Merge commit 'origin/master' into olesenm

applications/solvers/incompressible/icoDyMFoam/icoDyMFoam.C

@@ -56,32 +56,35 @@ int main(int argc, char *argv[])
     {
 #       include "readControls.H"
 #       include "CourantNo.H"
-
-        p.storePrevIter();
-
-        // Make the fluxes absolute
-        fvc::makeAbsolute(phi, U);
-
 #       include "setDeltaT.H"
 
         runTime++;
 
         Info<< "Time = " << runTime.timeName() << nl << endl;
 
-        bool meshChanged = mesh.update();
+        // Make the fluxes absolute
+        if (mesh.changing())
+        {
+            phi = fvc::interpolate(U) & mesh.Sf();
+        }
 
-        if (correctPhi && meshChanged)
+        mesh.update();
+
+        if (mesh.changing() && correctPhi)
         {
 #           include "correctPhi.H"
         }
 
         // Keep the absolute fluxes for use in ddtPhiCorr
-        surfaceScalarField phiAbs("phiAbs", phi);
+        surfaceScalarField phiAbs0("phiAbs0", phi);
 
         // Make the fluxes relative to the mesh motion
+        if (mesh.changing())
+        {
             fvc::makeRelative(phi, U);
+        }
 
-        if (meshChanged && checkMeshCourantNo)
+        if (mesh.changing() && checkMeshCourantNo)
         {
 #           include "meshCourantNo.H"
         }
@@ -89,6 +92,8 @@ int main(int argc, char *argv[])
         // --- PIMPLE loop
         for (int ocorr=0; ocorr<nOuterCorr; ocorr++)
         {
+            p.storePrevIter();
+
 #           include "UEqn.H"
 
             // --- PISO loop
@@ -101,10 +106,50 @@ int main(int argc, char *argv[])
 
                 if (ddtPhiCorr)
                 {
-                    phi += fvc::ddtPhiCorr(rAU, U, phiAbs);
+                    if (mesh.changing())
+                    {
+                        dimensionedScalar rDeltaT = 1.0/mesh.time().deltaT();
+
+                        volScalarField V0byV
+                        (
+                            IOobject
+                            (
+                                "V0byV",
+                                mesh.time().timeName(),
+                                mesh
+                            ),
+                            mesh,
+                            dimensionedScalar("V0byV", dimless, 1),
+                            zeroGradientFvPatchScalarField::typeName
+                        );
+                        V0byV.dimensionedInternalField() = mesh.V0()/mesh.V();
+                        V0byV.correctBoundaryConditions();
+
+                        phi += rDeltaT*
+                        (
+                            fvc::interpolate(rAU*V0byV)*phiAbs0
+                          - (fvc::interpolate(rAU*V0byV*U.oldTime()) & mesh.Sf())
+                        );
+                    }
+                    else
+                    {
+                        phi += fvc::ddtPhiCorr(rAU, U, phiAbs0);
+                    }
                 }
 
+                if (p.needReference())
+                {
+                    if (mesh.changing())
+                    {
+                        fvc::makeRelative(phi, U);
                         adjustPhi(phi, U, p);
+                        fvc::makeAbsolute(phi, U);
+                    }
+                    else
+                    {
+                        adjustPhi(phi, U, p);
+                    }
+                }
 
                 for (int nonOrth=0; nonOrth<=nNonOrthCorr; nonOrth++)
                 {
@@ -138,11 +183,11 @@ int main(int argc, char *argv[])
                     p.relax();
                 }
 
-                // Make the fluxes relative to the mesh motion
-                fvc::makeRelative(phi, U);
-
                 U -= rAU*fvc::grad(p);
                 U.correctBoundaryConditions();
+
+                // Make the fluxes relative to the mesh motion
+                fvc::makeRelative(phi, U);
             }
         }
 

applications/solvers/multiphase/interDyMFoam/interDyMFoam.C

@@ -41,6 +41,7 @@ Description
 #include "twoPhaseMixture.H"
 #include "incompressible/turbulenceModel/turbulenceModel.H"
 #include "probes.H"
+#include "EulerDdtScheme.H"
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
@@ -66,7 +67,6 @@ int main(int argc, char *argv[])
     {
         #include "readControls.H"
         #include "CourantNo.H"
-
         #include "setDeltaT.H"
 
         runTime++;
@@ -76,7 +76,7 @@ int main(int argc, char *argv[])
         // Make the fluxes absolute
         if (mesh.changing())
         {
-            fvc::makeAbsolute(phi, U);
+            phi = fvc::interpolate(U) & mesh.Sf();
         }
 
         scalar timeBeforeMeshUpdate = runTime.elapsedCpuTime();
@@ -100,7 +100,7 @@ int main(int argc, char *argv[])
         }
 
