Merge commit 'origin/master' into olesenm

applications/solvers/compressible/rhoPimpleFoam/rhoPimpleFoam.C

@@ -43,23 +43,20 @@ Description
 
 int main(int argc, char *argv[])
 {
-
+    #include "setRootCase.H"
-#   include "setRootCase.H"
+    #include "createTime.H"
-#   include "createTime.H"
+    #include "createMesh.H"
-#   include "createMesh.H"
+    #include "createFields.H"
-#   include "createFields.H"
+    #include "initContinuityErrs.H"
-#   include "initContinuityErrs.H"
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
     Info<< "\nStarting time loop\n" << endl;
 
     while (runTime.run())
     {
-#       include "readTimeControls.H"
+        #include "readTimeControls.H"
-#       include "readPIMPLEControls.H"
+        #include "readPIMPLEControls.H"
-#       include "compressibleCourantNo.H"
+        #include "compressibleCourantNo.H"
-#       include "setDeltaT.H"
+        #include "setDeltaT.H"
 
         runTime++;
 
@@ -75,13 +72,13 @@ int main(int argc, char *argv[])
         int oCorr=0;
         do
         {
-#           include "UEqn.H"
+            #include "UEqn.H"
-#           include "hEqn.H"
+            #include "hEqn.H"
 
             // --- PISO loop
             for (int corr=0; corr<nCorr; corr++)
             {
-#               include "pEqn.H"
+                #include "pEqn.H"
             }
 
             turbulence->correct();

applications/solvers/compressible/sonicLiquidFoam/createFields.H

@@ -37,8 +37,7 @@
             IOobject::NO_READ,
             IOobject::AUTO_WRITE
         ),
-        rho0 + psi*(p - p0),
+        rhoO + psi*p
-        p.boundaryField().types()
     );
 
 

applications/solvers/compressible/sonicLiquidFoam/sonicLiquidFoam.C

@@ -26,7 +26,7 @@ Application
     sonicLiquidFoam
 
 Description
-    Transient solver for trans-sonic/supersonic, laminar flow of a 
+    Transient solver for trans-sonic/supersonic, laminar flow of a
     compressible liquid.
 
 \*---------------------------------------------------------------------------*/

applications/solvers/heatTransfer/buoyantSimpleRadiationFoam/Make/files

@@ -1,4 +1,4 @@
 buoyantSimpleRadiationFoam.C
 
-EXE = $(FOAM_USER_APPBIN)/buoyantSimpleRadiationFoam
+EXE = $(FOAM_APPBIN)/buoyantSimpleRadiationFoam
 

applications/solvers/molecularDynamics/gnemdFoam/Make/files

@@ -0,0 +1,3 @@
+gnemdFoam.C
+
+EXE = $(FOAM_APPBIN)/gnemdFoam

applications/solvers/molecularDynamics/gnemdFoam/Make/options

@@ -0,0 +1,11 @@
+EXE_INC = \
+    -I$(LIB_SRC)/lagrangian/molecule/lnInclude \
+    -I$(LIB_SRC)/finiteVolume/lnInclude \
+    -I$(LIB_SRC)/lagrangian/basic/lnInclude \
+    -I$(LIB_SRC)/meshTools/lnInclude
+
+EXE_LIBS = \
+    -lmeshTools \
+    -lfiniteVolume \
+    -llagrangian \
+    -lmolecule

applications/solvers/molecularDynamics/gnemdFoam/gnemdFoam.C

@@ -0,0 +1,90 @@
+/*---------------------------------------------------------------------------*\
+ =========                   |
+ \\      /   F ield          | OpenFOAM: The Open Source CFD Toolbox
+  \\    /    O peration      |
+   \\  /     A nd            | Copyright (C) 1991-2005 OpenCFD Ltd.
+    \\/      M anipulation   |
+-------------------------------------------------------------------------------
+License
+    This file is part of OpenFOAM.
+
+    OpenFOAM is free software; you can redistribute it and/or modify it
+    under the terms of the GNU General Public License as published by the
+    Free Software Foundation; either version 2 of the License, or (at your
+    option) any later version.
+
+    OpenFOAM is distributed in the hope that it will be useful, but WITHOUT
+    ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+    FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
+    for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with OpenFOAM; if not, write to the Free Software Foundation,
+    Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+
+Application
+    gnemdFOAM
+
+Description
+    MD for Fluid Mechanics and hybridising with a continuum solver.
+
+\*---------------------------------------------------------------------------*/
+
+#include "fvCFD.H"
+#include "md.H"
+
+int main(int argc, char *argv[])
+{
+
+#   include "setRootCase.H"
+#   include "createTime.H"
+#   include "createMesh.H"
+
+    moleculeCloud molecules(mesh);
+
+#   include "createMDFields.H"
+
+    molecules.removeHighEnergyOverlaps();
+
+#   include "temperatureAndPressureVariables.H"
+
+    label nAveragingSteps = 0;
+
+    Info << "\nStarting time loop\n" << endl;
+
+    while (runTime.run())
+    {
+        runTime++;
+
+        nAveragingSteps++;
+
+        Info << "Time = " << runTime.timeName() << endl;
+
+        molecules.integrateEquationsOfMotion();
+
+#       include "meanMomentumEnergyAndNMols.H"
+
+#       include "temperatureAndPressure.H"
+
+#       include "calculateMDFields.H"
+
+#       include "averageMDFields.H"
+
+        runTime.write();
+
+#       include "resetMDFields.H"
+
+        if (runTime.outputTime())
+        {
+            nAveragingSteps = 0;
+        }
+
+        Info << "ExecutionTime = " << runTime.elapsedCpuTime() << " s"
+            << "  ClockTime = " << runTime.elapsedClockTime() << " s"
+            << nl << endl;
+    }
+
+    Info << "End\n" << endl;
+
+    return(0);
+}

applications/solvers/molecularDynamics/mdEquilibrationFoam/Make/files

@@ -0,0 +1,3 @@
+mdEquilibrationFoam.C
+
+EXE = $(FOAM_APPBIN)/mdEquilibrationFoam

applications/solvers/molecularDynamics/mdEquilibrationFoam/Make/options

@@ -0,0 +1,11 @@
+EXE_INC = \
+    -I$(LIB_SRC)/lagrangian/molecule/lnInclude \
+    -I$(LIB_SRC)/finiteVolume/lnInclude \
+    -I$(LIB_SRC)/lagrangian/basic/lnInclude \
+    -I$(LIB_SRC)/meshTools/lnInclude
+
+EXE_LIBS = \
+    -lmeshTools \
+    -lfiniteVolume \
+    -llagrangian \
+    -lmolecule

applications/solvers/molecularDynamics/mdEquilibrationFoam/mdEquilibrationFoam.C

@@ -0,0 +1,86 @@
+/*---------------------------------------------------------------------------*\
+ =========                   |
+ \\      /   F ield          | OpenFOAM: The Open Source CFD Toolbox
+  \\    /    O peration      |
+   \\  /     A nd            | Copyright (C) 1991-2005 OpenCFD Ltd.
+    \\/      M anipulation   |
+-------------------------------------------------------------------------------
+License
+    This file is part of OpenFOAM.
+
+    OpenFOAM is free software; you can redistribute it and/or modify it
+    under the terms of the GNU General Public License as published by the
+    Free Software Foundation; either version 2 of the License, or (at your
+    option) any later version.
+
+    OpenFOAM is distributed in the hope that it will be useful, but WITHOUT
+    ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+    FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
+    for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with OpenFOAM; if not, write to the Free Software Foundation,
+    Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+
+Application
+    mdEquilibrationFOAM
+
+Description
+    Equilibrates and/or preconditions MD systems
+
+\*---------------------------------------------------------------------------*/
+
+#include "fvCFD.H"
+#include "md.H"
+
+int main(int argc, char *argv[])
+{
+
+#   include "setRootCase.H"
+#   include "createTime.H"
+#   include "createMesh.H"
+
+    moleculeCloud molecules(mesh);
+
+    molecules.removeHighEnergyOverlaps();
+
+#   include "temperatureAndPressureVariables.H"
+
+#   include "readmdEquilibrationDict.H"
+
+    label nAveragingSteps = 0;
+
+    Info << "\nStarting time loop\n" << endl;
+
+    while (runTime.run())
+    {
+        runTime++;
+
+        nAveragingSteps++;
+
+        Info << "Time = " << runTime.timeName() << endl;
+
+        molecules.integrateEquationsOfMotion();
+
+#       include "meanMomentumEnergyAndNMols.H"
+
+#       include "temperatureAndPressure.H"
+
+#       include "temperatureEquilibration.H"
+
+        runTime.write();
+
+        if (runTime.outputTime())
+        {
+            nAveragingSteps = 0;
+        }
+
+        Info << "ExecutionTime = " << runTime.elapsedCpuTime() << " s"
+            << "  ClockTime = " << runTime.elapsedClockTime() << " s"
+            << nl << endl;
+    }
+
+    Info << "End\n" << endl;
+
+    return(0);
+}

applications/solvers/molecularDynamics/mdEquilibrationFoam/readmdEquilibrationDict.H

@@ -0,0 +1,18 @@
+Info<< "Reading MD Equilibration Dictionary" << nl << endl;
+
+IOdictionary mdEquilibrationDict
+(
+    IOobject
+    (
+        "mdEquilibrationDict",
+        runTime.system(),
+        mesh,
+        IOobject::MUST_READ,
+        IOobject::NO_WRITE
+    )
+);
+
+scalar targetTemperature = readScalar
+(
+    mdEquilibrationDict.lookup("equilibrationTargetTemperature")
+);

applications/solvers/multiphase/compressibleLesInterFoam/Make/files

@@ -1,3 +1,3 @@
 compressibleLesInterFoam.C
 
-EXE = $(FOAM_USER_APPBIN)/compressibleLesInterFoam
+EXE = $(FOAM_APPBIN)/compressibleLesInterFoam

applications/solvers/multiphase/lesCavitatingFoam/lesCavitatingFoam.C

@@ -23,9 +23,10 @@ License
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 Application
-    rasCavitatingFoam
+    lesCavitatingFoam
 
 Description
+    Transient cavitation code with LES turbulence.
 
