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
-        fvc::makeRelative(phi, U);
+        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);
+                    }
                 }
 
-                adjustPhi(phi, U, p);
+                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

@@ -2,21 +2,42 @@
     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 +
-        (
+    (
-            fvc::interpolate(interface.sigmaK())*fvc::snGrad(gamma)
+        fvc::interpolate(interface.sigmaK())*fvc::snGrad(gamma)
-          - ghf*fvc::snGrad(rho)
+      - ghf*fvc::snGrad(rho)
-        )*rAUf*mesh.magSf();
+    )*rAUf*mesh.magSf();
 
     if (pd.needReference())
     {
@@ -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:
-    setenv WM_COMPILER_DIR $FOAM_INST_DIR/$WM_ARCH/gcc-4.2.2$WM_COMPILER_ARCH
+    switch ("$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 "$WM_COMPILER_INST" in
 OpenFOAM)
-    export WM_COMPILER_DIR=$FOAM_INST_DIR/$WM_ARCH/gcc-4.2.2$WM_COMPILER_ARCH
+    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

@@ -272,7 +272,7 @@ inline vector triangle<Point, PointRef>::circumCentre() const
 
     scalar c = c1 + c2 + c3;
 
-    return 
+    return
     (
         ((c2 + c3)*a_ + (c3 + c1)*b_ + (c1 + c2)*c_)/(2*c)
     );
@@ -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)
@@ -434,7 +434,7 @@ template<class Point, class PointRef>
 inline pointHit triangle<Point, PointRef>::intersection
 (
     const point& orig,
-    const vector& dir,    
+    const vector& dir,
     const intersection::algorithm alg
 ) const
 {
@@ -617,7 +617,7 @@ inline bool triangle<Point, PointRef>::classify
     scalar beta = 0;
 
     bool hit = false;
-    
+
     if (Foam::mag(u1) < SMALL)
     {
         beta = u0/u2;

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/OpenFOAM/primitives/strings/string/stringI.H

@@ -103,7 +103,7 @@ inline bool Foam::string::stripInvalid(string& s)
                 ++nValid;
             }
         }
-    
+
         s.resize(nValid);
 
         return true;

src/finiteVolume/finiteVolume/ddtSchemes/EulerDdtScheme/EulerDdtScheme.C

@@ -471,8 +471,8 @@ EulerDdtScheme<Type>::fvcDdtPhiCorr
                        (
                            rA*rho.oldTime()*U.oldTime()
                        ) & mesh().Sf()
-                 )
+                   )
-               )
+                )
             )
         );
     }

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;
 
@@ -24,7 +25,7 @@ double d_epsilon ( void )
 //    D_EPSILON is a number R which is a power of 2 with the property that,
 //    to the precision of the computer's arithmetic,
 //      1 < 1 + R
-//    but 
+//    but
 //      1 = ( 1 + R / 2 )
 //
 //  Modified:
@@ -79,7 +80,7 @@ double d_max ( double x, double y )
   if ( y < x )
   {
     return x;
-  } 
+  }
   else
   {
     return y;
@@ -113,7 +114,7 @@ double d_min ( double x, double y )
   if ( y < x )
   {
     return y;
-  } 
+  }
   else
   {
     return x;
@@ -623,7 +624,7 @@ void d2vec_sort_quick_a ( int n, double a[] )
 }
 //******************************************************************************
 
-int diaedg ( double x0, double y0, double x1, double y1, double x2, double y2, 
+int diaedg ( double x0, double y0, double x1, double y1, double x2, double y2,
   double x3, double y3 )
 
 //******************************************************************************
@@ -660,7 +661,7 @@ int diaedg ( double x0, double y0, double x1, double y1, double x2, double y2,
 //
 //  Parameters:
 //
-//    Input, double X0, Y0, X1, Y1, X2, Y2, X3, Y3, the coordinates of the 
+//    Input, double X0, Y0, X1, Y1, X2, Y2, X3, Y3, the coordinates of the
 //    vertices of a quadrilateral, given in counter clockwise order.
 //
 //    Output, int DIAEDG, chooses a diagonal:
@@ -696,12 +697,12 @@ int diaedg ( double x0, double y0, double x1, double y1, double x2, double y2,
   dx32 = x3 - x2;
   dy32 = y3 - y2;
 
