Merge branch 'master' of ssh://noisy/home/noisy3/OpenFOAM/OpenFOAM-dev

applications/solvers/compressible/rhoSimplecFoam/UEqn.H

-    // Solve the Momentum equation
-
-    tmp<fvVectorMatrix> UEqn
-    (
-        fvm::div(phi, U)
-      + turbulence->divDevRhoReff(U)
-    );
-
-    UEqn().relax();
-
-    solve(UEqn() == -fvc::grad(p));

applications/solvers/compressible/rhoSimplecFoam/hEqn.H

-{
-    fvScalarMatrix hEqn
-    (
-        fvm::div(phi, h)
-      - fvm::Sp(fvc::div(phi), h)
-      - fvm::laplacian(turbulence->alphaEff(), h)
-     ==
-        fvc::div(phi/fvc::interpolate(rho)*fvc::interpolate(p, "div(U,p)"))
-      - p*fvc::div(phi/fvc::interpolate(rho))
-    );
-
-    hEqn.relax();
-
-    hEqn.solve();
-
-    thermo.correct();
-
-    rho = thermo.rho();
-
-    if (!transonic)
-    {
-        rho.relax();
-    }
-
-    Info<< "rho max/min : "
-        << max(rho).value() << " "
-        << min(rho).value() << endl;
-}

applications/solvers/compressible/rhoSimplecFoam/pEqn.H

+rho = thermo.rho();
+rho = max(rho, rhoMin);
+rho = min(rho, rhoMax);
+rho.relax();
+
 volScalarField p0 = p;
 
 volScalarField AU = UEqn().A();
@@ -24,8 +29,8 @@ if (transonic)
           + phid*(fvc::interpolate(p) - fvc::interpolate(p, "UD"))
         );
 
-        refCast<mixedFvPatchScalarField>(p.boundaryField()[1]).refValue()
-            = p.boundaryField()[1];
+        //refCast<mixedFvPatchScalarField>(p.boundaryField()[1]).refValue()
+        //    = p.boundaryField()[1];
 
         fvScalarMatrix pEqn
         (
@@ -35,6 +40,7 @@ if (transonic)
           + fvc::div(phid)*p
           - fvm::laplacian(rho/AtU, p)
         );
+        //pEqn.relax();
 
         pEqn.setReference(pRefCell, pRefValue);
 

applications/solvers/compressible/rhoSimplecFoam/rhoSimplecFoam.C

@@ -57,6 +57,7 @@ int main(int argc, char *argv[])
         #include "readSIMPLEControls.H"
 
         p.storePrevIter();
+        rho.storePrevIter();
 
         if (!transonic)
         {

applications/test/memInfo/Make/files

+memInfo.C
+
+EXE = $(FOAM_USER_APPBIN)/memInfo

applications/test/memInfo/memInfo.C

+#include "memInfo.H"
+#include "IOstreams.H"
+#include "List.H"
+#include "vector.H"
+
+using namespace Foam;
+
+int main()
+{
+    memInfo m;
+
+    Info<< m << endl;
+
+    List<vector> l(10000000, vector::one);
+
+    Info<< m.update() << endl;
+
+    return 0;
+}

applications/utilities/parallelProcessing/reconstructPar/reconstructPar.C

@@ -56,6 +56,14 @@ int main(int argc, char *argv[])
         "specify a list of fields to be reconstructed. Eg, '(U T p)' - "
         "regular expressions not currently supported"
     );
+    argList::addOption
+    (
+        "lagrangianFields",
+        "list",
+        "specify a list of lagrangian fields to be reconstructed. Eg, '(U d)' -"
+        "regular expressions not currently supported, "
+        "positions always included."
+    );
     argList::addBoolOption
     (
         "noLagrangian",
@@ -73,6 +81,20 @@ int main(int argc, char *argv[])
 
     const bool noLagrangian = args.optionFound("noLagrangian");
 