 \*---------------------------------------------------------------------------*/
 

applications/solvers/multiphase/rasCavitatingFoam/rasCavitatingFoam.C

@@ -26,6 +26,7 @@ Application
     rasCavitatingFoam
 
 Description
+    Transient cavitation code with RAS turbulence.
 
 \*---------------------------------------------------------------------------*/
 

applications/solvers/multiphase/twoPhaseEulerFoam/kineticTheoryModel/frictionalStressModel/Schaeffer/SchaefferFrictionalStress.C

@@ -71,8 +71,8 @@ frictionalPressure
     const dimensionedScalar& eta,
     const dimensionedScalar& p
 ) const
-{   
+{
-    return 
+    return
         dimensionedScalar("1e24", dimensionSet(1, -1, -2, 0, 0), 1e24)
        *pow(Foam::max(alpha - alphaMinFriction, scalar(0)), 10.0);
 }
@@ -89,7 +89,7 @@ frictionalPressurePrime
     const dimensionedScalar& p
 ) const
 {
-    return 
+    return
         dimensionedScalar("1e25", dimensionSet(1, -1, -2, 0, 0), 1e25)
        *pow(Foam::max(alpha - alphaMinFriction, scalar(0)), 9.0);
 }
@@ -129,8 +129,8 @@ Foam::tmp<Foam::volScalarField> Foam::SchaefferFrictionalStress::muf
     {
         if (alpha[celli] > alphaMax.value()-5e-2)
         {
-            muf_[celli] = 
+            muf_[celli] =
-                0.5*alpha[celli]*pf[celli]*sin(phi.value())
+                0.5*pf[celli]*sin(phi.value())
                /(
                     sqrt(1.0/6.0*(sqr(D[celli].xx() - D[celli].yy())
                   + sqr(D[celli].yy() - D[celli].zz())

applications/test/dataEntry/Make/files

@@ -0,0 +1,3 @@
+testDataEntry.C
+
+EXE = $(FOAM_APPBIN)/testDataEntry

applications/test/dataEntry/Make/options

@@ -0,0 +1,11 @@
+EXE_INC = \
+    -I$(LIB_SRC)/finiteVolume/lnInclude \
+    -I$(LIB_SRC)/lagrangian/intermediate/lnInclude \
+    -I$(LIB_SRC)/thermophysicalModels/radiation/lnInclude \
+    -I$(LIB_SRC)/thermophysicalModels/thermophysicalFunctions/lnInclude
+
+EXE_LIBS = \
+    -lfiniteVolume \
+    -llagrangianIntermediate \
+    -lradiation \
+    -lthermophysicalFunctions

applications/test/dataEntry/files

@@ -0,0 +1,4 @@
+testTable.C
+
+EXE=$(FOAM_USER_APPBIN)/testTable
+

applications/test/dataEntry/testDataEntry.C

@@ -23,83 +23,64 @@ License
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 Application
-    Rcomponents
+    testDataEntry
 
 Description
-    Calculates and writes the scalar fields of the six components of the 
+    Tests lagrangian/intermediate/submodels/IO/DataEntry
-    Reynolds stress R for each time.
 
 \*---------------------------------------------------------------------------*/
 
 #include "fvCFD.H"
+#include "DataEntry.H"
+#include "IOdictionary.H"
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
 int main(int argc, char *argv[])
 {
-
-#   include "addTimeOptions.H"
 #   include "setRootCase.H"
-
 #   include "createTime.H"
-
-    // Get times list
-    instantList Times = runTime.times();
-
-    // set startTime and endTime depending on -time and -latestTime options
-#   include "checkTimeOptions.H"
-
-    runTime.setTime(Times[startTime], startTime);
-
 #   include "createMesh.H"
 
-    for (label i=startTime; i<endTime; i++)
+    IOdictionary dataEntryProperties
-    {
+    (
-        runTime.setTime(Times[i], i);
+        IOobject
-
-        Info<< "Time = " << runTime.timeName() << endl;
-
-        IOobject Rheader
         (
-            "R",
+            "dataEntryProperties",
-            runTime.timeName(),
+            runTime.constant(),
             mesh,
-            IOobject::MUST_READ
+            IOobject::MUST_READ,
-        );
+            IOobject::NO_WRITE
+        )
+    );
 
-        // Check R exists
+    autoPtr<DataEntry<scalar> > dataEntry
-        if (Rheader.headerOk())
+    (
-        {
+        DataEntry<scalar>::New
-            mesh.readUpdate();
+        (
+            "dataEntry",
+            dataEntryProperties
+        )
+    );
 
-            Info<< "    Reading R" << endl;
+    scalar x0 = readScalar(dataEntryProperties.lookup("x0"));
-            volSymmTensorField R(Rheader, mesh);
+    scalar x1 = readScalar(dataEntryProperties.lookup("x1"));
 
-            for (direction i=0; i<tensor::nComponents; i++)
+    Info<< "Data entry type: " << dataEntry().type() << nl << endl;
-            {
-                Info<< "    Calculating R" << tensor::componentNames[i] << endl;
 
-                volScalarField Ri
+    Info<< "Inputs" << nl
-                (
+        << "    x0 = " << x0 << nl
-                    IOobject
+        << "    x1 = " << x1 << nl
-                    (
+        << endl;
-                        "R" + word(tensor::componentNames[i]),
-                        runTime.timeName(),
-                        mesh,
-                        IOobject::NO_READ
-                    ),
-                    R.component(i)
-                );
-                Ri.write();
-            }
-        }
-        else
-        {
-            Info<< "    No R" << endl;
-        }
 
-        Info<< endl;
+    Info<< "Interpolation" << nl
-    }
+        << "    f(x0) = " << dataEntry().value(x0) << nl
+        << "    f(x1) = " << dataEntry().value(x1) << nl
+        << endl;
+
+    Info<< "Integration" << nl
+        << "    int(f(x)) lim(x0->x1) = " << dataEntry().integrate(x0, x1) << nl
+        << endl;
 
     return(0);
 }

applications/utilities/mesh/advanced/refineHexMesh/Make/files

@@ -0,0 +1,3 @@
+refineHexMesh.C
+EXE = $(FOAM_APPBIN)/refineHexMesh
+

applications/utilities/mesh/advanced/refineHexMesh/Make/options

@@ -0,0 +1,10 @@
+EXE_INC = \
+    -I$(LIB_SRC)/finiteVolume/lnInclude \
+    -I$(LIB_SRC)/dynamicMesh/lnInclude \
+    -I$(LIB_SRC)/meshTools/lnInclude
+
+
+EXE_LIBS = \
+    -ldynamicMesh \
+    -lmeshTools \
+    -lfiniteVolume

