merge Mark's branch

ReleaseNotes-1.5

@@ -2,7 +2,7 @@
 #
 #+TITLE:          *OpenFOAM release notes for version 1.5*
 #+AUTHOR:                      OpenCFD Ltd.
-#+DATE:                       26 August 2008
+#+DATE:                       07 October 2008
 #+LINK:                  http://www.opencfd.co.uk
 #+OPTIONS: author:nil ^:{}
 
@@ -34,7 +34,7 @@
     and $WM_COMPILER_ARCH environment variables in the OpenFOAM-1.5/etc/bashrc
     (or cshrc) file.
   + The location of the installation of the compiler is controlled by the
-    $WM_COMPILER_INST environment variable in the OpenFOAM-1.5/etc/settings.sh
+    $compilerInstall environment variable in the OpenFOAM-1.5/etc/settings.sh
     (or settings.csh) file.
 
 * Developments to solvers (applications)

ReleaseNotes-1.5.html

@@ -49,7 +49,7 @@ quires the installation of Qt 4.3.? for ParaView-3 to run.
     $WM_COMPILER and $WM_COMPILER_ARCH environment variables in the
     OpenFOAM-1.5/etc/bashrc (or cshrc) file.
   * The location of the installation of the compiler is controlled by the
-    $WM_COMPILER_INST environment variable in the OpenFOAM-1.5/etc/settings.sh
+    $compilerInstall environment variable in the OpenFOAM-1.5/etc/settings.sh
     (or settings.csh) file.
 
 4 Developments to solvers (applications)
@@ -202,7 +202,7 @@ To aid common monitoring and post-processing activities.
   * Non-blocking, non-buffered, parallel transfers with potential scaling
     benefits for larger number of processors.
 
-Date: 26 August 2008
+Date: 07 October 2008
 
 HTML generated by org-mode 6.06b in emacs 23
 

applications/test/List/ListLoop.s

@@ -1,224 +0,0 @@
-	.file	"ListLoop.C"
-	.section	.ctors,"aw",@progbits
-	.align 4
-	.long	_GLOBAL__I__Z4funcRN4Foam4ListIdEERKS1_RKNS0_IiEES7_
-	.text
-	.align 2
-	.p2align 4,,15
-	.type	_Z41__static_initialization_and_destruction_0ii, @function
-_Z41__static_initialization_and_destruction_0ii:
-.LFB2550:
-	pushl	%ebp
-.LCFI0:
-	movl	%esp, %ebp
-.LCFI1:
-	pushl	%ebx
-.LCFI2:
-	call	__i686.get_pc_thunk.bx
-	addl	$_GLOBAL_OFFSET_TABLE_, %ebx
-	subl	$20, %esp
-.LCFI3:
-	decl	%eax
-	je	.L7
-.L5:
-	addl	$20, %esp
-	popl	%ebx
-	leave
-	ret
-	.p2align 4,,7
-.L7:
-	cmpl	$65535, %edx
-	jne	.L5
-	leal	_ZSt8__ioinit@GOTOFF(%ebx), %eax
-	movl	%eax, (%esp)
-	call	_ZNSt8ios_base4InitC1Ev@PLT
-	movl	__dso_handle@GOT(%ebx), %eax
-	movl	$0, 4(%esp)
-	movl	%eax, 8(%esp)
-	leal	__tcf_0@GOTOFF(%ebx), %eax
-	movl	%eax, (%esp)
-	call	__cxa_atexit@PLT
-	addl	$20, %esp
-	popl	%ebx
-	leave
-	ret
-.LFE2550:
-	.size	_Z41__static_initialization_and_destruction_0ii, .-_Z41__static_initialization_and_destruction_0ii
-.globl __gxx_personality_v0
-	.align 2
-	.p2align 4,,15
-	.type	_GLOBAL__I__Z4funcRN4Foam4ListIdEERKS1_RKNS0_IiEES7_, @function
-_GLOBAL__I__Z4funcRN4Foam4ListIdEERKS1_RKNS0_IiEES7_:
-.LFB2552:
-	pushl	%ebp
-.LCFI4:
-	movl	$65535, %edx
-	movl	$1, %eax
-	movl	%esp, %ebp
-.LCFI5:
-	leave
-	jmp	_Z41__static_initialization_and_destruction_0ii
-.LFE2552:
-	.size	_GLOBAL__I__Z4funcRN4Foam4ListIdEERKS1_RKNS0_IiEES7_, .-_GLOBAL__I__Z4funcRN4Foam4ListIdEERKS1_RKNS0_IiEES7_
-	.align 2
-	.p2align 4,,15
-	.type	__tcf_0, @function
-__tcf_0:
-.LFB2551:
-	pushl	%ebp
-.LCFI6:
-	movl	%esp, %ebp
-.LCFI7:
-	pushl	%ebx
-.LCFI8:
-	call	__i686.get_pc_thunk.bx
-	addl	$_GLOBAL_OFFSET_TABLE_, %ebx
-	subl	$4, %esp
-.LCFI9:
-	leal	_ZSt8__ioinit@GOTOFF(%ebx), %eax
-	movl	%eax, (%esp)
-	call	_ZNSt8ios_base4InitD1Ev@PLT
-	addl	$4, %esp
-	popl	%ebx
-	leave
-	ret
-.LFE2551:
-	.size	__tcf_0, .-__tcf_0
-	.align 2
-	.p2align 4,,15
-.globl _Z4funcRN4Foam4ListIdEERKS1_RKNS0_IiEES7_
-	.type	_Z4funcRN4Foam4ListIdEERKS1_RKNS0_IiEES7_, @function
-_Z4funcRN4Foam4ListIdEERKS1_RKNS0_IiEES7_:
-.LFB2352:
-	pushl	%ebp
-.LCFI10:
-	movl	%esp, %ebp
-.LCFI11:
-	pushl	%edi
-.LCFI12:
-	pushl	%esi
-.LCFI13:
-	subl	$12, %esp
-.LCFI14:
-	movl	8(%ebp), %edx
-	movl	(%edx), %eax
-	testl	%eax, %eax
-	movl	%eax, -20(%ebp)
-	jle	.L16
-	movl	16(%ebp), %eax
-	movl	4(%edx), %edx
-	xorl	%ecx, %ecx
-	movl	4(%eax), %eax
-	movl	%edx, -12(%ebp)
-	movl	%eax, -16(%ebp)
-	movl	20(%ebp), %eax
-	movl	4(%eax), %edi
-	movl	12(%ebp), %eax
-	movl	4(%eax), %esi
-	.p2align 4,,7
-.L15:
-	movl	-16(%ebp), %edx
-	movl	(%edx,%ecx,4), %eax
-	movl	-12(%ebp), %edx
-	leal	(%edx,%eax,8), %eax
-	movl	(%edi,%ecx,4), %edx
-	incl	%ecx
-	cmpl	%ecx, -20(%ebp)
-	fldl	(%eax)
-	fsubl	(%esi,%edx,8)
-	fstpl	(%eax)
-	jne	.L15
-.L16:
-	addl	$12, %esp
-	popl	%esi
-	popl	%edi
-	leave
-	ret
-.LFE2352:
-	.size	_Z4funcRN4Foam4ListIdEERKS1_RKNS0_IiEES7_, .-_Z4funcRN4Foam4ListIdEERKS1_RKNS0_IiEES7_
-	.local	_ZSt8__ioinit
-	.comm	_ZSt8__ioinit,1,1
-	.section	.eh_frame,"a",@progbits
-.Lframe1:
-	.long	.LECIE1-.LSCIE1
-.LSCIE1:
-	.long	0x0
-	.byte	0x1
-	.string	"zPR"
-	.uleb128 0x1
-	.sleb128 -4
-	.byte	0x8
-	.uleb128 0x6
-	.byte	0x9b
-	.long	DW.ref.__gxx_personality_v0-.
-	.byte	0x1b
-	.byte	0xc
-	.uleb128 0x4
-	.uleb128 0x4
-	.byte	0x88
-	.uleb128 0x1
-	.align 4
-.LECIE1:
-.LSFDE1:
-	.long	.LEFDE1-.LASFDE1
-.LASFDE1:
-	.long	.LASFDE1-.Lframe1
-	.long	.LFB2550-.
-	.long	.LFE2550-.LFB2550
-	.uleb128 0x0
-	.byte	0x4
-	.long	.LCFI0-.LFB2550
-	.byte	0xe
-	.uleb128 0x8
-	.byte	0x85
-	.uleb128 0x2
-	.byte	0x4
-	.long	.LCFI1-.LCFI0
-	.byte	0xd
-	.uleb128 0x5
-	.byte	0x4
-	.long	.LCFI2-.LCFI1
-	.byte	0x83
-	.uleb128 0x3
-	.align 4
-.LEFDE1:
-.LSFDE5:
-	.long	.LEFDE5-.LASFDE5
-.LASFDE5:
-	.long	.LASFDE5-.Lframe1
-	.long	.LFB2551-.
-	.long	.LFE2551-.LFB2551
-	.uleb128 0x0
-	.byte	0x4
-	.long	.LCFI6-.LFB2551
-	.byte	0xe
-	.uleb128 0x8
-	.byte	0x85
-	.uleb128 0x2
-	.byte	0x4
-	.long	.LCFI7-.LCFI6
-	.byte	0xd
-	.uleb128 0x5
-	.byte	0x4
-	.long	.LCFI8-.LCFI7
-	.byte	0x83
-	.uleb128 0x3
-	.align 4
-.LEFDE5:
-	.hidden DW.ref.__gxx_personality_v0
-	.weak	DW.ref.__gxx_personality_v0
-	.section	.data.DW.ref.__gxx_personality_v0,"awG",@progbits,DW.ref.__gxx_personality_v0,comdat
-	.align 4
-	.type	DW.ref.__gxx_personality_v0, @object
-	.size	DW.ref.__gxx_personality_v0, 4
-DW.ref.__gxx_personality_v0:
-	.long	__gxx_personality_v0
-	.ident	"GCC: (GNU) 4.1.1"
-	.section	.text.__i686.get_pc_thunk.bx,"axG",@progbits,__i686.get_pc_thunk.bx,comdat
-.globl __i686.get_pc_thunk.bx
-	.hidden	__i686.get_pc_thunk.bx
-	.type	__i686.get_pc_thunk.bx, @function
-__i686.get_pc_thunk.bx:
-	movl	(%esp), %ebx
-	ret
-	.section	.note.GNU-stack,"",@progbits

applications/test/xfer/Make/files

@@ -0,0 +1,4 @@
+xferListTest.C
+
+/* EXE = $(FOAM_USER_APPBIN)/xferListTest */
+EXE = ./xferListTest

applications/test/xfer/xferListTest.C

@@ -0,0 +1,88 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2008 OpenCFD Ltd.
+     \\/     M anipulation  |
+-------------------------------------------------------------------------------
+License
+    This file is part of OpenFOAM.
+
+    OpenFOAM is free software; you can redistribute it and/or modify it
+    under the terms of the GNU General Public License as published by the
+    Free Software Foundation; either version 2 of the License, or (at your
+    option) any later version.
+
+    OpenFOAM is distributed in the hope that it will be useful, but WITHOUT
+    ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+    FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
+    for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with OpenFOAM; if not, write to the Free Software Foundation,
+    Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+
+Application
+
+Description
+
+\*---------------------------------------------------------------------------*/
+
+#include "OSspecific.H"
+
+#include "IOstreams.H"
+#include "IStringStream.H"
+#include "labelList.H"
+
+using namespace Foam;
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+//  Main program:
+
+int main(int argc, char *argv[])
+{
+    List<label> lstA(10);
+    List<label> lstC(IStringStream("(1 2 3 4)")());
+    
+    forAll(lstA, i)
+    {
+        lstA[i] = i;
+    }
+        
+    Info<< "lstA: " << lstA << endl;
+    Info<< "lstC: " << lstC << endl;
+
+    xfer<List<label> > xA(lstA, true);
+    xfer<List<label> > xB;
+
+//    List<label> lstB( xferTmp(List<label>, lstC) );
+//    List<label> lstB( xfer<List<label> >(lstC) );
+    List<label> lstB( xA );
+
+    Info<< "xA: " << *xA << endl;
+    Info<< "xB: " << *xB << endl;
+    Info<< "lstA: " << lstA << endl;
+    Info<< "lstB: " << lstB << endl;
+    Info<< "lstC: " << lstC << endl;
+
+    xA = lstB;
+
+    Info<< "xA: " << *xA << endl;
+    Info<< "xB: " << *xB << endl;
+    Info<< "lstA: " << lstA << endl;
+    Info<< "lstB: " << lstB << endl;
+    Info<< "lstC: " << lstC << endl;
+
+    xB = xA;
+
+    Info<< "xA: " << *xA << endl;
+    Info<< "xB: " << *xB << endl;
+    Info<< "lstA: " << lstA << endl;
+    Info<< "lstB: " << lstB << endl;
+    Info<< "lstC: " << lstC << endl;
+
+    return 0;
+}
+
+
+// ************************************************************************* //

applications/utilities/mesh/generation/extrudeMesh/Make/options

@@ -1,8 +1,8 @@
 EXE_INC = \
     -IextrudedMesh \
     -IextrudeModel/lnInclude \
-    -I$(FOAM_SRC)/meshTools/lnInclude \
+    -I$(LIB_SRC)/meshTools/lnInclude \
-    -I$(FOAM_SRC)/dynamicMesh/lnInclude 
+    -I$(LIB_SRC)/dynamicMesh/lnInclude
 
