Merge branch 'master' of /home/noisy3/OpenFOAM/OpenFOAM-dev

.gitignore

@@ -60,6 +60,8 @@ doc/[Dd]oxygen/man
 # untracked configuration files
 /etc/prefs.csh
 /etc/prefs.sh
+/etc/config/*.csh
+/etc/config/*.sh
 
 # source packages - anywhere
 *.tar.bz2

applications/utilities/miscellaneous/expandDictionary/expandDictionary.C

@@ -2,7 +2,7 @@
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 2004-2010 OpenCFD Ltd.
+    \\  /    A nd           | Copyright (C) 2008-2011 OpenCFD Ltd.
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -28,12 +28,33 @@ Description
     Read the dictionary provided as an argument, expand the macros etc. and
     write the resulting dictionary to standard output.
 
+Usage
+    - expandDictionary inputDict [OPTION]
+
+    \param -list \n
+    Report the #include/#includeIfPresent to stdout only.
+
+Note
+    The \c -list option can be useful when determining which files
+    are actually included by a directory. It can also be used to
+    determine which files may need to be copied when transferring
+    simulation to another environment. The following code snippet
+    could be a useful basis for such cases:
+
+    \verbatim
+        for i in . 0 constant system
+        do
+            find $i -maxdepth 1 -type f -exec expandDictionary -list '{}' \;
+        done | sed -ne '/^"\//!{ s/^"//; s/"$//; p }' | sort | uniq
+    \endverbatim
+
 \*---------------------------------------------------------------------------*/
 
 #include "argList.H"
 #include "IFstream.H"
 #include "IOobject.H"
 #include "dictionary.H"
+#include "includeEntry.H"
 
 using namespace Foam;
 
@@ -48,6 +69,12 @@ int main(int argc, char *argv[])
         "the resulting dictionary to standard output."
     );
 
+    argList::addBoolOption
+    (
+        "list",
+        "Report the #include/#includeIfPresent to stdout only"
+    );
+
     argList::noBanner();
     argList::noParallel();
     argList::validArgs.append("inputDict");
@@ -55,12 +82,22 @@ int main(int argc, char *argv[])
 
     const string dictName = args[1];
 
-    IOobject::writeBanner(Info)
-        <<"//\n// " << dictName << "\n//\n";
+    const bool listOpt = args.optionFound("list");
+
+    if (listOpt)
+    {
+        Foam::functionEntries::includeEntry::report = true;
+    }
 
-    dictionary(IFstream(dictName)(), true).write(Info, false);
+    dictionary dict(IFstream(dictName)(), true);
 
-    IOobject::writeDivider(Info);
+    if (!listOpt)
+    {
+        IOobject::writeBanner(Info)
+            <<"//\n// " << dictName << "\n//\n";
+        dict.write(Info, false);
+        IOobject::writeDivider(Info);
+    }
 
     return 0;
 }

applications/utilities/surface/surfaceMeshInfo/Make/files

+surfaceMeshInfo.C
+
+EXE = $(FOAM_APPBIN)/surfaceMeshInfo

applications/utilities/surface/surfaceMeshInfo/Make/options

+EXE_INC = \
+    -I$(LIB_SRC)/meshTools/lnInclude \
+    -I$(LIB_SRC)/surfMesh/lnInclude
+
+EXE_LIBS = -lmeshTools -lsurfMesh