-  tola = tol * d_max ( fabs ( dx10 ), 
+  tola = tol * d_max ( fabs ( dx10 ),
-               d_max ( fabs ( dy10 ), 
+               d_max ( fabs ( dy10 ),
                d_max ( fabs ( dx30 ), fabs ( dy30 ) ) ) );
 
-  tolb = tol * d_max ( fabs ( dx12 ), 
+  tolb = tol * d_max ( fabs ( dx12 ),
-               d_max ( fabs ( dy12 ), 
+               d_max ( fabs ( dy12 ),
                d_max ( fabs ( dx32 ), fabs ( dy32 ) ) ) );
 
   ca = dx10 * dx30 + dy10 * dy30;
@@ -718,7 +719,7 @@ int diaedg ( double x0, double y0, double x1, double y1, double x2, double y2,
   else
   {
     tola = d_max ( tola, tolb );
-    s = ( dx10 * dy30 - dx30 * dy10 ) * cb 
+    s = ( dx10 * dy30 - dx30 * dy10 ) * cb
       + ( dx32 * dy12 - dx12 * dy32 ) * ca;
 
     if ( tola < s )
@@ -771,7 +772,7 @@ void dmat_transpose_print ( int m, int n, double a[], const char *title )
 }
 //******************************************************************************
 
-void dmat_transpose_print_some ( int m, int n, double a[], int ilo, int jlo, 
+void dmat_transpose_print_some ( int m, int n, double a[], int ilo, int jlo,
   int ihi, int jhi, const char *title )
 
 //******************************************************************************
@@ -909,7 +910,7 @@ void dmat_uniform ( int m, int n, double b, double c, int *seed, double r[] )
 //
 //    Input/output, int *SEED, the "seed" value.  Normally, this
 //    value should not be 0, otherwise the output value of SEED
-//    will still be 0, and D_UNIFORM will be 0.  On output, SEED has 
+//    will still be 0, and D_UNIFORM will be 0.  On output, SEED has
 //    been updated.
 //
 //    Output, double DMAT_UNIFORM[M*N], a matrix of pseudorandom values.
@@ -943,7 +944,7 @@ void dmat_uniform ( int m, int n, double b, double c, int *seed, double r[] )
 }
 //******************************************************************************
 
-int dtris2 ( int point_num, double point_xy[], int *tri_num, 
+int dtris2 ( int point_num, double point_xy[], int *tri_num,
   int tri_vert[], int tri_nabe[] )
 
 //******************************************************************************
@@ -1046,11 +1047,11 @@ int dtris2 ( int point_num, double point_xy[], int *tri_num,
 
     for ( j = 0; j <= 1; j++ )
     {
-      cmax = d_max ( fabs ( point_xy[2*(m-1)+j] ), 
+      cmax = d_max ( fabs ( point_xy[2*(m-1)+j] ),
                      fabs ( point_xy[2*(m1-1)+j] ) );
 
-      if ( tol * ( cmax + 1.0 ) 
+      if ( tol * ( cmax + 1.0 )
-           < fabs ( point_xy[2*(m-1)+j] - point_xy[2*(m1-1)+j] ) ) 
+           < fabs ( point_xy[2*(m-1)+j] - point_xy[2*(m1-1)+j] ) )
       {
         k = j;
         break;
@@ -1095,7 +1096,7 @@ int dtris2 ( int point_num, double point_xy[], int *tri_num,
     m = j;
 
     lr = lrline ( point_xy[2*(m-1)+0], point_xy[2*(m-1)+1],
-      point_xy[2*(m1-1)+0], point_xy[2*(m1-1)+1], 
+      point_xy[2*(m1-1)+0], point_xy[2*(m1-1)+1],
       point_xy[2*(m2-1)+0], point_xy[2*(m2-1)+1], 0.0 );
 
     if ( lr != 0 )
@@ -1182,8 +1183,8 @@ int dtris2 ( int point_num, double point_xy[], int *tri_num,
       m2 = tri_vert[3*(ltri-1)+0];
     }
 