 EXE_LIBS = \
     -lmeshTools \

applications/utilities/mesh/generation/extrudeMesh/extrudeModel/Make/options

@@ -1,6 +1,6 @@
 EXE_INC = \
-    -I$(FOAM_SRC)/meshTools/lnInclude \
+    -I$(LIB_SRC)/meshTools/lnInclude \
-    -I$(FOAM_SRC)/dynamicMesh/lnInclude
+    -I$(LIB_SRC)/dynamicMesh/lnInclude
 
 EXE_LIBS = \
     -lmeshTools \

applications/utilities/miscellaneous/foamFormatConvert/Make/options

@@ -1,8 +1,7 @@
 EXE_INC = \
-    -I$(FOAM_SRC)/finiteVolume/lnInclude \
+    -I$(LIB_SRC)/finiteVolume/lnInclude \
-    -I$(FOAM_SRC)/meshTools/lnInclude \
+    -I$(LIB_SRC)/meshTools/lnInclude \
-    -I$(FOAM_SRC)/lagrangian/basic/lnInclude \
+    -I$(LIB_SRC)/lagrangian/basic/lnInclude
-
 
 EXE_LIBS = \
     -lmeshTools \

applications/utilities/postProcessing/dataConversion/foamToEnsightParts/foamToEnsightParts.C

@@ -39,6 +39,14 @@ Usage
     @param -zeroTime \n
     Include the often incomplete initial conditions.
 
+    @param -index \<start\>\n
+    Ignore the time index contained in the time file and use a
+    simple indexing when creating the @c Ensight/data/######## files.
+
+    @param -noMesh \n
+    Suppress writing the geometry. Can be useful for converting partial
+    results for a static geometry.
+
 Note
     - no parallel data.
     - writes to @a Ensight directory to avoid collisions with foamToEnsight.
@@ -70,6 +78,8 @@ int main(int argc, char *argv[])
     timeSelector::addOptions(true, false);
     argList::noParallel();
     argList::validOptions.insert("ascii", "");
+    argList::validOptions.insert("index",  "start");
+    argList::validOptions.insert("noMesh", "");
 
     const word volFieldTypes[] =
     {
@@ -104,6 +114,18 @@ int main(int argc, char *argv[])
         format = IOstream::ASCII;
     }
 
+    // control for renumbering iterations
+    bool optIndex = false;
+    label indexingNumber = 0;
+    if (args.options().found("index"))
+    {
+        optIndex = true;
+        indexingNumber = readLabel(IStringStream(args.options()["index"])());
+    }
+
+    // always write the geometry, unless the -noMesh option is specified
+    bool optNoMesh = args.options().found("noMesh");
+
     fileName ensightDir = args.rootPath()/args.globalCaseName()/"Ensight";
     fileName dataDir = ensightDir/"data";
     fileName caseFileName = "Ensight.case";
@@ -146,6 +168,13 @@ int main(int argc, char *argv[])
 #   include "findFields.H"
 #   include "validateFields.H"
 
+    if (hasMovingMesh && optNoMesh)
+    {
+        Info<< "mesh is moving: ignoring '-noMesh' option" << endl;
+        optNoMesh = false;
+    }
+
+
     // map times used
     Map<scalar>  timeIndices;
 
@@ -192,6 +221,8 @@ int main(int argc, char *argv[])
                 partsList.recalculate(mesh);
             }
 
+            if (!optNoMesh)
+            {
                 fileName geomDir;
                 if (hasMovingMesh)
                 {
@@ -200,7 +231,8 @@ int main(int argc, char *argv[])
 
                 ensightGeoFile geoFile(ensightDir/geomDir/geometryName, format);
                 partsList.writeGeometry(geoFile);
-            Info << nl;
+                Info<< nl;
+            }
         }
 
         Info<< "write volume field (" << flush;

applications/utilities/postProcessing/dataConversion/foamToEnsightParts/getTimeIndex.H

@@ -1,9 +1,13 @@
-// Read time index from */uniform/time,
+// Read time index from */uniform/time, but treat 0 and constant specially
-// but treat 0 and constant specially
+// or simply increment from the '-index' option if it was supplied
 
     label timeIndex = 0;
 
-    if
+    if (optIndex)
+    {
+        timeIndex = indexingNumber++;
+    }
+    else if
     (
         runTime.timeName() != "constant"
      && runTime.timeName() != "0"
@@ -22,19 +26,8 @@
 
         if (io.headerOk())
         {
-            IOdictionary timeObject
+            io.readOpt() = IOobject::MUST_READ;
-            (
+            IOdictionary timeObject(io);
-                IOobject
-                (
-                    "time",
-                    runTime.timeName(),
-                    "uniform",
-                    runTime,
-                    IOobject::MUST_READ,
-                    IOobject::NO_WRITE,
-                    false
-                )
-            );
 
             timeObject.lookup("index") >> timeIndex;
         }

applications/utilities/postProcessing/dataConversion/foamToEnsightParts/moveMesh.H

@@ -1,5 +1,5 @@
 {
-    IOobject ioPoints
+    IOobject io
     (
         "points",
         runTime.timeName(),
@@ -7,21 +7,11 @@
         mesh
     );
 
-    if (ioPoints.headerOk())
+    if (io.headerOk())
     {
-        // Reading new points
+        // Read new points
-        pointIOField newPoints
+        io.readOpt() = IOobject::MUST_READ;
-        (
+        pointIOField newPoints(io);
-            IOobject
-            (
-                "points",
-                mesh.time().timeName(),
-                polyMesh::meshSubDir,
-                mesh,
-                IOobject::MUST_READ,
-                IOobject::NO_WRITE
-            )
-        );
 
         mesh.movePoints(newPoints);
     }

applications/utilities/postProcessing/dataConversion/foamToEnsightParts/validateFields.H

@@ -5,7 +5,8 @@ forAllIter(HashTable<word>, volumeFields, fieldIter)
     const word& fieldName = fieldIter.key();
     const word& fieldType = fieldIter();
 
-    if (fieldName.size() > 2 &&  fieldName(fieldName.size() - 2, 2) != "_0")
+    // ignore _0 fields
+    if (fieldName.size() > 2 && fieldName(fieldName.size() - 2, 2) == "_0")
     {
         volumeFields.erase(fieldIter);
     }

applications/utilities/postProcessing/graphics/PV3FoamReader/PV3FoamReader/CMakeLists.txt

@@ -1,4 +1,3 @@
-
 # create a plugin that adds a reader to the ParaView GUI
 # it is added in the file dialog when doing opens/saves.
 
@@ -16,8 +15,8 @@ LINK_DIRECTORIES(
 )
 
 INCLUDE_DIRECTORIES(
-    $ENV{FOAM_SRC}/OpenFOAM/lnInclude
+    $ENV{WM_PROJECT_DIR}/src/OpenFOAM/lnInclude
-    $ENV{FOAM_SRC}/finiteVolume/lnInclude
+    $ENV{WM_PROJECT_DIR}/src/finiteVolume/lnInclude
     ${PROJECT_SOURCE_DIR}/../vtkPV3Foam
 )
 
@@ -52,3 +51,4 @@ TARGET_LINK_LIBRARIES(
     finiteVolume
     vtkPV3Foam
 )
+#-----------------------------------------------------------------------------

applications/utilities/postProcessing/graphics/PVFoamReader/PVFoamReader/CMakeLists.txt

@@ -16,8 +16,12 @@ SET(PVFoamReader_LIBS
   vtkGraphics
 )
 
-INCLUDE_DIRECTORIES($ENV{FOAM_SRC}/OpenFOAM/lnInclude $ENV{FOAM_SRC}/finiteVolume/lnInclude)
+INCLUDE_DIRECTORIES(
-INCLUDE_DIRECTORIES($ENV{ParaView_INST_DIR}/include ../vtkFoam/lnInclude)
+    $ENV{WM_PROJECT_DIR}/src/OpenFOAM/lnInclude
+    $ENV{WM_PROJECT_DIR}/src/finiteVolume/lnInclude
+    $ENV{ParaView_INST_DIR}/include
+    ../vtkFoam/lnInclude
+)
 ADD_DEFINITIONS(-D$ENV{WM_PRECISION_OPTION})
 
 #-----------------------------------------------------------------------------
@@ -72,3 +76,4 @@ CONFIGURE_FILE(${PROJECT_SOURCE_DIR}/PVFoamReader.pvsm.in
                ${PROJECT_BINARY_DIR}/../${PROJECT_NAME}.pvsm @ONLY IMMEDIATE)
 
 TARGET_LINK_LIBRARIES(${PROJECT_NAME} OpenFOAM finiteVolume vtkFoam)
+#-----------------------------------------------------------------------------

applications/utilities/postProcessing/graphics/fieldview9Reader/Make/options

@@ -94,7 +94,7 @@ EXE_INC = \
     -I$(LIB_SRC)/finiteVolume/lnInclude \
     -I$(LIB_SRC)/meshTools/lnInclude \
     -I$(LIB_SRC)/browser/lnInclude \
-    -I$(FOAM_SRC)/lagrangian/basic/lnInclude
+    -I$(LIB_SRC)/lagrangian/basic/lnInclude
 
 EXE_LIBS = \
     $(FV_LIBS) \

applications/utilities/postProcessing/miscellaneous/execFlowFunctionObjects/Make/options

@@ -1,5 +1,5 @@
 EXE_INC = \
-    -I$(FOAM_SRC)/postProcessing/postCalc \
+    -I$(LIB_SRC)/postProcessing/postCalc \
     -I$(LIB_SRC)/finiteVolume/lnInclude \
     -I$(LIB_SRC)/transportModels \
     -I$(LIB_SRC)/turbulenceModels/RAS \

applications/utilities/postProcessing/velocityField/Co/Make/options

@@ -1,5 +1,5 @@
 EXE_INC = \
-    -I$(FOAM_SRC)/postProcessing/postCalc \
+    -I$(LIB_SRC)/postProcessing/postCalc \
     -I$(LIB_SRC)/finiteVolume/lnInclude 
 
 EXE_LIBS = \

applications/utilities/postProcessing/velocityField/Lambda2/Make/options

@@ -1,5 +1,5 @@
 EXE_INC = \
-    -I$(FOAM_SRC)/postProcessing/postCalc \
+    -I$(LIB_SRC)/postProcessing/postCalc \
     -I$(LIB_SRC)/finiteVolume/lnInclude
 
 EXE_LIBS = \

applications/utilities/postProcessing/velocityField/Mach/Make/options

@@ -1,5 +1,5 @@
 EXE_INC = \
-    -I$(FOAM_SRC)/postProcessing/postCalc \
+    -I$(LIB_SRC)/postProcessing/postCalc \
     -I$(LIB_SRC)/finiteVolume/lnInclude \
     -I$(LIB_SRC)/thermophysicalModels/basic/lnInclude
 

applications/utilities/postProcessing/velocityField/Pe/Make/options

@@ -1,5 +1,5 @@
 EXE_INC = \
-    -I$(FOAM_SRC)/postProcessing/postCalc \
+    -I$(LIB_SRC)/postProcessing/postCalc \
     -I$(LIB_SRC)/finiteVolume/lnInclude \
     -I$(LIB_SRC)/meshTools/lnInclude \
     -I$(LIB_SRC)/sampling/lnInclude \

applications/utilities/postProcessing/velocityField/Q/Make/options

@@ -1,5 +1,5 @@
 EXE_INC = \
-    -I$(FOAM_SRC)/postProcessing/postCalc \
+    -I$(LIB_SRC)/postProcessing/postCalc \
     -I$(LIB_SRC)/finiteVolume/lnInclude
 