applications/utilities/surface/surfaceMeshInfo/surfaceMeshInfo.C

+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 2011-2011 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 3 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, see <http://www.gnu.org/licenses/>.
+
+Application
+    surfaceMeshInfo
+
+Description
+    Miscellaneous information about surface meshes
+
+Usage
+    - surfaceMeshInfo surfaceFile [OPTION]
+
+    \param -areas \n
+    Report area for each face.
+
+    \param -scale \<scale\> \n
+    Specify a scaling factor when reading files.
+
+    \param -xml \n
+    Write output in XML format.
+
+Note
+    The filename extensions are used to determine the file format type.
+
+    The XML-like output can be useful for extraction with other tools,
+    but either output format can be easily extracted with a simple sed
+    command:
+    \verbatim
+        surfaceMeshInfo surfaceFile -areas | \
+            sed -ne '/areas/,/:/{ /:/!p }'
+
+        surfaceMeshInfo surfaceFile -areas -xml | \
+            sed -ne '/<areas/,/</{ /</!p }'
+    \endverbatim
+
+\*---------------------------------------------------------------------------*/
+
+#include "argList.H"
+#include "timeSelector.H"
+#include "Time.H"
+
+#include "UnsortedMeshedSurfaces.H"
+
+using namespace Foam;
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+//  Main program:
+
+int main(int argc, char *argv[])
+{
+    argList::addNote
+    (
+        "information about surface meshes"
+    );
+
+    argList::noBanner();
+    argList::noParallel();
+    argList::validArgs.append("surfaceFile");
+
+    argList::addOption
+    (
+        "scale",
+        "factor",
+        "geometry scaling factor - default is 1"
+    );
+    argList::addBoolOption
+    (
+        "areas",
+        "display area of each face"
+    );
+    argList::addBoolOption
+    (
+        "xml",
+        "write output in XML format"
+    );
+
+    argList args(argc, argv);
+    Time runTime(args.rootPath(), args.caseName());
+
+    const fileName importName = args[1];
+
+    // check that reading is supported
+    if (!UnsortedMeshedSurface<face>::canRead(importName, true))
+    {
+        return 1;
+    }
+
+    const bool writeXML = args.optionFound("xml");
+    const bool writeAreas = args.optionFound("areas");
+
+
+    // use UnsortedMeshedSurface, not MeshedSurface to maintain ordering
+    UnsortedMeshedSurface<face> surf(importName);
+
+    scalar scaling = 0;
+    if (args.optionReadIfPresent("scale", scaling) && scaling > 0)
+    {
+        Info<< " -scale " << scaling << endl;
+        surf.scalePoints(scaling);
+    }
+
+    scalar areaTotal = 0;
+
+    if (writeXML)
+    {
+        Info<<"<?xml version='1.0' encoding='utf-8'?>" << nl
+            <<"<surfaceMeshInfo>" << nl
+            << "<npoints>" << surf.nPoints() << "</npoints>" << nl
+            << "<nfaces>"  << surf.size() << "</nfaces>" << nl;
+
+        if (writeAreas)
+        {
+            Info<<"<areas size='" << surf.size() << "'>" << nl;
+        }
+    }
+    else
+    {
+        Info<< "nPoints   : " << surf.nPoints() << nl
+            << "nFaces    : " << surf.size() << nl;
+
+        if (writeAreas)
+        {
+            Info<< "areas     : " << nl;
+        }
+    }
+
+    forAll(surf, faceI)
+    {
+        const scalar fArea(surf[faceI].mag(surf.points()));
+        areaTotal += fArea;
+
+        if (writeAreas)
+        {
+            Info<< fArea << nl;
+        }
+    }
+
+    if (writeXML)
+    {
+        if (writeAreas)
+        {
+            Info<<"</areas>" << nl;
+        }
+
+        Info<< "<area>" << areaTotal << "</area>" << nl
+            << "</surfaceMeshInfo>" << nl;
+    }
+    else
+    {
+        Info<< "area      : " << areaTotal << nl;
+    }
+
+    return 0;
+}
+
+// ************************************************************************* //

bin/foamEtcFile

@@ -38,9 +38,13 @@
 #            && _foamSource $foamPrefs
 #     \endcode
 #
+# Note
+#     This script must exist in <foamInstall>/OpenFOAM-<VERSION>/bin/
+#     or <foamInstall>/openfoam<VERSION>/bin/ (for the debian version)
+#
 #-------------------------------------------------------------------------------
 usage() {
-    [ "$quietOpt" = true ] && exit 1
+    [ "${quietOpt:-$silentOpt}" = true ] && exit 1
 