+    HashSet<word> selectedLagrangianFields;
+    if (args.optionFound("lagrangianFields"))
+    {
+        if (noLagrangian)
+        {
+            FatalErrorIn(args.executable())
+                << "Cannot specify noLagrangian and lagrangianFields "
+                << "options together."
+                << exit(FatalError);
+        }
+
+        args.optionLookup("lagrangianFields")() >> selectedLagrangianFields;
+    }
+
     // determine the processor count directly
     label nProcs = 0;
     while (isDir(args.path()/(word("processor") + name(nProcs))))
@@ -403,84 +425,96 @@ int main(int argc, char *argv[])
                         cloudName,
                         mesh,
                         procMeshes.meshes(),
-                        sprayObjs
+                        sprayObjs,
+                        selectedLagrangianFields
                     );
                     reconstructLagrangianFieldFields<label>
                     (
                         cloudName,
                         mesh,
                         procMeshes.meshes(),
-                        sprayObjs
+                        sprayObjs,
+                        selectedLagrangianFields
                     );
                     reconstructLagrangianFields<scalar>
                     (
                         cloudName,
                         mesh,
                         procMeshes.meshes(),
-                        sprayObjs
+                        sprayObjs,
+                        selectedLagrangianFields
                     );
                     reconstructLagrangianFieldFields<scalar>
                     (
                         cloudName,
                         mesh,
                         procMeshes.meshes(),
-                        sprayObjs
+                        sprayObjs,
+                        selectedLagrangianFields
                     );
                     reconstructLagrangianFields<vector>
                     (
                         cloudName,
                         mesh,
                         procMeshes.meshes(),
-                        sprayObjs
+                        sprayObjs,
+                        selectedLagrangianFields
                     );
                     reconstructLagrangianFieldFields<vector>
                     (
                         cloudName,
                         mesh,
                         procMeshes.meshes(),
-                        sprayObjs
+                        sprayObjs,
+                        selectedLagrangianFields
                     );
                     reconstructLagrangianFields<sphericalTensor>
                     (
                         cloudName,
                         mesh,
                         procMeshes.meshes(),
-                        sprayObjs
+                        sprayObjs,
+                        selectedLagrangianFields
                     );
                     reconstructLagrangianFieldFields<sphericalTensor>
                     (
                         cloudName,
                         mesh,
                         procMeshes.meshes(),
-                        sprayObjs
+                        sprayObjs,
+                        selectedLagrangianFields
                     );
                     reconstructLagrangianFields<symmTensor>
                     (
                         cloudName,
                         mesh,
                         procMeshes.meshes(),
-                        sprayObjs
+                        sprayObjs,
+                        selectedLagrangianFields
                     );
                     reconstructLagrangianFieldFields<symmTensor>
                     (
                         cloudName,
                         mesh,
                         procMeshes.meshes(),
-                        sprayObjs
+                        sprayObjs,
+                        selectedLagrangianFields
                     );
                     reconstructLagrangianFields<tensor>
                     (
                         cloudName,
                         mesh,
                         procMeshes.meshes(),
-                        sprayObjs
+                        sprayObjs,
+                        selectedLagrangianFields
                     );
                     reconstructLagrangianFieldFields<tensor>
                     (
                         cloudName,
                         mesh,
                         procMeshes.meshes(),
-                        sprayObjs
+                        sprayObjs,
+                        selectedLagrangianFields
                     );
                 }
             }

bin/foamJob

@@ -188,12 +188,12 @@ then
     fi
     mpiopts="-np $NPROCS"
 
-    # 
+    #
     # is the machine ready to run parallel?
     #
     echo "Parallel processing using $WM_MPLIB with $NPROCS processors"
     case "$WM_MPLIB" in
-    OPENMPI)
+    *OPENMPI)
         # add hostfile info
         for hostfile in \
             hostfile \

bin/mpirunDebug

@@ -221,7 +221,7 @@ done
 unset cmd
 
 case "$WM_MPLIB" in
-OPENMPI)
+*OPENMPI)
     cmd="mpirun -app $PWD/mpirun.schema </dev/null"
     ;;
 MPICH)

bin/tools/pre-commit-hook

@@ -146,13 +146,20 @@ checkIllegalCode()
     badFiles=$(
     for f in $fileList
     do
-        # parse line numbers from grep output:
-        #        <lineNr>:   contents
-        lines=$(git grep -E -hn -e "$reBad" $scope"$f" |
-            sed -e 's@:.*@@' |
-            tr '\n' ' '
-        )
-        [ -n "$lines" ] && echo "$Indent$f -- lines: $lines"
+        case "$f" in
+        # exclude potential makefiles
+        (wmake/[Mm]akefile* | wmake/rules/*)
+        ;;
+        (*)
+            # parse line numbers from grep output:
+            #        <lineNr>:   contents
+            lines=$(git grep -E -hn -e "$reBad" $scope"$f" |
+                sed -e 's@:.*@@' |
+                tr '\n' ' '
+            )
+            [ -n "$lines" ] && echo "$Indent$f -- lines: $lines"
+        ;;
+        esac
     done
     )
 
