Merge branch 'development' into bugfix/cumulativeBugFix

ListOfContributors

@@ -1,8 +1,8 @@
 #                            -*- mode: org; -*-
 #
-#+TITLE:          *Cumulative List of Contributors for foam-extend-3.0*
+#+TITLE:          *Cumulative List of Contributors for foam-extend
 #+AUTHOR:                      Hrvoje Jasak.
-#+DATE:                       10 January 2014
+#+DATE:                       9 February 2017
 #+LINK:                  http://foam-extend.org
 #+OPTIONS: author:nil
 
@@ -91,4 +91,7 @@ Contents:
     Alexander Vakhrushev
     Vuko Vukcevic
     Niklas Wikstrom
-
+    Celio Fernandes
+    Luis Ferras
+    Manoel de Araujo
+    J.Miguel Nobrega

ThirdParty/AllMake.stage2

@@ -40,8 +40,8 @@
 # Requirements:
 #     1: Your foam-extend environment must be properly initialized
 #     2: AllMake.stage1 if you are overriding your system compiler
-#     3: The file etc/prefs.sh should be used for setting the variables enabling
-#        the compilation of the various packages
+#     3: The file etc/prefs.sh should be used for setting the variables
+#        enabling the compilation of the various packages
 #
 # Author:
 #     Martin Beaudoin, Hydro-Quebec, (2015)
@@ -104,6 +104,13 @@ then
 	( rpm_make -p openmpi-1.8.8 -s openmpi-1.8.8.spec  -u http://www.open-mpi.org/software/ompi/v1.8/downloads/openmpi-1.8.8.tar.gz \
           -f --define '_configureAdditionalArgs "$WM_THIRD_PARTY_USE_OPENMPI_188_ConfigureAdditionalArgs"')
     }
+    # mvipich2-2.2
+    #
+    [ ! -z "$WM_THIRD_PARTY_USE_MVAPICH2_22" ] && {
+        echo "Building mvapich2 2.2"
+        ( rpm_make -p mvapich2-2.2 -s mvapich2-2.2.spec -u http://mvapich.cse.ohio-state.edu/download/mvapich/mv2/mvapich2-2.2.tar.gz \
+          -f --define '_configureAdditionalArgs "$WM_THIRD_PARTY_USE_MVAPICH2_22_ConfigureAdditionalArgs"')
+    }
 else
     echo "Using system installed OpenMPI"
     echo ""

ThirdParty/rpmBuild/SPECS/mvapich2-2.2.spec

@@ -0,0 +1,268 @@
+#------------------------------------------------------------------------------
+# =========                 |
+# \\      /  F ield         | foam-extend: Open Source CFD
+#  \\    /   O peration     |
+#   \\  /    A nd           | For copyright notice see file Copyright
+#    \\/     M anipulation  |
+#------------------------------------------------------------------------------
+# License
+#     This file is part of foam-extend.
+#
+#     foam-extend 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 3 of the License, or (at your
+#     option) any later version.
+#
+#     foam-extend 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 foam-extend.  If not, see <http://www.gnu.org/licenses/>.
+#
+# Script
+#     RPM spec file for mvapich2-2.2
+#
+# Description
+#     RPM spec file for creating a relocatable RPM
+#
+# Author:
+#     Martin Beaudoin, Hydro-Quebec, (2015)
+#
+#------------------------------------------------------------------------------
+
+# We grab the value of WM_THIRD_PARTY and WM_OPTIONS from the environment variable
+%{expand:%%define _WM_THIRD_PARTY_DIR %(echo $WM_THIRD_PARTY_DIR)}
+%{expand:%%define _WM_OPTIONS         %(echo $WM_OPTIONS)}
+
+# Disable the generation of debuginfo packages
+%define debug_package %{nil}
+
+# The topdir needs to point to the $WM_THIRD_PARTY/rpmbuild directory
+%define _topdir	 	%{_WM_THIRD_PARTY_DIR}/rpmBuild
+%define _tmppath	%{_topdir}/tmp
+
+# Will install the package directly $WM_THIRD_PARTY_DIR
+#   Some comments about package relocation:
+#   By using this prefix for the Prefix:  parameter in this file, you will make this
+#   package relocatable.
+#
+#   This is fine, as long as your software is itself relocatable.
+#
+#   Simply take note that libraries built with libtool are not relocatable because the
+#   prefix we specify will be hard-coded in the library .la files.
+#   Ref: http://sourceware.org/autobook/autobook/autobook_80.html
+#
+#   In that case, if you ever change the value of the $WM_THIRD_PARTY_DIR, you will
+#   not be able to reutilize this RPM, even though it is relocatable. You will need to
+#   regenerate the RPM.
+#
+%define _prefix         %{_WM_THIRD_PARTY_DIR}
+
+%define name		mvapich2
+%define release		%{_WM_OPTIONS}
+%define version 	2.2
+
+%define buildroot       %{_topdir}/BUILD/%{name}-%{version}-root
+
+BuildRoot:	        %{buildroot}
+Summary: 		mvapich2
+License: 		BSD
+Name: 			%{name}
+Version: 		%{version}
+Release: 		%{release}
+URL:            http://mvapich.cse.ohio-state.edu/download/mvapich/mv2/
+Source: 		%url/%{name}-%{version}.tar.gz
+Prefix: 		%{_prefix}
+Group: 			Development/Tools
+
+
+%define _installPrefix  %{_prefix}/packages/%{name}-%{version}/platforms/%{_WM_OPTIONS}
+
+#--------------------------------------------------------------------------
+#
+# Here, we define default compiling options for mvapich2
+#
+# One can override the option on the commande line : --define='MACRO EXPR'
+#
+%{!?_configureAdditionalArgs: %define _configureAdditionalArgs Undefined}
+
+
+%description
+%{summary}
+
+%prep
+%setup -q
+
+
+%build
+    # export WM settings in a form that GNU configure recognizes
+    [ -n "$WM_CC" ]         &&  export CC="$WM_CC"
+    [ -n "$WM_CXX" ]        &&  export CXX="$WM_CXX"
+    [ -n "$WM_CFLAGS" ]     &&  export CFLAGS="$WM_CFLAGS"
+    [ -n "$WM_CXXFLAGS" ]   &&  export CXXFLAGS="$WM_CXXFLAGS"
+    [ -n "$WM_LDFLAGS" ]    &&  export LDFLAGS="$WM_LDFLAGS"
+
+    set +x
+    echo ""
+    echo "Compilation options:"
+    echo "     _configureAdditionalArgs : %{_configureAdditionalArgs}"
+    echo ""
+    set -x
+
+    unset mpiWith
+    # Enable GridEngine if it appears to be in use
+    # If you don't want any integration with SGE, simply unset the SGE
+    # environment variable
+    if [ -n "$SGE_ROOT" ]
+    then
+        mpiWith="$mpiWith --with-sge"
+    else
+        mpiWith="$mpiWith --without-sge"
+	mpiWith="$mpiWith --enable-mca-no-build=ras-gridengine,pls-gridengine"
+    fi
+
+    # Infiniband support
+    # Adjust according to your local paths
+    # if [ -d /usr/local/ofed -a -d /usr/local/ofed/lib64 ]
+    # then
+    #     mpiWith="$mpiWith --with-openib=/usr/local/ofed"
+    #     mpiWith="$mpiWith --with-openib-libdir=/usr/local/ofed/lib64"
+    # fi
+
+    # NOTE. Option --disable-mcast disables Infiniband when libs are not present
+
+    ./configure \
+        --prefix=%{_installPrefix}  \
+        --exec_prefix=%{_installPrefix}  \
+        --enable-mpirun-prefix-by-default \
+        --enable-orterun-prefix-by-default \
+        --enable-shared \
+        --enable-mpi-cxx \
+        --disable-static \
+        --disable-mpi-f77 \
+        --disable-mpi-f90 \
+        --without-slurm \
+        --enable-mpi-profile $mpiWith \
+        --disable-vt \
+        echo %{?_configureAdditionalArgs}`
+
+    [ -z "$WM_NCOMPPROCS" ] && WM_NCOMPPROCS=1
+    make -j $WM_NCOMPPROCS
+
+%install
+    make install DESTDIR=$RPM_BUILD_ROOT
+
+    # Creation of foam-extend specific .csh and .sh files"
+
+    echo ""
+    echo "Generating foam-extend specific .csh and .sh files for the package %{name}-%{version}"
+    echo ""
+    #
+    # Generate package specific .sh file for foam-extend
+    #
+mkdir -p $RPM_BUILD_ROOT/%{_installPrefix}/etc
+cat << DOT_SH_EOF > $RPM_BUILD_ROOT/%{_installPrefix}/etc/%{name}-%{version}.sh
+# Load %{name}-%{version} libraries and binaries
+# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+export MVAPICH2_DIR=\$WM_THIRD_PARTY_DIR/packages/%{name}-%{version}/platforms/\$WM_OPTIONS
+export MVAPICH2_BIN_DIR=\$MVAPICH2_DIR/bin
+export MVAPICH2_LIB_DIR=\$MVAPICH2_DIR/lib
+
+# Enable access to the package runtime applications and libraries
+[ -d \$MVAPICH2_BIN_DIR ] && _foamAddPath \$MVAPICH2_BIN_DIR
+[ -d \$MVAPICH2_LIB_DIR ] && _foamAddLib  \$MVAPICH2_LIB_DIR
+
+export MPI_HOME=\$MVAPICH2_DIR
+export MPI_ARCH_PATH=\$MPI_HOME
+export OPAL_PREFIX=\$MPI_ARCH_PATH
+
+# We initialize the rest of the environment using mpicc --showme:
+# This does not work with MVAPICH2
+#export MVAPICH2_INCLUDE_DIR="\`mpicc --showme:incdirs\`"
+#export MVAPICH2_COMPILE_FLAGS="\`mpicc --showme:compile\`"
+#export MVAPICH2_LINK_FLAGS="\`mpicc --showme:link\`"
+
+# Set the foam-extend compilation flags
+export PINC=\$MVAPICH2_COMPILE_FLAGS
+export PLIBS=\$MVAPICH2_LINK_FLAGS
+
+
+if [ "\$FOAM_VERBOSE" -a "\$PS1" ]
+then
+    echo "  Environment variables defined for OpenMPI:"
+    echo "    MVAPICH2_BIN_DIR       : \$MVAPICH2_BIN_DIR"
+    echo "    MVAPICH2_LIB_DIR       : \$MVAPICH2_LIB_DIR"
+    echo "    MVAPICH2_INCLUDE_DIR   : \$MVAPICH2_INCLUDE_DIR"
+    echo "    MVAPICH2_COMPILE_FLAGS : \$MVAPICH2_COMPILE_FLAGS"
+    echo "    MVAPICH2_LINK_FLAGS    : \$MVAPICH2_LINK_FLAGS"
+    echo ""
+    echo "    MPI_HOME              : \$MPI_HOME"
+    echo "    MPI_ARCH_PATH         : \$MPI_ARCH_PATH"
+    echo "    OPAL_PREFIX           : \$OPAL_PREFIX"
+    echo "    PINC                  : \$PINC"
+    echo "    PLIBS                 : \$PLIBS"
+fi
+DOT_SH_EOF
+
+    #
+    # Generate package specific .csh file for foam-extend
+    #
+cat << DOT_CSH_EOF > $RPM_BUILD_ROOT/%{_installPrefix}/etc/%{name}-%{version}.csh
+# Load %{name}-%{version} libraries and binaries
+# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+setenv MVAPICH2_DIR \$WM_THIRD_PARTY_DIR/packages/%{name}-%{version}/platforms/\$WM_OPTIONS
+setenv MVAPICH2_BIN_DIR \$MVAPICH2_DIR/bin
+setenv MVAPICH2_LIB_DIR \$MVAPICH2_DIR/lib
+
+# Enable access to the package runtime applications and libraries
+if ( -e \$MVAPICH2_BIN_DIR ) then
+    _foamAddPath \$MVAPICH2_BIN_DIR
+endif
+
+if ( -e \$MVAPICH2_LIB_DIR ) then
+    _foamAddLib \$MVAPICH2_LIB_DIR
+endif
+
+setenv MPI_HOME \$MVAPICH2_DIR
+setenv MPI_ARCH_PATH \$MPI_HOME
+setenv OPAL_PREFIX \$MPI_ARCH_PATH
+
+# We initialize the rest of the environment using mpicc --showme:
+setenv MVAPICH2_INCLUDE_DIR "\`mpicc --showme:incdirs\`"
+setenv MVAPICH2_COMPILE_FLAGS "\`mpicc --showme:compile\`"
+setenv MVAPICH2_LINK_FLAGS "\`mpicc --showme:link\`"
+
+# Set the foam-extend compilation flags
+setenv PINC "\$MVAPICH2_COMPILE_FLAGS"
+setenv PLIBS "\$MVAPICH2_LINK_FLAGS"
+
+
+if (\$?FOAM_VERBOSE && \$?prompt) then
+    echo "  Environment variables defined for OpenMPI:"
+    echo "    MVAPICH2_BIN_DIR       : \$MVAPICH2_BIN_DIR"
+    echo "    MVAPICH2_LIB_DIR       : \$MVAPICH2_LIB_DIR"
+    echo "    MVAPICH2_INCLUDE_DIR   : \$MVAPICH2_INCLUDE_DIR"
+    echo "    MVAPICH2_COMPILE_FLAGS : \$MVAPICH2_COMPILE_FLAGS"
+    echo "    MVAPICH2_LINK_FLAGS    : \$MVAPICH2_LINK_FLAGS"
+    echo ""
+    echo "    MPI_HOME              : \$MPI_HOME"
+    echo "    MPI_ARCH_PATH         : \$MPI_ARCH_PATH"
+    echo "    OPAL_PREFIX           : \$OPAL_PREFIX"
+    echo "    PINC                  : \$PINC"
+    echo "    PLIBS                 : \$PLIBS"
+endif
+DOT_CSH_EOF
+
+    #finally, generate a .tgz file for systems where using rpm for installing packages
+    # as a non-root user might be a problem.
+    (mkdir -p  %{_topdir}/TGZS/%{_target_cpu}; cd $RPM_BUILD_ROOT/%{_prefix}; tar -zcvf %{_topdir}/TGZS/%{_target_cpu}/%{name}-%{version}.tgz  packages/%{name}-%{version})
+
+
+%clean
+rm -rf %{buildroot}
+
+%files
+%defattr(-,root,root)
+%{_installPrefix}

