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

-	.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

+xferListTest.C
+
+/* EXE = $(FOAM_USER_APPBIN)/xferListTest */
+EXE = ./xferListTest

applications/test/xfer/xferListTest.C

+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  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

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

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

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

applications/utilities/miscellaneous/foamFormatConvert/Make/options

 EXE_INC = \
-    -I$(FOAM_SRC)/finiteVolume/lnInclude \
-    -I$(FOAM_SRC)/meshTools/lnInclude \
-    -I$(FOAM_SRC)/lagrangian/basic/lnInclude \
-
+    -I$(LIB_SRC)/finiteVolume/lnInclude \
+    -I$(LIB_SRC)/meshTools/lnInclude \
+    -I$(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;
 
@@ -192,15 +221,18 @@ int main(int argc, char *argv[])
                 partsList.recalculate(mesh);
             }
 
-            fileName geomDir;
-            if (hasMovingMesh)
+            if (!optNoMesh)
             {
-                geomDir = dataDir/subDir;
-            }
+                fileName geomDir;
+                if (hasMovingMesh)
+                {
+                    geomDir = dataDir/subDir;
+                }
 
-            ensightGeoFile geoFile(ensightDir/geomDir/geometryName, format);
-            partsList.writeGeometry(geoFile);
-            Info << nl;
+                ensightGeoFile geoFile(ensightDir/geomDir/geometryName, format);
+                partsList.writeGeometry(geoFile);
+                Info<< nl;
+            }
         }
 
         Info<< "write volume field (" << flush;

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

-// Read time index from */uniform/time,
-// but treat 0 and constant specially
+// Read time index from */uniform/time, 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
-            (
-                IOobject
-                (
-                    "time",
-                    runTime.timeName(),
-                    "uniform",
-                    runTime,
-                    IOobject::MUST_READ,
-                    IOobject::NO_WRITE,
-                    false
-                )
-            );
+            io.readOpt() = IOobject::MUST_READ;
+            IOdictionary timeObject(io);
 
             timeObject.lookup("index") >> timeIndex;
         }

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

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

-
 # 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{FOAM_SRC}/finiteVolume/lnInclude
+    $ENV{WM_PROJECT_DIR}/src/OpenFOAM/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 $ENV{FOAM_SRC}/finiteVolume/lnInclude)
-INCLUDE_DIRECTORIES($ENV{ParaView_INST_DIR}/include ../vtkFoam/lnInclude)
+INCLUDE_DIRECTORIES(
+    $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 = \