 EXE_LIBS = \

applications/utilities/postProcessing/velocityField/enstrophy/Make/options

@@ -1,5 +1,5 @@
 EXE_INC = \
-    -I$(FOAM_SRC)/postProcessing/postCalc \
+    -I$(LIB_SRC)/postProcessing/postCalc \
     -I$(LIB_SRC)/finiteVolume/lnInclude
 
 EXE_LIBS = \

applications/utilities/postProcessing/velocityField/flowType/Make/options

@@ -1,5 +1,5 @@
 EXE_INC = \
-    -I$(FOAM_SRC)/postProcessing/postCalc \
+    -I$(LIB_SRC)/postProcessing/postCalc \
     -I$(LIB_SRC)/finiteVolume/lnInclude
 
 EXE_LIBS = \

applications/utilities/postProcessing/velocityField/uprime/Make/options

@@ -1,5 +1,5 @@
 EXE_INC = \
-    -I$(FOAM_SRC)/postProcessing/postCalc \
+    -I$(LIB_SRC)/postProcessing/postCalc \
     -I$(LIB_SRC)/finiteVolume/lnInclude
 
 EXE_LIBS = \

applications/utilities/postProcessing/velocityField/vorticity/Make/options

@@ -1,5 +1,5 @@
 EXE_INC = \
-    -I$(FOAM_SRC)/postProcessing/postCalc \
+    -I$(LIB_SRC)/postProcessing/postCalc \
     -I$(LIB_SRC)/finiteVolume/lnInclude
 
 EXE_LIBS = \

etc/bashrc

@@ -23,16 +23,17 @@
 #     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 #
 # Script
-#     bashrc
+#     etc/bashrc
 #
 # Description
 #     Startup file for OpenFOAM
 #     Sourced from ~/.profile or ~/.bashrc
+#     Should be usable by any POSIX-compliant shell (eg, ksh)
 #
 #------------------------------------------------------------------------------
 
 export WM_PROJECT=OpenFOAM
-#export WM_PROJECT_VERSION=1.5
+#export WM_PROJECT_VERSION=1.5.x
 : ${WM_PROJECT_VERSION:=dev}; export WM_PROJECT_VERSION
 
 
@@ -53,7 +54,7 @@ foamInstall=$HOME/$WM_PROJECT
 # Location of site/user files
 # ~~~~~~~~~~~~~~~~~~~~~~~~~~~
 export WM_PROJECT_INST_DIR=$FOAM_INST_DIR
-export WM_PROJECT_DIR=$FOAM_INST_DIR/$WM_PROJECT-$WM_PROJECT_VERSION
+export WM_PROJECT_DIR=$WM_PROJECT_INST_DIR/$WM_PROJECT-$WM_PROJECT_VERSION
 export WM_PROJECT_USER_DIR=$HOME/$WM_PROJECT/$USER-$WM_PROJECT_VERSION
 
 
@@ -163,7 +164,7 @@ esac
 cleanProg=$WM_PROJECT_DIR/bin/foamCleanPath
 
 # Remove anything under top-level foam directory
-wildCards="$FOAM_INST_DIR $HOME/$WM_PROJECT/$USER"
+wildCards="$WM_PROJECT_INST_DIR $HOME/$WM_PROJECT/$USER"
 
 #- Clean path/PATH
 cleanPath=`$cleanProg "$PATH" "$wildCards"` && PATH="$cleanPath"
@@ -182,9 +183,7 @@ _foamSource()
 {
    while [ $# -ge 1 ]
    do
-      if [ "$FOAM_VERBOSE" -a "$PS1" ]; then
+      [ "$FOAM_VERBOSE" -a "$PS1" ] && echo "Sourcing: $1"
-         echo "Sourcing: $1"
-      fi
       . $1
       shift
    done

etc/cshrc

@@ -23,7 +23,7 @@
 #     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 #
 # Script
-#     cshrc
+#     etc/cshrc
 #
 # Description
 #     Startup file for OpenFOAM
@@ -32,7 +32,7 @@
 #------------------------------------------------------------------------------
 
 setenv WM_PROJECT OpenFOAM
-#setenv WM_PROJECT_VERSION 1.5
+#setenv WM_PROJECT_VERSION 1.5.x
 if ( ! $?WM_PROJECT_VERSION ) setenv WM_PROJECT_VERSION dev
 
 #!!User:
@@ -52,7 +52,7 @@ if ( ! $?FOAM_INST_DIR ) setenv FOAM_INST_DIR $foamInstall
 # Location of site/user files
 # ~~~~~~~~~~~~~~~~~~~~~~~~~~~
 setenv WM_PROJECT_INST_DIR $FOAM_INST_DIR
-setenv WM_PROJECT_DIR $FOAM_INST_DIR/$WM_PROJECT-$WM_PROJECT_VERSION
+setenv WM_PROJECT_DIR $WM_PROJECT_INST_DIR/$WM_PROJECT-$WM_PROJECT_VERSION
 setenv WM_PROJECT_USER_DIR $HOME/$WM_PROJECT/$LOGNAME-$WM_PROJECT_VERSION
 
 
@@ -167,7 +167,7 @@ if (! $?MANPATH) then
 endif
 
 # Remove anything under top-level foam directory
-set wildCards="$FOAM_INST_DIR $HOME/$WM_PROJECT/$LOGNAME"
+set wildCards="$WM_PROJECT_INST_DIR $HOME/$WM_PROJECT/$LOGNAME"
 
 #- Clean path/PATH
 set colonPath=`echo "$path" | sed -e 's/ /:/g'`
@@ -219,5 +219,8 @@ endif
 
 # cleanup environment:
 # ~~~~~~~~~~~~~~~~~~~~
+unset cleanProg
+unset wildCards
+unset colonPath
 unalias _foamSource
 # -----------------------------------------------------------------------------

etc/settings.csh

@@ -23,7 +23,7 @@
 #     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 #
 # Script
-#     settings.csh
+#     etc/settings.csh
 #
 # Description
 #     Startup file for OpenFOAM
@@ -31,60 +31,70 @@
 #
 #------------------------------------------------------------------------------
 
-alias _foamAddPath 'set path=(\!* $path) ; if ( ! -d \!* ) mkdir -p \!*'
+# prefix to PATH
-alias _foamAddLib 'setenv LD_LIBRARY_PATH \!*\:${LD_LIBRARY_PATH} ; set xx=`echo $LD_LIBRARY_PATH | sed -e "s/:.*//"`; if ( ! -d  $xx ) mkdir -p $xx'
+alias _foamAddPath 'set path=(\!* $path)'
+# prefix to LD_LIBRARY_PATH
+alias _foamAddLib 'setenv LD_LIBRARY_PATH \!*\:${LD_LIBRARY_PATH}'
+# make directory if it doesn't already exist
+alias _foamMkDir 'if ( ! -d \!* ) mkdir -p \!*'
 
+# location of the jobControl directory
+setenv FOAM_JOB_DIR $WM_PROJECT_INST_DIR/jobControl
 
-#- Add the system-specific executables path to the path
+# wmake configuration
-set path=($WM_PROJECT_DIR/bin $FOAM_INST_DIR/$WM_ARCH/bin $path)
-
-#- Location of the jobControl directory
-setenv FOAM_JOB_DIR $FOAM_INST_DIR/jobControl
-
 setenv WM_DIR $WM_PROJECT_DIR/wmake
 setenv WM_LINK_LANGUAGE c++
 setenv WM_OPTIONS $WM_ARCH$WM_COMPILER$WM_PRECISION_OPTION$WM_COMPILE_OPTION
-set path=($WM_DIR $path)
 
+# base configuration
 setenv FOAM_SRC $WM_PROJECT_DIR/src
 setenv FOAM_LIB $WM_PROJECT_DIR/lib
-setenv FOAM_LIBBIN $FOAM_LIB/$WM_OPTIONS
+setenv FOAM_LIBBIN $WM_PROJECT_DIR/lib/$WM_OPTIONS
-_foamAddLib $FOAM_LIBBIN
-
 setenv FOAM_APP $WM_PROJECT_DIR/applications
 setenv FOAM_APPBIN $WM_PROJECT_DIR/applications/bin/$WM_OPTIONS
-_foamAddPath $FOAM_APPBIN
 
+# user configuration
+setenv FOAM_USER_LIBBIN $WM_PROJECT_USER_DIR/lib/$WM_OPTIONS
+setenv FOAM_USER_APPBIN $WM_PROJECT_USER_DIR/applications/bin/$WM_OPTIONS
+
+# convenience
 setenv FOAM_TUTORIALS $WM_PROJECT_DIR/tutorials
 setenv FOAM_UTILITIES $FOAM_APP/utilities
 setenv FOAM_SOLVERS $FOAM_APP/solvers
+setenv FOAM_RUN $WM_PROJECT_USER_DIR/run
 
-setenv FOAM_USER_LIBBIN $WM_PROJECT_USER_DIR/lib/$WM_OPTIONS
+# add OpenFOAM scripts and wmake to the path
+set path=($WM_DIR $WM_PROJECT_DIR/bin $path)
+
+_foamAddPath $FOAM_APPBIN
+_foamAddPath $FOAM_USER_APPBIN
+_foamAddLib  $FOAM_LIBBIN
 _foamAddLib  $FOAM_USER_LIBBIN
 
-setenv FOAM_USER_APPBIN $WM_PROJECT_USER_DIR/applications/bin/$WM_OPTIONS
+# create these directories if necessary:
-_foamAddPath $FOAM_USER_APPBIN
+_foamMkDir $FOAM_LIBBIN
-
+_foamMkDir $FOAM_APPBIN
-setenv FOAM_RUN $WM_PROJECT_USER_DIR/run
+_foamMkDir $FOAM_USER_LIBBIN
+_foamMkDir $FOAM_USER_APPBIN
 
 
 # Compiler settings
 # ~~~~~~~~~~~~~~~~~
-set WM_COMPILER_BIN=
+set compilerBin=
-set WM_COMPILER_LIB=
+set compilerLib=
 
 # Select compiler installation
 # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-# WM_COMPILER_INST = OpenFOAM | System
+# compilerInstall = OpenFOAM | System
-set WM_COMPILER_INST=OpenFOAM
+set compilerInstall=OpenFOAM
 
-switch ("$WM_COMPILER_INST")
+switch ("$compilerInstall")
 case OpenFOAM:
     switch ("$WM_COMPILER")
     case Gcc:
         setenv WM_COMPILER_DIR $WM_THIRD_PARTY_DIR/gcc-4.3.2/platforms/$WM_ARCH$WM_COMPILER_ARCH
         _foamAddLib $WM_THIRD_PARTY_DIR/mpfr-2.3.2/platforms/$WM_ARCH$WM_COMPILER_ARCH/lib
-        _foamAddLib $WM_THIRD_PARTY_DIR/gmp-4.2.3/platforms/$WM_ARCH$WM_COMPILER_ARCH/lib
+        _foamAddLib $WM_THIRD_PARTY_DIR/gmp-4.2.4/platforms/$WM_ARCH$WM_COMPILER_ARCH/lib
     breaksw
     case Gcc42:
         setenv WM_COMPILER_DIR $WM_THIRD_PARTY_DIR/gcc-4.2.4/platforms/$WM_ARCH$WM_COMPILER_ARCH
@@ -97,22 +107,22 @@ case OpenFOAM:
         echo "Warning in $WM_PROJECT_DIR/etc/settings.csh:"
         echo "    Cannot find $WM_COMPILER_DIR installation."
         echo "    Please install this compiler version or if you wish to use the system compiler,"
-        echo "    change the WM_COMPILER_INST setting to 'System' in this file"
+        echo "    change the 'compilerInstall' setting to 'System' in this file"
         echo
     endif
 
-    set WM_COMPILER_BIN="$WM_COMPILER_DIR/bin"
+    set compilerBin=$WM_COMPILER_DIR/bin
-    set WM_COMPILER_LIB=$WM_COMPILER_DIR/lib${WM_COMPILER_LIB_ARCH}:$WM_COMPILER_DIR/lib
+    set compilerLib=$WM_COMPILER_DIR/lib$WM_COMPILER_LIB_ARCH:$WM_COMPILER_DIR/lib
     breaksw
 endsw
 
-if ($?WM_COMPILER_BIN) then
+if ($?compilerBin) then
-    _foamAddPath $WM_COMPILER_BIN
+    _foamAddPath $compilerBin
-    _foamAddLib $WM_COMPILER_LIB
+    _foamAddLib  $compilerLib
 endif
 
