscellaneous/execFlowFunctionObjects/execFlowFunctionObjects.C

@@ -139,7 +139,7 @@ void Foam::calc(const argList& args, const Time& runTime, const fvMesh& mesh)
 
         IOobject LESPropertiesHeader
         (
-            "RASProperties",
+            "LESProperties",
             runTime.constant(),
             mesh,
             IOobject::MUST_READ,

src/ODE/ODE/ODE.H

@@ -34,7 +34,7 @@ Description
 #define ODE_H
 
 #include "scalarField.H"
-#include "Matrix.H"
+#include "scalarMatrices.H"
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
@@ -80,7 +80,7 @@ public:
             const scalar x,
             const scalarField& y,
             scalarField& dfdx,
-            Matrix<scalar>& dfdy
+            scalarSquareMatrix& dfdy
         ) const = 0;
 };
 

src/ODE/ODESolvers/KRR4/KRR4.C

@@ -25,7 +25,6 @@ License
 \*---------------------------------------------------------------------------*/
 
 #include "KRR4.H"
-#include "simpleMatrix.H"
 #include "addToRunTimeSelectionTable.H"
 
 // * * * * * * * * * * * * * * Static Data Members * * * * * * * * * * * * * //
@@ -36,11 +35,11 @@ namespace Foam
 {
     addToRunTimeSelectionTable(ODESolver, KRR4, ODE);
 
-const scalar 
+const scalar
     KRR4::safety = 0.9, KRR4::grow = 1.5, KRR4::pgrow = -0.25,
     KRR4::shrink = 0.5, KRR4::pshrink = (-1.0/3.0), KRR4::errcon = 0.1296;
 
-const scalar 
+const scalar
     KRR4::gamma = 1.0/2.0,
     KRR4::a21 = 2.0, KRR4::a31 = 48.0/25.0, KRR4::a32 = 6.0/25.0,
     KRR4::c21 = -8.0, KRR4::c31 = 372.0/25.0, KRR4::c32 = 12.0/5.0,
@@ -81,8 +80,8 @@ void Foam::KRR4::solve
     const ODE& ode,
     scalar& x,
     scalarField& y,
-    scalarField& dydx, 
-    const scalar eps, 
+    scalarField& dydx,
+    const scalar eps,
     const scalarField& yScale,
     const scalar hTry,
     scalar& hDid,
@@ -109,14 +108,14 @@ void Foam::KRR4::solve
             a_[i][i] += 1.0/(gamma*h);
         }
 
-        simpleMatrix<scalar>::LUDecompose(a_, pivotIndices_);
+        LUDecompose(a_, pivotIndices_);
 
         for (register label i=0; i<n_; i++)
         {
             g1_[i] = dydxTemp_[i] + h*c1X*dfdx_[i];
         }
 
-        simpleMatrix<scalar>::LUBacksubstitute(a_, pivotIndices_, g1_);
+        LUBacksubstitute(a_, pivotIndices_, g1_);
 
         for (register label i=0; i<n_; i++)
         {
@@ -131,7 +130,7 @@ void Foam::KRR4::solve
             g2_[i] = dydx_[i] + h*c2X*dfdx_[i] + c21*g1_[i]/h;
         }
 
-        simpleMatrix<scalar>::LUBacksubstitute(a_, pivotIndices_, g2_);
+        LUBacksubstitute(a_, pivotIndices_, g2_);
 
         for (register label i=0; i<n_; i++)
         {
@@ -146,7 +145,7 @@ void Foam::KRR4::solve
             g3_[i] = dydx[i] + h*c3X*dfdx_[i] + (c31*g1_[i] + c32*g2_[i])/h;
         }
 
-        simpleMatrix<scalar>::LUBacksubstitute(a_, pivotIndices_, g3_);
+        LUBacksubstitute(a_, pivotIndices_, g3_);
 
         for (register label i=0; i<n_; i++)
         {
@@ -154,7 +153,7 @@ void Foam::KRR4::solve
                 + (c41*g1_[i] + c42*g2_[i] + c43*g3_[i])/h;
         }
 