     exec 1>&2
     while [ "$#" -ge 1 ]; do echo "$1"; shift; done
@@ -53,6 +57,7 @@ options:
   -mode <mode>      any combination of u(user), g(group), o(other)
   -prefix <dir>     specify an alternative installation prefix
   -quiet            suppress all normal output
+  -silent           suppress all stderr output
   -version <ver>    specify an alternative OpenFOAM version
                     in the form Maj.Min.Rev (eg, 1.7.0)
   -help             print the usage
@@ -72,13 +77,9 @@ USAGE
     exit 1
 }
 
-#
-# This script must exist in <foamInstall>/OpenFOAM-<VERSION>/bin/
-# or <foamInstall>/openfoam<VERSION>/bin/ (for the debian version)
-#
 #-------------------------------------------------------------------------------
 
-# the bindir:
+# the bin dir:
 binDir="${0%/*}"
 
 # the project dir:
@@ -128,7 +129,7 @@ esac
 
 # default mode is 'ugo'
 mode=ugo
-unset listOpt quietOpt
+unset listOpt quietOpt silentOpt
 
 # parse options
 while [ "$#" -gt 0 ]
@@ -162,6 +163,9 @@ do
     -q | -quiet)
         quietOpt=true
         ;;
+    -s | -silent)
+        silentOpt=true
+        ;;
     -v | -version)
         [ "$#" -ge 2 ] || usage "'$1' option requires an argument"
         version="$2"
@@ -241,7 +245,7 @@ then
     # list directories, or potential file locations
     [ "$nArgs" -le 1 ] || usage
 
-    # a silly combination, but -quiet has precedence
+    # a silly combination, but -quiet does have precedence
     [ "$quietOpt" = true ] && exit 0
 
     for dir

bin/foamExec

@@ -31,12 +31,21 @@
 #     Runs the <foamVersion> version of executable <foamCommand>
 #     with the rest of the arguments.
 #
-#     Can also be used for parallel runs e.g.
-#     mpirun -np <nProcs> \
-#         foamExec -v <foamVersion> <foamCommand> ... -parallel
+#     Can also be used for parallel runs. For example,
+#     \code
+#         mpirun -np <nProcs> \
+#             foamExec -version <foamVersion> <foamCommand> ... -parallel
+#     \endcode
+#
+# Note
+#     This script must exist in <foamInstall>/OpenFOAM-<VERSION>/bin/
+#     or <foamInstall>/openfoam<VERSION>/bin/ (for the debian version)
+#
+#     foamEtcFile must be found in the same directory as this script
 #
 # SeeAlso
 #    foamEtcFile
+#
 #------------------------------------------------------------------------------
 usage() {
     exec 1>&2
@@ -46,9 +55,11 @@ usage() {
 Usage: ${0##*/} [OPTION] <application> ...
 
 options:
+  -prefix <dir>     specify an alternative installation prefix
+                    pass through to foamEtcFile and set as FOAM_INST_DIR
   -version <ver>    specify an alternative OpenFOAM version
                     pass through to foamEtcFile
-  -help             this usage
+  -help             print the usage
 
 * run a particular OpenFOAM version of <application>
 
@@ -56,13 +67,21 @@ USAGE
     exit 1
 }
 
-#
-# This script must exist in <foamInstall>/OpenFOAM-<VERSION>/bin/
-# or <foamInstall>/openfoam<VERSION>/bin/ (for the debian version)
-#
-# foamEtcFile must be found in the same directory as this script
 #-------------------------------------------------------------------------------
 