         // Keep the absolute fluxes for use in ddtPhiCorr
-        surfaceScalarField phiAbs("phiAbs", phi);
+        surfaceScalarField phiAbs0("phiAbs0", phi);
 
         // Make the fluxes relative to the mesh motion
         if (mesh.changing())
@@ -125,8 +125,6 @@ int main(int argc, char *argv[])
             #include "pEqn.H"
         }
 
-        #include "continuityErrs.H"
-
         p = pd + rho*gh;
 
         if (pd.needReference())

applications/solvers/multiphase/interDyMFoam/pEqn.H

@@ -2,14 +2,35 @@
     volScalarField rAU = 1.0/UEqn.A();
     surfaceScalarField rAUf = fvc::interpolate(rAU);
 
-    volVectorField HU = UEqn.H();
+    U = rAU*UEqn.H();
-    U = rAU*HU;
-
     surfaceScalarField phiU("phiU", (fvc::interpolate(U) & mesh.Sf()));
 
     if (ddtPhiCorr)
     {
-        phiU += fvc::ddtPhiCorr(rAU, rho, U, phiAbs);
+        //phiU += fvc::ddtPhiCorr(rAU, rho, U, phiAbs0);
+
+        dimensionedScalar rDeltaT = 1.0/mesh.time().deltaT();
+
+        volScalarField V0byV
+        (
+            IOobject
+            (
+                "V0byV",
+                mesh.time().timeName(),
+                mesh
+            ),
+            mesh,
+            dimensionedScalar("V0byV", dimless, 1),
+            zeroGradientFvPatchScalarField::typeName
+        );
+        V0byV.dimensionedInternalField() = mesh.V0()/mesh.V();
+        V0byV.correctBoundaryConditions();
+
+        phiU += rDeltaT*
+        (
+            fvc::interpolate(rAU*rho.oldTime()*V0byV)*phiAbs0
+          - (fvc::interpolate(rAU*rho.oldTime()*V0byV*U.oldTime()) & mesh.Sf())
+        );
     }
 
     phi = phiU +
@@ -59,6 +80,8 @@
     U += rAU*fvc::reconstruct((phi - phiU)/rAUf);
     U.correctBoundaryConditions();
 
+    #include "continuityErrs.H"
+
     // Make the fluxes relative to the mesh motion
     fvc::makeRelative(phi, U);
 }

applications/utilities/postProcessing/velocityField/magGradU/FoamX/magGradU.cfg

@@ -1,27 +0,0 @@
-/*---------------------------------------------------------------------------*\
-| =========                 |                                                 |
-| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  1.0                                   |
-|   \\  /    A nd           | Web:      http://www.openfoam.org               |
-|    \\/     M anipulation  |                                                 |
-\*---------------------------------------------------------------------------*/
-// magGradU tool definition
-
-description     "Magnitude of grad(U) calculation";
-
-magGradUDict
-{
-    type            dictionary;
-    description     "magGradU control dictionary";
-    dictionaryPath  "system";
-
-    entries
-    {
-        arguments
-        {
-            type        rootCaseTimeArguments;
-        }
-    }
-}
-
-// ************************************************************************* //

applications/utilities/postProcessing/velocityField/magGradU/Make/files

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

applications/utilities/postProcessing/velocityField/magGradU/Make/options

@@ -1,7 +0,0 @@
-EXE_INC = \
-    -I$(FOAM_SRC)/postProcessing/postCalc \
-    -I$(LIB_SRC)/finiteVolume/lnInclude
-
-EXE_LIBS = \
-    $(FOAM_LIBBIN)/postCalc.o \
-    -lfiniteVolume