-    lr = lrline ( point_xy[2*(m-1)+0], point_xy[2*(m-1)+1], 
+    lr = lrline ( point_xy[2*(m-1)+0], point_xy[2*(m-1)+1],
-      point_xy[2*(m1-1)+0], point_xy[2*(m1-1)+1], 
+      point_xy[2*(m1-1)+0], point_xy[2*(m1-1)+1],
       point_xy[2*(m2-1)+0], point_xy[2*(m2-1)+1], 0.0 );
 
     if ( 0 < lr )
@@ -1199,7 +1200,7 @@ int dtris2 ( int point_num, double point_xy[], int *tri_num,
       redg = (l % 3) + 1;
     }
 
-    vbedg ( point_xy[2*(m-1)+0], point_xy[2*(m-1)+1], point_num, 
+    vbedg ( point_xy[2*(m-1)+0], point_xy[2*(m-1)+1], point_num,
       point_xy, *tri_num, tri_vert, tri_nabe, &ltri, &ledg, &rtri, &redg );
 
     n = *tri_num + 1;
@@ -1255,7 +1256,7 @@ int dtris2 ( int point_num, double point_xy[], int *tri_num,
     ltri = n;
     ledg = 2;
 
-    error = swapec ( m, &top, &ltri, &ledg, point_num, point_xy, *tri_num, 
+    error = swapec ( m, &top, &ltri, &ledg, point_num, point_xy, *tri_num,
       tri_vert, tri_nabe, stack );
 
     if ( error != 0 )
@@ -1473,9 +1474,9 @@ void dvec_print ( int n, double a[], const char *title )
   }
 
   cout << "\n";
-  for ( i = 0; i <= n-1; i++ ) 
+  for ( i = 0; i <= n-1; i++ )
   {
-    cout << setw(6)  << i + 1 << "  " 
+    cout << setw(6)  << i + 1 << "  "
          << setw(14) << a[i]  << "\n";
   }
 
@@ -1600,8 +1601,8 @@ int i_modp ( int i, int j )
 //
 //  Formula:
 //
-//    If 
+//    If
-//      NREM = I_MODP ( I, J ) 
+//      NREM = I_MODP ( I, J )
 //      NMULT = ( I - NREM ) / J
 //    then
 //      I = J * NMULT + NREM
@@ -1620,7 +1621,7 @@ int i_modp ( int i, int j )
 //  Examples:
 //
 //        I         J     MOD  I_MODP   I_MODP Factorization
-// 
+//
 //      107        50       7       7    107 =  2 *  50 + 7
 //      107       -50       7       7    107 = -2 * -50 + 7
 //     -107        50      -7      43   -107 = -3 *  50 + 43
@@ -1640,7 +1641,7 @@ int i_modp ( int i, int j )
 //
 //    Input, int J, the number that divides I.
 //
-//    Output, int I_MODP, the nonnegative remainder when I is 
+//    Output, int I_MODP, the nonnegative remainder when I is
 //    divided by J.
 //
 {
@@ -1692,7 +1693,7 @@ int i_sign ( int i )
 //
 //    Output, int I_SIGN, the sign of I.
 {
-  if ( i < 0 ) 
+  if ( i < 0 )
   {
     return (-1);
   }
@@ -1809,7 +1810,7 @@ void imat_transpose_print ( int m, int n, int a[], const char *title )
 }
 //******************************************************************************
 
-void imat_transpose_print_some ( int m, int n, int a[], int ilo, int jlo, 
+void imat_transpose_print_some ( int m, int n, int a[], int ilo, int jlo,
   int ihi, int jhi, const char *title )
 