applications/utilities/mesh/advanced/refineHexMesh/refineHexMesh.C

@@ -0,0 +1,185 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2007 OpenCFD Ltd.
+     \\/     M anipulation  |
+-------------------------------------------------------------------------------
+License
+    This file is part of OpenFOAM.
+
+    OpenFOAM is free software; you can redistribute it and/or modify it
+    under the terms of the GNU General Public License as published by the
+    Free Software Foundation; either version 2 of the License, or (at your
+    option) any later version.
+
+    OpenFOAM is distributed in the hope that it will be useful, but WITHOUT
+    ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+    FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
+    for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with OpenFOAM; if not, write to the Free Software Foundation,
+    Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+
+Description
+    Hex 2x2x2 refiner
+
+\*---------------------------------------------------------------------------*/
+
+#include "fvMesh.H"
+#include "pointMesh.H"
+#include "argList.H"
+#include "Time.H"
+#include "hexRef8.H"
+#include "cellSet.H"
+#include "OFstream.H"
+#include "meshTools.H"
+#include "IFstream.H"
+#include "polyTopoChange.H"
+#include "mapPolyMesh.H"
+#include "volMesh.H"
+#include "surfaceMesh.H"
+#include "volFields.H"
+#include "surfaceFields.H"
+#include "pointFields.H"
+#include "ReadFields.H"
+
+using namespace Foam;
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+// Main program:
+int main(int argc, char *argv[])
+{
+    argList::validArgs.append("cellSet");
+#   include "setRootCase.H"
+#   include "createTime.H"
+#   include "createMesh.H"
+    pointMesh pMesh(mesh);
+
+    word cellSetName(args.args()[1]);
+
+    Info<< "Reading cells to refine from cellSet " << cellSetName
+        << nl << endl;
+
+    cellSet cellsToRefine(mesh, cellSetName);
+
+    Info<< "Read " << returnReduce(cellsToRefine.size(), sumOp<label>())
+        << " cells to refine from cellSet " << cellSetName << nl
+        << endl;
+
+
+    // Read objects in time directory
+    IOobjectList objects(mesh, runTime.timeName());
+
+    // Read vol fields.
+
+    PtrList<volScalarField> vsFlds;
+    ReadFields(mesh, objects, vsFlds);
+
+    PtrList<volVectorField> vvFlds;
+    ReadFields(mesh, objects, vvFlds);
+
+    PtrList<volSphericalTensorField> vstFlds;
+    ReadFields(mesh, objects, vstFlds);
+
+    PtrList<volSymmTensorField> vsymtFlds;
+    ReadFields(mesh, objects, vsymtFlds);
+
+    PtrList<volTensorField> vtFlds;
+    ReadFields(mesh, objects, vtFlds);
+
+    // Read surface fields.
+
+    PtrList<surfaceScalarField> ssFlds;
+    ReadFields(mesh, objects, ssFlds);
+
+    PtrList<surfaceVectorField> svFlds;
+    ReadFields(mesh, objects, svFlds);
+
+    PtrList<surfaceSphericalTensorField> sstFlds;
+    ReadFields(mesh, objects, sstFlds);
+
+    PtrList<surfaceSymmTensorField> ssymtFlds;
+    ReadFields(mesh, objects, ssymtFlds);
+
+    PtrList<surfaceTensorField> stFlds;
+    ReadFields(mesh, objects, stFlds);
+
+    // Read point fields
+    PtrList<pointScalarField> psFlds;
+    ReadFields(pMesh, objects, psFlds);
+    
+    PtrList<pointVectorField> pvFlds;
+    ReadFields(pMesh, objects, pvFlds);
+
+
+
+    // Construct refiner without unrefinement. Read existing point/cell level.
+    hexRef8 meshCutter(mesh);
+
+    // Some stats
+    Info<< "Read mesh:" << nl
+        << "    cells:" << mesh.globalData().nTotalCells() << nl
+        << "    faces:" << mesh.globalData().nTotalFaces() << nl
+        << "    points:" << mesh.globalData().nTotalPoints() << nl
+        << "    cellLevel :"
+        << " min:" << gMin(meshCutter.cellLevel())
+        << " max:" << gMax(meshCutter.cellLevel()) << nl
+        << "    pointLevel :"
+        << " min:" << gMin(meshCutter.pointLevel())
+        << " max:" << gMax(meshCutter.pointLevel()) << nl
+        << endl;
+
+
+    // Maintain 2:1 ratio
+    labelList newCellsToRefine
+    (
+        meshCutter.consistentRefinement
+        (
+            cellsToRefine.toc(),
+            true                  // extend set
+        )
+    );
+
+    // Mesh changing engine.
+    polyTopoChange meshMod(mesh);
+
+    // Play refinement commands into mesh changer.
+    meshCutter.setRefinement(newCellsToRefine, meshMod);
+
+    runTime++;
+
+    // Create mesh, return map from old to new mesh.
+    autoPtr<mapPolyMesh> map = meshMod.changeMesh(mesh, false);
+
+    // Update fields
+    mesh.updateMesh(map);
+    pMesh.updateMesh(map);
+
+    // Update numbering of cells/vertices.
+    meshCutter.updateMesh(map);
+
+    // Optionally inflate mesh
+    if (map().hasMotionPoints())
+    {
+        mesh.movePoints(map().preMotionPoints());
+        pMesh.movePoints(map().preMotionPoints());
+    }
+
+    Pout<< "Refined from " << returnReduce(map().nOldCells(), sumOp<label>())
+        << " to " << mesh.globalData().nTotalCells() << " cells." << nl << endl;
+
+    Info<< "Writing mesh to " << runTime.timeName() << endl;
+
+    mesh.write();
+    meshCutter.write();
+
+    Info<< "End\n" << endl;
+
+    return 0;
+}
+
+
+// ************************************************************************* //

applications/utilities/mesh/conversion/tetgenToFoam/tetgenToFoam.C

@@ -56,18 +56,14 @@ NOTE:
 always. Might use some geometric check instead.
 - marked faces might not actually be boundary faces of mesh. This is not handled
 and you'll have to run without face file (-noFaceFile option)
-- default is to have indices starting at 1. Use -startAt0 if starting at 0.
+
-- all input is expected to be ordered.
 \*---------------------------------------------------------------------------*/
 
 #include "argList.H"
 #include "Time.H"
 #include "polyMesh.H"
 #include "IFstream.H"
-#include "polyPatch.H"
 #include "cellModeller.H"
-#include "ListOps.H"
-#include <fstream>
 
 using namespace Foam;
 
@@ -79,7 +75,6 @@ int main(int argc, char *argv[])
 {
     argList::validArgs.append("file prefix");
     argList::validOptions.insert("noFaceFile", "");
-    argList::validOptions.insert("startAt0", "");
 
 #   include "setRootCase.H"
 #   include "createTime.H"
@@ -87,34 +82,29 @@ int main(int argc, char *argv[])
 
     bool readFaceFile = !args.options().found("noFaceFile");
 
-    bool startAt1 = !args.options().found("startAt0");
-
     fileName prefix(args.additionalArgs()[0]);
 
     fileName nodeFile(prefix + ".node");
     fileName eleFile(prefix + ".ele");
     fileName faceFile(prefix + ".face");
 
-    Info<< "Files:" << endl
+    if (!readFaceFile)
-        << "    nodes : " << nodeFile << endl
-        << "    elems : " << eleFile << endl
-        << "    faces : " << faceFile << endl
-        << endl;
-
-
-    if (readFaceFile)
     {
-        Info<< "Reading .file for boundary information" << nl << endl;
+        Info<< "Files:" << endl
-    }
+            << "    nodes : " << nodeFile << endl
-    if (startAt1)
+            << "    elems : " << eleFile << endl
-    {
+            << endl;
-        Info<< "Numbering in files starts at 1" << nl << endl;
     }
     else
     {
-        Info<< "Numbering in files starts at 0" << nl << endl;
+        Info<< "Files:" << endl
-    }
+            << "    nodes : " << nodeFile << endl
+            << "    elems : " << eleFile << endl
+            << "    faces : " << faceFile << endl
+            << endl;
 
+        Info<< "Reading .face file for boundary information" << nl << endl;
+    }
 
     if (!exists(nodeFile) || !exists(eleFile))
     {
@@ -134,7 +124,7 @@ int main(int argc, char *argv[])
     }
 
 
-    std::ifstream nodeStream(nodeFile.c_str());
+    IFstream nodeStream(nodeFile);
 
     //
     // Read nodes.
@@ -145,7 +135,7 @@ int main(int argc, char *argv[])
 
     do
     {
-        std::getline(nodeStream, line);
+        nodeStream.getLine(line);
     }
     while((line.size() > 0) && (line[0] == '#'));
 
@@ -169,61 +159,60 @@ int main(int argc, char *argv[])
     //
 
     pointField points(nNodes);
+    Map<label> nodeToPoint(nNodes);
 
-    label pointI = 0;
-
-    while (nodeStream.good())
     {
-        std::getline(nodeStream, line);
+        labelList pointIndex(nNodes);
 
-        if ((line.size() > 0) && (line[0] != '#'))
+        label pointI = 0;
+
+        while (nodeStream.good())
         {
-            IStringStream nodeLine(line);
+            nodeStream.getLine(line);
 
-            label nodeI;
+            if ((line.size() > 0) && (line[0] != '#'))
-            scalar x, y, z;
-            label dummy;
-
-            nodeLine >> nodeI >> x >> y >> z;
-
-            for (label i = 0; i < nNodeAttr; i++)
             {
-                nodeLine >> dummy;
+                IStringStream nodeLine(line);
-            }
 
-            if (hasRegion)
+                label nodeI;
-            {
+                scalar x, y, z;
-                nodeLine >> dummy;
+                label dummy;
-            }
 
-            // Store point and node number.
+                nodeLine >> nodeI >> x >> y >> z;
-            if
-            (
-                 (!startAt1 && nodeI != pointI)
-              || (startAt1 && nodeI-1 != pointI)
-            )
-            {
-                FatalErrorIn(args.executable())
-                    << "point numbering not consecutive for node " << nodeI
-                    << " or numbering starts"
-                    << " at 0 or 1. Perhaps rerun w/o -startAt0 option?"
-                    << exit(FatalError);
-            }
 
-            points[pointI++] = point(x, y, z);
+                for (label i = 0; i < nNodeAttr; i++)
+                {
+                    nodeLine >> dummy;
+                }
+
+                if (hasRegion)
+                {
+                    nodeLine >> dummy;
+                }
+
+                // Store point and node number.
+                points[pointI] = point(x, y, z);
+                nodeToPoint.insert(nodeI, pointI);
+                pointI++;
+            }
+        }
+        if (pointI != nNodes)
+        {
+            FatalIOErrorIn(args.executable().c_str(), nodeStream)
+                << "Only " << pointI << " nodes present instead of " << nNodes
+                << " from header." << exit(FatalIOError);
         }
     }
 
-
     //
     // read elements
     //
 
-    std::ifstream eleStream(eleFile.c_str());
+    IFstream eleStream(eleFile);
 
     do
     {
-        std::getline(eleStream, line);
+        eleStream.getLine(line);
     }
     while((line.size() > 0) && (line[0] == '#'));
 