applications/utilities/postProcessing/velocityField/magGradU/magGradU.C

@@ -1,87 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  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
-
-Application
-    magGradU
-
-Description
-    Calculates and writes the scalar magnitude of the gradient of the
-    velocity field U.
-    The -noWrite option just outputs the max/min values without writing
-    the field.
-
-\*---------------------------------------------------------------------------*/
-
-#include "calc.H"
-#include "fvc.H"
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-void Foam::calc(const argList& args, const Time& runTime, const fvMesh& mesh)
-{
-    bool writeResults = !args.options().found("noWrite");
-
-    IOobject Uheader
-    (
-        "U",
-        runTime.timeName(),
-        mesh,
-        IOobject::MUST_READ
-    );
-
-    if (Uheader.headerOk())
-    {
-        Info<< "    Reading U" << endl;
-        volVectorField U(Uheader, mesh);
-
-        Info<< "    Calculating magGradU" << endl;
-        volScalarField magGradU
-        (
-            IOobject
-            (
-                "magGradU",
-                runTime.timeName(),
-                mesh,
-                IOobject::NO_READ
-            ),
-            mag(fvc::grad(U))
-        );
-
-        Info<< "magGrad(U) max/min : "
-            << max(magGradU).value() << " "
-            << min(magGradU).value() << endl;
-
-        if (writeResults)
-        {
-            magGradU.write();
-        }
-    }
-    else
-    {
-        Info<< "    No U" << endl;
-    }
-}
-
-
-// ************************************************************************* //

applications/utilities/thermophysical/chemkinToFoam/chemkinToFoam.C

@@ -58,7 +58,7 @@ int main(int argc, char *argv[])
         << "reactions" << cr.reactions() << ';' << endl;
 
     OFstream thermoFile(FOAMThermodynamicsFileName);
-    thermoFile<< cr.specieThermo() << endl;
+    thermoFile<< cr.speciesThermo() << endl;
 
     Info << "End\n" << endl;
 

etc/apps/paraview3/bashrc

@@ -45,10 +45,9 @@ else
     unset CMAKE_HOME
 fi
 
-# export ParaView_VERSION="3.3-cvs"
+export ParaView_VERSION="3.3-cvs"
-export ParaView_VERSION=3.3
 
-export ParaView_INST_DIR=$WM_PROJECT_INST_DIR/paraview-$ParaView_VERSION
+export ParaView_INST_DIR=$WM_PROJECT_INST_DIR/ParaView$ParaView_VERSION
 export ParaView_DIR=$ParaView_INST_DIR/platforms/$WM_OPTIONS
 
 if [ "$PYTHONPATH" ]; then
@@ -60,7 +59,9 @@ fi
 
 if [ -r $ParaView_DIR ]; then
     export PATH=$ParaView_DIR/bin:$PATH
-    export LD_LIBRARY_PATH=$ParaView_DIR/lib/paraview-$ParaView_VERSION:$LD_LIBRARY_PATH
+
+    # LD_LIBRARY_PATH may not be necessary
+    ## export LD_LIBRARY_PATH=$ParaView_DIR/lib/paraview-3.3:$LD_LIBRARY_PATH
 
     export PV_PLUGIN_PATH=$FOAM_LIBBIN
 fi

etc/apps/paraview3/cshrc

@@ -42,13 +42,12 @@ setenv CMAKE_HOME $WM_PROJECT_INST_DIR/$WM_ARCH/cmake-2.4.6
 if ( -r $CMAKE_HOME ) then
     set path=($CMAKE_HOME/bin $path)
 else
-    unset CMAKE_HOME
+    unsetenv CMAKE_HOME
 endif
 
-# setenv ParaView_VERSION 3.3-cvs
+setenv ParaView_VERSION 3.3-cvs
-setenv ParaView_VERSION 3.3
 
-export ParaView_INST_DIR=$WM_PROJECT_INST_DIR/paraview-$ParaView_VERSION
+export ParaView_INST_DIR=$WM_PROJECT_INST_DIR/ParaView$ParaView_VERSION
 setenv ParaView_DIR $ParaView_INST_DIR/platforms/$WM_OPTIONS
 
 if ($?PYTHONPATH) then
@@ -59,7 +58,9 @@ endif
 
 if ( -r $ParaView_INST_DIR ) then
     set path=($ParaView_DIR/bin $path)
-    setenv LD_LIBRARY_PATH $ParaView_DIR/lib/paraview-$ParaView_VERSION:$LD_LIBRARY_PATH
+
+    # LD_LIBRARY_PATH may not be necessary
+    ## setenv LD_LIBRARY_PATH $ParaView_DIR/lib/paraview-3.3:$LD_LIBRARY_PATH
 
     setenv PV_PLUGIN_PATH $FOAM_LIBBIN
 endif

etc/bashrc

@@ -33,6 +33,8 @@
 
 export WM_PROJECT=OpenFOAM
 #export WM_PROJECT_VERSION=dev
+: ${WM_PROJECT_VERSION:=dev}; export WM_PROJECT_VERSION
+
 