 //******************************************************************************
@@ -1962,7 +1963,7 @@ void ivec_heap_d ( int n, int a[] )
 //  Only nodes (N/2)-1 down to 0 can be "parent" nodes.
 //
   for ( i = (n/2)-1; 0 <= i; i-- )
-  { 
+  {
 //
 //  Copy the value out of the parent node.
 //  Position IFREE is now "open".
@@ -2180,7 +2181,7 @@ void ivec_sorted_unique ( int n, int a[], int *nuniq )
 
   for ( i = 1; i < n; i++ )
   {
-    if ( a[i] != a[*nuniq] ) 
+    if ( a[i] != a[*nuniq] )
     {
       *nuniq = *nuniq + 1;
       a[*nuniq] = a[i];
@@ -2192,7 +2193,7 @@ void ivec_sorted_unique ( int n, int a[], int *nuniq )
 }
 //******************************************************************************
 
-int lrline ( double xu, double yu, double xv1, double yv1, double xv2, 
+int lrline ( double xu, double yu, double xv1, double yv1, double xv2,
   double yv2, double dv )
 
 //******************************************************************************
@@ -2253,9 +2254,9 @@ int lrline ( double xu, double yu, double xv1, double yv1, double xv2,
   dxu = xu - xv1;
   dyu = yu - yv1;
 
-  tolabs = tol * d_max ( fabs ( dx ), 
+  tolabs = tol * d_max ( fabs ( dx ),
-                 d_max ( fabs ( dy ), 
+                 d_max ( fabs ( dy ),
-                 d_max ( fabs ( dxu ), 
+                 d_max ( fabs ( dxu ),
                  d_max ( fabs ( dyu ), fabs ( dv ) ) ) ) );
 
   t = dy * dxu - dx * dyu + dv * sqrt ( dx * dx + dy * dy );
@@ -2426,7 +2427,7 @@ int *points_delaunay_naive_2d ( int n, double p[], int *ntri )
 
 //********************************************************************
 //
-//  Purpose:  
+//  Purpose:
 //
 //    POINTS_DELAUNAY_NAIVE_2D computes the Delaunay triangulation in 2D.
 //
@@ -2456,7 +2457,7 @@ int *points_delaunay_naive_2d ( int n, double p[], int *ntri )
 //
 //    Joseph O'Rourke,
 //    Computational Geometry,
-//    Cambridge University Press, 
+//    Cambridge University Press,
 //    Second Edition, 1998, page 187.
 //
 //  Parameters:
@@ -2467,7 +2468,7 @@ int *points_delaunay_naive_2d ( int n, double p[], int *ntri )
 //
 //    Output, int *NTRI, the number of triangles.
 //
-//    Output, int POINTS_DELAUNAY_NAIVE_2D[3*NTRI], the indices of the 
+//    Output, int POINTS_DELAUNAY_NAIVE_2D[3*NTRI], the indices of the
 //    nodes making each triangle.
 //
 {
@@ -2506,34 +2507,34 @@ int *points_delaunay_naive_2d ( int n, double p[], int *ntri )
 //
 //  For each triple (I,J,K):
 //
-    for ( i = 0; i < n - 2; i++ ) 
+    for ( i = 0; i < n - 2; i++ )
     {
-      for ( j = i+1; j < n; j++ ) 
+      for ( j = i+1; j < n; j++ )
       {
-        for ( k = i+1; k < n; k++ ) 
+        for ( k = i+1; k < n; k++ )
         {
-          if ( j != k ) 
+          if ( j != k )
           {
-            xn = ( p[1+j*2] - p[1+i*2] ) * ( z[k] - z[i] ) 
+            xn = ( p[1+j*2] - p[1+i*2] ) * ( z[k] - z[i] )
                - ( p[1+k*2] - p[1+i*2] ) * ( z[j] - z[i] );
-            yn = ( p[0+k*2] - p[0+i*2] ) * ( z[j] - z[i] ) 
+            yn = ( p[0+k*2] - p[0+i*2] ) * ( z[j] - z[i] )
                - ( p[0+j*2] - p[0+i*2] ) * ( z[k] - z[i] );
-            zn = ( p[0+j*2] - p[0+i*2] ) * ( p[1+k*2] - p[1+i*2] ) 
+            zn = ( p[0+j*2] - p[0+i*2] ) * ( p[1+k*2] - p[1+i*2] )
                - ( p[0+k*2] - p[0+i*2] ) * ( p[1+j*2] - p[1+i*2] );
 
             flag = ( zn < 0 );
 