ThirdParty/rpmBuild/SPECS/openmpi-1.8.8.spec

@@ -138,7 +138,7 @@ Group: 			Development/Tools
         --enable-orterun-prefix-by-default \
         --enable-shared \
         --enable-mpi-cxx \
-	--disable-static \
+        --disable-static \
         --disable-mpi-f77 \
         --disable-mpi-f90 \
         --without-slurm \

ThirdParty/tools/makeThirdPartyFunctionsForRPM

@@ -82,6 +82,7 @@ rpm_make()
     echo "Package name      : $_PACKAGE"
     echo "Package URL       : $_PACKAGE_URL"
     echo "RPM spec file name: $_SPECFILE"
+    echo "RPM file name     : $_RPMFILENAME"
     echo "Additional flags  : $_ADDITIONALFLAGS"
 
     # Shift options

applications/solvers/combustion/rhoReactingFoam/YEqn.H

@@ -13,7 +13,7 @@ tmp<fv::convectionScheme<scalar> > mvConvection
     label inertIndex = -1;
     volScalarField Yt("Yt", 0.0*Y[0]);
 
-    for (label i=0; i<Y.size(); i++)
+    for (label i = 0; i < Y.size(); i++)
     {
         if (Y[i].name() != inertSpecie)
         {

applications/solvers/compressible/rhoPorousMRFPimpleFoam/pEqn.H

@@ -3,6 +3,9 @@ rho = thermo.rho();
 volScalarField rUA = 1.0/UEqn().A();
 U = rUA*UEqn().H();
 
+// Update boundary velocity for consistency with the flux
+mrfZones.correctBoundaryVelocity(U);
+
 if (pimple.nCorrPISO() <= 1)
 {
     UEqn.clear();

applications/solvers/compressible/steadyCompressibleFoam/pEqn.H

@@ -13,7 +13,7 @@
         U = rUA*UEqn.H();
 
         // Calculate phi for boundary conditions
-        phi = rhof*fvc::interpolate(U) & mesh.Sf();
+        phi = rhof*(fvc::interpolate(U) & mesh.Sf());
 
         surfaceScalarField phid2 = rhoReff/rhof*phi;
 

applications/solvers/compressible/steadyCompressibleMRFFoam/pEqn.H

@@ -12,6 +12,9 @@
     {
         U = rUA*UEqn.H();
 
+        // Update boundary velocity for consistency with the flux
+        mrfZones.correctBoundaryVelocity(U);
+
         // Calculate phi for boundary conditions
         phi = rhof*fvc::interpolate(U) & mesh.Sf();
 

applications/solvers/compressible/steadyUniversalMRFFoam/pEqn.H

@@ -12,6 +12,9 @@
     {
         U = rUA*UEqn.H();
 
+        // Update boundary velocity for consistency with the flux
+        mrfZones.correctBoundaryVelocity(U);
+
         // Calculate phi for boundary conditions
         phi = rhof*fvc::interpolate(U) & mesh.Sf();
 

applications/solvers/coupled/Allwmake

@@ -1,13 +0,0 @@
-#!/bin/sh
-cd ${0%/*} || exit 1    # run from this directory
-set -x
-
-wmake libso conjugateHeatTransfer
-
-wmake blockCoupledScalarTransportFoam
-wmake conjugateHeatFoam
-wmake conjugateHeatSimpleFoam
-wmake pUCoupledFoam
-wmake MRFPorousFoam
-
-# ----------------------------------------------------------------- end-of-file

applications/solvers/coupled/MRFPorousFoam/MRFPorousFoam.C

@@ -81,17 +81,40 @@ int main(int argc, char *argv[])
 #       include "couplingTerms.H"
 
         // Solve the block matrix
-        maxResidual = cmptMax(UpEqn.solve().initialResidual());
+        residual = UpEqn.solve();
+        maxResidual = cmptMax(residual.initialResidual());
 