 #!!User:
 #    either set $FOAM_INST_DIR before sourcing this file or set
@@ -63,7 +65,7 @@ export WM_PROJECT_USER_DIR=$HOME/$WM_PROJECT/$USER-$WM_PROJECT_VERSION
 
 # Compiler (if set to "" use the system compiler)
 # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-export WM_COMPILER=Gcc
+export WM_COMPILER=Gcc43
 export WM_COMPILER_ARCH=
 export WM_COMPILER_LIB_ARCH=
 

etc/settings.csh

@@ -86,7 +86,14 @@ set WM_COMPILER_INST=OpenFOAM
 
 switch ("$WM_COMPILER_INST")
 case OpenFOAM:
+    switch ("$WM_COMPILER")
+    case Gcc43:
+        setenv WM_COMPILER_DIR $FOAM_INST_DIR/$WM_ARCH/gcc-4.3.0$WM_COMPILER_ARCH
+    breaksw
+    case Gcc:
         setenv WM_COMPILER_DIR $FOAM_INST_DIR/$WM_ARCH/gcc-4.2.2$WM_COMPILER_ARCH
+    breaksw
+    endsw
 
     # Check that the compiler directory can be found
     if ( ! -d "$WM_COMPILER_DIR" ) then
@@ -128,7 +135,6 @@ setenv FOAMX_PATH $FOAM_UTILITIES/preProcessing/FoamX
 #
 # need csh equivalent for this?
 # for FOAMX_CONFIG in \
-#     $HOME/.$WM_PROJECT-$WM_PROJECT_VERSION/apps/FoamX \
 #     $HOME/.$WM_PROJECT/$WM_PROJECT_VERSION/apps/FoamX \
 #     $HOME/.$WM_PROJECT/apps/FoamX \
 #     $WM_PROJECT_INST_DIR/site/$WM_PROJECT_VERSION/apps/FoamX \

etc/settings.sh

@@ -97,7 +97,14 @@ WM_COMPILER_INST=OpenFOAM
 
 case "$WM_COMPILER_INST" in
 OpenFOAM)
+    case "$WM_COMPILER" in
+    Gcc43)
+        export WM_COMPILER_DIR=$FOAM_INST_DIR/$WM_ARCH/gcc-4.3.0$WM_COMPILER_ARCH
+        ;;
+    Gcc)
         export WM_COMPILER_DIR=$FOAM_INST_DIR/$WM_ARCH/gcc-4.2.2$WM_COMPILER_ARCH
+        ;;
+    esac
 
     # Check that the compiler directory can be found
     if [ ! -d "$WM_COMPILER_DIR" ]
@@ -134,7 +141,6 @@ export PATH=$MICO_ARCH_PATH/bin:$PATH
 export FOAMX_PATH=$FOAM_UTILITIES/preProcessing/FoamX
 # perhaps we can cut down a bit here
 for FOAMX_CONFIG in \
-    $HOME/.$WM_PROJECT-$WM_PROJECT_VERSION/apps/FoamX \
     $HOME/.$WM_PROJECT/$WM_PROJECT_VERSION/apps/FoamX \
     $HOME/.$WM_PROJECT/apps/FoamX \
     $WM_PROJECT_INST_DIR/site/$WM_PROJECT_VERSION/apps/FoamX \

src/OpenFOAM/containers/HashTables/HashTable/HashTable.C

@@ -318,7 +318,8 @@ bool HashTable<T, Key, Hash>::erase(const iterator& cit)
             delete it.elmtPtr_;
 
             // Search back for previous non-zero table entry
-            while (--it.hashIndex_ >= 0 && !table_[it.hashIndex_]);
+            while (--it.hashIndex_ >= 0 && !table_[it.hashIndex_])
+            {}
 
             if (it.hashIndex_ >= 0)
             {

src/OpenFOAM/containers/HashTables/HashTable/HashTableI.H

@@ -220,7 +220,8 @@ HashTable<T, Key, Hash>::iterator::operator++()
     (
         ++hashIndex_ < curHashTable_.tableSize_
      && !(elmtPtr_ = curHashTable_.table_[hashIndex_])
-    );
+    )
+    {}
 
     if (hashIndex_ == curHashTable_.tableSize_)
     {
@@ -259,7 +260,8 @@ HashTable<T, Key, Hash>::begin()
 {
     label i = 0;
 