@@ -242,10 +231,11 @@ int main(int argc, char *argv[])
 
     if (nPtsPerTet != 4)
     {
-        FatalErrorIn(args.executable()) << "Cannot handle tets with "
+        FatalIOErrorIn(args.executable().c_str(), eleStream)
+            << "Cannot handle tets with "
             << nPtsPerTet << " points per tetrahedron in .ele file" << endl
             << "Can only handle tetrahedra with four points"
-            << exit(FatalError);
+            << exit(FatalIOError);
     }
 
     if (nElemAttr != 0)
@@ -262,39 +252,27 @@ int main(int argc, char *argv[])
     labelList tetPoints(4);
 
     cellShapeList cells(nTets);
+    label cellI = 0;
 
     while (eleStream.good())
     {
-        std::getline(eleStream, line);
+        eleStream.getLine(line);
 
         if ((line.size() > 0) && (line[0] != '#'))
         {
             IStringStream eleLine(line);
 
             label elemI;
-
             eleLine >> elemI;
 
-            if (startAt1)
-            {
-                --elemI;
-            }
-
             for (label i = 0; i < 4; i++)
             {
                 label nodeI;
-
                 eleLine >> nodeI;
-
+                tetPoints[i] = nodeToPoint[nodeI];
-                if (startAt1)
-                {
-                    --nodeI;
-                }
-
-                tetPoints[i] = nodeI;
             }
 
-            cells[elemI] = cellShape(tet, tetPoints);
+            cells[cellI++] = cellShape(tet, tetPoints);
 
             // Skip attributes
             for (label i = 0; i < nElemAttr; i++)
@@ -321,11 +299,11 @@ int main(int argc, char *argv[])
         // read boundary faces
         //
 
-        std::ifstream faceStream(faceFile.c_str());
+        IFstream faceStream(faceFile);
 
         do
         {
-            std::getline(faceStream, line);
+            faceStream.getLine(line);
         }
         while((line.size() > 0) && (line[0] == '#'));
 
@@ -344,10 +322,11 @@ int main(int argc, char *argv[])
 
         if (nFaceAttr != 1)
         {
-            FatalErrorIn(args.executable()) << "Expect boundary markers to be"
+            FatalIOErrorIn(args.executable().c_str(), faceStream)
+                << "Expect boundary markers to be"
                 << " present in .face file." << endl
                 << "This is the second number in the header which is now:"
-                << nFaceAttr << exit(FatalError);
+                << nFaceAttr << exit(FatalIOError);
         }
 
         // List of Foam vertices per boundary face
@@ -357,6 +336,8 @@ int main(int argc, char *argv[])
         boundaryPatch.setSize(nFaces);
         boundaryPatch = -1;
 
+        label faceI = 0;
+
         // Region to patch conversion
         Map<label> regionToPatch;
 
@@ -364,35 +345,23 @@ int main(int argc, char *argv[])
 
         while (faceStream.good())
         {
-            std::getline(faceStream, line);
+            faceStream.getLine(line);
 
             if ((line.size() > 0) && (line[0] != '#'))
             {
                 IStringStream faceLine(line);
 
-                label faceI, dummy, region;
+                label tetGenFaceI, dummy, region;
 
-                faceLine >> faceI;
+                faceLine >> tetGenFaceI;
-
-                if (startAt1)
-                {
-                    --faceI;
-                }
 
                 // Read face and reverse orientation (Foam needs outwards
                 // pointing)
                 for (label i = 0; i < 3; i++)
                 {
                     label nodeI;
-
                     faceLine >> nodeI;
-
+                    f[2-i] = nodeToPoint[nodeI];
-                    if (startAt1)
-                    {
-                        --nodeI;
-                    }
-
-                    f[2-i] = nodeI;
                 }
 
                 boundaryFaces[faceI] = f;
@@ -431,6 +400,8 @@ int main(int argc, char *argv[])
                         faceLine >> dummy;
                     }
                 }
+
+                faceI++;
             }
         }
 

applications/utilities/mesh/generation/autoHexMesh/Make/files

@@ -1,3 +0,0 @@
-autoHexMesh.C
-
-EXE = $(FOAM_APPBIN)/autoHexMesh

applications/utilities/mesh/generation/blockMesh/genBlockMesh.C

@@ -105,16 +105,39 @@ int main(int argc, char *argv[])
 
     if (writeTopo)
     {
-        word objMeshFile(runTime.path()/"blockTopology.obj");
-
-        Info<< nl << "Dumping block structure as Lightwave obj format"
-            << " to " << objMeshFile << endl;
-
         // Write mesh as edges.
+        {
+            fileName objMeshFile("blockTopology.obj");
 
-        OFstream objStream(objMeshFile);
+            OFstream str(runTime.path()/objMeshFile);
 
-        blocks.writeTopology(objStream);
+            Info<< nl << "Dumping block structure as Lightwave obj format"
+                << " to " << objMeshFile << endl;
+
+            blocks.writeTopology(str);
+        }
+
+        // Write centres of blocks
+        {
+            fileName objCcFile("blockCentres.obj");
+
+            OFstream str(runTime.path()/objCcFile);
+
+            Info<< nl << "Dumping block centres as Lightwave obj format"
+                << " to " << objCcFile << endl;
+
+            const polyMesh& topo = blocks.topology();
+
+            const pointField& cellCentres = topo.cellCentres();
+
+            forAll(cellCentres, cellI)
+            {
+                //point cc = b.blockShape().centre(b.points());
+                const point& cc = cellCentres[cellI];
+
+                str << "v " << cc.x() << ' ' << cc.y() << ' ' << cc.z() << nl;
+            }
+        }
 
         Info<< nl << "end" << endl;
 

applications/utilities/mesh/generation/snappyHexMesh/Make/files

@@ -0,0 +1,3 @@
+snappyHexMesh.C
+
+EXE = $(FOAM_APPBIN)/snappyHexMesh

applications/utilities/mesh/generation/snappyHexMesh/Make/options

@@ -1,6 +1,6 @@
 EXE_INC = \
     /* -g -DFULLDEBUG -O0 */ \
-    -I$(FOAM_UTILITIES)/parallelProcessing/decompositionMethods/decompositionMethods/lnInclude \
+    -I$(LIB_SRC)/decompositionAgglomeration/decompositionMethods/lnInclude \
     -I$(LIB_SRC)/autoMesh/lnInclude \
     -I$(LIB_SRC)/meshTools/lnInclude \
     -I$(LIB_SRC)/triSurface/lnInclude \

applications/utilities/mesh/generation/snappyHexMesh/snappyHexMesh.C

@@ -23,10 +23,10 @@ License
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 Application
-    autoHexMesh
+    snappyHexMesh
 
 Description
-    Automatic split hex mesher.
+    Automatic split hex mesher. Refines and snaps to surface.
 
 \*---------------------------------------------------------------------------*/
 
@@ -58,7 +58,7 @@ int main(int argc, char *argv[])
     (
        IOobject
        (
-            "autoHexMeshDict",
+            "snappyHexMeshDict",
             runTime.system(),
             mesh,
             IOobject::MUST_READ,

applications/utilities/mesh/manipulation/Optional/setSet/setSet.C

@@ -47,7 +47,7 @@ Description
 #include <stdio.h>
 
 
-#ifdef READLINE
+#if READLINE != 0
 #include <readline/readline.h>
 #include <readline/history.h>
 #endif
@@ -57,7 +57,7 @@ using namespace Foam;
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
 
-#ifdef READLINE
+#if READLINE != 0
 static const char* historyFile = ".setSet";
 #endif
 
@@ -739,7 +739,7 @@ int main(int argc, char *argv[])
 
         fileStreamPtr = new std::ifstream(batchFile.c_str());
     }
-#ifdef READLINE
+#if READLINE != 0
     else if (!read_history(historyFile))
     {
         Info<< "Successfully read history from " << historyFile << endl;
@@ -784,7 +784,7 @@ int main(int argc, char *argv[])
         }
         else
         {
-#           ifdef READLINE
+#           if READLINE != 0
             {
                 char* linePtr = readline("readline>");
 

applications/utilities/mesh/manipulation/checkMesh/checkMesh.C

@@ -101,7 +101,7 @@ int main(int argc, char *argv[])
 
             if (!noTopology)
             {
-                noFailedChecks += checkTopology(mesh, allTopology);
+                noFailedChecks += checkTopology(mesh, allTopology, allGeometry);
             }
 
             noFailedChecks += checkGeometry(mesh, allGeometry);

applications/utilities/mesh/manipulation/checkMesh/checkTopology.C

@@ -7,7 +7,12 @@
 #include "pointSet.H"
 #include "IOmanip.H"
 
-Foam::label Foam::checkTopology(const polyMesh& mesh, const bool allTopology)
+Foam::label Foam::checkTopology
+(
+    const polyMesh& mesh,
+    const bool allTopology,
+    const bool allGeometry
+)
 {
     label noFailedChecks = 0;
 
@@ -142,39 +147,38 @@ Foam::label Foam::checkTopology(const polyMesh& mesh, const bool allTopology)
             << setw(20) << "Patch"
             << setw(9) << "Faces"
             << setw(9) << "Points"
-            << " Surface" << endl;
+            << setw(34) << "Surface topology";
+        if (allGeometry)
+        {
+            Pout<< " Bounding box";
+        }
+        Pout<< endl;
 
         forAll(patches, patchI)
         {
             const polyPatch& pp = patches[patchI];
 