-        // Retrieve solution
-        UpEqn.retrieveSolution(0, U.internalField());
-        UpEqn.retrieveSolution(3, p.internalField());
+        // Check for divergence
+        if (mag(residual.finalResidual() - residual.initialResidual()) > 1)
+        {
+            Info<< "DIVERGENCE: rescue step" << endl;
 
-        U.correctBoundaryConditions();
-        p.correctBoundaryConditions();
+            // Solving potential flow equation and correcting velocities
+            phi = (fvc::interpolate(U) & mesh.Sf());
+            
+            solve
+            (
+                tpEqn
+             ==
+              - fvc::div(U)
+            );
 
-        phi = (fvc::interpolate(U) & mesh.Sf()) + tpEqn().flux() + tpresSource;
+            phi += tpEqn().flux() + tpresSource;
 
+            U = fvc::reconstruct(phi);
+        }
+        else
+        {
+            // Retrieve solution
+            UpEqn.retrieveSolution(0, U.internalField());
+            UpEqn.retrieveSolution(3, p.internalField());
+
+            U.correctBoundaryConditions();
+            p.correctBoundaryConditions();
+
+            phi = (fvc::interpolate(U) & mesh.Sf()) + tpEqn().flux() + tpresSource;
+        }
+        
         // Make flux relative in rotating zones
         mrfZones.relativeFlux(phi);
 

applications/solvers/coupled/MRFPorousFoam/UEqn.H

@@ -5,6 +5,9 @@
         fvc::div(phi)
     );
 
+    // Update boundary velocity for consistency with the flux
+    mrfZones.correctBoundaryVelocity(U);
+
     // Momentum equation
     fvVectorMatrix UEqn
     (
@@ -49,9 +52,7 @@
         trAU().rename("rAU");
     }
 
-    // Insert the additional components. Note this will destroy the H and A
-
-    UEqn += fvm::SuSp(-divPhi, U) + divPhi*U;
+    // Under-relax momentum. Note this will destroy the H and A
     UEqn.relax();
 
     // Insert momentum equation
@@ -67,28 +68,38 @@
 
         const scalarField& V = mesh.V().field();
 
-        // Note: this insertion should only happen in porous cell zones
-        // A rewrite of the porousZones class interface is needed.
+        // Note: insertion should only happen in porous cell zones
         // HJ, 14/Mar/2016
-        forAll (TUIn, cellI)
+
+        register label cellI;
+
+        forAll (pZones, pZoneI)
         {
-            const scalar& cellV = V[cellI];
+            const labelList& curZoneCells = pZones[pZoneI].zone();
 
-            const tensor& cellTU = TUIn[cellI];
+            // Loop over all cells in the zone
+            forAll (curZoneCells, zcI)
+            {
+                cellI = curZoneCells[zcI];
 
-            CoeffField<vector4>::squareType& cellDD = DD[cellI];
+                const scalar& cellV = V[cellI];
 
-            cellDD(0, 0) += cellV*cellTU.xx();
-            cellDD(0, 1) += cellV*cellTU.xy();
-            cellDD(0, 2) += cellV*cellTU.xz();
+                const tensor& cellTU = TUIn[cellI];
 
-            cellDD(1, 0) += cellV*cellTU.yx();
-            cellDD(1, 1) += cellV*cellTU.yy();
-            cellDD(2, 2) += cellV*cellTU.yz();
+                CoeffField<vector4>::squareType& cellDD = DD[cellI];
 
-            cellDD(2, 0) += cellV*cellTU.zx();
-            cellDD(2, 1) += cellV*cellTU.zy();
-            cellDD(2, 2) += cellV*cellTU.zz();
+                cellDD(0, 0) += cellV*cellTU.xx();
+                cellDD(0, 1) += cellV*cellTU.xy();
+                cellDD(0, 2) += cellV*cellTU.xz();
+
+                cellDD(1, 0) += cellV*cellTU.yx();
+                cellDD(1, 1) += cellV*cellTU.yy();
+                cellDD(2, 2) += cellV*cellTU.yz();
+
+                cellDD(2, 0) += cellV*cellTU.zx();
+                cellDD(2, 1) += cellV*cellTU.zy();
+                cellDD(2, 2) += cellV*cellTU.zz();
+            }
         }
     }
 }

applications/solvers/coupled/MRFPorousFoam/initConvergenceCheck.H

@@ -1,4 +1,5 @@
-// initialize values for convergence checks
+    // initialize values for convergence checks
+    BlockSolverPerformance<vector4> residual;
 
     scalar maxResidual = 0;
     scalar convergenceCriterion = 0;

applications/solvers/coupled/conjugateHeatFoam/Make/options

@@ -1,5 +1,4 @@
 EXE_INC = \
-    -I../conjugateHeatTransfer/lnInclude \
     -I$(LIB_SRC)/turbulenceModels \
     -I$(LIB_SRC)/turbulenceModels/incompressible/RAS/RASModel \
     -I$(LIB_SRC)/turbulenceModels/incompressible/turbulenceModel \
@@ -7,8 +6,9 @@ EXE_INC = \
     -I$(LIB_SRC)/transportModels/incompressible/singlePhaseTransportModel \
     -I$(LIB_SRC)/coupledMatrix/lnInclude \
     -I$(LIB_SRC)/finiteVolume/lnInclude \
+    -I$(LIB_SRC)/thermophysicalModels/basic/lnInclude \
     -I$(LIB_SRC)/thermophysicalModels/radiation/lnInclude \
-    -I$(LIB_SRC)/thermophysicalModels/basic/lnInclude
+    -I$(LIB_SRC)/conjugateHeatTransfer/lnInclude
 
 EXE_LIBS = \
     -lincompressibleTurbulenceModel \

applications/solvers/coupled/conjugateHeatFoam/solveEnergy.H

@@ -14,15 +14,12 @@
               + fvm::div(phi, T)
             )
           - fvm::laplacian(kappaEff, T)
-            ==
+         ==
             radiation->Ru()
           - fvm::Sp(4.0*radiation->Rp()*pow3(T), T)
           + 3.0*radiation->Rp()*pow4(T)
         );
 
-        //Done automatically in 1.6.1-ext
-        //TFluidEqn->boundaryManipulate(T.boundaryField());
-
         fvScalarMatrix* TSolidEqn = new fvScalarMatrix
         (
             fvm::ddt(rhoCpsolid, Tsolid)
@@ -30,10 +27,6 @@
           + fvm::SuSp(-solidThermo.S()/Tsolid, Tsolid)
         );
 
-        //Done automatically in 1.6.1-ext
-        //TSolidEqn->boundaryManipulate(Tsolid.boundaryField());
-
-
         // Add fluid equation
         TEqns.set(0, TFluidEqn);
 

applications/solvers/coupled/conjugateHeatSimpleFoam/Make/options

@@ -1,5 +1,4 @@
 EXE_INC = \
-    -I../conjugateHeatTransfer/lnInclude \
     -I$(LIB_SRC)/turbulenceModels \
     -I$(LIB_SRC)/turbulenceModels/incompressible/RAS/RASModel \
     -I$(LIB_SRC)/turbulenceModels/incompressible/turbulenceModel \
@@ -7,8 +6,9 @@ EXE_INC = \
     -I$(LIB_SRC)/transportModels/incompressible/singlePhaseTransportModel \
     -I$(LIB_SRC)/coupledMatrix/lnInclude \
     -I$(LIB_SRC)/finiteVolume/lnInclude \
+    -I$(LIB_SRC)/thermophysicalModels/basic/lnInclude \
     -I$(LIB_SRC)/thermophysicalModels/radiation/lnInclude \
-    -I$(LIB_SRC)/thermophysicalModels/basic/lnInclude
+    -I$(LIB_SRC)/conjugateHeatTransfer/lnInclude
 
 EXE_LIBS = \
     -lincompressibleTurbulenceModel \

applications/solvers/coupled/conjugateHeatSimpleFoam/solveEnergy.H

@@ -14,7 +14,7 @@
               + fvm::SuSp(-fvc::div(phi), T)
             )
           - fvm::laplacian(kappaEff, T)
-            ==
+         ==
             radiation->Ru()
           - fvm::Sp(4.0*radiation->Rp()*pow3(T), T)
           + 3.0*radiation->Rp()*pow4(T)

applications/solvers/coupled/pUCoupledFoam/UEqn.H

@@ -14,9 +14,7 @@
 
     rAU = 1.0/UEqn.A();
 
-    // Insert the additional components. Note this will destroy the H and A
-
-    UEqn += fvm::SuSp(-divPhi, U) + divPhi*U;
+    // Under-relax momentum. Note this will destroy the H and A
     UEqn.relax();
 