-    while (table_ && !table_[i] && ++i < tableSize_);
+    while (table_ && !table_[i] && ++i < tableSize_)
+    {}
 
     if (i == tableSize_)
     {
@@ -396,7 +398,8 @@ HashTable<T, Key, Hash>::const_iterator::operator++()
         (
             ++hashIndex_ < curHashTable_.tableSize_
          && !(elmtPtr_ = curHashTable_.table_[hashIndex_])
-        );
+        )
+        {}
     }
 
     return *this;
@@ -430,7 +433,8 @@ HashTable<T, Key, Hash>::begin() const
 {
     label i = 0;
 
-    while (table_ && !table_[i] && ++i < tableSize_);
+    while (table_ && !table_[i] && ++i < tableSize_)
+    {}
 
     if (i == tableSize_)
     {

src/OpenFOAM/global/argList/argList.C

@@ -34,6 +34,7 @@ License
 #include "JobInfo.H"
 #include "labelList.H"
 
+
 // * * * * * * * * * * * * * * Static Data Members * * * * * * * * * * * * * //
 
 namespace Foam
@@ -389,7 +390,8 @@ Foam::argList::argList
                         rootPath_/globalCase_/"processor"
                       + name(++nProcDirs)
                     )
-                );
+                )
+                {}
 
                 if (nProcDirs != Pstream::nProcs())
                 {

src/OpenFOAM/global/new.C

@@ -29,6 +29,7 @@ Description
 
 #include <new>
 #include <iostream>
+#include <cstdlib>
 
 namespace Foam
 {

src/OpenFOAM/interpolations/interpolateXY/interpolateXY.C

@@ -64,7 +64,8 @@ Type interpolateXY
     label n = xOld.size();
 
     label lo = 0;
-    for (lo=0; lo<n && xOld[lo]>x; ++lo);
+    for (lo=0; lo<n && xOld[lo]>x; ++lo)
+    {}
 
     label low = lo;
     if (low < n)
@@ -79,7 +80,8 @@ Type interpolateXY
     }
 
     label hi = 0;
-    for (hi=0; hi<n && xOld[hi]<x; ++hi);
+    for (hi=0; hi<n && xOld[hi]<x; ++hi)
+    {}
 
     label high = hi;
     if (high < n)

src/OpenFOAM/meshes/polyMesh/zones/ZoneMesh/ZoneMesh.H

@@ -49,8 +49,6 @@ namespace Foam
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
-class polyMesh;
-
 // Forward declaration of friend functions and operators
 
 template<class ZoneType, class MeshType> class ZoneMesh;
@@ -94,7 +92,7 @@ public:
 
     // Constructors
 
-        //- Read constructor given IOobject and a mesh reference
+        //- Read constructor given IOobject and a MeshType reference
         ZoneMesh
         (
             const IOobject&,

src/OpenFOAM/meshes/primitiveShapes/triangle/triangleI.H

@@ -397,7 +397,7 @@ inline pointHit triangle<Point, PointRef>::ray
 
     bool eligible =
         alg == intersection::FULL_RAY
-     || alg == intersection::HALF_RAY && dist > -planarPointTol
+     || (alg == intersection::HALF_RAY && dist > -planarPointTol)
      || (
             alg == intersection::VISIBLE
          && ((q1 & normal()) < -VSMALL)

src/OpenFOAM/primitives/longLong/longLongIO.C

@@ -73,7 +73,8 @@ long long readLongLong(Istream& is)
     static const label zeroOffset = int('0');
 
     // Get next non-whitespace character
-    while (is.read(c) && isspace(c));
+    while (is.read(c) && isspace(c))
+    {}
 
     do
     {

src/OpenFOAM/primitives/strings/string/string.H

@@ -49,6 +49,8 @@ SourceFiles
 #include "char.H"
 
