From 2d3e61abf890bed6e70896fd3a9da6b6e2754a62 Mon Sep 17 00:00:00 2001
From: henry <Henry Weller h.weller@opencfd.co.uk>
Date: Fri, 28 Aug 2009 17:54:50 +0100
Subject: [PATCH 1/6] Corrected handling of species with parentheses in their
 names.

---
 .../chemistryReaders/chemkinReader/chemkinLexer.L          | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/src/thermophysicalModels/reactionThermo/chemistryReaders/chemkinReader/chemkinLexer.L b/src/thermophysicalModels/reactionThermo/chemistryReaders/chemkinReader/chemkinLexer.L
index f7ec61e331..17529cdb64 100644
--- a/src/thermophysicalModels/reactionThermo/chemistryReaders/chemkinReader/chemkinLexer.L
+++ b/src/thermophysicalModels/reactionThermo/chemistryReaders/chemkinReader/chemkinLexer.L
@@ -67,8 +67,9 @@ int yyFlexLexer::yywrap()
 Foam::string foamSpecieString(const char* YYText)
 {
     Foam::string specieString(YYText);
-    specieString.replaceAll('(', '<');
-    specieString.replaceAll(')', '>');
+    // Transforming parentheses is no longer necessary
+    //specieString.replaceAll('(', '<');
+    //specieString.replaceAll(')', '>');
     return specieString;
 }
 
@@ -804,7 +805,7 @@ bool finishReaction = false;
         }
         else
         {
-            currentSpecieName = keyword;
+            currentSpecieName = foamName(foamSpecieString(YYText()));
 
             HashTable<label>::iterator specieIndexIter
             (

From a51e412ea8c52fd7c098898ca248d76ce464c204 Mon Sep 17 00:00:00 2001
From: henry <Henry Weller h.weller@opencfd.co.uk>
Date: Fri, 28 Aug 2009 17:55:03 +0100
Subject: [PATCH 2/6] Added comment.

---
 tutorials/mesh/snappyHexMesh/Allrun | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/tutorials/mesh/snappyHexMesh/Allrun b/tutorials/mesh/snappyHexMesh/Allrun
index e69de29bb2..13813aeae7 100755
--- a/tutorials/mesh/snappyHexMesh/Allrun
+++ b/tutorials/mesh/snappyHexMesh/Allrun
@@ -0,0 +1,2 @@
+# These cases are links to solver test cases and are run when the Allrun scripts of those solvers are run.
+# This empty Allrun script avoids the meshing of theses cases to be run twice.

From 47ac4180c95adbf1569775178f2d53fa304a5edb Mon Sep 17 00:00:00 2001
From: henry <Henry Weller h.weller@opencfd.co.uk>
Date: Fri, 28 Aug 2009 17:55:25 +0100
Subject: [PATCH 3/6] Corrected handling of the initial time and header.

---
 .../functionObjects/forces/forces/forces.C         | 14 +++++---------
 1 file changed, 5 insertions(+), 9 deletions(-)

diff --git a/src/postProcessing/functionObjects/forces/forces/forces.C b/src/postProcessing/functionObjects/forces/forces/forces.C
index 6baace3863..462116ca4a 100644
--- a/src/postProcessing/functionObjects/forces/forces/forces.C
+++ b/src/postProcessing/functionObjects/forces/forces/forces.C
@@ -211,12 +211,6 @@ Foam::forces::forces
     }
 
     read(dict);
-
-    if (active_)
-    {
-        // Create the forces file if not already created
-        makeFile();
-    }
 }
 
 
@@ -317,16 +311,18 @@ void Foam::forces::makeFile()
         if (Pstream::master())
         {
             fileName forcesDir;
+            word startTimeName =
+                obr_.time().timeName(obr_.time().startTime().value());
+
             if (Pstream::parRun())
             {
                 // Put in undecomposed case (Note: gives problems for
                 // distributed data running)
-                forcesDir =
-                obr_.time().path()/".."/name_/obr_.time().timeName();
+                forcesDir = obr_.time().path()/".."/name_/startTimeName;
             }
             else
             {
-                forcesDir = obr_.time().path()/name_/obr_.time().timeName();
+                forcesDir = obr_.time().path()/name_/startTimeName;
             }
 
             // Create directory if does not exist.

From 0d33a7eb464e415716f20da0856302c0ff18fea0 Mon Sep 17 00:00:00 2001
From: henry <Henry Weller h.weller@opencfd.co.uk>
Date: Tue, 1 Sep 2009 10:44:37 +0100
Subject: [PATCH 4/6] Corrected conversion of tensor fields of all types.