-unset WM_COMPILER_BIN
+unset compilerBin
-unset WM_COMPILER_LIB
+unset compilerLib
 
 
 # Communications library
@@ -129,8 +139,8 @@ case OPENMPI:
     # Tell OpenMPI where to find its install directory
     setenv OPAL_PREFIX $MPI_ARCH_PATH
 
-    _foamAddLib  $MPI_ARCH_PATH/lib
     _foamAddPath $MPI_ARCH_PATH/bin
+    _foamAddLib  $MPI_ARCH_PATH/lib
 
     setenv FOAM_MPI_LIBBIN $FOAM_LIBBIN/$mpi_version
     unset mpi_version
@@ -143,8 +153,8 @@ case LAM:
     setenv LAMHOME $WM_THIRD_PARTY_DIR/$mpi_version
     # note: LAMHOME is deprecated, should probably point to MPI_ARCH_PATH too
 
-    _foamAddLib  $MPI_ARCH_PATH/lib
     _foamAddPath $MPI_ARCH_PATH/bin
+    _foamAddLib  $MPI_ARCH_PATH/lib
 
     setenv FOAM_MPI_LIBBIN $FOAM_LIBBIN/$mpi_version
     unset mpi_version
@@ -156,8 +166,8 @@ case MPICH:
     setenv MPI_ARCH_PATH $MPI_HOME/platforms/$WM_OPTIONS
     setenv MPICH_ROOT $MPI_ARCH_PATH
 
-    _foamAddLib  $MPI_ARCH_PATH/lib
     _foamAddPath $MPI_ARCH_PATH/bin
+    _foamAddLib  $MPI_ARCH_PATH/lib
 
     setenv FOAM_MPI_LIBBIN $FOAM_LIBBIN/$mpi_version
     unset mpi_version
@@ -169,9 +179,9 @@ case MPICH-GM:
     setenv MPICH_ROOT $MPI_ARCH_PATH
     setenv GM_LIB_PATH /opt/gm/lib64
 
+    _foamAddPath $MPI_ARCH_PATH/bin
     _foamAddLib  $MPI_ARCH_PATH/lib
     _foamAddLib  $GM_LIB_PATH
-    _foamAddPath $MPI_ARCH_PATH/bin
 
     setenv FOAM_MPI_LIBBIN $FOAM_LIBBIN/mpich-gm
     breaksw
@@ -215,8 +225,8 @@ endif
 
 # cleanup environment:
 # ~~~~~~~~~~~~~~~~~~~~
-unalias _foamAddLib
 unalias _foamAddPath
-
+unalias _foamAddLib
+unalias _foamMkDir
 
 # -----------------------------------------------------------------------------

etc/settings.sh

@@ -23,7 +23,7 @@
 #     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 #
 # Script
-#     settings.sh
+#     etc/settings.sh
 #
 # Description
 #     Startup file for OpenFOAM
@@ -31,95 +31,89 @@
 #
 #------------------------------------------------------------------------------
 
+# prefix to PATH
 _foamAddPath()
 {
-   if [ $# -eq 1 ]
-   then
-      oldIFS="$IFS"
-      IFS=':'    # split on ':'
-      set -- $1
-      IFS="$oldIFS"
-      unset oldIFS
-   fi
-
    while [ $# -ge 1 ]
    do
-      [ -d $1 ] || mkdir -p $1
       export PATH=$1:$PATH
       shift
    done
 }
 
+# prefix to LD_LIBRARY_PATH
 _foamAddLib()
 {
-   if [ $# -eq 1 ]
-   then
-      oldIFS="$IFS"
-      IFS=':'    # split on ':'
-      set -- $1
-      IFS="$oldIFS"
-      unset oldIFS
-   fi
-
    while [ $# -ge 1 ]
    do
-      [ -d $1 ] || mkdir -p $1
       export LD_LIBRARY_PATH=$1:$LD_LIBRARY_PATH
       shift
    done
 }
 
 
-#- Add the system-specific executables path to the path
+# make directories if they don't already exist
-export PATH=$WM_PROJECT_DIR/bin:$FOAM_INST_DIR/$WM_ARCH/bin:$PATH
+_foamMkDir()
+{
+   while [ $# -ge 1 ]
+   do
+      [ -d $1 ] || mkdir -p $1
+      shift
+   done
+}
 
-#- Location of the jobControl directory
-export FOAM_JOB_DIR=$FOAM_INST_DIR/jobControl
 
+# location of the jobControl directory
+export FOAM_JOB_DIR=$WM_PROJECT_INST_DIR/jobControl
+
+# wmake configuration
 export WM_DIR=$WM_PROJECT_DIR/wmake
 export WM_LINK_LANGUAGE=c++
-export WM_OPTIONS=$WM_ARCH${WM_COMPILER}$WM_PRECISION_OPTION$WM_COMPILE_OPTION
+export WM_OPTIONS=$WM_ARCH$WM_COMPILER$WM_PRECISION_OPTION$WM_COMPILE_OPTION
-export PATH=$WM_DIR:$PATH
 
+# base configuration
 export FOAM_SRC=$WM_PROJECT_DIR/src
 export FOAM_LIB=$WM_PROJECT_DIR/lib
-export FOAM_LIBBIN=$FOAM_LIB/$WM_OPTIONS
+export FOAM_LIBBIN=$WM_PROJECT_DIR/lib/$WM_OPTIONS
-_foamAddLib $FOAM_LIBBIN
-
 export FOAM_APP=$WM_PROJECT_DIR/applications
 export FOAM_APPBIN=$WM_PROJECT_DIR/applications/bin/$WM_OPTIONS
-_foamAddPath $FOAM_APPBIN
 
+# user configuration
+export FOAM_USER_LIBBIN=$WM_PROJECT_USER_DIR/lib/$WM_OPTIONS
+export FOAM_USER_APPBIN=$WM_PROJECT_USER_DIR/applications/bin/$WM_OPTIONS
+
+# convenience
 export FOAM_TUTORIALS=$WM_PROJECT_DIR/tutorials
 export FOAM_UTILITIES=$FOAM_APP/utilities
 export FOAM_SOLVERS=$FOAM_APP/solvers
-
-export FOAM_USER_LIBBIN=$WM_PROJECT_USER_DIR/lib/$WM_OPTIONS
-_foamAddLib $FOAM_USER_LIBBIN
-
-export FOAM_USER_APPBIN=$WM_PROJECT_USER_DIR/applications/bin/$WM_OPTIONS
-_foamAddPath $FOAM_USER_APPBIN
-
 export FOAM_RUN=$WM_PROJECT_USER_DIR/run
 
+# add OpenFOAM scripts and wmake to the path
+export PATH=$WM_DIR:$WM_PROJECT_DIR/bin:$PATH
+
+_foamAddPath $FOAM_APPBIN $FOAM_USER_APPBIN
+_foamAddLib  $FOAM_LIBBIN $FOAM_USER_LIBBIN
+
+# create these directories if necessary:
+_foamMkDir $FOAM_LIBBIN $FOAM_USER_LIBBIN $FOAM_APPBIN $FOAM_USER_APPBIN
+
 
 # Compiler settings
 # ~~~~~~~~~~~~~~~~~
-WM_COMPILER_BIN=
+unset compilerBin compilerLib
-WM_COMPILER_LIB=
 
 # Select compiler installation
 # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-# WM_COMPILER_INST = OpenFOAM | System
+# compilerInstall = OpenFOAM | System
-WM_COMPILER_INST=OpenFOAM
+compilerInstall=OpenFOAM
 
-case "$WM_COMPILER_INST" in
+case "$compilerInstall" in
 OpenFOAM)
     case "$WM_COMPILER" in
     Gcc)
         export WM_COMPILER_DIR=$WM_THIRD_PARTY_DIR/gcc-4.3.2/platforms/$WM_ARCH$WM_COMPILER_ARCH
         _foamAddLib $WM_THIRD_PARTY_DIR/mpfr-2.3.2/platforms/$WM_ARCH$WM_COMPILER_ARCH/lib
-        _foamAddLib $WM_THIRD_PARTY_DIR/gmp-4.2.3/platforms/$WM_ARCH$WM_COMPILER_ARCH/lib
+        _foamAddLib $WM_THIRD_PARTY_DIR/gmp-4.2.4/platforms/$WM_ARCH$WM_COMPILER_ARCH/lib
         ;;
     Gcc42)
         export WM_COMPILER_DIR=$WM_THIRD_PARTY_DIR/gcc-4.2.4/platforms/$WM_ARCH$WM_COMPILER_ARCH
@@ -133,21 +127,22 @@ OpenFOAM)
         echo "Warning in $WM_PROJECT_DIR/etc/settings.sh:"
         echo "    Cannot find $WM_COMPILER_DIR installation."
         echo "    Please install this compiler version or if you wish to use the system compiler,"
-        echo "    change the WM_COMPILER_INST setting to 'System' in this file"
+        echo "    change the 'compilerInstall' setting to 'System' in this file"
         echo
     fi
 
-    WM_COMPILER_BIN=$WM_COMPILER_DIR/bin
+    compilerBin=$WM_COMPILER_DIR/bin
-    WM_COMPILER_LIB=$WM_COMPILER_DIR/lib$WM_COMPILER_LIB_ARCH:$WM_COMPILER_DIR/lib
+    compilerLib=$WM_COMPILER_DIR/lib$WM_COMPILER_LIB_ARCH:$WM_COMPILER_DIR/lib
     ;;
 esac
 
-if [ -d "$WM_COMPILER_BIN" ]; then
+if [ -d "$compilerBin" ]
-    _foamAddPath $WM_COMPILER_BIN
+then
-    _foamAddLib  $WM_COMPILER_LIB
+    _foamAddPath $compilerBin
+    _foamAddLib  $compilerLib
 fi
 
-unset WM_COMPILER_BIN WM_COMPILER_LIB
+unset compilerBin compilerLib compilerInstall
 
 # Communications library
 # ~~~~~~~~~~~~~~~~~~~~~~
@@ -163,8 +158,8 @@ OPENMPI)
     # Tell OpenMPI where to find its install directory
     export OPAL_PREFIX=$MPI_ARCH_PATH
 
-    _foamAddLib  $MPI_ARCH_PATH/lib
     _foamAddPath $MPI_ARCH_PATH/bin
+    _foamAddLib  $MPI_ARCH_PATH/lib
 
     export FOAM_MPI_LIBBIN=$FOAM_LIBBIN/$mpi_version
     unset mpi_version
@@ -177,8 +172,8 @@ LAM)
     export LAMHOME=$WM_THIRD_PARTY_DIR/$mpi_version
     # note: LAMHOME is deprecated, should probably point to MPI_ARCH_PATH too
 
-    _foamAddLib  $MPI_ARCH_PATH/lib
     _foamAddPath $MPI_ARCH_PATH/bin
+    _foamAddLib  $MPI_ARCH_PATH/lib
 
     export FOAM_MPI_LIBBIN=$FOAM_LIBBIN/$mpi_version
     unset mpi_version
@@ -190,8 +185,8 @@ MPICH)
     export MPI_ARCH_PATH=$MPI_HOME/platforms/$WM_OPTIONS
     export MPICH_ROOT=$MPI_ARCH_PATH
 
-    _foamAddLib  $MPI_ARCH_PATH/lib
     _foamAddPath $MPI_ARCH_PATH/bin
+    _foamAddLib  $MPI_ARCH_PATH/lib
 
     export FOAM_MPI_LIBBIN=$FOAM_LIBBIN/$mpi_version
     unset mpi_version
@@ -203,9 +198,9 @@ MPICH-GM)
     export MPICH_ROOT=$MPI_ARCH_PATH
     export GM_LIB_PATH=/opt/gm/lib64
 
+    _foamAddPath $MPI_ARCH_PATH/bin
     _foamAddLib  $MPI_ARCH_PATH/lib
     _foamAddLib  $GM_LIB_PATH
-    _foamAddPath $MPI_ARCH_PATH/bin
 
     export FOAM_MPI_LIBBIN=$FOAM_LIBBIN/mpich-gm
     ;;
@@ -247,6 +242,6 @@ export MPI_BUFFER_SIZE=20000000
 
 # cleanup environment:
 # ~~~~~~~~~~~~~~~~~~~~
-unset _foamAddLib _foamAddPath
+unset _foamAddPath _foamAddLib _foamMkDir
 