-            if ( flag ) 
+            if ( flag )
             {
-              for ( m = 0; m < n; m++ )  
+              for ( m = 0; m < n; m++ )
               {
-                flag = flag && ( ( p[0+m*2] - p[0+i*2] ) * xn 
+                flag = flag && ( ( p[0+m*2] - p[0+i*2] ) * xn
-                               + ( p[1+m*2] - p[1+i*2] ) * yn 
+                               + ( p[1+m*2] - p[1+i*2] ) * yn
                                + ( z[m] - z[i] ) * zn <= 0 );
               }
             }
 
-            if ( flag ) 
+            if ( flag )
             {
               if ( pass == 2 )
               {
@@ -2545,8 +2546,8 @@ int *points_delaunay_naive_2d ( int n, double p[], int *ntri )
             }
 
           }
-        }    
+        }
-      } 
+      }
     }
   }
 
@@ -2587,7 +2588,7 @@ int s_len_trim ( const char *s )
   n = strlen ( s );
   t = const_cast<char*>(s) + n - 1;
 
-  while ( 0 < n ) 
+  while ( 0 < n )
   {
     if ( *t != ' ' )
     {
@@ -2601,8 +2602,8 @@ int s_len_trim ( const char *s )
 }
 //******************************************************************************
 
-int swapec ( int i, int *top, int *btri, int *bedg, int point_num, 
+int swapec ( int i, int *top, int *btri, int *bedg, int point_num,
-  double point_xy[], int tri_num, int tri_vert[], int tri_nabe[], 
+  double point_xy[], int tri_num, int tri_vert[], int tri_nabe[],
   int stack[] )
 
 //******************************************************************************
@@ -2698,7 +2699,7 @@ int swapec ( int i, int *top, int *btri, int *bedg, int point_num,
 
   for ( ; ; )
   {
-    if ( *top <= 0 ) 
+    if ( *top <= 0 )
     {
       break;
     }
@@ -2741,7 +2742,7 @@ int swapec ( int i, int *top, int *btri, int *bedg, int point_num,
       c = tri_vert[3*(u-1)+1];
     }
 
-    swap = diaedg ( x, y, 
+    swap = diaedg ( x, y,
       point_xy[2*(a-1)+0], point_xy[2*(a-1)+1],
       point_xy[2*(c-1)+0], point_xy[2*(c-1)+1],
       point_xy[2*(b-1)+0], point_xy[2*(b-1)+1] );
@@ -3021,16 +3022,16 @@ double *triangle_circumcenter_2d ( double t[] )
 
   center = new double[DIM_NUM];
 
-  asq = ( t[0+1*2] - t[0+0*2] ) * ( t[0+1*2] - t[0+0*2] ) 
+  asq = ( t[0+1*2] - t[0+0*2] ) * ( t[0+1*2] - t[0+0*2] )
       + ( t[1+1*2] - t[1+0*2] ) * ( t[1+1*2] - t[1+0*2] );
 
-  csq = ( t[0+2*2] - t[0+0*2] ) * ( t[0+2*2] - t[0+0*2] ) 
+  csq = ( t[0+2*2] - t[0+0*2] ) * ( t[0+2*2] - t[0+0*2] )
       + ( t[1+2*2] - t[1+0*2] ) * ( t[1+2*2] - t[1+0*2] );
-  
+
   top1 =  ( t[1+1*2] - t[1+0*2] ) * csq - ( t[1+2*2] - t[1+0*2] ) * asq;
   top2 =  ( t[0+1*2] - t[0+0*2] ) * csq - ( t[0+2*2] - t[0+0*2] ) * asq;
 