---
 .../postProcessing/dataConversion/foamToVTK/foamToVTK.C     | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/applications/utilities/postProcessing/dataConversion/foamToVTK/foamToVTK.C b/applications/utilities/postProcessing/dataConversion/foamToVTK/foamToVTK.C
index 74ac3c5676..33d3fc5742 100644
--- a/applications/utilities/postProcessing/dataConversion/foamToVTK/foamToVTK.C
+++ b/applications/utilities/postProcessing/dataConversion/foamToVTK/foamToVTK.C
@@ -1010,9 +1010,9 @@ int main(int argc, char *argv[])
                 writer.writeIOField<label>(labelNames);
                 writer.writeIOField<scalar>(scalarNames);
                 writer.writeIOField<vector>(vectorNames);
-                writer.writeIOField<vector>(sphereNames);
-                writer.writeIOField<vector>(symmNames);
-                writer.writeIOField<vector>(tensorNames);
+                writer.writeIOField<sphericalTensor>(sphereNames);
+                writer.writeIOField<symmTensor>(symmNames);
+                writer.writeIOField<tensor>(tensorNames);
             }
         }
     }

From 73b0912087ea80b163b72b3d9cc17a6c0e35760d Mon Sep 17 00:00:00 2001
From: andy <a.heather@opencfd.co.uk>
Date: Tue, 1 Sep 2009 10:57:48 +0100
Subject: [PATCH 5/6] do not export WM_PROJECT_VERSION if already set

---
 etc/bashrc | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/etc/bashrc b/etc/bashrc
index b4af75e716..df864b40e1 100644
--- a/etc/bashrc
+++ b/etc/bashrc
@@ -33,7 +33,7 @@
 #------------------------------------------------------------------------------
 
 export WM_PROJECT=OpenFOAM
-export WM_PROJECT_VERSION=dev
+[ -z "$WM_PROJECT_VERSION" ] && export WM_PROJECT_VERSION=1.6
 
 ################################################################################
 # USER EDITABLE PART

From 33a2ec60de376e0d6d8f5448a89e789df81cf003 Mon Sep 17 00:00:00 2001
From: henry <Henry Weller h.weller@opencfd.co.uk>
Date: Wed, 2 Sep 2009 11:34:58 +0100
Subject: [PATCH 6/6] Changed the time-selection so that it works correctly
 with the -parallel option for when the time directories only exist in the
 processor sub-directories.

---
 .../preProcessing/mapFields/mapFields.C       | 27 ++++++-------------
 .../preProcessing/mapFields/setTimeIndex.H    |  6 +++++
 2 files changed, 14 insertions(+), 19 deletions(-)

diff --git a/applications/utilities/preProcessing/mapFields/mapFields.C b/applications/utilities/preProcessing/mapFields/mapFields.C
index fde815d76f..111c871958 100644
--- a/applications/utilities/preProcessing/mapFields/mapFields.C
+++ b/applications/utilities/preProcessing/mapFields/mapFields.C
@@ -228,15 +228,8 @@ wordList addProcessorPatches
 
 int main(int argc, char *argv[])
 {
-#   include "setRoots.H"
-#   include "createTimes.H"
-#   include "setTimeIndex.H"
-
-    runTimeSource.setTime(sourceTimes[sourceTimeIndex], sourceTimeIndex);
-
-    Info<< "\nSource time: " << runTimeSource.value()
-        << "\nTarget time: " << runTimeTarget.value()
-        << endl;
+    #include "setRoots.H"
+    #include "createTimes.H"
 
     HashTable<word> patchMap;
     wordList cuttingPatches;
@@ -302,11 +295,7 @@ int main(int argc, char *argv[])
                 caseDirSource/fileName(word("processor") + name(procI))
             );
 
-            runTimeSource.setTime
-            (
-                sourceTimes[sourceTimeIndex],
-                sourceTimeIndex
-            );
+            #include "setTimeIndex.H"
 
             fvMesh meshSource
             (
@@ -348,6 +337,8 @@ int main(int argc, char *argv[])
 
         Info<< "Create source mesh\n" << endl;
 
+        #include "setTimeIndex.H"
+
         fvMesh meshSource
         (
             IOobject
@@ -450,11 +441,7 @@ int main(int argc, char *argv[])
                 caseDirSource/fileName(word("processor") + name(procISource))
             );
 
-            runTimeSource.setTime
-            (
-                sourceTimes[sourceTimeIndex],
-                sourceTimeIndex
-            );
+            #include "setTimeIndex.H"
 
             fvMesh meshSource
             (
@@ -529,6 +516,8 @@ int main(int argc, char *argv[])
     }
     else
     {
+        #include "setTimeIndex.H"
+
         Info<< "Create meshes\n" << endl;
 
         fvMesh meshSource
diff --git a/applications/utilities/preProcessing/mapFields/setTimeIndex.H b/applications/utilities/preProcessing/mapFields/setTimeIndex.H
index 19efd9ff5b..80dfb3efca 100644
--- a/applications/utilities/preProcessing/mapFields/setTimeIndex.H
+++ b/applications/utilities/preProcessing/mapFields/setTimeIndex.H
@@ -23,3 +23,9 @@
             runTimeTarget.time().value()
         );
     }
+
+    runTimeSource.setTime(sourceTimes[sourceTimeIndex], sourceTimeIndex);
+
+    Info<< "\nSource time: " << runTimeSource.value()
+        << "\nTarget time: " << runTimeTarget.value()
+        << endl;