@@ -243,7 +250,7 @@ checkLineLengthNonComments()
             # parse line numbers from grep output:
             #        <lineNr>:   contents
             lines=$(git grep -hn -e '^.\{81,\}' \
-                --and --not -e "^ *//" \
+                --and --not -e '^ *//' \
                 $scope"$f" |
                 sed -e 's@:.*@@' |
                 tr '\n' ' '
@@ -276,7 +283,7 @@ checkLineLengthNonDirective()
             # parse line numbers from grep output:
             #        <lineNr>:   contents
             lines=$(git grep -hn -e '^.\{81,\}' \
-                --and --not -e "^ *#" \
+                --and --not -e '^ *#' \
                 $scope"$f" |
                 sed -e 's@:.*@@' |
                 tr '\n' ' '

bin/tools/pre-receive-hook

@@ -109,13 +109,20 @@ checkIllegalCode()
     badFiles=$(
     for f in $fileList
     do
-        # parse line numbers from grep output:
-        #        <lineNr>:   contents
-        lines=$(git grep -E -hn -e "$reBad" $scope"$f" |
-            sed -e 's@:.*@@' |
-            tr '\n' ' '
-        )
-        [ -n "$lines" ] && echo "$Indent$f -- lines: $lines"
+        case "$f" in
+        # exclude potential makefiles
+        (wmake/[Mm]akefile* | wmake/rules/*)
+        ;;
+        (*)
+            # parse line numbers from grep output:
+            #        <lineNr>:   contents
+            lines=$(git grep -E -hn -e "$reBad" $scope"$f" |
+                sed -e 's@:.*@@' |
+                tr '\n' ' '
+            )
+            [ -n "$lines" ] && echo "$Indent$f -- lines: $lines"
+        ;;
+        esac
     done
     )
 
@@ -206,7 +213,7 @@ checkLineLengthNonComments()
             # parse line numbers from grep output:
             #        <lineNr>:   contents
             lines=$(git grep -hn -e '^.\{81,\}' \
-                --and --not -e "^ *//" \
+                --and --not -e '^ *//' \
                 $scope"$f" |
                 sed -e 's@:.*@@' |
                 tr '\n' ' '
@@ -239,7 +246,7 @@ checkLineLengthNonDirective()
             # parse line numbers from grep output:
             #        <lineNr>:   contents
             lines=$(git grep -hn -e '^.\{81,\}' \
-                --and --not -e "^ *#" \
+                --and --not -e '^ *#' \
                 $scope"$f" |
                 sed -e 's@:.*@@' |
                 tr '\n' ' '

doc/changes/inotify.txt

@@ -24,21 +24,63 @@ be quite a gain on large numbers of processors.
 
 
 - all file monitoring is done by an instance of 'fileMonitor' in the Time
-class. The fileMonitor class can be found in OSspecific. Default is
-to use the (linux-specific) 'inotify' system calls.
-If compiled with -DFOAM_USE_STAT it will revert to the current 'stat' system
-calls.
+class. The fileMonitor class can be found in OSspecific. It uses either
+timestamps as before or the (linux-specific) 'inotify' system framework
+(available only if compiled with -DFOAM_USE_INOTIFY).
 