 #include <string>
+#include <cstring>
+#include <cstdlib>
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 

src/lagrangian/basic/Cloud/Cloud.H

@@ -180,7 +180,7 @@ public:
                 return meshInfo_;
             }
 
-            const label size() const
+            label size() const
             {
                 return IDLList<ParticleType>::size();
             };

src/meshTools/indexedOctree/indexedOctree.C

@@ -1055,7 +1055,7 @@ pointIndexHit indexedOctree<Type>::findLine
         direction startBit = treeBb.posBits(start);
         direction endBit = treeBb.posBits(end);
 
-        if (startBit&endBit != 0)
+        if ((startBit & endBit) != 0)
         {
             // Both start and end outside domain and in same block.
             return pointIndexHit(false, vector::zero, -1);

src/meshTools/triSurface/triSurfaceTools/geompack/geompack.C

@@ -4,6 +4,7 @@
 # include <fstream>
 # include <cmath>
 # include <ctime>
+# include <cstring>
 
 using namespace std;
 

src/thermophysicalModels/combustion/chemistryReaders/chemistryReader/chemistryReader.H

@@ -118,7 +118,7 @@ public:
     // Member Functions
 
         virtual const speciesTable& species() const = 0;
-        virtual const HashPtrTable<reactionThermo>& specieThermo() const = 0;
+        virtual const HashPtrTable<reactionThermo>& speciesThermo() const = 0;
         virtual const SLPtrList<reaction>& reactions() const = 0;
 };
 

src/thermophysicalModels/combustion/chemistryReaders/chemkinReader/chemkinLexer.L

@@ -607,15 +607,15 @@ bool finishReaction = false;
 
         HashPtrTable<reactionThermo>::iterator specieThermoIter
         (
-            specieThermo_.find(currentSpecieName)
+            speciesThermo_.find(currentSpecieName)
         );
 
-        if (specieThermoIter != specieThermo_.end())
+        if (specieThermoIter != speciesThermo_.end())
         {
-            specieThermo_.erase(specieThermoIter);
+            speciesThermo_.erase(specieThermoIter);
         }
 
-        specieThermo_.insert
+        speciesThermo_.insert
         (
             currentSpecieName,
             new reactionThermo

src/thermophysicalModels/combustion/chemistryReaders/chemkinReader/chemkinReader.C

@@ -182,7 +182,7 @@ void Foam::chemkinReader::addReactionType
                         speciesTable_,
                         lhs.shrink(),
                         rhs.shrink(),
-                        specieThermo_
+                        speciesThermo_
                     ),
                     rr
                 )
@@ -201,7 +201,7 @@ void Foam::chemkinReader::addReactionType
                         speciesTable_,
                         lhs.shrink(),
                         rhs.shrink(),
-                        specieThermo_
+                        speciesThermo_
                     ),
                     rr
                 )
@@ -500,7 +500,7 @@ void Foam::chemkinReader::addReaction
                             speciesTable_,
                             lhs.shrink(),
                             rhs.shrink(),
-                            specieThermo_
+                            speciesThermo_
                         ),
                         ArrheniusReactionRate
                         (
@@ -553,7 +553,7 @@ void Foam::chemkinReader::addReaction
                             speciesTable_,
                             lhs.shrink(),
                             rhs.shrink(),
-                            specieThermo_
+                            speciesThermo_
                         ),
                         thirdBodyArrheniusReactionRate
                         (
@@ -658,7 +658,7 @@ void Foam::chemkinReader::addReaction
                             speciesTable_,
                             lhs.shrink(),
                             rhs.shrink(),
-                            specieThermo_
+                            speciesThermo_
                         ),
                         LandauTellerReactionRate
                         (
@@ -814,7 +814,8 @@ void Foam::chemkinReader::read
         yy_buffer_state* bufferPtr(yy_create_buffer(&thermoStream, yyBufSize));
         yy_switch_to_buffer(bufferPtr);
 
-        while(lex() != 0);
+        while(lex() != 0)
+        {}
 
         yy_delete_buffer(bufferPtr);
 
@@ -838,7 +839,8 @@ void Foam::chemkinReader::read
 
     initReactionKeywordTable();
 
-    while(lex() != 0);
+    while(lex() != 0)
+    {}
 
     yy_delete_buffer(bufferPtr);
 }

src/thermophysicalModels/combustion/chemistryReaders/chemkinReader/chemkinReader.H

@@ -198,7 +198,7 @@ private:
         HashTable<phase> speciePhase_;
 
         //- Table of the thermodynamic data given in the CHEMKIN file
-        HashPtrTable<reactionThermo> specieThermo_;
+        HashPtrTable<reactionThermo> speciesThermo_;
 