+# the bin dir:
+binDir="${0%/*}"
+
+# the project dir:
+projectDir="${binDir%/bin}"
+
+# the prefix dir (same as foamInstall):
+prefixDir="${projectDir%/*}"
+
+# # the name used for the project directory
+# projectDirName="${projectDir##*/}"
+
+
 unset etcOpts version
 # parse options
 while [ "$#" -gt 0 ]
@@ -71,15 +90,21 @@ do
     -h | -help)
         usage
         ;;
-    -v | -version)
+    -m | -mode)
+        [ "$#" -ge 2 ] || usage "'$1' option requires an argument"
+        etcOpts="$etcOpts $1 $2"    # pass-thru to foamEtcFile
+        shift
+        ;;
+    -p | -prefix)
         [ "$#" -ge 2 ] || usage "'$1' option requires an argument"
-        version="$2"
         etcOpts="$etcOpts $1 $2"    # pass-thru to foamEtcFile
+        prefixDir="$2"
         shift
         ;;
-    -m | -mode | -p | -prefix)
+    -v | -version)
         [ "$#" -ge 2 ] || usage "'$1' option requires an argument"
         etcOpts="$etcOpts $1 $2"    # pass-thru to foamEtcFile
+        version="$2"
         shift
         ;;
     --)
@@ -96,22 +121,21 @@ do
     shift
 done
 
-
 #
 # Find and source OpenFOAM settings (bashrc)
 # placed in function to preserve command-line arguments
 #
 sourceRc()
 {
-    # default is the current version
-    : ${version:=${WM_PROJECT_VERSION:-unknown}}
-
-    foamDotFile="$(${0%/*}/foamEtcFile $etcOpts bashrc)" || {
-        echo "Error : bashrc file could not be found for OpenFOAM-$version" 1>&2
+    foamDotFile="$($binDir/foamEtcFile $etcOpts bashrc)" || {
+        echo "Error : bashrc file could not be found for OpenFOAM-${version:-${WM_PROJECT_VERSION:-???}}" 1>&2
         exit 1
     }
 
-    . $foamDotFile
+    # set to consistent value before sourcing the bashrc
+    export FOAM_INST_DIR="$prefixDir"
+
+    . $foamDotFile $FOAM_SETTINGS
 }
 
 

bin/foamJob

@@ -26,6 +26,8 @@
 #     foamJob
 #
 # Description
+#     Run an OpenFOAM job in background.
+#     Redirects the output to 'log' in the case directory.
 #
 #------------------------------------------------------------------------------
 usage() {
@@ -36,9 +38,9 @@ usage() {
 Usage: ${0##*/} [OPTION] <application> ...
 options:
   -case <dir>       specify alternative case directory, default is the cwd
-  -p                parallel run of processors
-  -s                also sends output to screen
-  -v <ver>          specify OpenFOAM version
+  -parallel         parallel run of processors
+  -screen           also sends output to screen
+  -version <ver>    specify an alternative OpenFOAM version
   -help             print the usage
 
 * run an OpenFOAM job in background.
@@ -95,23 +97,22 @@ do
       usage
       ;;
    -case)
-      [ "$#" -ge 2 ] || usage "'-case' option requires an argument"
-      caseDir=$2
+      [ "$#" -ge 2 ] || usage "'$1' option requires an argument"
+      cd "$2" 2>/dev/null || usage "directory does not exist:  '$2'"
       shift 2
-      cd "$caseDir" 2>/dev/null || usage "directory does not exist:  '$caseDir'"
       ;;
-   -p)
+   -p | -parallel)
       parallelOpt=true
       shift
       ;;
-   -s)
+   -s | -screen)
       screenOpt=true
       shift
       ;;
-   -v)
-      shift
-      version=$1
-      shift
+   -v | -version)
+      [ "$#" -ge 2 ] || usage "'$1' option requires an argument"
+      version="$2"
+      shift 2
       ;;
    --)
       shift
@@ -126,29 +127,32 @@ do
    esac
 done
 