     UpEqn.insertEquation(0, UEqn);

applications/solvers/coupled/pUCoupledFoam/createFields.H

@@ -1,69 +1,71 @@
-Info << "Reading field p\n" << endl;
-volScalarField p
-(
-    IOobject
+    Info << "Reading field p\n" << endl;
+    volScalarField p
     (
-        "p",
-        runTime.timeName(),
+        IOobject
+        (
+            "p",
+            runTime.timeName(),
+            mesh,
+            IOobject::MUST_READ,
+            IOobject::AUTO_WRITE
+        ),
+        mesh
+    );
+
+    Info << "Reading field U\n" << endl;
+    volVectorField U
+    (
+        IOobject
+        (
+            "U",
+            runTime.timeName(),
+            mesh,
+            IOobject::MUST_READ,
+            IOobject::AUTO_WRITE
+        ),
+        mesh
+    );
+
+#   include "createPhi.H"
+
+    singlePhaseTransportModel laminarTransport(U, phi);
+
+    autoPtr<incompressible::RASModel> turbulence
+    (
+        incompressible::RASModel::New(U, phi, laminarTransport)
+    );
+
+    // Block vector field for velocity (first entry) and pressure (second
+    // entry).
+    Info << "Creating field Up\n" << endl;
+    volVector4Field Up
+    (
+        IOobject
+        (
+            "Up",
+            runTime.timeName(),
+            mesh,
+            IOobject::NO_READ,
+            IOobject::NO_WRITE
+        ),
         mesh,
-        IOobject::MUST_READ,
-        IOobject::AUTO_WRITE
-    ),
-    mesh
-);
+        dimensionedVector4("zero", dimless, vector4::zero)
+    );
 
-Info << "Reading field U\n" << endl;
-volVectorField U
-(
-    IOobject
+    Info<< "Creating field rAU\n" << endl;
+    volScalarField rAU
     (
-        "U",
-        runTime.timeName(),
+        IOobject
+        (
+            "rAU",
+            runTime.timeName(),
+            mesh,
+            IOobject::NO_READ,
+            IOobject::NO_WRITE
+        ),
         mesh,
-        IOobject::MUST_READ,
-        IOobject::AUTO_WRITE
-    ),
-    mesh
-);
+        runTime.deltaT()
+    );
 
-#include "createPhi.H"
-
-singlePhaseTransportModel laminarTransport(U, phi);
-autoPtr<incompressible::RASModel> turbulence
-(
-    incompressible::RASModel::New(U, phi, laminarTransport)
-);
-
-// Block vector field for velocity (first entry) and pressure (second
-// entry).
-Info << "Creating field Up\n" << endl;
-volVector4Field Up
-(
-    IOobject
-    (
-       "Up",
-       runTime.timeName(),
-       mesh,
-       IOobject::NO_READ,
-       IOobject::NO_WRITE
-    ),
-    mesh,
-    dimensionedVector4("zero", dimless, vector4::zero)
-);
-
-Info<< "Creating field rAU\n" << endl;
-volScalarField rAU
-(
-    IOobject
-    (
-        "rAU",
-        runTime.timeName(),
-        mesh,
-        IOobject::NO_READ,
-        IOobject::NO_WRITE
-    ),
-    mesh,
-    runTime.deltaT()
-);
-
-mesh.schemesDict().setFluxRequired(p.name());
+    mesh.schemesDict().setFluxRequired(p.name());
+    mesh.schemesDict().setFluxRequired("pcorr");

applications/solvers/incompressible/MRFSimpleFoam/MRFSimpleFoam.C

@@ -61,54 +61,14 @@ int main(int argc, char *argv[])
 
         // Pressure-velocity SIMPLE corrector
         {
-            // Momentum predictor
-
-            tmp<fvVectorMatrix> UEqn
-            (
-                fvm::div(phi, U)
-              + turbulence->divDevReff()
-            );
-            mrfZones.addCoriolis(UEqn());
-
-            UEqn().relax();
-
-            solve(UEqn() == -fvc::grad(p));
-
-            volScalarField rAU = 1.0/UEqn().A();
-            U = rAU*UEqn().H();
-            UEqn.clear();
-
-            phi = fvc::interpolate(U, "interpolate(HbyA)") & mesh.Sf();
-            mrfZones.relativeFlux(phi);
-            adjustPhi(phi, U, p);
-
-            // Non-orthogonal pressure corrector loop
-            while (simple.correctNonOrthogonal())
-            {
-                fvScalarMatrix pEqn
-                (
-                    fvm::laplacian(rAU, p) == fvc::div(phi)
-                );
-
-                pEqn.setReference(pRefCell, pRefValue);
-                pEqn.solve();
-
-                if (simple.finalNonOrthogonalIter())
-                {
-                    phi -= pEqn.flux();
-                }
-            }
-
-#           include "continuityErrs.H"
-
-            // Explicitly relax pressure for momentum corrector
-            p.relax();
-
-            // Momentum corrector
-            U -= rAU*fvc::grad(p);
-            U.correctBoundaryConditions();
+#           include "UEqn.H"
+#           include "pEqn.H"
         }
 
+        // Calculate relative velocity
+        Urel == U;
+        mrfZones.relativeVelocity(Urel);
+
         turbulence->correct();
 
         runTime.write();

applications/solvers/incompressible/MRFSimpleFoam/UEqn.H

@@ -0,0 +1,19 @@
+    // Solve the momentum equation
+
+    tmp<fvVectorMatrix> HUEqn
+    (
+        fvm::div(phi, U)
+      + turbulence->divDevReff()
+    );
+    mrfZones.addCoriolis(HUEqn());
+
+    // Get under-relaxation factor
+    const scalar UUrf = mesh.solutionDict().equationRelaxationFactor(U.name());
+
+    // Momentum solution
+    solve
+    (
+        relax(HUEqn(), UUrf)
+     ==
+        -fvc::grad(p)
+    );

applications/solvers/incompressible/MRFSimpleFoam/createFields.H

@@ -44,3 +44,19 @@
 
     MRFZones mrfZones(mesh);
     mrfZones.correctBoundaryVelocity(U);
+
+    // Create Urel as a permanent field to make it available for on-the-fly
+    // post-processing operations
+    volVectorField Urel
+    (
+        IOobject
+        (
+            "Urel",
+            runTime.timeName(),
+            mesh,
+            IOobject::NO_READ,
+            IOobject::AUTO_WRITE
+        ),
+        U
+    );
+    mrfZones.relativeVelocity(Urel);

applications/solvers/incompressible/MRFSimpleFoam/pEqn.H

@@ -0,0 +1,54 @@
+{
+    p.boundaryField().updateCoeffs();
+
+    // Prepare clean 1/Ap without contribution from under-relaxation
+    // HJ, 26/Oct/2015
+    volScalarField rAU
+    (
+        "(1|A(U))",
+        1/HUEqn().A()
+    );
+
+    // Update boundary velocity for consistency with the flux
+    // This is needed for a ramped MRF
+    mrfZones.correctBoundaryVelocity(U);
+
+    // Store velocity under-relaxation point before using U for
+    // the flux precursor
+    U.storePrevIter();
+
+    U = rAU*HUEqn().H();
+    HUEqn.clear();
+
+     phi = fvc::interpolate(U) & mesh.Sf();
+     mrfZones.relativeFlux(phi);
+     adjustPhi(phi, U, p);
+
+     // Non-orthogonal pressure corrector loop
+     while (simple.correctNonOrthogonal())
+     {
+         fvScalarMatrix pEqn
+         (
+             fvm::laplacian(rAU, p) == fvc::div(phi)
+         );
+
+         pEqn.setReference(pRefCell, pRefValue);
+         pEqn.solve();
+
+         if (simple.finalNonOrthogonalIter())
+         {
+             phi -= pEqn.flux();
+         }
+     }
+
+#   include "continuityErrs.H"
+
+    // Explicitly relax pressure for momentum corrector
+    p.relax();
+
+    // Momentum corrector
+    // Note: since under-relaxation does not change aU, H/a in U can be
+    // re-used.  HJ, 22/Jan/2016
+    U = UUrf*(U - rAU*fvc::grad(p)) + (1 - UUrf)*U.prevIter();
+    U.correctBoundaryConditions();
+}

applications/solvers/incompressible/simpleFoam/pEqn.H

@@ -1,8 +1,9 @@
+{
     p.boundaryField().updateCoeffs();
 
     // Prepare clean 1/Ap without contribution from under-relaxation
     // HJ, 26/Oct/2015
-    volScalarField rUA
+    volScalarField rAU
     (
         "(1|A(U))",
         1/HUEqn().A()
@@ -12,8 +13,9 @@
     // the flux precursor
     U.storePrevIter();
 
-    U = rUA*HUEqn().H();
+    U = rAU*HUEqn().H();
     HUEqn.clear();
+
     phi = fvc::interpolate(U) & mesh.Sf();
     adjustPhi(phi, U, p);
 
@@ -22,7 +24,7 @@
     {
         fvScalarMatrix pEqn
         (
-            fvm::laplacian(rUA, p) == fvc::div(phi)
+            fvm::laplacian(rAU, p) == fvc::div(phi)
         );
 
         pEqn.setReference(pRefCell, pRefValue);
@@ -43,6 +45,6 @@
     // Momentum corrector
     // Note: since under-relaxation does not change aU, H/a in U can be
     // re-used.  HJ, 22/Jan/2016
-    U = UUrf*(U - rUA*fvc::grad(p)) + (1 - UUrf)*U.prevIter();
+    U = UUrf*(U - rAU*fvc::grad(p)) + (1 - UUrf)*U.prevIter();
     U.correctBoundaryConditions();
-
+}

applications/solvers/multiphase/MRFInterFoam/pEqn.H

@@ -4,6 +4,9 @@
 
     U = rUA*UEqn.H();
 