-  bot  =  ( t[1+1*2] - t[1+0*2] ) * ( t[0+2*2] - t[0+0*2] )  
+  bot  =  ( t[1+1*2] - t[1+0*2] ) * ( t[0+2*2] - t[0+0*2] )
         - ( t[1+2*2] - t[1+0*2] ) * ( t[0+1*2] - t[0+0*2] );
 
   center[0] = t[0+0*2] + 0.5 * top1 / bot;
@@ -3042,7 +3043,7 @@ double *triangle_circumcenter_2d ( double t[] )
 }
 //******************************************************************************
 
-bool triangulation_plot_eps ( const char *file_out_name, int g_num, double g_xy[], 
+bool triangulation_plot_eps ( const char *file_out_name, int g_num, double g_xy[],
   int tri_num, int nod_tri[] )
 
 //******************************************************************************
@@ -3140,7 +3141,7 @@ bool triangulation_plot_eps ( const char *file_out_name, int g_num, double g_xy[
   file_out << "%%Title: " << file_out_name << "\n";
   file_out << "%%CreationDate: " << date_time << "\n";
   file_out << "%%Pages: 1\n";
-  file_out << "%%Bounding Box: " << x_ps_min << "  " << y_ps_min << "  " 
+  file_out << "%%Bounding Box: " << x_ps_min << "  " << y_ps_min << "  "
            << x_ps_max << "  " << y_ps_max << "\n";
   file_out << "%%Document-Fonts: Times-Roman\n";
   file_out << "%%LanguageLevel: 1\n";
@@ -3199,17 +3200,17 @@ bool triangulation_plot_eps ( const char *file_out_name, int g_num, double g_xy[
 
   for ( g = 0; g < g_num; g++ )
   {
-    x_ps = int(  
+    x_ps = int(
-      ( ( x_max - g_xy[0+g*2] ) * double( x_ps_min )  
+      ( ( x_max - g_xy[0+g*2] ) * double( x_ps_min )
-      + ( g_xy[0+g*2] - x_min ) * double( x_ps_max ) ) 
+      + ( g_xy[0+g*2] - x_min ) * double( x_ps_max ) )
       / ( x_max - x_min ) );
 
-    y_ps = int(  
+    y_ps = int(
-      ( ( y_max - g_xy[1+g*2] ) * double( y_ps_min )  
+      ( ( y_max - g_xy[1+g*2] ) * double( y_ps_min )
-      + ( g_xy[1+g*2] - y_min ) * double( y_ps_max ) ) 
+      + ( g_xy[1+g*2] - y_min ) * double( y_ps_max ) )
       / ( y_max - y_min ) );
 
-    file_out << "newpath " << x_ps << "  " 
+    file_out << "newpath " << x_ps << "  "
              << y_ps << " 5 0 360 arc closepath fill\n";
   }
 
@@ -3231,14 +3232,14 @@ bool triangulation_plot_eps ( const char *file_out_name, int g_num, double g_xy[
 
       k = nod_tri[3*(t-1)+e-1];
 
-      x_ps = int(  
+      x_ps = int(
-        ( ( x_max - g_xy[0+(k-1)*2] ) * double( x_ps_min )  
+        ( ( x_max - g_xy[0+(k-1)*2] ) * double( x_ps_min )
-        + ( g_xy[0+(k-1)*2] - x_min ) * double( x_ps_max ) ) 
+        + ( g_xy[0+(k-1)*2] - x_min ) * double( x_ps_max ) )
         / ( x_max - x_min ) );
 
-      y_ps = int( 
+      y_ps = int(
-        ( ( y_max - g_xy[1+(k-1)*2] ) * double( y_ps_min )  
+        ( ( y_max - g_xy[1+(k-1)*2] ) * double( y_ps_min )
-        + ( g_xy[1+(k-1)*2] - y_min ) * double( y_ps_max ) ) 
+        + ( g_xy[1+(k-1)*2] - y_min ) * double( y_ps_max ) )
         / ( y_max - y_min ) );
 
       if ( j == 1 )
@@ -3269,7 +3270,7 @@ bool triangulation_plot_eps ( const char *file_out_name, int g_num, double g_xy[
 }
 //******************************************************************************
 