-if [ "$#" -lt 1 ]
-then
-    usage "No application specified"
-fi
+[ "$#" -ge 1 ] || usage "No application specified"
+
 
-# use foamExec for a specified version and for remote (parallel) runs
+# use foamExec for a specified version
+# also need foamExec for remote (parallel) runs
 if [ -n "$version" -o "$parallelOpt" = true ]
 then
-    APPLICATION=`findExec foamExec`
-    if [ $? -ne 0 ]
+    # when possible, determine if application even exists
+    if [ -z "$version" ]
     then
-        usage "'foamExec' not found"
+        findExec $1 >/dev/null || usage "Application '$1' not found"
     fi
-    if [ -n "$version" ]
+
+    # use foamExec for dispatching
+    APPLICATION=`findExec foamExec` || usage "'foamExec' not found"
+
+    [ -n "$version" ] && APPLICATION="$APPLICATION -version $version"
+
+    # attempt to preserve the installation directory 'FOAM_INST_DIR'
+    if [ -d "$FOAM_INST_DIR" ]
     then
-        APPLICATION="$APPLICATION -v $version"
+        APPLICATION="$APPLICATION -prefix $FOAM_INST_DIR"
     fi
+
 else
-    APPLICATION=`findExec $1`
-    if [ $? -ne 0 ]
-    then
-        usage "Application '$1' executable not found"
-    fi
+    APPLICATION=`findExec $1` || usage "Application '$1' not found"
     echo "Application : $1"
     shift
 fi
@@ -182,11 +186,7 @@ then
     #
     # locate mpirun
     #
-    mpirun=`findExec mpirun`
-    if [ $? -ne 0 ]
-    then
-        usage "'mpirun' not found"
-    fi
+    mpirun=`findExec mpirun` || usage "'mpirun' not found"
     mpiopts="-np $NPROCS"
 
     #
@@ -217,10 +217,10 @@ then
     #
     if [ "$screenOpt" = true ]
     then
-        echo "Executing: mpirun $mpiopts $APPLICATION $@ -parallel | tee log"
-        $mpirun $mpiopts $APPLICATION $@ -parallel  | tee log
+        echo "Executing: $mpirun $mpiopts $APPLICATION $@ -parallel | tee log"
+        $mpirun $mpiopts $APPLICATION $@ -parallel | tee log
     else
-        echo "Executing: mpirun $mpiopts $APPLICATION $@ -parallel > log 2>&1"
+        echo "Executing: $mpirun $mpiopts $APPLICATION $@ -parallel > log 2>&1"
         $mpirun $mpiopts $APPLICATION $@ -parallel > log 2>&1 &
     fi
 

doc/changes/inotify.txt

@@ -55,15 +55,25 @@ timestamps as before or the (linux-specific) 'inotify' system framework
         - 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:
+      (so one fewer than the number of processors) with
+      the -roots command-line option:
 
-        mpirun -np 2 icoFoam -roots '("/tmp")' -parallel
+        mpirun -np 4 icoFoam -roots '("/tmp" "/tmp" "/tmp")' -parallel
 
     - the alternative to the -roots option is to have a
       cavity/system/decomposeParDict on the master with
             distributed     yes;
-            roots           ("/tmp");
+            roots           ("/tmp" "/tmp" "/tmp");
+
+    - as a convenience for cases when the slave roots are identical,
+      a single root entry is interpreted as being the same for all slaves.
+      With the -roots command-line option, this can take one of two forms:
+
+        mpirun -np 4 icoFoam -roots '("/tmp")' -parallel
+
+      or simply
+
+        mpirun -np 4 icoFoam -roots '"/tmp"' -parallel
 
 
 Details:

etc/apps/paraview3/bashrc

@@ -56,16 +56,22 @@ export ParaView_MAJOR=detect
 
 
 # Evaluate command-line parameters for ParaView
-while [ $# -gt 0 ]
-do
-    case "$1" in
-    ParaView*=*)