 # -----------------------------------------------------------------------------

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

@@ -83,6 +83,19 @@ HashTable<T, Key, Hash>::HashTable(const HashTable<T, Key, Hash>& ht)
     }
 }
 
+template<class T, class Key, class Hash>
+HashTable<T, Key, Hash>::HashTable(const xfer<HashTable<T, Key, Hash> >& ht)
+:
+    HashTableName(),
+    tableSize_(0),
+    table_(NULL),
+    nElmts_(0),
+    endIter_(*this, NULL, 0),
+    endConstIter_(*this, NULL, 0)
+{
+    transfer(*ht);
+}
+
 
 // * * * * * * * * * * * * * * * * Destructor  * * * * * * * * * * * * * * * //
 

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

@@ -41,6 +41,7 @@ SourceFiles
 #include "label.H"
 #include "word.H"
 #include "className.H"
+#include "xfer.H"
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
@@ -155,6 +156,9 @@ public:
         //- Construct as copy
         HashTable(const HashTable<T, Key, Hash>&);
 
+        //- Construct by transferring the parameter contents
+        HashTable(const xfer<HashTable<T, Key, Hash> >&);
+
 
     // Destructor
 

src/OpenFOAM/containers/HashTables/StaticHashTable/StaticHashTable.C

@@ -76,6 +76,24 @@ StaticHashTable<T, Key, Hash>::StaticHashTable
 {}
 
 
+
+template<class T, class Key, class Hash>
+StaticHashTable<T, Key, Hash>::StaticHashTable
+(
+    const xfer<StaticHashTable<T, Key, Hash> >& ht
+)
+:
+    StaticHashTableName(),
+    keys_(0),
+    objects_(0),
+    nElmts_(0),
+    endIter_(*this, 0, 0),
+    endConstIter_(*this, 0, 0)
+{
+    transfer(*ht);
+}
+
+
 // * * * * * * * * * * * * * * * * Destructor  * * * * * * * * * * * * * * * //
 
 template<class T, class Key, class Hash>

src/OpenFOAM/containers/HashTables/StaticHashTable/StaticHashTable.H

@@ -46,6 +46,7 @@ SourceFiles
 #include "label.H"
 #include "word.H"
 #include "className.H"
+#include "xfer.H"
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
@@ -146,6 +147,8 @@ public:
         //- Construct as copy
         StaticHashTable(const StaticHashTable<T, Key, Hash>&);
 
+        //- Construct as copy
+        StaticHashTable(const xfer<StaticHashTable<T, Key, Hash> >&);
 
     // Destructor
 

src/OpenFOAM/containers/Lists/CompactListList/CompactListList.C

@@ -92,6 +92,12 @@ CompactListList<T>::CompactListList(const UList<label>& rowSizes, const T& t)
 }
 
 
+template<class T>
+CompactListList<T>::CompactListList(const xfer<CompactListList<T> >& lst)
+{
+    transfer(*lst);
+}
+
 template<class T>
 CompactListList<T>::CompactListList(CompactListList<T>& cll, bool reUse)
 :

src/OpenFOAM/containers/Lists/CompactListList/CompactListList.H

@@ -103,6 +103,9 @@ public:
         //- Construct given list of row-sizes
         CompactListList(const UList<label>& rowSizes, const T&);
 
+        //- Construct by transferring the parameter contents
+        CompactListList(const xfer<CompactListList<T> >&);
+
         //- Construct as copy or re-use as specified.
         CompactListList(CompactListList<T>&, bool reUse);
 

src/OpenFOAM/containers/Lists/DynamicList/DynamicList.H

@@ -84,6 +84,10 @@ class DynamicList
         //- Allocated size for underlying List.
         label allocSize_;
 
+    // Private Member Functions
+
+        // Disabled, since the usefulness and semantics are not quite clear
+        void setSize(const label, const T&);
 
 public:
 
@@ -117,12 +121,14 @@ public:
 
         // Edit
 
-            //- Reset size of List.
+            //- Alter the list size.
+            //  When the new size is greater than the addressed list size, the
+            //  allocated list sizes is adjusted and the
+            //  addressed size does not change.
+            //  Otherwise the addressed list size is just reduced and the
+            //  allocated size does not change.
             inline void setSize(const label);
 
-            //- Reset size of List and value for new elements.
-            inline void setSize(const label, const T&);
-
             //- Clear the list, i.e. set the size to zero.
             //  Allocated size does not change
             inline void clear();
@@ -156,7 +162,7 @@ public:
         //  resizing the list if necessary
         inline T& operator()(const label);
 
-        //- Assignment of all entries to the given value
+        //- Assignment of all addressed entries to the given value
         inline void operator=(const T&);
 
         //- Assignment from List<T>. Also handles assignment from DynamicList.

src/OpenFOAM/containers/Lists/DynamicList/DynamicListI.H

@@ -33,7 +33,7 @@ inline Foam::DynamicList<T, SizeInc, SizeMult, SizeDiv>::DynamicList()
     List<T>(SizeInc),
     allocSize_(SizeInc)
 {
-    List<T>::size() = 0;
+    List<T>::size(0);
 }
 
 
@@ -47,7 +47,7 @@ inline Foam::DynamicList<T, SizeInc, SizeMult, SizeDiv>::DynamicList
     List<T>(s),
     allocSize_(s)
 {
-    List<T>::size() = 0;
+    List<T>::size(0);
 }
 
 
@@ -79,18 +79,19 @@ inline void Foam::DynamicList<T, SizeInc, SizeMult, SizeDiv>::setSize
     const label s
 )
 {
-    if (s <= List<T>::size())
+    label nextFree = List<T>::size();
+    if (s <= nextFree)
     {
-        // shrink addressable size, leave allocated size untouched
+        // adjust addressed size, leave allocated size untouched
-        List<T>::size() = s;
+        nextFree = s;
     }
     else
     {
-        label nextFree = List<T>::size();
+        // adjust allocated size, leave addressed size untouched
         allocSize_ = s;
         List<T>::setSize(allocSize_);
-        List<T>::size() = nextFree;
     }
+    List<T>::size(nextFree);
 }
 
 
@@ -112,14 +113,17 @@ inline void Foam::DynamicList<T, SizeInc, SizeMult, SizeDiv>::setSize
         allocSize_ = s;
         List<T>::setSize(allocSize_, t);
         List<T>::size() = nextFree;
+=======
+>>>>>>> olesenm:src/OpenFOAM/containers/Lists/DynamicList/DynamicListI.H
     }
+    List<T>::size(nextFree);
 }
 
 
 template<class T, unsigned SizeInc, unsigned SizeMult, unsigned SizeDiv>
 inline void Foam::DynamicList<T, SizeInc, SizeMult, SizeDiv>::clear()
 {
-    List<T>::size() = 0;
+    List<T>::size(0);
 }
 
 
@@ -193,7 +197,7 @@ inline void Foam::DynamicList<T, SizeInc, SizeMult, SizeDiv>::append(const T& e)
         List<T>::setSize(allocSize_);
     }
 
-    List<T>::size() = nextFree;
+    List<T>::size(nextFree);
 
     this->operator[](nextFree - 1) = e;
 }
@@ -214,7 +218,7 @@ inline T Foam::DynamicList<T, SizeInc, SizeMult, SizeDiv>::remove()
 
     const T& val = List<T>::operator[](nextFree);
 
-    List<T>::size() = nextFree;
+    List<T>::size(nextFree);
 
     return val;
 }
@@ -242,7 +246,7 @@ inline T& Foam::DynamicList<T, SizeInc, SizeMult, SizeDiv>::operator()
         List<T>::setSize(allocSize_);
     }
 
-    List<T>::size() = nextFree;
+    List<T>::size(nextFree);
 
     return this->operator[](i);
 }
@@ -255,7 +259,6 @@ inline void Foam::DynamicList<T, SizeInc, SizeMult, SizeDiv>::operator=
 )
 {
     List<T>::operator=(t);
-    allocSize_ = List<T>::size();
 }
 
 

src/OpenFOAM/containers/Lists/List/List.C

@@ -125,6 +125,14 @@ Foam::List<T>::List(const List<T>& a)
 }
 
 
+// Construct by transferring the parameter contents
+template<class T>
+Foam::List<T>::List(const xfer<List<T> >& lst)
+{
+    transfer(*lst);
+}
+
+
 // Construct as copy or re-use as specified.
 template<class T>
 Foam::List<T>::List(List<T>& a, bool reUse)

src/OpenFOAM/containers/Lists/List/List.H

@@ -43,6 +43,7 @@ SourceFiles
 
 #include "UList.H"
 #include "autoPtr.H"
+#include "xfer.H"
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
@@ -77,6 +78,12 @@ class List
     public UList<T>
 {
 
+protected:
+
+    //- Override size to be inconsistent with allocated storage.
+    //  Use with care.
+    inline void size(const label);
+
 public:
 
     // Constructors
@@ -93,6 +100,9 @@ public:
         //- Copy constructor.
         List(const List<T>&);
 
+        //- Construct by transferring the parameter contents
+        List(const xfer<List<T> >&);
+
         //- Construct as copy or re-use as specified.
         List(List<T>&, bool reUse);
 
@@ -142,9 +152,6 @@ public:
         //- Return the number of elements in the UList.
         inline label size() const;
 
-        //- Override size to be inconsistent with allocated storage.
-        //  Use with care.
-        inline label& size();
 
         // Edit
 

src/OpenFOAM/containers/Lists/List/ListI.H

@@ -53,19 +53,18 @@ inline T& Foam::List<T>::newElmt(const label i)
 
 
 template<class T>
-inline Foam::label Foam::List<T>::size() const
+inline void Foam::List<T>::size(const label n)
 {
-    return UList<T>::size_;
+    UList<T>::size_ = n;
 }
 
 
 template<class T>
-inline Foam::label& Foam::List<T>::size()
+inline Foam::label Foam::List<T>::size() const
 {
     return UList<T>::size_;
 }
 
-
 // * * * * * * * * * * * * * * * Member Operators  * * * * * * * * * * * * * //
 
 template<class T>

src/OpenFOAM/containers/Lists/PackedList/PackedList.C

@@ -44,6 +44,7 @@ PackedList<nBits>::PackedList(const label size, const unsigned int val)
 }
 
 
+
 //- Copy constructor.
 template<int nBits>
 PackedList<nBits>::PackedList(const PackedList<nBits>& PList)
@@ -53,6 +54,13 @@ PackedList<nBits>::PackedList(const PackedList<nBits>& PList)
 {}
 
 
+template<int nBits>
+PackedList<nBits>::PackedList(const xfer<PackedList<nBits> >& lst)
+{
+    transfer(*lst);
+}
+
+
 //- Construct from labelList
 template<int nBits>
 PackedList<nBits>::PackedList(const labelList& lst)

src/OpenFOAM/containers/Lists/PackedList/PackedList.H

@@ -134,6 +134,9 @@ public:
         //- Copy constructor.
         PackedList(const PackedList<nBits>& PList);
 
+        //- Construct by transferring the parameter contents
+        PackedList(const xfer<PackedList<nBits> >&);
+
         //- Construct from labelList.
         PackedList(const labelList&);
 

src/OpenFOAM/containers/Lists/PtrList/PtrList.C

@@ -71,6 +71,13 @@ Foam::PtrList<T>::PtrList(const PtrList<T>& a, const CloneArg& cloneArg)
 }
 
 
+template<class T>
+Foam::PtrList<T>::PtrList(const xfer<PtrList<T> >& lst)
+{
+    transfer(*lst);
+}
+
+
 template<class T>
 Foam::PtrList<T>::PtrList(PtrList<T>& a, bool reUse)
 :

src/OpenFOAM/containers/Lists/PtrList/PtrList.H

@@ -129,6 +129,9 @@ public:
         template<class CloneArg>
         PtrList(const PtrList<T>&, const CloneArg&);
 
+        //- Construct by transferring the parameter contents
+        PtrList(const xfer<PtrList<T> >&);
+
         //- Construct as copy or re-use as specified.
         PtrList(PtrList<T>&, bool reUse);
 

src/OpenFOAM/containers/Lists/SortableList/SortableList.C

@@ -40,6 +40,17 @@ Foam::SortableList<Type>::SortableList(const List<Type>& values)
     sort();
 }
 
+// Construct from List by transferring
+template <class Type>
+Foam::SortableList<Type>::SortableList(const xfer<List<Type> >& values)
+:
+    List<Type>(),
+    indices_((*values).size())
+{
+    List<Type>::transfer(*values);
+    sort();
+}
+
 
 // Construct given size. Sort later on.
 template <class Type>
@@ -86,7 +97,7 @@ void Foam::SortableList<Type>::sort()
         indices_[i] = i;
     }
 
-    //Foam::sort(indices_, less(*this));
+    // Foam::sort(indices_, less(*this));
     Foam::stableSort(indices_, less(*this));
 
     List<Type> tmpValues(this->size());

src/OpenFOAM/containers/Lists/SortableList/SortableList.H

@@ -29,6 +29,8 @@ Description
     A list that is sorted upon construction or when explicitly requested
     with the sort() method.
 