-void triangulation_print ( int point_num, double xc[], int tri_num, 
+void triangulation_print ( int point_num, double xc[], int tri_num,
   int tri_vert[], int tri_nabe[] )
 
 //******************************************************************************
@@ -3356,7 +3357,7 @@ void triangulation_print ( int point_num, double xc[], int tri_num,
 
   imat_transpose_print ( 3, tri_num, tri_nabe, "  Triangle neighbors" );
 //
-//  Determine VERTEX_NUM, the number of vertices.  This is not 
+//  Determine VERTEX_NUM, the number of vertices.  This is not
 //  the same as the number of points!
 //
   vertex_list = new int[3*tri_num];
@@ -3439,7 +3440,7 @@ void triangulation_print ( int point_num, double xc[], int tri_num,
 }
 //******************************************************************************
 
-void vbedg ( double x, double y, int point_num, double point_xy[], int tri_num, 
+void vbedg ( double x, double y, int point_num, double point_xy[], int tri_num,
   int tri_vert[], int tri_nabe[], int *ltri, int *ledg, int *rtri, int *redg )
 
 //******************************************************************************

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
@@ -742,7 +742,7 @@ bool finishReaction = false;
                         << "Plasma momentum-transfer in reaction on line "
                         << lineNo_ << "not yet supported"
                         << exit(FatalError);
-                            
+
                     BEGIN(readReactionKeyword);
                     break;
                 }
@@ -894,7 +894,7 @@ bool finishReaction = false;
                         FatalErrorIn("chemkinReader::lex()")
                             << "HIGH keyword given for a chemically"
                                " activated bimolecular reaction which does not"
-                               " contain a pressure dependent specie" 
+                               " contain a pressure dependent specie"
                             << " on line " << lineNo_
                             << exit(FatalError);
                     }
@@ -935,7 +935,7 @@ bool finishReaction = false;
                             << exit(FatalError);
                     }
 
-                    if 
+                    if
                     (
                         fofType == unknownFallOffFunctionType
                      || fofType == Lindemann
@@ -969,7 +969,7 @@ bool finishReaction = false;
                             << exit(FatalError);
                     }
 
-                    if 
+                    if
                     (
                         fofType == unknownFallOffFunctionType
                      || fofType == Lindemann
@@ -1046,7 +1046,7 @@ bool finishReaction = false;
                     }
 
                     rrType = LandauTeller;
-                    reactionCoeffsName = 
+                    reactionCoeffsName =
                         word(reactionTypeNames[rType])
                       + reactionRateTypeNames[rrType];
                     BEGIN(readReactionCoeffs);
@@ -1316,7 +1316,7 @@ bool finishReaction = false;
 <readPDependentSpecie>{pDependentSpecie} {
 
         word rhsPDependentSpecieName = pDependentSpecieName;
-        pDependentSpecieName = 
+        pDependentSpecieName =
             foamName(foamSpecieString(YYText()));
         pDependentSpecieName =
             pDependentSpecieName(0, pDependentSpecieName.size() - 1);
@@ -1412,7 +1412,7 @@ bool finishReaction = false;
         else
         {
             FatalErrorIn("chemkinReader::lex()")
-                << "unknown specie " << currentSpecieName 
+                << "unknown specie " << currentSpecieName
                 << " given in reaction-order specification"
                 << " on line " << lineNo_ << nl
                 << "Valid species are : " << nl
@@ -1449,7 +1449,7 @@ bool finishReaction = false;
             }
 
             FatalErrorIn("chemkinReader::lex()")
-                << "Specie " << currentSpecieName 
+                << "Specie " << currentSpecieName
                 << " on line " << lineNo_
                 << " not present in " << side << " of reaction " << nl << lrhs
                 << exit(FatalError);

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