 
-- inotify does not need timestamps. There is no need for fileModificationSkew
-to allow for time differences. (there can still temporarily be a difference
-in modified status between different processors due to nfs lagging)
+- the monitoring can be done in one of four modes as set by
+    OptimisationSwitches::fileModificationChecking
+
+    - timeStamp : old behaviour : all nodes check the timestamp
+    - inotify   : using inotify instead of timestamps
+    - timeStampMaster,inotifyMaster : only the master node checks the file
+                and only the master node reads it and distribute it to the
+                slaves. This makes runTimeModifiable possible on distributed
+                running (see below).
+
+- distributed running:
+    - set fileModificationChecking to e.g. timeStampMaster
+    - decompose a case, e.g. cavity
+    - copy system and constant to processor0/
+    - put the all the processor* directories on the wanted nodes inside
+      the case directory. E.g.
+        - on master have /tmp/cavity/processor0
+        - on slaveN have /tmp/cavity/processorN
+    - so to reiterate:
+        - there is no need for cavity/constant or cavity/system, all the
+          dictionaries are only in processor0/constant or processor0/system
+        - the slave processor directories have no system directory and the
+          constant directory only contains the mesh.
+    - start the job in distributed mode by specifying the slave roots
+      (so one less than the number of processors) with
+      the -roots command line option:
+
+        mpirun -np 2 icoFoam -roots '("/tmp")' -parallel
+
+    - the alternative to the -roots option is to have a
+      cavity/system/decomposeParDict on the master with
+            distributed     yes;
+            roots           ("/tmp");
 
 
+Details:
+- timeStampMaster, inotifyMaster : this works only for IOdictionaries that
+are READ_IF_MODIFIED. It means that slaves read exactly the same dictionary
+as the master so cannot be used for dictionaries that contain e.g. mesh
+specific information.
+
+- inotify is a monitoring framework used to monitor changes in
+lots of files (e.g. used in desktop searched like beagle). You specify
+files to monitor and then get warned for any changes to these files.
+It does not need timestamps. There is no need for fileModificationSkew
+to allow for time differences. (there can still temporarily be a difference
+in modified status between different processors due to nfs lagging). The big
+problem is that it does not work over nfs3 (not sure about nfs4).
+
 - fileMonitor stores two hashtables per file so there is a small overhead
 adding and removing files from monitoring.
 
-
 - if runTimeModifiable is false at start of run no files will get monitored,
 however if runTimeModified gets set to false during the run the files
 will still get monitored (though never reloaded). This is only a hypothetical
@@ -46,7 +88,6 @@ problem in that the kernel still stores events for the monitored files. However
 inotify is very efficient - e.g. it gets used to track changes on file systems
 for desktop search engines.
 
-
 - in the old system one could call modified() on any object and get
 and uptodate state. In the new system it will return the state from
 the last runTime++ (which if it triggered any re-reads will have reset the

etc/controlDict

@@ -872,6 +872,14 @@ InfoSwitches
 OptimisationSwitches
 {
     fileModificationSkew 10;
+
+    //- Modification checking:
+    //  - timeStamp         : use modification time on file
+    //  - inotify           : use inotify framework
+    //  - timeStampMaster   : do time stamp (and file reading) only on master.
+    //  - inotifyMaster     : do inotify (and file reading) only on master.
+    fileModificationChecking timeStampMaster;//inotify;timeStamp;inotifyMaster;
+
     commsType       nonBlocking; //scheduled; //blocking;
     floatTransfer   0;
     nProcsSimpleSum 0;

etc/settings.csh

@@ -90,17 +90,20 @@ switch ("$compilerInstall")
 case OpenFOAM:
     switch ("$WM_COMPILER")
     case Gcc:
+    case Gcc++0x:
         set gcc_version=gcc-4.4.3
         set gmp_version=gmp-5.0.1
         set mpfr_version=mpfr-2.4.2
         breaksw
     case Gcc45:
+    case Gcc45++0x:
         set gcc_version=gcc-4.5.0
         set gmp_version=gmp-5.0.1
         set mpfr_version=mpfr-2.4.2
         set mpc_version=mpc-0.8.1
         breaksw
     case Gcc44:
+    case Gcc44++0x:
         set gcc_version=gcc-4.4.3
         set gmp_version=gmp-5.0.1
         set mpfr_version=mpfr-2.4.2
@@ -190,6 +193,18 @@ case OpenFOAM:
 endsw
 
 
+#
+# add c++0x flags for external programs
+#
+if ( $?WM_CXXFLAGS ) then
+    switch ("$WM_COMPILER")
+    case Gcc*++0x:
+        setenv WM_CXXFLAGS "$WM_CXXFLAGS -std=c++0x"
+        breaksw
+    endsw
+endif
+
+
 # boost and CGAL
 # ~~~~~~~~~~~~~~
 