+    Uses the Foam::stableSort() algorithm.
+
 SourceFiles
     SortableList.C
 
@@ -84,10 +86,14 @@ public:
 
     // Constructors
 
-        //- Construct from List, sorting the elements. Starts with indices set
+        //- Construct from List, sorting the elements.
-        //  to index in argument
+        //  Starts with indices set to index in argument
         explicit SortableList(const List<Type>&);
 
+        //- Construct from tranferred List, sorting the elements.
+        //  Starts with indices set to index in argument
+        explicit SortableList(const xfer<List<Type> >&);
+
         //- Construct given size. Sort later on.
         explicit SortableList(const label size);
 

src/OpenFOAM/containers/Lists/UList/UListIO.C

@@ -60,7 +60,7 @@ void Foam::UList<T>::writeEntry(const word& keyword, Ostream& os) const
 
 
 template<class T>
-Foam::Ostream& Foam:: operator<<(Foam::Ostream& os, const Foam::UList<T>& L)
+Foam::Ostream& Foam::operator<<(Foam::Ostream& os, const Foam::UList<T>& L)
 {
     // Write list contents depending on data format
     if (os.format() == IOstream::ASCII || !contiguous<T>())

src/OpenFOAM/containers/Lists/UPtrList/UPtrList.C

@@ -50,6 +50,13 @@ UPtrList<T>::UPtrList(const label s)
 {}
 
 
+template<class T>
+UPtrList<T>::UPtrList(const xfer<UPtrList<T> >& lst)
+{
+    transfer(*lst);
+}
+
+
 template<class T>
 UPtrList<T>::UPtrList(UPtrList<T>& a, bool reUse)
 :

src/OpenFOAM/containers/Lists/UPtrList/UPtrList.H

@@ -110,6 +110,9 @@ public:
         //- Construct with length specified.
         explicit UPtrList(const label);
 
+        //- Construct by transferring the parameter contents
+        UPtrList(const xfer<UPtrList<T> >&);
+
         //- Construct as copy or re-use as specified.
         UPtrList(UPtrList<T>&, bool reUse);
 

src/OpenFOAM/containers/misc/xfer.H

@@ -0,0 +1,155 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2008 OpenCFD Ltd.
+     \\/     M anipulation  |
+-------------------------------------------------------------------------------
+License
+    This file is part of OpenFOAM.
+
+    OpenFOAM is free software; you can redistribute it and/or modify it
+    under the terms of the GNU General Public License as published by the
+    Free Software Foundation; either version 2 of the License, or (at your
+    option) any later version.
+
+    OpenFOAM is distributed in the hope that it will be useful, but WITHOUT
+    ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+    FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
+    for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with OpenFOAM; if not, write to the Free Software Foundation,
+    Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+
+Class
+    Foam::xfer
+
+Description
+    A simple container that can be used to copy or transfer the contents
+    of objects of type \<T\>.
+
+    Since it is decided upon construction of the xfer object whether the
+    parameter is to be copied or transferred, the contents of resulting
+    object can be transferred unconditionally.
+
+    This greatly simplifies defining the constructors for other classes
+    with mixed transfer/copy semantics.
+
+    The wrapped object of type \<T\> must implement a transfer() method and
+    an operator=() copy method.
+
+Note
+    The macros xferCopy(T,arg) and xferMove(T,arg) can be used as
+    workarounds for passing temporaries to copy-constructors.
+
+SourceFiles
+    xferI.H
+
+\*---------------------------------------------------------------------------*/
+
+#ifndef xfer_H
+#define xfer_H
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+namespace Foam
+{
+
+/*---------------------------------------------------------------------------*\
+                           Class xfer Declaration
+\*---------------------------------------------------------------------------*/
+
+template<class T>
+class xfer
+{
+    // Private data
+
+        //- Pointer to temporary object
+        mutable T* ptr_;
+
+public:
+
+    // Constructors
+
+        //- Store object pointer and manage its deletion
+        //  Can also be used later to transfer by assignment
+        inline explicit xfer(T* = 0);
+
+        //- Construct by copying or by transferring the parameter contents
+        inline xfer(T&, bool allowTransfer=false);
+
+        //- Construct by copying the parameter contents
+        inline xfer(const T&);
+
+        //- Construct by transferring the contents
+        inline xfer(const xfer<T>&);
+
+    // Destructor
+
+        inline ~xfer();
+
+    // Member Operators
+
+        //- Transfer the contents into the object
+        inline void operator=(T&);
+
+        //- Transfer the contents into the object
+        inline void operator=(const xfer<T>&);
+
+        //- Return a non-const reference to const object
+        //  @sa xferCopy, xferMove macros alternatives for copy-constructors
+        inline const xfer<T>& operator()() const;
+
+        //- Reference to the underlying datatype
+        inline T& operator*() const;
+
+};
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace Foam
+
+/**
+ * @def xferCopy(T,arg)
+ * Construct by copying the contents of the @a arg
+ * and return a const reference to an xfer of type \<T\>
+ *
+ * Useful for constructors where the argument is temporary.
+ * This is a workaround for a template resolution issue.
+ *
+ * @sa xferMove and Foam::xfer
+*/
+#define xferCopy(T,arg) \
+    (static_cast<const Foam::xfer< T >&>(Foam::xfer< T >(arg)()))
+
+/**
+ * @def xferMove(T,arg)
+ * Construct by transferring the contents of the @a arg
+ * and return a const reference to an xfer of type \<T\>
+ *
+ * Useful for constructors where the argument is temporary.
+ * This is a workaround for a template resolution issue.
+ *
+ * @par Example Use
+ * @code
+ *     List<label> a;
+ *     ...
+ *     List<label> b(xferMove(List<label>, a));
+ * @endcode
+ *
+ * @sa xferCopy and Foam::xfer
+*/
+#define xferMove(T,arg) \
+    (static_cast<const Foam::xfer< T >&>(Foam::xfer< T >(arg, true)()))
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+#include "xferI.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+#endif
+
+// ************************************************************************* //

src/OpenFOAM/containers/misc/xferI.H

@@ -0,0 +1,113 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2008 OpenCFD Ltd.
+     \\/     M anipulation  |
+-------------------------------------------------------------------------------
+License
+    This file is part of OpenFOAM.
+
+    OpenFOAM is free software; you can redistribute it and/or modify it
+    under the terms of the GNU General Public License as published by the
+    Free Software Foundation; either version 2 of the License, or (at your
+    option) any later version.
+
+    OpenFOAM is distributed in the hope that it will be useful, but WITHOUT
+    ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+    FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
+    for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with OpenFOAM; if not, write to the Free Software Foundation,
+    Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+
+\*---------------------------------------------------------------------------*/
+
+// * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
+
+template<class T>
+inline Foam::xfer<T>::xfer(T* p)
+:
+    ptr_(p ? p : new T)
+{}
+
+
+template<class T>
+inline Foam::xfer<T>::xfer(T& t, bool allowTransfer)
+:
+    ptr_(new T)
+{
+    if (allowTransfer)
+    {
+        ptr_->transfer(t);
+    }
+    else
+    {
+        ptr_->operator=(t);
+    }
+}
+
+
+template<class T>
+inline Foam::xfer<T>::xfer(const T& t)
+:
+    ptr_(new T)
+{
+    ptr_->operator=(t);
+}
+
+
+template<class T>
+inline Foam::xfer<T>::xfer(const xfer<T>& t)
+:
+    ptr_(new T)
+{
+    ptr_->transfer(*(t.ptr_));
+}
+
+
+// * * * * * * * * * * * * * * * * Destructor  * * * * * * * * * * * * * * * //
+
+template<class T>
+inline Foam::xfer<T>::~xfer()
+{
+    delete ptr_;
+    ptr_ = 0;
+}
+
+
+// * * * * * * * * * * * * * * * Member Operators  * * * * * * * * * * * * * //
+
+template<class T>
+inline void Foam::xfer<T>::operator=(T& t)
+{
+    ptr_->transfer(t);
+}
+
+
+template<class T>
+inline void Foam::xfer<T>::operator=(const xfer<T>& t)
+{
+    // silently ignore copy to self
+    if (this != &t)
+    {
+        ptr_->transfer(*(t.ptr_));
+    }
+}
+
+
+template<class T>
+inline const Foam::xfer<T>& Foam::xfer<T>::operator()() const
+{
+    return *this;
+}
+
+
+template<class T>
+inline T& Foam::xfer<T>::operator*() const
+{
+    return *ptr_;
+}
+
+// ************************************************************************* //

src/OpenFOAM/db/IOobject/IOobject.H

@@ -155,7 +155,7 @@ protected:
     // Protected member functions
 
         //- Construct and return an IFstream for the object.
-        //  The results is NULL if the stream constuction failed
+        //  The results is NULL if the stream construction failed
         Istream* objectStream();
 
         //- Set the object state to bad

src/OpenFOAM/db/IOobjects/IOField/IOField.C

@@ -29,41 +29,15 @@ License
 // * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
 
 template<class Type>
-Foam::IOField<Type>::IOField
+Foam::IOField<Type>::IOField(const IOobject& io)
-(
-    const IOobject& io
-)
 :
-    regIOobject(io),
+    regIOobject(io)
-    Field<Type>(readStream(typeName))
 {
-    close();
+    if
-}
+    (
-
+        io.readOpt() == IOobject::MUST_READ
-
+     || (io.readOpt() == IOobject::READ_IF_PRESENT && headerOk())
-template<class Type>
+    )
-Foam::IOField<Type>::IOField
-(
-    const IOobject& io,
-    const label size
-)
-:
-    regIOobject(io),
-    Field<Type>(size)
-{}
-
-
-template<class Type>
-Foam::IOField<Type>::IOField
-(
-    const IOobject& io,
-    const Field<Type>& f
-)
-:
-    regIOobject(io),
-    Field<Type>(f)
-{
-    if (io.readOpt() == IOobject::READ_IF_PRESENT && headerOk())
     {
         readStream(typeName) >> *this;
         close();
@@ -71,11 +45,77 @@ Foam::IOField<Type>::IOField
 }
 
 
+template<class Type>
+Foam::IOField<Type>::IOField(const IOobject& io, const label size)
+:
+    regIOobject(io)
+{
+    if
+    (
+        io.readOpt() == IOobject::MUST_READ
+     || (io.readOpt() == IOobject::READ_IF_PRESENT && headerOk())
+    )
+    {
+        readStream(typeName) >> *this;
+        close();
+    }
+    else
+    {
+        Field<Type>::setSize(size);
+    }
+}
+
+
+template<class Type>
+Foam::IOField<Type>::IOField(const IOobject& io, const Field<Type>& f)
+:
+    regIOobject(io)
+{
+    if
+    (
+        io.readOpt() == IOobject::MUST_READ
+     || (io.readOpt() == IOobject::READ_IF_PRESENT && headerOk())
+    )
+    {
+        readStream(typeName) >> *this;
+        close();
+    }
+    else
+    {
+        Field<Type>::operator=(f);
+    }
+}
+
+
 // * * * * * * * * * * * * * * * Destructor  * * * * * * * * * * * * * * * * //
 
-template<class T>
+template<class Type>
-Foam::IOField<T>::~IOField()
+Foam::IOField<Type>::~IOField()
 {}
 
+// * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
+
+template<class Type>
+bool Foam::IOField<Type>::writeData(Ostream& os) const
+{
+    return (os << static_cast<const Field<Type>&>(*this)).good();
+}
+
+
+// * * * * * * * * * * * * * * * Member Operators  * * * * * * * * * * * * * //
+
+template<class Type>
+void Foam::IOField<Type>::operator=(const IOField<Type>& rhs)
+{
+    Field<Type>::operator=(rhs);
+}
+
+
+template<class Type>
+void Foam::IOField<Type>::operator=(const Field<Type>& rhs)
+{
+    Field<Type>::operator=(rhs);
+}
+
 