+    // Update boundary velocity for consistency with the flux
+    mrfZones.correctBoundaryVelocity(U);
+
     surfaceScalarField phiU
     (
         "phiU",

applications/utilities/finiteArea/makeFaMesh/makeFaMesh.C

@@ -314,6 +314,26 @@ int main(int argc, char *argv[])
         }
     }
 
+    if (args.optionFound("addEmptyPatch"))
+    {
+        word emptyPatchName(args.optionLookup("addEmptyPatch")());
+        dictionary emptyPatchDict;
+        emptyPatchDict.add("type", "empty");
+        emptyPatchDict.add("edgeLabels", labelList());
+        emptyPatchDict.add("ngbPolyPatchIndex", -1);
+
+        faPatchLst.append
+        (
+            faPatch::New
+            (
+                emptyPatchName,
+                emptyPatchDict,
+                faPatchLst.size(),
+                areaMesh.boundary()
+            ).ptr()
+        );
+    }
+
     Info << "Add faPatches ... ";
     areaMesh.addFaPatches(List<faPatch*>(faPatchLst));
     Info << "Done" << endl;

applications/utilities/parallelProcessing/reconstructParMesh/reconstructParMesh.C

@@ -119,12 +119,12 @@ int main(int argc, char *argv[])
             << exit(FatalError);
     }
 
-    Foam::word regionName = polyMesh::defaultRegion;
+    word regionName = polyMesh::defaultRegion;
 
     if (args.optionReadIfPresent("region", regionName))
     {
         Info<< "Selecting region " << regionName << " for time = "
-            << runTime.timeName() << Foam::nl << Foam::endl;
+            << runTime.timeName() << nl << endl;
     }
 
     // Set all times on processor meshes equal to reconstructed mesh

applications/utilities/preProcessing/convertPhi/convertPhi.C

@@ -46,7 +46,6 @@ int main(int argc, char *argv[])
         FatalError.exit();
     }
 
-
     dimensionedScalar rhoRef
     (
         "rhoRef",

bin/plotForces.py

@@ -53,6 +53,21 @@ for i in range(1,len(t)):
         my[i] += mvy[i]
         mz[i] += mvz[i]
 
+# write clean data file
+outForces=open('forces.dat','w')
+
+for data in zip(t,fx,fy,fz):
+        outForces.write(' '.join([str(d) for d in data])+'\n')
+
+outForces.close()
+
+outMoments=open('moments.dat','w')
+
+for data in zip(t,mx,my,mz):
+        outMoments.write(' '.join([str(d) for d in data])+'\n')
+
+outMoments.close()
+
 # plot forces
 import pylab
 pylab.xlabel('iteration')

bin/plotResidual.py

@@ -62,6 +62,7 @@ for line in lines:
                 tepsilon.append(iepsilon)
                 epsilon.append(float(matchepsilon.group(2)))
 
+# write clean data file
 outfile=open('residual.dat','w')
 
 if iomega > 0:

etc/bashrc

@@ -91,11 +91,11 @@ export WM_THIRD_PARTY_DIR=$WM_PROJECT_DIR/ThirdParty
 # Use 'set' and 'unset' to adjust for your environent
 # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 # For AllMake.stage1
-export WM_THIRD_PARTY_USE_CMAKE_322=1
+#export WM_THIRD_PARTY_USE_CMAKE_322=1
 
 #
 # For AllMake.stage2
-export WM_THIRD_PARTY_USE_OPENMPI_165=1
+export WM_THIRD_PARTY_USE_OPENMPI_188=1
 
 #
 # For AllMake.stage3

etc/controlDict-EXAMPLE

@@ -943,7 +943,7 @@ Tolerances
     slidingEdgeEndCutoffTol         0.0001;
     slidingEdgeCoPlanarTol          0.8;
 
-     GGIAreaErrorTol                 1e-8;
+    GGIAreaErrorTol                 1e-8;
 }
 
 DimensionedConstants

etc/cshrc

@@ -77,11 +77,11 @@ setenv WM_THIRD_PARTY_DIR $WM_PROJECT_DIR/ThirdParty
 # This can be overriden in prefs.sh
 # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 # For AllMake.stage1
-setenv WM_THIRD_PARTY_USE_CMAKE_322 1
+#setenv WM_THIRD_PARTY_USE_CMAKE_322 1
 
 #
 # For AllMake.stage2
-setenv WM_THIRD_PARTY_USE_OPENMPI_165 1
+setenv WM_THIRD_PARTY_USE_OPENMPI_188 1
 
 #
 # For AllMake.stage3
@@ -152,7 +152,7 @@ if ( ! $?WM_PRECISION_OPTION ) setenv WM_PRECISION_OPTION DP
 
 # WM_COMPILE_OPTION = Opt | Debug | Prof
 if ( ! $?WM_COMPILE_OPTION ) setenv WM_COMPILE_OPTION Opt
-#setenv WM_COMPILE_OPTION Opt
+setenv WM_COMPILE_OPTION Opt
 #setenv WM_COMPILE_OPTION Debug
 
 # WM_MPLIB = SYSTEMOPENMPI | OPENMPI | MPICH | MPICH-GM | HPMPI | GAMMA | MPI | QSMPI | MVAPICH2

etc/prefs.csh-EXAMPLE

@@ -210,6 +210,9 @@ setenv WM_THIRD_PARTY_USE_OPENMPI_188 1
 #setenv WM_THIRD_PARTY_USE_OPENMPI_15 1
 #setenv WM_THIRD_PARTY_USE_OPENMPI_143 1
 #setenv WM_THIRD_PARTY_USE_OPENMPI_141 1
+#setenv WM_THIRD_PARTY_USE_MVAPICH2_22 1
+#setenv WM_THIRD_PARTY_USE_MVAPICH2_22_ConfigureAdditionalArgs '--disable-mcast'
+
 
 #
 # For AllMake.stage3

etc/prefs.sh-EXAMPLE

@@ -220,6 +220,9 @@ export WM_THIRD_PARTY_USE_OPENMPI_188=1
 #export WM_THIRD_PARTY_USE_OPENMPI_15=1
 #export WM_THIRD_PARTY_USE_OPENMPI_143=1
 #export WM_THIRD_PARTY_USE_OPENMPI_141=1
+#export WM_THIRD_PARTY_USE_MVAPICH2_22=1
+#export WM_THIRD_PARTY_USE_MVAPICH2_22_ConfigureAdditionalArgs='--disable-mcast'
+
 
 #
 # For AllMake.stage3

etc/settings.csh

@@ -173,7 +173,7 @@ case OPENMPI:
         if ($?FOAM_VERBOSE && $?prompt) then
             echo "Using openmpi-1.8.8 from the ThirdParty package: $WM_THIRD_PARTY_DIR/packages/$mpi_version"
         endif
-        _foamSource  $WM_THIRD_PARTY_DIR/packages/$mpi_version/platforms/$WM_OPTIONS/etc/$mpi_version.csh
+        _foamSource $WM_THIRD_PARTY_DIR/packages/$mpi_version/platforms/$WM_OPTIONS/etc/$mpi_version.csh
 
     else if ($?WM_THIRD_PARTY_USE_OPENMPI_165 != 0 && -d $WM_THIRD_PARTY_DIR/packages/openmpi-1.6.5/platforms/$WM_OPTIONS ) then
         set mpi_version=openmpi-1.6.5
@@ -181,7 +181,7 @@ case OPENMPI:
         if ($?FOAM_VERBOSE && $?prompt) then
             echo "Using openmpi-1.6.5 from the ThirdParty package: $WM_THIRD_PARTY_DIR/packages/$mpi_version"
         endif
-        _foamSource  $WM_THIRD_PARTY_DIR/packages/$mpi_version/platforms/$WM_OPTIONS/etc/$mpi_version.csh
+        _foamSource $WM_THIRD_PARTY_DIR/packages/$mpi_version/platforms/$WM_OPTIONS/etc/$mpi_version.csh
 
     else if ($?WM_THIRD_PARTY_USE_OPENMPI_143 != 0 && -d $WM_THIRD_PARTY_DIR/packages/openmpi-1.4.3/platforms/$WM_OPTIONS ) then
         set mpi_version=openmpi-1.4.3
@@ -189,7 +189,7 @@ case OPENMPI:
         if ($?FOAM_VERBOSE && $?prompt) then
             echo "Using openmpi-1.4.3 from the ThirdParty package: $WM_THIRD_PARTY_DIR/packages/$mpi_version"
         endif
-        _foamSource  $WM_THIRD_PARTY_DIR/packages/$mpi_version/platforms/$WM_OPTIONS/etc/$mpi_version.csh
+        _foamSource $WM_THIRD_PARTY_DIR/packages/$mpi_version/platforms/$WM_OPTIONS/etc/$mpi_version.csh
 
     else if ($?WM_THIRD_PARTY_USE_OPENMPI_143 != 0 && -d $WM_THIRD_PARTY_DIR/packages/openmpi-1.5/platforms/$WM_OPTIONS ) then
         set mpi_version=openmpi-1.5
@@ -197,7 +197,7 @@ case OPENMPI:
         if ($?FOAM_VERBOSE && $?prompt) then
             echo "Using openmpi-1.5 from the ThirdParty package: $WM_THIRD_PARTY_DIR/packages/$mpi_version"
         endif
-        _foamSource  $WM_THIRD_PARTY_DIR/packages/$mpi_version/platforms/$WM_OPTIONS/etc/$mpi_version.csh
+        _foamSource $WM_THIRD_PARTY_DIR/packages/$mpi_version/platforms/$WM_OPTIONS/etc/$mpi_version.csh
     endif
 
     unset mpi_version
@@ -576,8 +576,8 @@ endif
 
 # zoltan
 # ~~~~~
-if ( $?ZOLTAN_SYSTEM == 0 && $?WM_THIRD_PARTY_USE_ZOLTAN_36 != 0 && -e "$WM_THIRD_PARTY_DIR"/packages/zoltan-3.6/platforms/$WM_OPTIONS ) then
-    _foamSource $WM_THIRD_PARTY_DIR/packages/zoltan-3.6/platforms/$WM_OPTIONS/etc/zoltan-3.6.csh
+if ( $?ZOLTAN_SYSTEM == 0 && $?WM_THIRD_PARTY_USE_ZOLTAN_35 != 0 && -e "$WM_THIRD_PARTY_DIR"/packages/zoltan-3.5/platforms/$WM_OPTIONS ) then
+    _foamSource $WM_THIRD_PARTY_DIR/packages/zoltan-3.5/platforms/$WM_OPTIONS/etc/zoltan-3.5.csh
 endif
 