+                Pout<< "    "
+                    << setw(20) << pp.name()
+                    << setw(9) << pp.size()
+                    << setw(9) << pp.nPoints();
+
+
             primitivePatch::surfaceTopo pTyp = pp.surfaceType();
 
             if (pp.size() == 0)
             {
-                Pout<< "    "
+                Pout<< setw(34) << "ok (empty)";
-                    << setw(20) << pp.name()
-                    << setw(9) << pp.size()
-                    << setw(9) << pp.nPoints()
-                    << " ok (empty)" << endl;
             }
             else if (pTyp == primitivePatch::MANIFOLD)
             {
                 if (pp.checkPointManifold(true, &points))
                 {
-                    Pout<< "    " 
+                    Pout<< setw(34) << "multiply connected (shared point)";
-                        << setw(20) << pp.name()
-                        << setw(9) << pp.size()
-                        << setw(9) << pp.nPoints()
-                        << " multiply connected (shared point)" << endl;
                 }
                 else
                 {
-                    Pout<< "    "
+                    Pout<< setw(34) << "ok (closed singly connected)";
-                        << setw(20) << pp.name()
-                        << setw(9) << pp.size()
-                        << setw(9) << pp.nPoints()
-                        << " ok (closed singly connected surface)" << endl;
                 }
 
                 // Add points on non-manifold edges to make set complete
@@ -186,22 +190,35 @@ Foam::label Foam::checkTopology(const polyMesh& mesh, const bool allTopology)
 
                 if (pTyp == primitivePatch::OPEN)
                 {
-                    Pout<< "    "
+                    Pout<< setw(34) << "ok (non-closed singly connected)";
-                        << setw(20) << pp.name()
-                        << setw(9) << pp.size()
-                        << setw(9) << pp.nPoints()
-                        << " ok (not multiply connected)" << endl;
                 }
                 else
                 {
-                    Pout<< "    "
+                    Pout<< setw(34) << "multiply connected (shared edge)";
-                        << setw(20) << pp.name()
-                        << setw(9) << pp.size()
-                        << setw(9) << pp.nPoints()
-                        << " multiply connected surface (shared edge)"
-                        << endl;
                 }
             }
+
+            if (allGeometry)
+            {
+                const pointField& pts = pp.points();
+                const labelList& mp = pp.meshPoints();
+
+                boundBox bb(vector::zero, vector::zero);
+                if (returnReduce(mp.size(), sumOp<label>()) > 0)
+                {
+                    bb.min() = pts[mp[0]];
+                    bb.max() = pts[mp[0]];
+                    for (label i = 1; i < mp.size(); i++)
+                    {
+                        bb.min() = min(bb.min(), pts[mp[i]]);
+                        bb.max() = max(bb.max(), pts[mp[i]]);
+                    }
+                    reduce(bb.min(), minOp<vector>());
+                    reduce(bb.max(), maxOp<vector>());
+                }
+                Pout<< ' ' << bb;
+            }
+            Pout<< endl;
         }
 
         if (points.size() > 0)

applications/utilities/mesh/manipulation/checkMesh/checkTopology.H

@@ -4,5 +4,5 @@ namespace Foam
 {
     class polyMesh;
 
-    label checkTopology(const polyMesh& mesh, const bool allTopology);
+    label checkTopology(const polyMesh&, const bool, const bool);
 }

applications/utilities/mesh/manipulation/renumberMesh/Make/options

@@ -2,8 +2,7 @@ EXE_INC = \
     -I$(LIB_SRC)/meshTools/lnInclude \
     -I$(LIB_SRC)/dynamicMesh/lnInclude \
     -I$(LIB_SRC)/finiteVolume/lnInclude \
-    -I$(FOAM_UTILITIES)/parallelProcessing/decompositionMethods/decompositionMethods/lnInclude
+    -I$(LIB_SRC)/decompositionAgglomeration/decompositionMethods/lnInclude
-
 
 EXE_LIBS = \
     -lmeshTools \

applications/utilities/mesh/manipulation/subsetMesh/subsetMesh.C

@@ -60,7 +60,7 @@ void subsetVolFields
 
         Info<< "Subsetting field " << fieldName << endl;
 
-        GeometricField<Type, fvPatchField, volMesh> volField    
+        GeometricField<Type, fvPatchField, volMesh> fld    
         (
             IOobject
             (
@@ -73,7 +73,7 @@ void subsetVolFields
             baseMesh
         );
 
-        subFields.set(i, subsetter.interpolate(volField));
+        subFields.set(i, subsetter.interpolate(fld));
     }
 }
 
@@ -94,7 +94,7 @@ void subsetSurfaceFields
 
         Info<< "Subsetting field " << fieldName << endl;
 
-        GeometricField<Type, fvsPatchField, surfaceMesh> volField    
+        GeometricField<Type, fvsPatchField, surfaceMesh> fld    
         (
             IOobject
             (
@@ -107,7 +107,42 @@ void subsetSurfaceFields
             baseMesh
         );
 
-        subFields.set(i, subsetter.interpolate(volField));
+        subFields.set(i, subsetter.interpolate(fld));
+    }
+}
+
+
+template<class Type>
+void subsetPointFields
+(
+    const fvMeshSubset& subsetter,
+    const pointMesh& pMesh,
+    const wordList& fieldNames,
+    PtrList<GeometricField<Type, pointPatchField, pointMesh> >& subFields
+)
+{
+    const fvMesh& baseMesh = subsetter.baseMesh();
+
+    forAll(fieldNames, i)
+    {
+        const word& fieldName = fieldNames[i];
+
+        Info<< "Subsetting field " << fieldName << endl;
+
+        GeometricField<Type, pointPatchField, pointMesh> fld    
+        (
+            IOobject
+            (
+                fieldName,
+                baseMesh.time().timeName(),
+                baseMesh,
+                IOobject::MUST_READ,
+                IOobject::NO_WRITE
+            ),
+            pMesh
+        );
+
+        subFields.set(i, subsetter.interpolate(fld));
     }
 }
 
@@ -163,7 +198,9 @@ int main(int argc, char *argv[])
 
     IOobjectList objects(mesh, runTime.timeName());
 
-    // Read vol fields and subset.
+
+    // Read vol fields and subset
+    // ~~~~~~~~~~~~~~~~~~~~~~~~~~
 
     wordList scalarNames(objects.names(volScalarField::typeName));
     PtrList<volScalarField> scalarFlds(scalarNames.size());
@@ -191,7 +228,9 @@ int main(int argc, char *argv[])
     PtrList<volTensorField> tensorFlds(tensorNames.size());
     subsetVolFields(subsetter, tensorNames, tensorFlds);
 
-    // Read surface fields and subset.
+
+    // Read surface fields and subset
+    // ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
     wordList surfScalarNames(objects.names(surfaceScalarField::typeName));
     PtrList<surfaceScalarField> surfScalarFlds(surfScalarNames.size());
@@ -231,6 +270,59 @@ int main(int argc, char *argv[])
     subsetSurfaceFields(subsetter, surfTensorNames, surfTensorFlds);
 
 
+    // Read point fields and subset
+    // ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+    pointMesh pMesh(mesh);
+
+    wordList pointScalarNames(objects.names(pointScalarField::typeName));
+    PtrList<pointScalarField> pointScalarFlds(pointScalarNames.size());
+    subsetPointFields(subsetter, pMesh, pointScalarNames, pointScalarFlds);
+
+    wordList pointVectorNames(objects.names(pointVectorField::typeName));
+    PtrList<pointVectorField> pointVectorFlds(pointVectorNames.size());
+    subsetPointFields(subsetter, pMesh, pointVectorNames, pointVectorFlds);
+
+    wordList pointSphericalTensorNames
+    (
+        objects.names(pointSphericalTensorField::typeName)
+    );
+    PtrList<pointSphericalTensorField> pointSphericalTensorFlds
+    (
+        pointSphericalTensorNames.size()
+    );
+    subsetPointFields
+    (
+        subsetter,
+        pMesh,
+        pointSphericalTensorNames,
+        pointSphericalTensorFlds
+    );
+
+    wordList pointSymmTensorNames
+    (
+        objects.names(pointSymmTensorField::typeName)
+    );
+    PtrList<pointSymmTensorField> pointSymmTensorFlds
+    (
+        pointSymmTensorNames.size()
+    );
+    subsetPointFields
+    (
+        subsetter,
+        pMesh,
+        pointSymmTensorNames,
+        pointSymmTensorFlds
+    );
+
+    wordList pointTensorNames(objects.names(pointTensorField::typeName));
+    PtrList<pointTensorField> pointTensorFlds(pointTensorNames.size());
+    subsetPointFields(subsetter, pMesh, pointTensorNames, pointTensorFlds);
+
+
+
+    // Write mesh and fields to new time
+    // ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
     runTime++;
 
@@ -252,6 +344,18 @@ int main(int argc, char *argv[])
 
         vectorFlds[i].write();
     }
+    forAll(sphericalTensorFlds, i)
+    {
+        sphericalTensorFlds[i].rename(sphericalTensorNames[i]);
+
+        sphericalTensorFlds[i].write();
+    }
+    forAll(symmTensorFlds, i)
+    {
+        symmTensorFlds[i].rename(symmTensorNames[i]);
+
+        symmTensorFlds[i].write();
+    }
     forAll(tensorFlds, i)
     {
         tensorFlds[i].rename(tensorNames[i]);
@@ -272,6 +376,18 @@ int main(int argc, char *argv[])
 
         surfVectorFlds[i].write();
     }
+    forAll(surfSphericalTensorFlds, i)
+    {
+        surfSphericalTensorFlds[i].rename(surfSphericalTensorNames[i]);
+
+        surfSphericalTensorFlds[i].write();
+    }
+    forAll(surfSymmTensorFlds, i)
+    {
+        surfSymmTensorFlds[i].rename(surfSymmTensorNames[i]);
+
+        surfSymmTensorFlds[i].write();
+    }
     forAll(surfTensorNames, i)
     {
         surfTensorFlds[i].rename(surfTensorNames[i]);
@@ -279,6 +395,39 @@ int main(int argc, char *argv[])
         surfTensorFlds[i].write();
     }
 