-        simpleMatrix<scalar>::LUBacksubstitute(a_, pivotIndices_, g4_);
+        LUBacksubstitute(a_, pivotIndices_, g4_);
 
         for (register label i=0; i<n_; i++)
         {

src/ODE/ODESolvers/KRR4/KRR4.H

@@ -62,15 +62,15 @@ class KRR4
         mutable scalarField g4_;
         mutable scalarField yErr_;
         mutable scalarField dfdx_;
-        mutable Matrix<scalar> dfdy_;
-        mutable Matrix<scalar> a_;
+        mutable scalarSquareMatrix dfdy_;
+        mutable scalarSquareMatrix a_;
         mutable labelList pivotIndices_;
 
         static const int maxtry = 40;
 
         static const scalar safety, grow, pgrow, shrink, pshrink, errcon;
 
-        static const scalar 
+        static const scalar
             gamma,
             a21, a31, a32,
             c21, c31, c32, c41, c42, c43,

src/ODE/ODESolvers/SIBS/SIBS.H

@@ -60,8 +60,8 @@ class SIBS
         static const scalar safe1, safe2, redMax, redMin, scaleMX;
 
         mutable scalarField a_;
-        mutable Matrix<scalar> alpha_;
-        mutable Matrix<scalar> d_p_;
+        mutable scalarSquareMatrix alpha_;
+        mutable scalarSquareMatrix d_p_;
         mutable scalarField x_p_;
         mutable scalarField err_;
 
@@ -69,7 +69,7 @@ class SIBS
         mutable scalarField ySeq_;
         mutable scalarField yErr_;
         mutable scalarField dfdx_;
-        mutable Matrix<scalar> dfdy_;
+        mutable scalarSquareMatrix dfdy_;
 
         mutable label first_, kMax_, kOpt_;
         mutable scalar epsOld_, xNew_;
@@ -82,7 +82,7 @@ void SIMPR
     const scalarField& y,
     const scalarField& dydx,
     const scalarField& dfdx,
-    const Matrix<scalar>& dfdy, 
+    const scalarSquareMatrix& dfdy,
     const scalar deltaX,
     const label nSteps,
     scalarField& yEnd
@@ -97,7 +97,7 @@ void polyExtrapolate
     scalarField& yz,
     scalarField& dy,
     scalarField& x_p,
-    Matrix<scalar>& d_p
+    scalarSquareMatrix& d_p
 ) const;
 
 

src/ODE/ODESolvers/SIBS/SIMPR.C

@@ -25,7 +25,6 @@ License
 \*---------------------------------------------------------------------------*/
 
 #include "SIBS.H"
-#include "simpleMatrix.H"
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
@@ -36,7 +35,7 @@ void Foam::SIBS::SIMPR
     const scalarField& y,
     const scalarField& dydx,
     const scalarField& dfdx,
-    const Matrix<scalar>& dfdy,
+    const scalarSquareMatrix& dfdy,
     const scalar deltaX,
     const label nSteps,
     scalarField& yEnd
@@ -44,7 +43,7 @@ void Foam::SIBS::SIMPR
 {
     scalar h = deltaX/nSteps;
 
-    Matrix<scalar> a(n_, n_);
+    scalarSquareMatrix a(n_);
     for (register label i=0; i<n_; i++)
     {
         for (register label j=0; j<n_; j++)
@@ -55,14 +54,14 @@ void Foam::SIBS::SIMPR
     }
 
     labelList pivotIndices(n_);
-    simpleMatrix<scalar>::LUDecompose(a, pivotIndices);
+    LUDecompose(a, pivotIndices);
 
     for (register label i=0; i<n_; i++)
     {
         yEnd[i] = h*(dydx[i] + h*dfdx[i]);
     }
 