 # Python

etc/settings.sh

@@ -220,7 +220,7 @@ OPENMPI)
         then
             echo "Using openmpi-1.8.8 from the ThirdParty package: $WM_THIRD_PARTY_DIR/packages/$mpi_version"
         fi
-        _foamSource  $WM_THIRD_PARTY_DIR/packages/$mpi_version/platforms/$WM_OPTIONS/etc/$mpi_version.sh
+        _foamSource $WM_THIRD_PARTY_DIR/packages/$mpi_version/platforms/$WM_OPTIONS/etc/$mpi_version.sh
 
     elif [ ! -z $WM_THIRD_PARTY_USE_OPENMPI_165 ] && [ -e $WM_THIRD_PARTY_DIR/packages/openmpi-1.6.5/platforms/$WM_OPTIONS ]
         then
@@ -229,7 +229,7 @@ OPENMPI)
         then
             echo "Using openmpi-1.6.5 from the ThirdParty package: $WM_THIRD_PARTY_DIR/packages/$mpi_version"
         fi
-        _foamSource  $WM_THIRD_PARTY_DIR/packages/$mpi_version/platforms/$WM_OPTIONS/etc/$mpi_version.sh
+        _foamSource $WM_THIRD_PARTY_DIR/packages/$mpi_version/platforms/$WM_OPTIONS/etc/$mpi_version.sh
 
     elif [ ! -z $WM_THIRD_PARTY_USE_OPENMPI_143 ] && [ -e $WM_THIRD_PARTY_DIR/packages/openmpi-1.4.3/platforms/$WM_OPTIONS ]
         then
@@ -238,7 +238,7 @@ OPENMPI)
         then
             echo "Using openmpi-1.4.3 from the ThirdParty package: $WM_THIRD_PARTY_DIR/packages/$mpi_version"
         fi
-        _foamSource  $WM_THIRD_PARTY_DIR/packages/$mpi_version/platforms/$WM_OPTIONS/etc/$mpi_version.sh
+        _foamSource $WM_THIRD_PARTY_DIR/packages/$mpi_version/platforms/$WM_OPTIONS/etc/$mpi_version.sh
 
     elif [ ! -z $WM_THIRD_PARTY_USE_OPENMPI_15 ] && [ -e $WM_THIRD_PARTY_DIR/packages/openmpi-1.5/platforms/$WM_OPTIONS ]
         then
@@ -247,7 +247,7 @@ OPENMPI)
         then
             echo "Using openmpi-1.5 from the ThirdParty package: $WM_THIRD_PARTY_DIR/packages/$mpi_version"
         fi
-        _foamSource  $WM_THIRD_PARTY_DIR/packages/$mpi_version/platforms/$WM_OPTIONS/etc/$mpi_version.sh
+        _foamSource $WM_THIRD_PARTY_DIR/packages/$mpi_version/platforms/$WM_OPTIONS/etc/$mpi_version.sh
     fi
 
     # On Windows set mpi_version from value defined in bashrc.mingw:
@@ -375,22 +375,16 @@ SYSTEMOPENMPI)
     unset mpi_version
     ;;
 
+
 MVAPICH2)
-    mpi_version=mvapich2
-
-    if [ -n "${MVAPICH2_BIN_DIR}" ] && [ -d "${MVAPICH2_BIN_DIR}" ]
-    then
-        _foamAddPath $MVAPICH2_BIN_DIR
-    else
-        MVAPICH2_BIN_DIR=$(dirname `which mpicc`)
-    fi
-
-    if which mpicc >/dev/null
-    then
-        mpicc -v 2>/dev/null | grep -q "mpicc for MVAPICH2" ||
-            echo "Warning: `which mpicc` does not appear to be for MVAPICH2"
-    else
-        echo "Warning: mpicc not available"
+    mpi_version=mvapich2-2.2
+    if [ ! -z $WM_THIRD_PARTY_USE_MVAPICH2_20 ] && [ -e $WM_THIRD_PARTY_DIR/packages/mvapich2-2.2/platforms/$WM_OPTIONS ]
+        then
+        if [ "$FOAM_VERBOSE" -a "$PS1" ]
+        then
+            echo "Using mvapich2 from the ThirdParty package: $WM_THIRD_PARTY_DIR/packages/$mpi_version"
+        fi
+        _foamSource $WM_THIRD_PARTY_DIR/packages/$mpi_version/platforms/$WM_OPTIONS/etc/$mpi_version.sh
     fi
 
     export MPI_HOME=`dirname $MVAPICH2_BIN_DIR`

src/Allwmake

@@ -59,6 +59,8 @@ thermophysicalModels/Allwmake
 transportModels/Allwmake
 turbulenceModels/Allwmake
 lagrangian/Allwmake
+wmake libso conjugateHeatTransfer
+
 postProcessing/Allwmake
 conversion/Allwmake
 

src/ODE/sixDOF/sixDOFqODE/sixDOFqODE.C

@@ -598,7 +598,7 @@ void Foam::sixDOFqODE::relaxAcceleration
     const scalar maxRelFactor
 )
 {
-    if (minRelFactor - maxRelFactor < SMALL)
+    if (mag(minRelFactor - maxRelFactor) < SMALL)
     {
         // Fixed relaxation
        relaxFactorT_ = minRelFactor;

src/conjugateHeatTransfer/fvPatchFields/chtRcTemperature/chtRcTemperatureFvPatchScalarField.H

@@ -47,7 +47,7 @@ namespace Foam
 {
 
 /*---------------------------------------------------------------------------*\
-                  Class chtRcTemperatureFvPatchScalarField Declaration
+             Class chtRcTemperatureFvPatchScalarField Declaration
 \*---------------------------------------------------------------------------*/
 
 class chtRcTemperatureFvPatchScalarField
@@ -60,7 +60,7 @@ class chtRcTemperatureFvPatchScalarField
         word kName_;
 
         //- Take radiation into account for this patch
-        bool radiation_;
+        Switch radiation_;
 
 
 public:
@@ -86,7 +86,8 @@ public:
             const dictionary&
         );
 
-        //- Construct by mapping given chtRcTemperatureFvPatchScalarField onto a new patch
+        //- Construct by mapping given chtRcTemperatureFvPatchScalarField
+        //  onto a new patch
         chtRcTemperatureFvPatchScalarField
         (
             const chtRcTemperatureFvPatchScalarField&,
@@ -128,8 +129,26 @@ public:
 
         // Access functions
 
+            //- Return kName
+            const word& kName() const
+            {
+                return kName_;
+            }
+
+            //- Return access to kName
+            word& kName()
+            {
+                return kName_;
+            }
+
             //- Return radiation
-            bool radiation() const
+            const Switch& radiation() const
+            {
+                return radiation_;
+            }
+
+            //- Return access to radiation
+            Switch& radiation()
             {
                 return radiation_;
             }
@@ -158,7 +177,6 @@ public:
 
         //- Write
         virtual void write(Ostream&) const;
-
 };
 
 

src/conjugateHeatTransfer/fvPatchFields/chtRcThermalDiffusivity/chtRcThermalDiffusivityFvPatchScalarField.C

@@ -36,14 +36,10 @@ Author
 #include "radiationConstants.H"
 #include "VectorN.H"
 
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-namespace Foam
-{
-
 // * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
 
-chtRcThermalDiffusivityFvPatchScalarField::chtRcThermalDiffusivityFvPatchScalarField
+Foam::chtRcThermalDiffusivityFvPatchScalarField::
+chtRcThermalDiffusivityFvPatchScalarField
 (
     const fvPatch& p,
     const DimensionedField<scalar, volMesh>& iF
@@ -53,7 +49,8 @@ chtRcThermalDiffusivityFvPatchScalarField::chtRcThermalDiffusivityFvPatchScalarF
 {}
 
 
-chtRcThermalDiffusivityFvPatchScalarField::chtRcThermalDiffusivityFvPatchScalarField
+Foam::chtRcThermalDiffusivityFvPatchScalarField::
+chtRcThermalDiffusivityFvPatchScalarField
 (
     const fvPatch& p,
     const DimensionedField<scalar, volMesh>& iF,
@@ -64,7 +61,8 @@ chtRcThermalDiffusivityFvPatchScalarField::chtRcThermalDiffusivityFvPatchScalarF
 {}
 