+    // Point ones
+    forAll(pointScalarFlds, i)
+    {
+        pointScalarFlds[i].rename(pointScalarNames[i]);
+
+        pointScalarFlds[i].write();
+    }
+    forAll(pointVectorFlds, i)
+    {
+        pointVectorFlds[i].rename(pointVectorNames[i]);
+
+        pointVectorFlds[i].write();
+    }
+    forAll(pointSphericalTensorFlds, i)
+    {
+        pointSphericalTensorFlds[i].rename(pointSphericalTensorNames[i]);
+
+        pointSphericalTensorFlds[i].write();
+    }
+    forAll(pointSymmTensorFlds, i)
+    {
+        pointSymmTensorFlds[i].rename(pointSymmTensorNames[i]);
+
+        pointSymmTensorFlds[i].write();
+    }
+    forAll(pointTensorNames, i)
+    {
+        pointTensorFlds[i].rename(pointTensorNames[i]);
+
+        pointTensorFlds[i].write();
+    }
+
+
     Info << nl << "End" << endl;
 
     return 0;

applications/utilities/parallelProcessing/Allwmake

@@ -1,8 +0,0 @@
-#!/bin/sh
-set -x
-
-(cd decompositionMethods; ./Allwmake)
-wmake decomposePar
-wmake reconstructPar
-wmake reconstructParMesh
-wmake redistributeMeshPar

applications/utilities/parallelProcessing/decomposePar/Make/options

@@ -1,5 +1,5 @@
 EXE_INC = \
-    -I../decompositionMethods/decompositionMethods/lnInclude \
+    -I$(LIB_SRC)/decompositionAgglomeration/decompositionMethods/lnInclude \
     -I$(LIB_SRC)/finiteVolume/lnInclude \
     -I$(LIB_SRC)/lagrangian/basic/lnInclude
 

applications/utilities/parallelProcessing/decomposePar/decomposeParDict

@@ -21,6 +21,9 @@ FoamFile
 
 numberOfSubdomains   4;
 
+//preservePatches (inlet);
+//preserveFaceZones (heater solid1 solid3);
+
 method               simple;
 //method               hierarchical;
 //method               metis;
@@ -39,6 +42,17 @@ hierarchicalCoeffs
     order                xyz;
 }
 
+metisCoeffs
+{
+    //processorWeights 
+    //(
+    //    1
+    //    1
+    //    1
+    //    1
+    //);
+}
+
 manualCoeffs
 {
     dataFile             "decompositionData";

applications/utilities/parallelProcessing/decompositionMethods/Allwmake

@@ -1,8 +0,0 @@
-#!/bin/sh
-set -x
-
-wmake libso metis-5.0pre2/GKlib
-wmake libso metis-5.0pre2/libmetis
-
-wmake libso decompositionMethods
-(cd parMetisDecomp; ./Allwmake)

applications/utilities/parallelProcessing/decompositionMethods/metis-5.0pre2/CHANGES.v4

@@ -1,155 +0,0 @@
-
-
-METIS 4.0.2, 3/10/04
-------------------------------------------------------------------------------
-- Fixed a problem with weighted graphs and ometis.c
-
-
-METIS 4.0.1, 11/29/98
-------------------------------------------------------------------------------
-This is mostly a bug-fix release
-
-  - Fixed some bugs in the multi-constraint partitioning routines
-  - Fixed some bugs in the volume-minimization routines
-
-
-
-METIS 4.0.0, 9/20/98
-------------------------------------------------------------------------------
-METIS 4.0 contains a number of changes over the previous major release (ver 
-3.0.x). Most of these changes are concentrated on the graph and mesh 
-partitioning routines and they do not affect the sparse matrix re-ordering 
-routines. Here is a list of the major changes:
-
-  Multi-Constraint Partitioning
-  -----------------------------
-  METIS now includes partitioning routines that can be used to a partition
-  a graph in the presence of multiple balancing constraints.
-
-  Minimizing the Total Communication Volume
-  -----------------------------------------
-  METIS now includes partitioning routines whose objective is to minimize
-  the total communication volume (as opposed to minimizing the edge-cut).
-
-  Minimizing the Maximum Connectivity of the Subdomains
-  -----------------------------------------------------
-  The k-way partitioning routines in METIS can now directly minimize the number
-  of adjacent subdomains. For most graphs corresponding to finite element 
-  meshes, METIS is able to significantly reduce the maximum (and total) number of 
-  adjacent subdomains.
-
-
-
-
-METIS 3.0.6, 1/28/98
--------------------------------------------------------------------------------
-  - Fixed some problems when too many partitions were asked, and each partition
-    end up having 0 vertices
-  - Fixed some bugs in the I/O routines
-  - Added support for the g77 compiler under Linux
-
-
-METIS 3.0.5, 12/22/97
--------------------------------------------------------------------------------
-  - Fixed problems on 64-bit architectures (eg., -64 option on SGIs).
-  - Added some options in Makefile.in
-
-
-METIS 3.0.4, 12/1/97
--------------------------------------------------------------------------------
-  Fixed a memory leak in the ordering code.
-
-
-METIS 3.0.3, 11/5/97
--------------------------------------------------------------------------------
-  This is mostly a bug-fix release with just a few additions
-
-  Added functionality
-    - Added support for quadrilateral elements.
-    - Added a routine METIS_EstimateMemory that estimates the amount of
-      memory that will be allocated by METIS. This is useful in determining
-      if a problem can run on your system.
-    - Added hooks to allow PARMETIS to use the orderings produced by METIS.
-      This is hidden from the user but it will be used in the next release
-      of PARMETIS.
-
-  Bug-fixes
-    - Fixed a bug related to memory allocation. This should somewhat reduce the 
-      overall memory used by METIS.
-    - Fixed some bugs in the 'graphchk' program in the case of weighted graphs.
-    - Removed some code corresponding to unused options.
-    - Fixed some minor bugs in the node-refinement code
-      
-
-
--------------------------------------------------------------------------------
-METIS 3.0 contains a number of changes over METIS 2.0.
-The major changes are the following:
-
-  General Changes
-  ---------------
-    1.  Added code to directly partition finite element meshes.
-
-    2.  Added code to convert finite element meshes into graphs so they
-        can be used by METIS.
-
-    1.  The names, calling sequences, and options  of the routines in 
-        METISlib have been changed.
-
-    2.  Better support has been added for Fortran programs.
-
-    3.  Eliminated the 'metis' program. The only way to tune METIS's
-        behavior is to use METISlib.
-
-    4.  Improved memory management. METIS should now only abort if truly
-        there is no more memory left in the system.
-
-
-  Graph Partitioning
-  ------------------
-    1.  Added partitioning routines that can be used to compute a partition 
-        with prescribed partition weights. For example, they can be used to 
-        compute a 3-way partition such that partition 1 has 50% of the weight, 
-        partition 2 has 20% of the way, and partition 3 has 30% of the weight. 
-
-    2.  Improved the speed of the k-way partitioning algorithm (kmetis). The
-        new code has better cache locality which dramatically improves the 
-        speed for large graphs. A factor of 4 speedup can be obtained for
-        certain graphs. METIS can now partition a 4 million node graph
-        in well under a minute on a MIPS R10000.
-
-    3.  Eliminated some of the options that were seldom used. 
-  
-
-  Fill-Reducing Orderings
-  ----------------------
-    1.  Added a node based ordering code `onmetis' that greatly improves 
-        ordering quality.
-
-    2.  Improved the quality of the orderings produced by the original
-        edge-based ordering code (it is now called 'oemetis').
-
-    3.  METIS can now analyze the graph and try to compress together 
-        nodes with identical sparsity pattern. For some problems, this 
-        significantly reduces ordering time 
-
-    4.  METIS can now prune dense columns prior to ordering. This can be
-        helpful for LP matrices.
-        
-
-  Mesh Partitioning
-  -----------------
-    1.  METIS can now directly partition the element node array of finite
-        element meshes. It produces two partitioning vectors. One for the
-        elements and one for the nodes. METIS supports the following 
-        elements: triangles, tetrahedra, hexahedra
-
-
-  Mesh-To-Graph Conversion Routines
-  ---------------------------------
-    1.  METIS now includes a number of mesh conversion functions that can 
-        be used to create the dual and nodal graphs directly from the 
-        element connectivity arrays. These are highly optimized routines. 
-
-
-

applications/utilities/parallelProcessing/decompositionMethods/metis-5.0pre2/CHANGES.v5

@@ -1,28 +0,0 @@
-
-metis-5.0pre2
-------------------------------------------------------------------------
-r1437 | karypis | 2007-04-07 23:16:16 -0500 (Sat, 07 Apr 2007) | 3 lines
-
-- Added installation instructions and change-logs.
-- Tested 32bit & 64bit on 64bit architectures and passed tests.
-- Tested 32bit on 32bit architectures and passed tests.
-- strtoidx() addition for portable input file parsing
-- Restructured the internal memory allocation schemes for graph and
-  refinement data. This should enhance portability and make the code
-  easier to maintain.
-- Fixed some bad memory allocation calls (i.e., sizeof(x)/sizeof(idxtype). 
-  However, there are tons of those and need to be corrected once and for
-  all by eliminating workspace and the associated mallocs.
-- Added mprint/mscanf family of functions for portable formated I/O
-  of the idxtype datatype. The specifier for this datatype is %D.
-  All library routines use this function for printing. 
-  The implementation of these routines is not very efficient, but
-  that should do for now (in principle these routines should not be
-  used unless debugging).
-- Incorporated GKlib into METIS, which replaced many of its internal
-  functions. GKlib's malloc interface will enable graceful and clean
-  aborts (i.e., free all internally allocated memory) on fatal errors.
-  This will probably be available in the next pre-release.
-- Fixed the problems associated with metis.h that were identified by
-  David (flyspray Issue #9).
-

applications/utilities/parallelProcessing/decompositionMethods/metis-5.0pre2/GKlib/Make/files