 // ************************************************************************* //

src/OpenFOAM/db/IOobjects/IOField/IOField.H

@@ -63,24 +63,13 @@ public:
     // Constructors
 
         //- Construct from IOobject
-        IOField
+        IOField(const IOobject&);
-        (
-            const IOobject&
-        );
 
         //- Construct from components
-        IOField
+        IOField(const IOobject&, const Field<Type>&);
-        (
-            const IOobject&,
-            const Field<Type>&
-        );
 
         //- Construct from IOobject and size (does not set values)
-        IOField
+        IOField(const IOobject&, const label size);
-        (
-            const IOobject&,
-            const label size
-        );
 
 
     // Destructor
@@ -90,23 +79,14 @@ public:
 
     // Member functions
 
-        bool writeData(Ostream& os) const
+        bool writeData(Ostream&) const;
-        {
-            return (os << static_cast<const Field<Type>&>(*this)).good();
-        }
 
 
     // Member operators
 
-        void operator=(const IOField<Type>& iof)
+        void operator=(const IOField<Type>&);
-        {
-            Field<Type>::operator=(iof);
-        }
 
-        void operator=(const Field<Type>& f)
+        void operator=(const Field<Type>&);
-        {
-            Field<Type>::operator=(f);
-        }
 };
 
 

src/OpenFOAM/db/IOobjects/IOList/IOList.C

@@ -84,7 +84,6 @@ Foam::IOList<T>::IOList(const IOobject& io, const List<T>& list)
     {
         List<T>::operator=(list);
     }
-
 }
 
 
@@ -95,6 +94,16 @@ Foam::IOList<T>::~IOList()
 {}
 
 
+
+// * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
+
+template<class T>
+bool Foam::IOList<T>::writeData(Ostream& os) const
+{
+    return (os << *this).good();
+}
+
+
 // * * * * * * * * * * * * * * * Member Operators  * * * * * * * * * * * * * //
 
 template<class T>
@@ -111,11 +120,4 @@ void Foam::IOList<T>::operator=(const List<T>& rhs)
 }
 
 
-template<class T>
-bool Foam::IOList<T>::writeData(Ostream& os) const
-{
-    return (os << *this).good();
-}
-
-
 // ************************************************************************* //

src/OpenFOAM/db/IOobjects/IOMap/IOMap.C

@@ -31,8 +31,7 @@ License
 template<class T>
 Foam::IOMap<T>::IOMap(const IOobject& io)
 :
-    regIOobject(io),
+    regIOobject(io)
-    Map<T>()
 {
     if
     (

src/OpenFOAM/db/IOobjects/IOPtrList/IOPtrList.C

@@ -91,14 +91,7 @@ Foam::IOPtrList<T>::~IOPtrList()
 {}
 
 
-// * * * * * * * * * * * * * * * Member Operators  * * * * * * * * * * * * * //
+// * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
-
-template<class T>
-void Foam::IOPtrList<T>::operator=(const IOPtrList<T>& rhs)
-{
-    PtrList<T>::operator=(rhs);
-}
-
 
 template<class T>
 bool Foam::IOPtrList<T>::writeData(Ostream& os) const
@@ -107,4 +100,12 @@ bool Foam::IOPtrList<T>::writeData(Ostream& os) const
 }
 
 
+// * * * * * * * * * * * * * * * Member Operators  * * * * * * * * * * * * * //
+
+template<class T>
+void Foam::IOPtrList<T>::operator=(const IOPtrList<T>& rhs)
+{
+    PtrList<T>::operator=(rhs);
+}
+
 // ************************************************************************* //

src/OpenFOAM/db/IOobjects/IOdictionary/IOdictionary.C

@@ -42,15 +42,10 @@ namespace Foam
 
 // * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
 
-Foam::IOdictionary::IOdictionary
+Foam::IOdictionary::IOdictionary(const IOobject& io)
-(
-    const IOobject& io
-)
 :
     regIOobject(io)
 {
-    dictionary::name() = IOobject::objectPath();
-
     if
     (
         io.readOpt() == IOobject::MUST_READ
@@ -60,18 +55,29 @@ Foam::IOdictionary::IOdictionary
         readStream(typeName) >> *this;
         close();
     }
+
+    dictionary::name() = IOobject::objectPath();
 }
 
 
-Foam::IOdictionary::IOdictionary
+Foam::IOdictionary::IOdictionary(const IOobject& io, const dictionary& dict)
-(
-    const IOobject& io,
-    const dictionary& dict
-)
 :
-    regIOobject(io),
+    regIOobject(io)
-    dictionary(dict)
 {
+    if
+    (
+        io.readOpt() == IOobject::MUST_READ
+     || (io.readOpt() == IOobject::READ_IF_PRESENT && headerOk())
+    )
+    {
+        readStream(typeName) >> *this;
+        close();
+    }
+    else
+    {
+        dictionary::operator=(dict);
+    }
+
     dictionary::name() = IOobject::objectPath();
 }
 
@@ -92,9 +98,9 @@ const Foam::word& Foam::IOdictionary::name() const
 
 // * * * * * * * * * * * * * * * Member Operators  * * * * * * * * * * * * * //
 
-void Foam::IOdictionary::operator=(const IOdictionary& d)
+void Foam::IOdictionary::operator=(const IOdictionary& rhs)
 {
-    dictionary::operator=(d);
+    dictionary::operator=(rhs);
 }
 
 

src/OpenFOAM/db/IOobjects/IOdictionary/IOdictionaryIO.C

@@ -34,27 +34,17 @@ Description
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
-namespace Foam
+bool Foam::IOdictionary::readData(Istream& is)
-{
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-bool IOdictionary::readData(Istream& is)
 {
     is >> *this;
     return !is.bad();
 }
 
 
-bool IOdictionary::writeData(Ostream& os) const
+bool Foam::IOdictionary::writeData(Ostream& os) const
 {
     dictionary::write(os, false);
     return os.good();
 }
 
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-} // End namespace Foam
-
 // ************************************************************************* //

src/OpenFOAM/db/functionObjectList/functionObjectList.H

@@ -63,7 +63,7 @@ class functionObjectList
         //- Dictionary containing the list of function object specifications
         const dictionary& foDict_;
 
-        //- Switch for the execultion of the functionObjects
+        //- Switch for the execution of the functionObjects
         bool execution_;
 
 
@@ -84,7 +84,7 @@ public:
         //  The functionObject specifications are read from the controlDict
         functionObjectList
         (
-            const Time& t,
+            const Time&,
             const bool execution = true
         );
 
@@ -93,7 +93,7 @@ public:
         //  setting
         functionObjectList
         (
-            const Time& t,
+            const Time&,
             const dictionary& foDict,
             const bool execution = true
         );

src/OpenFOAM/db/regIOobject/regIOobject.H

@@ -101,7 +101,7 @@ public:
         //- Construct as copy
         regIOobject(const regIOobject&);
 
-        //- Construct as copy, and transfering registry registration to copy
+        //- Construct as copy, and transferring registry registration to copy
         //  if registerCopy is true
         regIOobject(const regIOobject&, bool registerCopy);
 

src/OpenFOAM/fields/GeometricFields/GeometricField/GeometricField.C

@@ -105,18 +105,15 @@ bool Foam::GeometricField<Type, PatchField, GeoMesh>::readIfPresent()
         (
             "GeometricField<Type, PatchField, GeoMesh>::readIfPresent()"
         )   << "read option IOobject::MUST_READ "
-            << "suggests that a read constuctor for field " << this->name()
+            << "suggests that a read constructor for field " << this->name()
             << " would be more appropriate." << endl;
     }
-    else if (this->readOpt() == IOobject::READ_IF_PRESENT)
+    else if (this->readOpt() == IOobject::READ_IF_PRESENT && this->headerOk())
-    {
-        if (this->headerOk())
     {
         boundaryField_.transfer(readField(this->readStream(typeName))());
         this->close();
 
         // Check compatibility between field and mesh
-
         if (this->size() != GeoMesh::size(this->mesh()))
         {
             FatalIOErrorIn
@@ -134,7 +131,6 @@ bool Foam::GeometricField<Type, PatchField, GeoMesh>::readIfPresent()
 
         return true;
     }
-    }
 
     return false;
 }
@@ -149,7 +145,7 @@ bool Foam::GeometricField<Type, PatchField, GeoMesh>::readOldTimeIfPresent()
         this->name()  + "_0",
         this->time().timeName(),
         this->db(),
-        IOobject::MUST_READ,
+        IOobject::READ_IF_PRESENT,
         IOobject::AUTO_WRITE
     );
 

src/OpenFOAM/meshes/polyMesh/polyMesh.H

@@ -214,7 +214,7 @@ public:
         //- Construct from IOobject
         explicit polyMesh(const IOobject& io);
 
-        //- Construct from components without boundary.
+        //- Construct without boundary from components.
         //  Boundary is added using addPatches() member function
         polyMesh
         (
@@ -226,8 +226,7 @@ public:
             const bool syncPar = true
         );
 
-        //- Construct from components with cells rather than owner
+        //- Construct without boundary with cells rather than owner/neighbour.
-        //  and neighbourwithout boundary.
         //  Boundary is added using addPatches() member function
         polyMesh
         (
@@ -263,8 +262,7 @@ public:
 
         // Database
 
-            //- Over-ride the objectRegistry dbDir
+            //- Override the objectRegistry dbDir for a single-region case
-            //  if this is single-region case
             virtual const fileName& dbDir() const;
 
             //- Return the local mesh directory (dbDir()/meshSubDir)
@@ -311,17 +309,17 @@ public:
                 return bounds_;
             }
 
-            //- Return the vector of valid directions in mesh
+            //- Return the vector of valid directions in mesh.
-            //  defined according to the presence of empty patches.
+            //  Defined according to the presence of empty patches.
             //  1 indicates valid direction and -1 an invalid direction.
             const Vector<label>& directions() const;
 
-            //- Return the number of valid geoemtric dimensions in the mesh
+            //- Return the number of valid geometric dimensions in the mesh
             label nGeometricD() const;
 
-            //- Return the number of valid solution dimensions in the mesh
+            //- Return the number of valid solution dimensions in the mesh.
             //  For wedge cases this includes the circumferential direction
-            //  in case of swirl
+            //  in case of swirl.
             label nSolutionD() const;
 
             //- Return point zone mesh

src/OpenFOAM/meshes/polyMesh/zones/cellZone/cellZone.C

@@ -114,6 +114,22 @@ Foam::cellZone::cellZone
 {}
 
 
+Foam::cellZone::cellZone
+(
+    const word& name,
+    const xfer<labelList>& addr,
+    const label index,
+    const cellZoneMesh& zm
+)
+:
+    labelList(addr),
+    name_(name),
+    index_(index),
+    zoneMesh_(zm),
+    cellLookupMapPtr_(NULL)
+{}
+
+
 // Construct from dictionary
 Foam::cellZone::cellZone
 (
@@ -148,6 +164,21 @@ Foam::cellZone::cellZone
     cellLookupMapPtr_(NULL)
 {}
 
+Foam::cellZone::cellZone
+(
+    const cellZone& cz,
+    const xfer<labelList>& addr,
+    const label index,
+    const cellZoneMesh& zm
+)
+:
+    labelList(addr),
+    name_(cz.name()),
+    index_(index),
+    zoneMesh_(zm),
+    cellLookupMapPtr_(NULL)
+{}
+
 
 // * * * * * * * * * * * * * * * * Destructor  * * * * * * * * * * * * * * * //
 

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

@@ -128,26 +128,45 @@ public:
             const word& name,
             const labelList& addr,
             const label index,
-            const cellZoneMesh& zm
+            const cellZoneMesh&
+        );
+
+        //- Construct from components, transferring contents
+        cellZone
+        (
+            const word& name,
+            const xfer<labelList>& addr,
+            const label index,
+            const cellZoneMesh&
         );
 
         //- Construct from dictionary
         cellZone
         (
             const word& name,
-            const dictionary& dict,
+            const dictionary&,
             const label index,
-            const cellZoneMesh& zm
+            const cellZoneMesh&
         );
 
         //- Construct given the original zone and resetting the
         //  cell list and zone mesh information
         cellZone
         (
-            const cellZone& cz,
+            const cellZone&,
             const labelList& addr,
             const label index,
-            const cellZoneMesh& zm
+            const cellZoneMesh&
+        );
+
+        //- Construct given the original zone, resetting the
+        //  cell list and zone mesh information
+        cellZone
+        (
+            const cellZone&,
+            const xfer<labelList>& addr,
+            const label index,
+            const cellZoneMesh&
         );
 