-    simpleMatrix<scalar>::LUBacksubstitute(a, pivotIndices, yEnd);
+    LUBacksubstitute(a, pivotIndices, yEnd);
 
     scalarField del(yEnd);
     scalarField ytemp(n_);
@@ -83,7 +82,7 @@ void Foam::SIBS::SIMPR
             yEnd[i] = h*yEnd[i] - del[i];
         }
 
-        simpleMatrix<scalar>::LUBacksubstitute(a, pivotIndices, yEnd);
+        LUBacksubstitute(a, pivotIndices, yEnd);
 
         for (register label i=0; i<n_; i++)
         {
@@ -99,7 +98,7 @@ void Foam::SIBS::SIMPR
         yEnd[i] = h*yEnd[i] - del[i];
     }
 
-    simpleMatrix<scalar>::LUBacksubstitute(a, pivotIndices, yEnd);
+    LUBacksubstitute(a, pivotIndices, yEnd);
 
     for (register label i=0; i<n_; i++)
     {

src/ODE/ODESolvers/SIBS/polyExtrapolate.C

@@ -36,7 +36,7 @@ void Foam::SIBS::polyExtrapolate
     scalarField& yz,
     scalarField& dy,
     scalarField& x,
-    Matrix<scalar>& d
+    scalarSquareMatrix& d
 ) const
 {
     label n = yz.size();

src/OpenFOAM/Make/files

@@ -177,9 +177,9 @@ dimensionedTypes/dimensionedTensor/dimensionedTensor.C
 
 matrices/solution/solution.C
 
-scalarMatrix = matrices/scalarMatrix
-$(scalarMatrix)/scalarMatrix.C
-$(scalarMatrix)/SVD/SVD.C
+scalarMatrices = matrices/scalarMatrices
+$(scalarMatrices)/scalarMatrices.C
+$(scalarMatrices)/SVD/SVD.C
 
 LUscalarMatrix = matrices/LUscalarMatrix
 $(LUscalarMatrix)/LUscalarMatrix.C

src/OpenFOAM/db/IOstreams/Pstreams/PstreamCommsStruct.C

@@ -22,8 +22,6 @@ License
     along with OpenFOAM; if not, write to the Free Software Foundation,
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
-Description
-
 \*---------------------------------------------------------------------------*/
 
 #include "Pstream.H"

src/OpenFOAM/matrices/DiagonalMatrix/DiagonalMatrix.C

@@ -29,7 +29,8 @@ License
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
 template<class Type>
-Foam::DiagonalMatrix<Type>::DiagonalMatrix(const Matrix<Type>& a)
+template<class Form>
+Foam::DiagonalMatrix<Type>::DiagonalMatrix(const Matrix<Form, Type>& a)
 :
     List<Type>(min(a.n(), a.m()))
 {

src/OpenFOAM/matrices/DiagonalMatrix/DiagonalMatrix.H

@@ -46,7 +46,7 @@ namespace Foam
 
 // * * * * * *  * * * * * * Class Forward declaration  * * * * * * * * * * * //
 
-template<class Type> class Matrix;
+template<class Form, class Type> class Matrix;
 
 /*---------------------------------------------------------------------------*\
                            Class DiagonalMatrix Declaration
@@ -62,7 +62,8 @@ public:
     // Constructors
 
         //- Construct from diagonal component of a Matrix
-        DiagonalMatrix<Type>(const Matrix<Type>&);
+        template<class Form>
+        DiagonalMatrix<Type>(const Matrix<Form, Type>&);
 
         //- Construct empty from size
         DiagonalMatrix<Type>(const label size);

src/OpenFOAM/matrices/LUscalarMatrix/LUscalarMatrix.C

@@ -31,9 +31,9 @@ License
 
 // * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
 
-Foam::LUscalarMatrix::LUscalarMatrix(const Matrix<scalar>& matrix)
+Foam::LUscalarMatrix::LUscalarMatrix(const scalarSquareMatrix& matrix)
 :
-    scalarMatrix(matrix),
+    scalarSquareMatrix(matrix),
     pivotIndices_(n())
 {
     LUDecompose(*this, pivotIndices_);
@@ -101,7 +101,7 @@ Foam::LUscalarMatrix::LUscalarMatrix
                 nCells += lduMatrices[i].size();
             }
 