@@ -1,21 +0,0 @@
-trunk/b64.c
-trunk/blas.c
-trunk/dfkvkselect.c
-trunk/dlmalloc.c
-trunk/error.c
-trunk/fs.c
-trunk/getopt.c
-trunk/htable.c
-trunk/io.c
-trunk/memory.c
-trunk/omp.c
-trunk/pdb.c
-trunk/pqueue.c
-trunk/seq.c
-trunk/sort.c
-trunk/string.c
-trunk/timers.c
-trunk/tokenizer.c
-trunk/util.c
-
-LIB = $(FOAM_LIBBIN)/libGKlib

applications/utilities/parallelProcessing/decompositionMethods/metis-5.0pre2/GKlib/Make/options

@@ -1 +0,0 @@
-/*EXE_INC = -Wno-unused-variables*/

applications/utilities/parallelProcessing/decompositionMethods/metis-5.0pre2/GKlib/trunk/GKlib.h

@@ -1,75 +0,0 @@
-/*
- * GKlib.h
- * 
- * George's library of most frequently used routines
- *
- * $Id: GKlib.h 1430 2007-04-07 17:53:07Z karypis $
- *
- */
-
-#ifndef _GKLIB_H_
-#define _GKLIB_H_ 1
-
-#define GKMSPACE
-
-#if defined(_MSC_VER)
-#define __MSC__
-#endif
-#if defined(__ICC)
-#define __ICC__
-#endif
-
-
-#include <gk_arch.h> /*!< This should be here, prior to the includes */
-
-
-/*************************************************************************
-* Header file inclusion section
-**************************************************************************/
-#include <stddef.h>
-#include <stdlib.h>
-#include <stdarg.h>
-#include <stdio.h>
-#include <errno.h>
-#include <ctype.h>
-#include <math.h>
-#include <float.h>
-#include <time.h>
-#include <string.h>
-#include <limits.h>
-#include <signal.h>
-#include <setjmp.h>
-#include <assert.h>
-#include <sys/stat.h>
-
-#if defined(__WITHPCRE__)
-#include <pcreposix.h>
-#else
-#include <regex.h>
-#endif
-
-
-#if defined(__OPENMP__) 
-#include <omp.h>
-#endif
-
-
-
-
-#include <gk_dlmalloc.h>
-#include <gk_types.h>
-#include <gk_struct.h>
-#include <gk_externs.h>
-#include <gk_defs.h>
-#include <gk_macros.h>
-#include <gk_getopt.h>
-
-#include <gk_sort.h>
-#include <gk_blas.h>
-#include <gk_memory.h>
-
-#include <gk_proto.h>
-
-#endif  /* GKlib.h */
-
-

applications/utilities/parallelProcessing/decompositionMethods/metis-5.0pre2/GKlib/trunk/Makefile

@@ -1,212 +0,0 @@
-#*************************************************************************
-# Global flags
-#*************************************************************************
-gdb         = yes
-debug       = no
-memdbg      = no
-openmp      = no
-pcre        = no
-x86compiler = gcc
-
-
-
-#*************************************************************************
-# System-specific compilation flags
-#*************************************************************************
-# Get some basic information about the system that you are working on
-cputype = $(shell uname -m | sed "s/\\ /_/g")
-systype = $(shell uname)
-ifeq ($(findstring CYGWIN, $(systype)),CYGWIN)
-  systype = MSWIN
-#  systype = CYGWIN
-  cputype = x86
-endif
-
-
-
-ifeq ($(systype),MSWIN)
-  #-------------------------------------------------------------------
-  # These defs are very much Visual Studio Specific
-  #-------------------------------------------------------------------
-  #Compiler information
-  CC = cl 
-  OPTFLAGS = /Ox 
-  COPTIONS = -DWIN32 -DMSC -D_CRT_SECURE_NO_DEPRECATE 
-
-  #Linker information
-  LDOPTIONS = 
-  LD = /cygdrive/c/Program\ Files/Microsoft\ Visual\ Studio\ 8/VC/BIN/link
-
-  #Library creation information
-  AR = lib /NODEFAULTLIB:LIBC /OUT:$@ 
-  RANLIB = 
-
-  ifeq ($(openmp),yes)
-    COPTIONS  += -D__OPENMP__ /openmp 
-    LDOPTIONS += /openmp
-  endif
-
-  #Compile input/output file specification
-  SOURCEFILE = /c $<
-  OUTPUTFILE = /Fo$@
-
-  # Standard file extensions
-  OBJEXT = .obj
-  LIBEXT = .lib
-  EXEEXT = .exe
-else
-  ifeq ($(systype),Linux)  
-    ifeq ($(x86compiler),gcc) 
-      #Compiler information
-      CC = gcc
-      OPTFLAGS = -O6
-      COPTIONS = -DLINUX -D_FILE_OFFSET_BITS=64 -Wall -std=c99 -pedantic
-
-      #Linker information
-      LDOPTIONS =
-      LD = gcc
-    else
-      #Compiler information
-      CC = icc
-      OPTFLAGS = -O3
-      COPTIONS = -DLINUX -D_FILE_OFFSET_BITS=64 -std=c99 
-
-      #Linker information
-      LDOPTIONS =
-      LD = icc
-
-      ifeq ($(openmp),yes)
-        COPTIONS  += -D__OPENMP__ -openmp -openmp-report2
-        LDOPTIONS += -openmp
-      endif
-    endif
-  endif
-
-
-  ifeq ($(systype),Darwin)  
-    #Compiler information
-    CC = gcc
-    OPTFLAGS = -O6
-    COPTIONS = -DDARWIN -D_FILE_OFFSET_BITS=64 -Wall -std=c99 -pedantic
-
-    #Linker information
-    LDOPTIONS =
-    LD = gcc
-
-    #Linker information
-    LDOPTIONS =
-    LD = gcc
-  endif
-
-
-  ifeq ($(systype),SunOS)
-    #Compiler information
-    CC = /opt/SUNWspro/bin/cc
-    OPTFLAGS = -xO4
-    COPTIONS = -DSUNOS 
-  
-    #Linker information
-    LDOPTIONS = 
-    LD = /opt/SUNWspro/bin/cc
-  endif
-
-  ifeq ($(systype),CYGWIN)
-    #Compiler information
-    CC = gcc 
-    OPTFLAGS = -O6
-    COPTIONS = -DCYGWIN -DWIN32 -D_FILE_OFFSET_BITS=64 -Wall -std=c99 -pedantic -mno-cygwin 
-
-    #Linker information
-    LDOPTIONS = -mno-cygwin 
-    LD = gcc
-  endif
-
-
-  #-------------------------------------------------------------------
-  # These defs are common among the GNU/GCC based systems
-  #-------------------------------------------------------------------
-  #Library creation information
-  AR = ar crv $@ 
-  RANLIB = ar -ts $@
-
-  #Compile input/output file specification
-  SOURCEFILE = -c $<
-  OUTPUTFILE = -o $@
-
-  # Standard file extensions
-  OBJEXT = .o
-  LIBEXT = .a
-  EXEEXT = 
-endif
-
-
-#**************************************************************************
-DMALLOCINC = 
-DMALLOCFLAGS =
-DEBUGFLAGS =
-XTRAFLAGS = 
-
-ifeq ($(dmalloc),yes)
-  DMALLOCINC = -I$(HOME)/local/include
-  DMALLOCFLAGS = -DDMALLOC
-  OPTFLAGS = -g
-endif
-
-ifeq ($(debug),yes)
-  DEBUGFLAGS = -DDEBUG
-  OPTFLAGS = -g
-endif
-
-ifeq ($(gdb),yes)
-  OPTFLAGS += -g
-endif
-
-ifeq ($(pcre),yes)
-  XTRAFLAGS += -D__WITHPCRE__
-endif
-#**************************************************************************
-
-
-
-#**************************************************************************
-INCLUDES = -I./ $(INCDIR) $(DMALLOCINC)
-CFLAGS = $(COPTIONS) $(OPTFLAGS) $(XTRAFLAGS) $(DMALLOCFLAGS) $(DEBUGFLAGS) $(INCLUDES)
-#**************************************************************************
-
-
-#**************************************************************************
-# Create the build directory if it does not exist
-#**************************************************************************
-BUILDDIR = ../builds/$(systype)-$(cputype)
-$(shell mkdir -p $(BUILDDIR))
-
-OBJS    = $(patsubst %.c, $(BUILDDIR)/%$(OBJEXT), $(wildcard *.c))
-HEADERS = $(wildcard *.h) Makefile
-
-
-$(BUILDDIR)/libGKlib$(LIBEXT): $(OBJS)
-	$(AR) $(OBJS)
-	$(RANLIB) 
-
-doc:
-	doxygen ../doxygen/Doxyfile
-
-pubdoc:
-	doxygen ../doxygen/Doxyfile
-	scp -r ../doxygen/html/* dminers.dtc.umn.edu:/var/www/wwwroot/dminers/files/doxy/GKlib 
-	ssh dminers.dtc.umn.edu "chmod -R a+rX /var/www/wwwroot/dminers/files/doxy/GKlib"
-
-clean:
-	rm -f $(OBJS)
-
-realclean:
-	rm -f $(OBJS) ; rm -f $(BUILDDIR)/libGKlib$(LIBEXT)
-
-
-$(OBJS) : $(HEADERS) Makefile
-
-
-$(BUILDDIR)/%$(OBJEXT) : %.c
-	$(CC) $(CFLAGS) $(SOURCEFILE) $(OUTPUTFILE)
-
-

applications/utilities/parallelProcessing/decompositionMethods/metis-5.0pre2/GKlib/trunk/b64.c