         //- Construct and return a clone, resetting the zone mesh
@@ -182,7 +201,7 @@ public:
         static autoPtr<cellZone> New
         (
             const word& name,
-            const dictionary& dict,
+            const dictionary&,
             const label index,
             const cellZoneMesh&
         );

src/OpenFOAM/meshes/polyMesh/zones/faceZone/faceZone.C

@@ -242,6 +242,30 @@ Foam::faceZone::faceZone
 }
 
 
+Foam::faceZone::faceZone
+(
+    const word& name,
+    const xfer<labelList>& addr,
+    const xfer<boolList>& fm,
+    const label index,
+    const faceZoneMesh& zm
+)
+:
+    labelList(addr),
+    name_(name),
+    flipMap_(fm),
+    index_(index),
+    zoneMesh_(zm),
+    patchPtr_(NULL),
+    masterCellsPtr_(NULL),
+    slaveCellsPtr_(NULL),
+    mePtr_(NULL),
+    faceLookupMapPtr_(NULL)
+{
+    checkAddressing();
+}
+
+
 // Construct from dictionary
 Foam::faceZone::faceZone
 (
@@ -292,6 +316,30 @@ Foam::faceZone::faceZone
 }
 
 
+Foam::faceZone::faceZone
+(
+    const faceZone& fz,
+    const xfer<labelList>& addr,
+    const xfer<boolList>& fm,
+    const label index,
+    const faceZoneMesh& zm
+)
+:
+    labelList(addr),
+    name_(fz.name()),
+    flipMap_(fm),
+    index_(index),
+    zoneMesh_(zm),
+    patchPtr_(NULL),
+    masterCellsPtr_(NULL),
+    slaveCellsPtr_(NULL),
+    mePtr_(NULL),
+    faceLookupMapPtr_(NULL)
+{
+    checkAddressing();
+}
+
+
 // * * * * * * * * * * * * * * * * Destructor  * * * * * * * * * * * * * * * //
 
 Foam::faceZone::~faceZone()

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

@@ -163,24 +163,45 @@ public:
             const faceZoneMesh& zm
         );
 
+        //- Construct from components, transferring contents
+        faceZone
+        (
+            const word& name,
+            const xfer<labelList>& addr,
+            const xfer<boolList>& fm,
+            const label index,
+            const faceZoneMesh&
+        );
+
         //- Construct from dictionary
         faceZone
         (
             const word& name,
-            const dictionary& dict,
+            const dictionary&,
             const label index,
-            const faceZoneMesh& zm
+            const faceZoneMesh&
         );
 
         //- Construct given the original zone and resetting the
         //  face list and zone mesh information
         faceZone
         (
-            const faceZone& fz,
+            const faceZone&,
             const labelList& addr,
             const boolList& fm,
             const label index,
-            const faceZoneMesh& zm
+            const faceZoneMesh&
+        );
+
+        //- Construct given the original zone, resetting the
+        //  face list and zone mesh information
+        faceZone
+        (
+            const faceZone&,
+            const xfer<labelList>& addr,
+            const xfer<boolList>& fm,
+            const label index,
+            const faceZoneMesh&
         );
 
         //- Construct and return a clone, resetting the zone mesh
@@ -216,9 +237,9 @@ public:
         static autoPtr<faceZone> New
         (
             const word& name,
-            const dictionary& dict,
+            const dictionary&,
             const label index,
-            const faceZoneMesh& zm
+            const faceZoneMesh&
         );
 
 

src/OpenFOAM/meshes/polyMesh/zones/pointZone/pointZone.C

@@ -112,6 +112,22 @@ Foam::pointZone::pointZone
 {}
 
 
+Foam::pointZone::pointZone
+(
+    const word& name,
+    const xfer<labelList>& addr,
+    const label index,
+    const pointZoneMesh& zm
+)
+:
+    labelList(addr),
+    name_(name),
+    index_(index),
+    zoneMesh_(zm),
+    pointLookupMapPtr_(NULL)
+{}
+
+
 // Construct from dictionary
 Foam::pointZone::pointZone
 (
@@ -147,6 +163,22 @@ Foam::pointZone::pointZone
 {}
 
 
+Foam::pointZone::pointZone
+(
+    const pointZone& pz,
+    const xfer<labelList>& addr,
+    const label index,
+    const pointZoneMesh& zm
+)
+:
+    labelList(addr),
+    name_(pz.name()),
+    index_(index),
+    zoneMesh_(zm),
+    pointLookupMapPtr_(NULL)
+{}
+
+
 // * * * * * * * * * * * * * * * * Destructor  * * * * * * * * * * * * * * * //
 
 Foam::pointZone::~pointZone()

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

@@ -130,26 +130,45 @@ public:
             const word& name,
             const labelList& addr,
             const label index,
-            const pointZoneMesh& zm
+            const pointZoneMesh&
+        );
+
+        //- Construct from components, transferring contents
+        pointZone
+        (
+            const word& name,
+            const xfer<labelList>& addr,
+            const label index,
+            const pointZoneMesh&
         );
 
         //- Construct from dictionary
         pointZone
         (
             const word& name,
-            const dictionary& dict,
+            const dictionary&,
             const label index,
-            const pointZoneMesh& zm
+            const pointZoneMesh&
         );
 
         //- Construct given the original zone and resetting the
         //  point list and zone mesh information
         pointZone
         (
-            const pointZone& pz,
+            const pointZone&,
             const labelList& addr,
             const label index,
-            const pointZoneMesh& zm
+            const pointZoneMesh&
+        );
+
+        //- Construct given the original zone, resetting the
+        //  face list and zone mesh information
+        pointZone
+        (
+            const pointZone&,
+            const xfer<labelList>& addr,
+            const label index,
+            const pointZoneMesh&
         );
 
         //- Construct and return a clone, resetting the zone mesh
@@ -184,7 +203,7 @@ public:
         static autoPtr<pointZone> New
         (
             const word& name,
-            const dictionary& dict,
+            const dictionary&,
             const label index,
             const pointZoneMesh&
         );

src/OpenFOAM/meshes/primitiveMesh/primitiveMeshPointCells.C

@@ -167,7 +167,7 @@ const labelList& primitiveMesh::pointCells
             }
         }
 
-        storage.size() = n;
+        storage.setSize(n);
 
         return storage;
     }

src/postProcessing/systemCall/systemCall.H

@@ -60,8 +60,7 @@ protected:
 
     // Private data
 
-        //- Name of this set of forces,
+        //- Name of this set of system calls
-        //  Also used as the name of the probes directory.
         word name_;
 
         const objectRegistry& obr_;

tutorials/XiFoam/Allrun

@@ -3,7 +3,7 @@
 . $WM_PROJECT_DIR/bin/tools/RunFunctions
 
 # Get application name from directory
-application=`basename $PWD`
+application=${PWD##*/}
 
 setControlDict () {
     controlDict="system/controlDict"

tutorials/icoFoam/Allrun

@@ -3,7 +3,7 @@
 . $WM_PROJECT_DIR/bin/tools/RunFunctions
 
 # Get application name from directory
-application=`basename $PWD`
+application=${PWD##*/}
 
 cavityCases="cavity cavityFine cavityGrade cavityHighRe cavityClipped"
 

tutorials/interFoam/Allrun

@@ -3,7 +3,7 @@
 . $WM_PROJECT_DIR/bin/tools/RunFunctions
 
 # Get application name from directory
-application=`basename $PWD`
+application=${PWD##*/}
 
 setDamBreakFine ()
 {

tutorials/laplacianFoam/flange/Allrun

@@ -5,9 +5,10 @@
 # Get application directory
 application="laplacianFoam"
 
-runIdeasToFoam ()
+runAnsysToFoam()
 {
-    if [ -f log.ideasToFoam ] ; then
+    if [ -f log.ansysToFoam ]
+    then
         echo "ansysToFoam already run on $PWD: remove log file to run"
     else
         echo "ansysToFoam: converting mesh $1"
@@ -15,7 +16,7 @@ runIdeasToFoam ()
     fi
 }
 
-runIdeasToFoam flange.ans 0.001
+runAnsysToFoam flange.ans 0.001
 runApplication $application
 runApplication foamToFieldview9
 runApplication foamToEnsight

tutorials/lesCavitatingFoam/Allrun

@@ -7,21 +7,21 @@ application="lesCavitatingFoam"
 
 refineMeshByCellSet()
 {
+   while [ $# -ge 1 ]
+   do
       echo "creating cell set for primary zone - $1"
       cp system/cellSetDict.$1 system/cellSetDict
-    cellSet >& log.cellSet.$1
+      cellSet > log.cellSet.$1 2>&1
 
       echo "refining primary zone - $1"
-    refineMesh -dict -overwrite >& log.refineMesh.$1
+      refineMesh -dict -overwrite > log.refineMesh.$1 2>&1
+      shift
+   done
 }
 
 cd throttle
     runApplication blockMesh
-
+    refineMeshByCellSet 1 2 3
-    refineMeshByCellSet 1
-    refineMeshByCellSet 2
-    refineMeshByCellSet 3
-
     runApplication $application
 cd ..
 
@@ -29,10 +29,7 @@ cd throttle3D
     cp -r 0.org 0
 
     runApplication blockMesh
-
+    refineMeshByCellSet 1 2 3
-    refineMeshByCellSet 1
-    refineMeshByCellSet 2
-    refineMeshByCellSet 3
 
     echo "mapping fields from 2D throttle case"
     mapFields ../throttle -sourceTime latestTime >& log.mapFields

tutorials/rasCavitatingFoam/throttle/Allrun

@@ -7,20 +7,19 @@ application="rasCavitatingFoam"
 
 refineMeshByCellSet()
 {
+   while [ $# -ge 1 ]
+   do
       echo "creating cell set for primary zone - $1"
       cp system/cellSetDict.$1 system/cellSetDict
-    cellSet >& log.cellSet.$1
+      cellSet > log.cellSet.$1 2>&1
 
       echo "refining primary zone - $1"
-    refineMesh -dict -overwrite >& log.refineMesh.$1
+      refineMesh -dict -overwrite > log.refineMesh.$1 2>&1
+      shift
+   done
 }
 
 runApplication blockMesh
-
+refineMeshByCellSet 1 2 3
-refineMeshByCellSet 1
-
-refineMeshByCellSet 2
-
-refineMeshByCellSet 3
-
 runApplication $application
+

tutorials/rhoCentralFoam/Allrun

@@ -1,10 +1,9 @@
 #!/bin/sh
-
 # Source tutorial run functions
 . $WM_PROJECT_DIR/bin/tools/RunFunctions
 
 # Get application name from directory
-application=`basename $PWD`
+application=${PWD##*/}
 
 cases=" \
 shockTube \
@@ -15,12 +14,13 @@ LadenburgJet60psi \
 biconic25-55Run35 \
 "
 
-moveTimeMeshToConstant () {
+moveTimeMeshToConstant ()
-DT=`foamInfoExec -times | tail -1`
+{
-if [ $DT != 0 ] ; then
+   DT=`foamInfoExec -times | tail -1`
+   if [ "$DT" != 0 ] ; then
        mv ${DT}/polyMesh/* constant/polyMesh
        rm -rf ${DT}
-fi
+   fi
 }
 
 for case in $cases

tutorials/sonicLiquidFoam/Allrun

@@ -3,7 +3,7 @@
 . $WM_PROJECT_DIR/bin/tools/RunFunctions
 
 # Get application name from directory
-application=`basename $PWD`
+application=${PWD##*/}
 
 setDecompressionTankFine ()
 {

tutorials/sonicTurbFoam/Allrun

@@ -3,7 +3,7 @@
 . $WM_PROJECT_DIR/bin/tools/RunFunctions
 
 # Get application name from directory
-application=`basename $PWD`
+application=${PWD##*/}
 
 runStarToFoam ()
 {

tutorials/sonicTurbFoam/nacaAirfoil/system/controlDict

@@ -55,7 +55,7 @@ functions
     //    patches     (WALL10);
     //    // Name of fields
     //    pName       p;
-    //    Uname   U;
+    //    UName       U;
     //    // Dump to file
     //    log         true;
     //    // Density
@@ -73,7 +73,7 @@ functions
         patches     (WALL10);
         // Name of fields
         pName       p;
-        Uname   U;
+        UName       U;
         // Dump to file
         log         true;
         // Density
@@ -95,9 +95,6 @@ functions
         Aref        1.0;
     }
 
-
 );
 
-
-
 // ************************************************************************* //