 
-chtRcThermalDiffusivityFvPatchScalarField::chtRcThermalDiffusivityFvPatchScalarField
+Foam::chtRcThermalDiffusivityFvPatchScalarField::
+chtRcThermalDiffusivityFvPatchScalarField
 (
     const chtRcThermalDiffusivityFvPatchScalarField& ptf,
     const fvPatch& p,
@@ -76,7 +74,8 @@ chtRcThermalDiffusivityFvPatchScalarField::chtRcThermalDiffusivityFvPatchScalarF
 {}
 
 
-chtRcThermalDiffusivityFvPatchScalarField::chtRcThermalDiffusivityFvPatchScalarField
+Foam::chtRcThermalDiffusivityFvPatchScalarField::
+chtRcThermalDiffusivityFvPatchScalarField
 (
     const chtRcThermalDiffusivityFvPatchScalarField& ptf,
     const DimensionedField<scalar, volMesh>& iF
@@ -88,7 +87,7 @@ chtRcThermalDiffusivityFvPatchScalarField::chtRcThermalDiffusivityFvPatchScalarF
 
 // * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
 
-void chtRcThermalDiffusivityFvPatchScalarField::evaluate
+void Foam::chtRcThermalDiffusivityFvPatchScalarField::evaluate
 (
     const Pstream::commsTypes
 )
@@ -97,7 +96,7 @@ void chtRcThermalDiffusivityFvPatchScalarField::evaluate
 }
 
 
-void chtRcThermalDiffusivityFvPatchScalarField::updateCoeffs()
+void Foam::chtRcThermalDiffusivityFvPatchScalarField::updateCoeffs()
 {
     if (updated())
     {
@@ -109,16 +108,18 @@ void chtRcThermalDiffusivityFvPatchScalarField::updateCoeffs()
 
 
 void
-chtRcThermalDiffusivityFvPatchScalarField::calcThermalDiffusivity
+Foam::chtRcThermalDiffusivityFvPatchScalarField::calcThermalDiffusivity
 (
     chtRegionCoupleBase& owner,
     const chtRegionCoupleBase& neighbour
 ) const
 {
-    if(debug)
+    if (debug)
     {
-        Info << "In chtRcThermalDiffusivityFvPatchScalarField::calcThermalDiffusivity on "
-            << this->dimensionedInternalField().name()
+        InfoIn
+        (
+            "chtRcThermalDiffusivityFvPatchScalarField::calcThermalDiffusivity"
+        )   << "for field " << this->dimensionedInternalField().name()
             << " in " << this->patch().boundaryMesh().mesh().name()
             << endl;
     }
@@ -158,19 +159,19 @@ chtRcThermalDiffusivityFvPatchScalarField::calcThermalDiffusivity
         const scalarField& lfNei = neighbour.originalPatchField();
         scalarField lTcNei = TwOwn.shadowPatchField().patchInternalField();
 
-        forAll(lData, facei)
+        forAll (lData, facei)
         {
             lData[facei][0] = lTcNei[facei];
             lData[facei][1] = lfNei[facei];
         }
 
-        if(TwOwn.shadowPatchField().radiation())
+        if (TwOwn.shadowPatchField().radiation())
         {
             const scalarField& lQrNei =
                 owner.lookupShadowPatchField<volScalarField, scalar>("Qr");
             const scalarField& lTwNei = TwOwn.shadowPatchField();
 
-            forAll(lData, facei)
+            forAll (lData, facei)
             {
                 lData[facei][2] = lTwNei[facei];
                 lData[facei][3] = lQrNei[facei];
@@ -180,15 +181,15 @@ chtRcThermalDiffusivityFvPatchScalarField::calcThermalDiffusivity
         const Field<VectorN<scalar, 4> > iData =
             owner.regionCouplePatch().interpolate(lData);
 
-        forAll(iData, facei)
+        forAll (iData, facei)
         {
             TcNei[facei] = iData[facei][0];
             fNei[facei] = iData[facei][1];
         }
 
-        if(TwOwn.shadowPatchField().radiation())
+        if (TwOwn.shadowPatchField().radiation())
         {
-            forAll(iData, facei)
+            forAll (iData, facei)
             {
                 Qr[facei] += iData[facei][3];
                 fourQro[facei] +=
@@ -205,46 +206,35 @@ chtRcThermalDiffusivityFvPatchScalarField::calcThermalDiffusivity
     const scalarField kOwn = fOwn/(1.0 - p.weights())/mld.magDelta(p.index());
     const scalarField kNei = fNei/p.weights()/mld.magDelta(p.index());
 
-    //Info << "kOwn = " << kOwn << endl;
-    //Info << "kNei = " << kNei << endl;
-    //Info << "TcOwn = " << TcOwn << endl;
-    //Info << "TcNei = " << TcNei << endl;
-    //Info << "DeltaT = " << TcNei - TcOwn << endl;
-
-    //Info << "Qr = " << Qr << endl;
-    //Info << "kOwn + kNei = " << (kOwn + kNei) << endl;
-
-    //Info << "k = " << k << endl;
-
     k = kOwn*(TwOwn*(kNei*(TcNei - TcOwn) + Qr + fourQro) - TcOwn*fourQro);
     k /= stabilise((fourQro + TwOwn*(kOwn + kNei))*(TcNei - TcOwn), SMALL);
     k /= p.deltaCoeffs();
 
     //Info << "k = " << k << endl;
 
-    forAll(k, facei)
+    forAll (k, facei)
     {
         k[facei] = max(min(k[facei], 100*kHarm[facei]), 0.01*kHarm[facei]);
     }
 
-    //Info << "k = " << k << endl;
-
     owner.fvPatchScalarField::updateCoeffs();
 }
 
 
 void
-chtRcThermalDiffusivityFvPatchScalarField::calcTemperature
+Foam::chtRcThermalDiffusivityFvPatchScalarField::calcTemperature
 (
     chtRcTemperatureFvPatchScalarField& TwOwn,
     const chtRcTemperatureFvPatchScalarField& neighbour,
     const chtRegionCoupleBase& ownerK
 ) const
 {
-    if(debug)
+    if (debug)
     {
-        Info << "In chtRcThermalDiffusivityFvPatchScalarField::calcTemperature on "
-            << this->dimensionedInternalField().name()
+        InfoIn
+        (
+            "chtRcThermalDiffusivityFvPatchScalarField::calcTemperature"
+        )   << "for field " << this->dimensionedInternalField().name()
             << " in " << this->patch().boundaryMesh().mesh().name()
             << endl;
     }
@@ -280,19 +270,19 @@ chtRcThermalDiffusivityFvPatchScalarField::calcTemperature
         scalarField lTcNei =
             TwOwn.shadowPatchField().patchInternalField();
 
-        forAll(lData, facei)
+        forAll (lData, facei)
         {
             lData[facei][0] = lTcNei[facei];
             lData[facei][1] = lfNei[facei];
         }
 
-        if(TwOwn.shadowPatchField().radiation())
+        if (TwOwn.shadowPatchField().radiation())
         {
             const scalarField& lTwNei = TwOwn.shadowPatchField();
             const scalarField& lQrNei =
                 TwOwn.lookupShadowPatchField<volScalarField, scalar>("Qr");
 
-            forAll(lData, facei)
+            forAll (lData, facei)
             {
                 lData[facei][2] = lTwNei[facei];
                 lData[facei][3] = lQrNei[facei];
@@ -302,15 +292,15 @@ chtRcThermalDiffusivityFvPatchScalarField::calcTemperature
         const Field<VectorN<scalar, 4> > iData =
             TwOwn.regionCouplePatch().interpolate(lData);
 
-        forAll(iData, facei)
+        forAll (iData, facei)
         {
             TcNei[facei] = iData[facei][0];
             fNei[facei] = iData[facei][1];
         }
 
-        if(TwOwn.shadowPatchField().radiation())
+        if (TwOwn.shadowPatchField().radiation())
         {
-            forAll(iData, facei)
+            forAll (iData, facei)
             {
                 fourQro[facei] +=
                     4.0*radiation::sigmaSB.value()*pow4(iData[facei][2]);
@@ -322,29 +312,15 @@ chtRcThermalDiffusivityFvPatchScalarField::calcTemperature
     const scalarField kOwn = fOwn/(1.0 - p.weights())/mld.magDelta(p.index());
     const scalarField kNei = fNei/p.weights()/mld.magDelta(p.index());
 
-    //Info << "kOwn = " << kOwn << endl;
-    //Info << "kNei = " << kNei << endl;
-    //Info << "TcOwn = " << TcOwn << endl;
-    //Info << "TcNei = " << TcNei << endl;
-    //Info << "Qr = " << Qr << " Sum = " << sum(Qr*p.magSf()) << endl;
-
     TwOwn *=
         (fourQro + Qr + kOwn*TcOwn + kNei*TcNei)
        /(TwOwn*(kOwn + kNei) + fourQro);
 
-    //Info << "TwOwn = " << TwOwn << endl;
-
-    //scalarField q1 = (TwOwn - TcOwn)*kOwn;
-    //Info << "q1 = " << q1 << " Sum = " << sum(q1*p.magSf()) << endl;
-
-    //scalarField q2 = (TcNei - TcOwn)*ownerK*p.deltaCoeffs();
-    //Info << "q2 = " << q2 << " Sum = " << sum(q2*p.magSf()) << endl;
-
     TwOwn.fvPatchScalarField::updateCoeffs();
 }
 