-            Matrix<scalar> m(nCells, nCells, 0.0);
+            scalarSquareMatrix m(nCells, nCells, 0.0);
             transfer(m);
             convert(lduMatrices);
         }
@@ -109,7 +109,7 @@ Foam::LUscalarMatrix::LUscalarMatrix
     else
     {
         label nCells = ldum.lduAddr().size();
-        Matrix<scalar> m(nCells, nCells, 0.0);
+        scalarSquareMatrix m(nCells, nCells, 0.0);
         transfer(m);
         convert(ldum, interfaceCoeffs, interfaces);
     }

src/OpenFOAM/matrices/LUscalarMatrix/LUscalarMatrix.H

@@ -36,7 +36,7 @@ SourceFiles
 #ifndef LUscalarMatrix_H
 #define LUscalarMatrix_H
 
-#include "scalarMatrix.H"
+#include "scalarMatrices.H"
 #include "labelList.H"
 #include "FieldField.H"
 #include "lduInterfaceFieldPtrsList.H"
@@ -55,7 +55,7 @@ class procLduMatrix;
 
 class LUscalarMatrix
 :
-    public scalarMatrix
+    public scalarSquareMatrix
 {
     // Private data
 
@@ -78,7 +78,7 @@ class LUscalarMatrix
         void convert(const PtrList<procLduMatrix>& lduMatrices);
 
 
-        //- Print the ratio of the mag-sum of the off-diagonal coefficients 
+        //- Print the ratio of the mag-sum of the off-diagonal coefficients
         //  to the mag-diagonal
         void printDiagonalDominance() const;
 
@@ -87,8 +87,8 @@ public:
 
     // Constructors
 
-        //- Construct from Matrix<scalar> and perform LU decomposition
-        LUscalarMatrix(const Matrix<scalar>&);
+        //- Construct from scalarSquareMatrix and perform LU decomposition
+        LUscalarMatrix(const scalarSquareMatrix&);
 
         //- Construct from lduMatrix and perform LU decomposition
         LUscalarMatrix

src/OpenFOAM/matrices/Matrix/Matrix.C

@@ -28,8 +28,8 @@ License
 
 // * * * * * * * * * * * * Private Member Functions  * * * * * * * * * * * * //
 
-template<class Type>
-void Foam::Matrix<Type>::allocate()
+template<class Form, class Type>
+void Foam::Matrix<Form, Type>::allocate()
 {
     if (n_ && m_)
     {
@@ -46,8 +46,8 @@ void Foam::Matrix<Type>::allocate()
 
 // * * * * * * * * * * * * * * * Destructor  * * * * * * * * * * * * * * * * //
 
-template<class Type>
-Foam::Matrix<Type>::~Matrix()
+template<class Form, class Type>
+Foam::Matrix<Form, Type>::~Matrix()
 {
     if (v_)
     {
@@ -59,16 +59,16 @@ Foam::Matrix<Type>::~Matrix()
 
 // * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
 
-template<class Type>
-const Foam::Matrix<Type>& Foam::Matrix<Type>::null()
+template<class Form, class Type>
+const Foam::Matrix<Form, Type>& Foam::Matrix<Form, Type>::null()
 {
-    Matrix<Type>* nullPtr = reinterpret_cast<Matrix<Type>*>(NULL);
+    Matrix<Form, Type>* nullPtr = reinterpret_cast<Matrix<Form, Type>*>(NULL);
     return *nullPtr;
 }
 
 
-template<class Type>
-Foam::Matrix<Type>::Matrix(const label n, const label m)
+template<class Form, class Type>
+Foam::Matrix<Form, Type>::Matrix(const label n, const label m)
 :
     n_(n),
     m_(m),
@@ -76,7 +76,7 @@ Foam::Matrix<Type>::Matrix(const label n, const label m)