         //- Table of species composition
         HashTable<List<specieElement> > specieComposition_;
@@ -363,9 +363,9 @@ public:
         }
 
         //- Table of the thermodynamic data given in the CHEMKIN file
-        const HashPtrTable<reactionThermo>& specieThermo() const
+        const HashPtrTable<reactionThermo>& speciesThermo() const
         {
-            return specieThermo_;
+            return speciesThermo_;
         }
 
         //- Table of species composition

src/thermophysicalModels/combustion/chemistryReaders/foamChemistryReader/foamChemistryReader.C

@@ -45,12 +45,12 @@ Foam::foamChemistryReader::foamChemistryReader
     const fileName& thermoFileName
 )
 :
-    specieThermo_(IFstream(thermoFileName)()),
+    speciesThermo_(IFstream(thermoFileName)()),
     speciesTable_(dictionary(IFstream(reactionsFileName)()).lookup("species")),
     reactions_
     (
         dictionary(IFstream(reactionsFileName)()).lookup("reactions"),
-        reaction::iNew(speciesTable_, specieThermo_)
+        reaction::iNew(speciesTable_, speciesThermo_)
     )
 {}
 
@@ -58,7 +58,7 @@ Foam::foamChemistryReader::foamChemistryReader
 // Construct from components
 Foam::foamChemistryReader::foamChemistryReader(const dictionary& thermoDict)
 :
-    specieThermo_
+    speciesThermo_
     (
         IFstream
         (
@@ -84,7 +84,7 @@ Foam::foamChemistryReader::foamChemistryReader(const dictionary& thermoDict)
                 fileName(thermoDict.lookup("foamChemistryFile")).expand()
             )()
         ).lookup("reactions"),
-        reaction::iNew(speciesTable_, specieThermo_)
+        reaction::iNew(speciesTable_, speciesThermo_)
     )
 {}
 

src/thermophysicalModels/combustion/chemistryReaders/foamChemistryReader/foamChemistryReader.H

@@ -60,7 +60,7 @@ class foamChemistryReader
     public chemistryReader
 {
         //- Table of the thermodynamic data given in the foamChemistry file
-        HashPtrTable<reactionThermo> specieThermo_;
+        HashPtrTable<reactionThermo> speciesThermo_;
 
         //- Table of species
         speciesTable speciesTable_;
@@ -113,9 +113,9 @@ public:
         }
 
         //- Table of the thermodynamic data given in the foamChemistry file
-        const HashPtrTable<reactionThermo>& specieThermo() const
+        const HashPtrTable<reactionThermo>& speciesThermo() const
         {
-            return specieThermo_;
+            return speciesThermo_;
         }
 
         //- List of the reactions

src/thermophysicalModels/combustion/mixtureThermos/mixtures/reactingMixture/reactingMixture.C

@@ -45,7 +45,7 @@ reactingMixture::reactingMixture
     (
         thermoDict,
         autoPtr<chemistryReader>::operator()().species(),
-        autoPtr<chemistryReader>::operator()().specieThermo(),
+        autoPtr<chemistryReader>::operator()().speciesThermo(),
         mesh
     ),
     PtrList<chemistryReader::reaction>

wmake/rules/linux64Gcc43/X

@@ -0,0 +1,3 @@
+XFLAGS     =
+XINC       = $(XFLAGS) -I/usr/X11R6/include
+XLIBS      = -L/usr/X11R6/lib64 -lXext -lX11

wmake/rules/linux64Gcc43/c

@@ -0,0 +1,16 @@
+.SUFFIXES: .c .h
+
+cWARN        = -Wall
+
+cc          = gcc -m64
+
+include $(RULES)/c$(WM_COMPILE_OPTION)
+
+cFLAGS      = $(GFLAGS) $(cWARN) $(cOPT) $(cDBUG) $(LIB_HEADER_DIRS) -fPIC
+
+ctoo        = $(WM_SCHEDULER) $(cc) $(cFLAGS) -c $$SOURCE -o $@
+
+LINK_LIBS   = $(cDBUG)
+
+LINKLIBSO   = $(cc) -shared
+LINKEXE     = $(cc) -Xlinker -z -Xlinker nodefs