@@ -1,90 +0,0 @@
-/*! 
-\file  b64.c
-\brief This file contains some simple 8bit-to-6bit encoding/deconding routines
-
-Most of these routines are outdated and should be converted using glibc's equivalent
-routines.
-
-\date   Started 2/22/05
-\author George
-\version\verbatim $Id: b64.c 1421 2007-04-06 14:37:41Z karypis $ \endverbatim
-*/
-
-
-#include <GKlib.h>
-
-#define B64OFFSET       48      /* This is the '0' number */
-
-
-
-/******************************************************************************
-* Encode 3 '8-bit' binary bytes as 4 '6-bit' characters
-*******************************************************************************/
-void encodeblock(unsigned char *in, unsigned char *out)
-{
-  out[0] = (in[0] >> 2);
-  out[1] = (((in[0] & 0x03) << 4) | (in[1] >> 4));
-  out[2] = (((in[1] & 0x0f) << 2) | (in[2] >> 6));
-  out[3] = (in[2] & 0x3f);
-
-  out[0] += B64OFFSET;
-  out[1] += B64OFFSET;
-  out[2] += B64OFFSET;
-  out[3] += B64OFFSET;
-
-//  printf("%c %c %c %c %2x %2x %2x %2x %2x %2x %2x\n", out[0], out[1], out[2], out[3], out[0], out[1], out[2], out[3], in[0], in[1], in[2]);
-}
-
-/******************************************************************************
-* Decode 4 '6-bit' characters into 3 '8-bit' binary bytes
-*******************************************************************************/
-void decodeblock(unsigned char *in, unsigned char *out)
-{   
-  in[0] -= B64OFFSET;
-  in[1] -= B64OFFSET;
-  in[2] -= B64OFFSET;
-  in[3] -= B64OFFSET;
-
-  out[0] = (in[0] << 2 | in[1] >> 4);
-  out[1] = (in[1] << 4 | in[2] >> 2);
-  out[2] = (in[2] << 6 | in[3]);
-}
-
-
-/******************************************************************************
-* This function encodes an input array of bytes into a base64 encoding. Memory
-* for the output array is assumed to have been allocated by the calling program
-* and be sufficiently large. The output string is NULL terminated.
-*******************************************************************************/
-void GKEncodeBase64(int nbytes, unsigned char *inbuffer, unsigned char *outbuffer)
-{
-  int i, j;
-
-  if (nbytes%3 != 0)
-    gk_errexit(SIGERR, "GKEncodeBase64: Input buffer size should be a multiple of 3! (%d)\n", nbytes);
-
-  for (j=0, i=0; i<nbytes; i+=3, j+=4) 
-    encodeblock(inbuffer+i, outbuffer+j);
-
-//printf("%d %d\n", nbytes, j);
-  outbuffer[j] = '\0';
-}
-
-
-
-/******************************************************************************
-* This function decodes an input array of base64 characters into their actual
-* 8-bit codes. Memory * for the output array is assumed to have been allocated 
-* by the calling program and be sufficiently large. The padding is discarded.
-*******************************************************************************/
-void GKDecodeBase64(int nbytes, unsigned char *inbuffer, unsigned char *outbuffer)
-{
-  int i, j;
-
-  if (nbytes%4 != 0)
-    gk_errexit(SIGERR, "GKDecodeBase64: Input buffer size should be a multiple of 4! (%d)\n", nbytes);
-
-  for (j=0, i=0; i<nbytes; i+=4, j+=3) 
-    decodeblock(inbuffer+i, outbuffer+j);
-}
-

applications/utilities/parallelProcessing/decompositionMethods/metis-5.0pre2/GKlib/trunk/blas.c

@@ -1,129 +0,0 @@
-/*!
-\file blas.c
-\brief This file contains GKlib's implementation of BLAS-like routines
-
-The BLAS routines that are currently implemented are mostly level-one.
-They follow a naming convention of the type gk_[type][name], where
-[type] is one of c, i, f, and d, based on C's four standard scalar
-datatypes of characters, integers, floats, and doubles.
-
-These routines are implemented using a generic macro template,
-which is used for code generation.
-
-\date   Started 9/28/95
-\author George
-\version\verbatim $Id: blas.c 1421 2007-04-06 14:37:41Z karypis $ \endverbatim
-*/
-
-#include <GKlib.h>
-
-
-
-/*************************************************************************/
-/*! Set the elements of an array to a specified value */
-/*************************************************************************/
-GK_SET(gk_cset,   char)
-GK_SET(gk_iset,   int)
-GK_SET(gk_fset,   float)
-GK_SET(gk_dset,   double)
-GK_SET(gk_idxset, gk_idx_t)
-
-
-
-/*************************************************************************/
-/*! Set the elements of an array in increasing order */
-/*************************************************************************/
-GK_INCSET(gk_cincset,   char)
-GK_INCSET(gk_iincset,   int)
-GK_INCSET(gk_fincset,   float)
-GK_INCSET(gk_dincset,   double)
-GK_INCSET(gk_idxincset, gk_idx_t)
-
-
-
-/*************************************************************************/
-/*! Return the index of the maximum element in a vector */
-/*************************************************************************/
-GK_ARGMAX(gk_cargmax,   char)
-GK_ARGMAX(gk_iargmax,   int)
-GK_ARGMAX(gk_fargmax,   float)
-GK_ARGMAX(gk_dargmax,   double)
-GK_ARGMAX(gk_idxargmax, gk_idx_t)
-
-
-
-/*************************************************************************/
-/*! Return the index of the minimum element in a vector */
-/*************************************************************************/
-GK_ARGMIN(gk_cargmin,   char)
-GK_ARGMIN(gk_iargmin,   int)
-GK_ARGMIN(gk_fargmin,   float)
-GK_ARGMIN(gk_dargmin,   double)
-GK_ARGMIN(gk_idxargmin, gk_idx_t)
-
-
-
-/*************************************************************************/
-/*! Return the index of the Kth largest element in a vector */
-/*************************************************************************/
-GK_ARGMAX_N(gk_cargmax_n,   char,     gk_ckv_t,   gk_ckvmalloc,   gk_dckvsort)
-GK_ARGMAX_N(gk_iargmax_n,   int,      gk_ikv_t,   gk_ikvmalloc,   gk_dikvsort)
-GK_ARGMAX_N(gk_fargmax_n,   float,    gk_fkv_t,   gk_fkvmalloc,   gk_dfkvsort)
-GK_ARGMAX_N(gk_dargmax_n,   double,   gk_dkv_t,   gk_dkvmalloc,   gk_ddkvsort)
-GK_ARGMAX_N(gk_idxargmax_n, gk_idx_t, gk_idxkv_t, gk_idxkvmalloc, gk_didxkvsort)
-
-
-/*************************************************************************/
-/*! Sums the entries of an array */
-/*************************************************************************/
-GK_SUM(gk_csum,   char,     intmax_t)
-GK_SUM(gk_isum,   int,      intmax_t)
-GK_SUM(gk_fsum,   float,    float)
-GK_SUM(gk_dsum,   double,   double)
-GK_SUM(gk_idxsum, gk_idx_t, intmax_t)
-
-
-
-/*************************************************************************/
-/*! Scales the elements of a vector by a constant */
-/*************************************************************************/
-GK_SCALE(gk_cscale,   char)
-GK_SCALE(gk_iscale,   int)
-GK_SCALE(gk_fscale,   float)
-GK_SCALE(gk_dscale,   double)
-GK_SCALE(gk_idxscale, gk_idx_t)
-
-
-/*************************************************************************/
-/*! Computes the 2-norm of a vector */
-/*************************************************************************/
-GK_NORM2(gk_cnorm2,   char,     intmax_t)
-GK_NORM2(gk_inorm2,   int,      intmax_t)
-GK_NORM2(gk_fnorm2,   float,    float)
-GK_NORM2(gk_dnorm2,   double,   double)
-GK_NORM2(gk_idxnorm2, gk_idx_t, intmax_t)
-
-
-
-
-/*************************************************************************/
-/*! Computes the dot-product of two vectors */
-/*************************************************************************/
-GK_DOT(gk_cdot,   char,     intmax_t)
-GK_DOT(gk_idot,   int,      intmax_t)
-GK_DOT(gk_fdot,   float,    float)
-GK_DOT(gk_ddot,   double,   double)
-GK_DOT(gk_idxdot, gk_idx_t, intmax_t)
-
-
-
-/*************************************************************************/
-/*! Computes y = ax+y */
-/*************************************************************************/
-GK_AXPY(gk_caxpy,   char)
-GK_AXPY(gk_iaxpy,   int)
-GK_AXPY(gk_faxpy,   float)
-GK_AXPY(gk_daxpy,   double)
-GK_AXPY(gk_idxaxpy, gk_idx_t)
-
-