@@ -236,9 +251,7 @@ case OPENMPI:
     breaksw
 
 case SYSTEMOPENMPI:
-
-    # This uses the installed openmpi. It needs mpicc installed!
-
+    # Use the system installed openmpi, get library directory via mpicc
     set mpi_version=openmpi-system
 
     # Set compilation flags here instead of in wmake/rules/../mplibSYSTEMOPENMPI

etc/settings.sh

@@ -111,18 +111,18 @@ unset MPFR_ARCH_PATH
 case "${compilerInstall:-OpenFOAM}" in
 OpenFOAM)
     case "$WM_COMPILER" in
-    Gcc)
+    Gcc | Gcc++0x)
         gcc_version=gcc-4.4.3
         gmp_version=gmp-5.0.1
         mpfr_version=mpfr-2.4.2
         ;;
-    Gcc45)
+    Gcc45 | Gcc45++0x)
         gcc_version=gcc-4.5.0
         gmp_version=gmp-5.0.1
         mpfr_version=mpfr-2.4.2
         mpc_version=mpc-0.8.1
         ;;
-    Gcc44)
+    Gcc44 | Gcc44++0x)
         gcc_version=gcc-4.4.3
         gmp_version=gmp-5.0.1
         mpfr_version=mpfr-2.4.2
@@ -213,6 +213,19 @@ OpenFOAM)
 esac
 
 
+#
+# add c++0x flags for external programs
+#
+if [ -n "$WM_CXXFLAGS" ]
+then
+    case "$WM_COMPILER" in
+    Gcc*++0x)
+        WM_CXXFLAGS="$WM_CXXFLAGS -std=c++0x"
+        ;;
+    esac
+fi
+
+
 # boost and CGAL
 # ~~~~~~~~~~~~~~
 
@@ -261,7 +274,7 @@ OPENMPI)
     ;;
 
 SYSTEMOPENMPI)
-    # use the system installed openmpi, get library directory via mpicc
+    # Use the system installed openmpi, get library directory via mpicc
     mpi_version=openmpi-system
 
     # Set compilation flags here instead of in wmake/rules/../mplibSYSTEMOPENMPI

src/OSspecific/POSIX/Allwmake

@@ -12,9 +12,9 @@ unset COMP_FLAGS LINK_FLAGS
 if [ -f /usr/include/sys/inotify.h -a "${1%USE_STAT}" = "$1" ]
 then
     echo "Found <sys/inotify.h>  --  using inotify for file monitoring."
-    unset COMP_FLAGS
+    export COMP_FLAGS="-DFOAM_USE_INOTIFY"
 else
-    export COMP_FLAGS="-DFOAM_USE_STAT"
+    unset COMP_FLAGS
 fi
 
 

src/OSspecific/POSIX/Make/files

@@ -8,6 +8,7 @@ fileStat.C
 POSIX.C
 cpuTime/cpuTime.C
 clockTime/clockTime.C
+memInfo/memInfo.C
 
 /*
  * Note: fileMonitor assumes inotify by default. Compile with -DFOAM_USE_STAT

src/OSspecific/POSIX/POSIX.C

@@ -36,6 +36,7 @@ Description
 #include "fileName.H"
 #include "fileStat.H"
 #include "timer.H"
+#include "IFstream.H"
 
 #include <fstream>
 #include <cstdlib>

src/OSspecific/POSIX/clockTime/clockTime.C

@@ -24,38 +24,25 @@ License
 \*---------------------------------------------------------------------------*/
 
 #include "clockTime.H"
-#include "scalar.H"
 #include <sys/time.h>
 
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-namespace Foam
-{
-
-// * * * * * * * * * * * * * * * Static Members  * * * * * * * * * * * * * * //
-
-
 // * * * * * * * * * * * * * Private Member Functions  * * * * * * * * * * * //
 
-void clockTime::getTime(struct timeval& t)
+void Foam::clockTime::getTime(timeType& t)
 {
-    gettimeofday(&t, NULL);
+    gettimeofday(&t, 0);
 }
 
 
-double clockTime::timeDifference
-(
-    const struct timeval& start,
-    const struct timeval& end