wmake/rules/linux64Gcc43/c++

@@ -0,0 +1,21 @@
+.SUFFIXES: .C .cxx .cc .cpp
+
+c++WARN     = -Wall -Wno-strict-aliasing -Wextra -Wno-unused-parameter -Wold-style-cast
+
+CC          = g++ -m64
+
+include $(RULES)/c++$(WM_COMPILE_OPTION)
+
+ptFLAGS     = -DNoRepository -ftemplate-depth-40
+
+c++FLAGS    = $(GFLAGS) $(c++WARN) $(c++OPT) $(c++DBUG) $(ptFLAGS) $(LIB_HEADER_DIRS) -fPIC
+
+Ctoo        = $(WM_SCHEDULER) $(CC) $(c++FLAGS) -c $$SOURCE -o $@
+cxxtoo      = $(Ctoo)
+cctoo       = $(Ctoo)
+cpptoo      = $(Ctoo)
+
+LINK_LIBS   = $(c++DBUG)
+
+LINKLIBSO   = $(CC) $(c++FLAGS) -shared
+LINKEXE     = $(CC) $(c++FLAGS)

wmake/rules/linux64Gcc43/c++Debug

@@ -0,0 +1,2 @@
+c++DBUG    = -ggdb3 -DFULLDEBUG
+c++OPT      = -O0 -fdefault-inline

wmake/rules/linux64Gcc43/c++Opt

@@ -0,0 +1,4 @@
+c++DBUG     = 
+c++OPT      = -march=opteron -O3
+#c++OPT      = -march=nocona -O3
+# -ftree-vectorize -ftree-vectorizer-verbose=3

wmake/rules/linux64Gcc43/c++Prof

@@ -0,0 +1,2 @@
+c++DBUG    = -pg
+c++OPT     = -O2

wmake/rules/linux64Gcc43/cDebug

@@ -0,0 +1,2 @@
+cDBUG       = -ggdb -DFULLDEBUG
+cOPT        = -O1 -fdefault-inline -finline-functions

wmake/rules/linux64Gcc43/cOpt

@@ -0,0 +1,2 @@
+cDBUG       = 
+cOPT        = -march=opteron -O3 -fno-gcse

wmake/rules/linux64Gcc43/cProf

@@ -0,0 +1,2 @@
+cDBUG       = -pg
+cOPT        = -O2

wmake/rules/linux64Gcc43/general

@@ -0,0 +1,11 @@
+CPP        = /lib/cpp $(GFLAGS)
+LD         = ld -A64
+
+PROJECT_LIBS = -l$(WM_PROJECT) -liberty -ldl
+
+include $(GENERAL_RULES)/standard
+
+include $(RULES)/X
+include $(RULES)/c
+include $(RULES)/c++
+include $(GENERAL_RULES)/cint

wmake/rules/linux64Gcc43/mplib

@@ -0,0 +1,3 @@
+PFLAGS     = 
+PINC       = 
+PLIBS      = 

wmake/rules/linux64Gcc43/mplibGAMMA

@@ -0,0 +1,3 @@
+PFLAGS     = 
+PINC       = -I$(GAMMA_ARCH_PATH)/include
+PLIBS      = -L$(GAMMA_ARCH_PATH)/lib -lgamma

wmake/rules/linux64Gcc43/mplibLAM

@@ -0,0 +1,3 @@
+PFLAGS     = 
+PINC       = -I$(LAM_ARCH_PATH)/include
+PLIBS      = -L$(LAM_ARCH_PATH)/lib -lmpi -llam -lpthread -lutil

wmake/rules/linux64Gcc43/mplibMPICH

@@ -0,0 +1,3 @@
+PFLAGS     = 
+PINC       = -I$(MPICH_ARCH_PATH)/include
+PLIBS      = -L$(MPICH_ARCH_PATH)/lib -lmpich -lrt

wmake/rules/linux64Gcc43/mplibMPICH-GM

@@ -0,0 +1,3 @@
+PFLAGS     =
+PINC       = -I$(MPICH_ARCH_PATH)/include
+PLIBS      = -L$(MPICH_ARCH_PATH)/lib -lmpich -L$(GM_LIB_PATH) -lgm

wmake/rules/linux64Gcc43/mplibOPENMPI

@@ -0,0 +1,3 @@
+PFLAGS     = -DOMPI_SKIP_MPICXX
+PINC       = -I$(OPENMPI_ARCH_PATH)/include
+PLIBS      = -L$(OPENMPI_ARCH_PATH)/lib -lmpi