 
-void chtRcThermalDiffusivityFvPatchScalarField::write(Ostream& os) const
+void Foam::chtRcThermalDiffusivityFvPatchScalarField::write(Ostream& os) const
 {
     fvPatchScalarField::write(os);
     os.writeKeyword("remoteField")
@@ -353,19 +329,18 @@ void chtRcThermalDiffusivityFvPatchScalarField::write(Ostream& os) const
 }
 
 
-//- Specify data associated with VectorN<scalar, 4> type is contiguous
-template<>
-inline bool contiguous<VectorN<scalar, 4> >() {return true;}
-
-
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
-makePatchTypeField
-(
-    fvPatchScalarField,
-    chtRcThermalDiffusivityFvPatchScalarField
-);
+namespace Foam
+{
+
+    makePatchTypeField
+    (
+        fvPatchScalarField,
+        chtRcThermalDiffusivityFvPatchScalarField
+    );
 
 } // End namespace Foam
 
+
 // ************************************************************************* //

src/conjugateHeatTransfer/fvPatchFields/chtRcThermalDiffusivity/chtRcThermalDiffusivityFvPatchScalarField.H

@@ -25,10 +25,12 @@ Class
     chtRcThermalDiffusivityFvPatchScalarField
 
 Description
-    Region couple patch field taking radiation into account
+    Diffusivity for the region couple patch field taking radiation into account
+    Master side
 
 Author
     Henrik Rusche, Wikki GmbH.  All rights reserved
+    Cleaned up by Hrvoje Jasak
 
 SourceFiles
     chtRcThermalDiffusivityFvPatchScalarField.C
@@ -46,16 +48,13 @@ namespace Foam
 {
 
 /*---------------------------------------------------------------------------*\
-        Class chtRcThermalDiffusivityFvPatchScalarField Declaration
+          Class chtRcThermalDiffusivityFvPatchScalarField Declaration
 \*---------------------------------------------------------------------------*/
 
 class chtRcThermalDiffusivityFvPatchScalarField
 :
     public chtRegionCoupleBase
 {
-    // Private data
-
-
 public:
 
     //- Runtime type information
@@ -79,7 +78,8 @@ public:
             const dictionary&
         );
 
-        //- Construct by mapping given chtRcThermalDiffusivityFvPatchScalarField onto a new patch
+        //- Construct by mapping given
+        //  chtRcThermalDiffusivityFvPatchScalarField onto a new patch
         chtRcThermalDiffusivityFvPatchScalarField
         (
             const chtRcThermalDiffusivityFvPatchScalarField&,
@@ -119,9 +119,6 @@ public:
 
     // Member functions
 
-        // Access
-
-
         // Evaluation functions
 
             //- Evaluate the patch field
@@ -148,7 +145,6 @@ public:
 
         //- Write
         virtual void write(Ostream&) const;
-
 };
 
 

src/conjugateHeatTransfer/fvPatchFields/chtRcThermalDiffusivitySlave/chtRcThermalDiffusivitySlaveFvPatchScalarField.C

@@ -31,14 +31,10 @@ Author
 #include "fvPatchFieldMapper.H"
 #include "volFields.H"
 
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-namespace Foam
-{
-
 // * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
 
-chtRcThermalDiffusivitySlaveFvPatchScalarField::chtRcThermalDiffusivitySlaveFvPatchScalarField
+Foam::chtRcThermalDiffusivitySlaveFvPatchScalarField::
+chtRcThermalDiffusivitySlaveFvPatchScalarField
 (
     const fvPatch& p,
     const DimensionedField<scalar, volMesh>& iF
@@ -48,7 +44,8 @@ chtRcThermalDiffusivitySlaveFvPatchScalarField::chtRcThermalDiffusivitySlaveFvPa
 {}
 
 
-chtRcThermalDiffusivitySlaveFvPatchScalarField::chtRcThermalDiffusivitySlaveFvPatchScalarField
+Foam::chtRcThermalDiffusivitySlaveFvPatchScalarField::
+chtRcThermalDiffusivitySlaveFvPatchScalarField
 (
     const fvPatch& p,
     const DimensionedField<scalar, volMesh>& iF,
@@ -59,7 +56,19 @@ chtRcThermalDiffusivitySlaveFvPatchScalarField::chtRcThermalDiffusivitySlaveFvPa
 {}
 
 
-chtRcThermalDiffusivitySlaveFvPatchScalarField::chtRcThermalDiffusivitySlaveFvPatchScalarField
+Foam::chtRcThermalDiffusivitySlaveFvPatchScalarField::
+chtRcThermalDiffusivitySlaveFvPatchScalarField
+(
+    const chtRcThermalDiffusivitySlaveFvPatchScalarField& ptf,
+    const DimensionedField<scalar, volMesh>& iF
+)
+:
+    chtRegionCoupleBase(ptf, iF)
+{}
+
+
+Foam::chtRcThermalDiffusivitySlaveFvPatchScalarField::
+chtRcThermalDiffusivitySlaveFvPatchScalarField
 (
     const chtRcThermalDiffusivitySlaveFvPatchScalarField& ptf,
     const fvPatch& p,
@@ -71,20 +80,10 @@ chtRcThermalDiffusivitySlaveFvPatchScalarField::chtRcThermalDiffusivitySlaveFvPa
 {}
 
 
-chtRcThermalDiffusivitySlaveFvPatchScalarField::chtRcThermalDiffusivitySlaveFvPatchScalarField
-(
-    const chtRcThermalDiffusivitySlaveFvPatchScalarField& ptf,
-    const DimensionedField<scalar, volMesh>& iF
-)
-:
-    chtRegionCoupleBase(ptf, iF)
-{}
-
-
 // * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
 
-const chtRegionCoupleBase&
-chtRcThermalDiffusivitySlaveFvPatchScalarField::shadowPatchField() const
+const Foam::chtRegionCoupleBase&
+Foam::chtRcThermalDiffusivitySlaveFvPatchScalarField::shadowPatchField() const
 {
     return dynamic_cast<const chtRegionCoupleBase&>
     (
@@ -93,7 +92,7 @@ chtRcThermalDiffusivitySlaveFvPatchScalarField::shadowPatchField() const
 }
 
 
-void chtRcThermalDiffusivitySlaveFvPatchScalarField::evaluate
+void Foam::chtRcThermalDiffusivitySlaveFvPatchScalarField::evaluate
 (
     const Pstream::commsTypes
 )
@@ -102,7 +101,7 @@ void chtRcThermalDiffusivitySlaveFvPatchScalarField::evaluate
 }
 
 
-void chtRcThermalDiffusivitySlaveFvPatchScalarField::updateCoeffs()
+void Foam::chtRcThermalDiffusivitySlaveFvPatchScalarField::updateCoeffs()
 {
     if (updated())
     {
@@ -115,12 +114,16 @@ void chtRcThermalDiffusivitySlaveFvPatchScalarField::updateCoeffs()
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
-makePatchTypeField
-(
-    fvPatchScalarField,
-    chtRcThermalDiffusivitySlaveFvPatchScalarField
-);
+namespace Foam
+{
+
+    makePatchTypeField
+    (
+        fvPatchScalarField,
+        chtRcThermalDiffusivitySlaveFvPatchScalarField
+    );
 
 } // End namespace Foam
 
+
 // ************************************************************************* //

src/conjugateHeatTransfer/fvPatchFields/chtRcThermalDiffusivitySlave/chtRcThermalDiffusivitySlaveFvPatchScalarField.H

@@ -25,10 +25,12 @@ Class
     chtRcThermalDiffusivitySlaveFvPatchScalarField
 
 Description
-    Region couple patch field taking radiation into account
+    Diffusivity for the region couple patch field taking radiation into account
+    Slave side
 
 Author
     Henrik Rusche, Wikki GmbH.  All rights reserved
+    Cleaned up by Hrvoje Jasak
 
 SourceFiles
     chtRcThermalDiffusivitySlaveFvPatchScalarField.C
@@ -49,15 +51,13 @@ class chtThermalDiffusivityRegionCoupleFvPatchScalarField;
 class chtTemperatureRegionCoupleFvPatchScalarField;
 
 /*---------------------------------------------------------------------------*\
-                  Class chtRcThermalDiffusivitySlaveFvPatchScalarField Declaration
+        Class chtRcThermalDiffusivitySlaveFvPatchScalarField Declaration
 \*---------------------------------------------------------------------------*/
 
 class chtRcThermalDiffusivitySlaveFvPatchScalarField
 :
     public chtRegionCoupleBase
 {
-    // Private data
-
 public:
 
     //- Runtime type information
@@ -81,7 +81,8 @@ public:
             const dictionary&
         );
 
-        //- Construct by mapping given chtRcThermalDiffusivitySlaveFvPatchScalarField onto a new patch
+        //- Construct by mapping given
+        //  chtRcThermalDiffusivitySlaveFvPatchScalarField onto a new patch
         chtRcThermalDiffusivitySlaveFvPatchScalarField
         (
             const chtRcThermalDiffusivitySlaveFvPatchScalarField&,