From 0bd12e060167a86ea3f1b0aa322873f43d347631 Mon Sep 17 00:00:00 2001
From: andy <a.heather@opencfd.co.uk>
Date: Tue, 13 May 2008 16:33:29 +0100
Subject: [PATCH 1/6] added sourceTime option to mapFields

---
 .../preProcessing/mapFields/mapFields.C       | 55 +++++++++++++++----
 .../preProcessing/mapFields/setRoots.H        |  1 +
 2 files changed, 46 insertions(+), 10 deletions(-)

diff --git a/applications/utilities/preProcessing/mapFields/mapFields.C b/applications/utilities/preProcessing/mapFields/mapFields.C
index f234a89d08..59563aa17b 100644
--- a/applications/utilities/preProcessing/mapFields/mapFields.C
+++ b/applications/utilities/preProcessing/mapFields/mapFields.C
@@ -43,6 +43,31 @@ Description
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
+int getTimeIndex
+(
+    const instantList& times,
+    const scalar t
+)
+{
+    int nearestIndex = -1;
+    scalar nearestDiff = Foam::GREAT;
+
+    forAll(times, timeIndex)
+    {
+        if (times[timeIndex].name() == "constant") continue;
+
+        scalar diff = fabs(times[timeIndex].value() - t);
+        if (diff < nearestDiff)
+        {
+            nearestDiff = diff;
+            nearestIndex = timeIndex;
+        }
+    }
+
+    return nearestIndex;
+}
+
+
 void mapConsistentMesh
 (
     const fvMesh& meshSource,
@@ -97,7 +122,7 @@ void mapConsistentMesh
 void mapSubMesh
 (
     const fvMesh& meshSource,
-    const fvMesh& meshTarget, 
+    const fvMesh& meshTarget,
     const HashTable<word>& patchMap,
     const wordList& cuttingPatches
 )
@@ -203,7 +228,7 @@ wordList addProcessorPatches
     {
         if (typeid(meshTarget.boundary()[patchi]) == typeid(processorFvPatch))
         {
-            if 
+            if
             (
                !cuttingPatchTable.found
                 (
@@ -219,7 +244,7 @@ wordList addProcessorPatches
             }
         }
     }
-    
+
     return cuttingPatchTable.toc();
 }
 
@@ -232,7 +257,9 @@ int main(int argc, char *argv[])
 
 #   include "createTimes.H"
 
-    runTimeSource.setTime(runTimeTarget);
+#   include "setTimeIndex.H"
+
+    runTimeSource.setTime(sourceTimes[sourceTimeIndex], sourceTimeIndex);
 
     Info<< "\nSource time: " << runTimeSource.value()
         << "\nTarget time: " << runTimeTarget.value()
@@ -255,9 +282,9 @@ int main(int argc, char *argv[])
                 false
             )
         );
-        
+
         mapFieldsDict.lookup("patchMap") >> patchMap;
-        
+
         mapFieldsDict.lookup("cuttingPatches") >>  cuttingPatches;
     }
 
@@ -302,7 +329,11 @@ int main(int argc, char *argv[])
                 caseDirSource/fileName(word("processor") + name(procI))
             );
 
-            runTimeSource.setTime(runTimeTarget);
+            runTimeSource.setTime
+            (
+                sourceTimes[sourceTimeIndex],
+                sourceTimeIndex
+            );
 
             fvMesh meshSource
             (
@@ -446,7 +477,11 @@ int main(int argc, char *argv[])
                 caseDirSource/fileName(word("processor") + name(procISource))
             );
 
-            runTimeSource.setTime(runTimeTarget);
+            runTimeSource.setTime
+            (
+                sourceTimes[sourceTimeIndex],
+                sourceTimeIndex
+            );
 
             fvMesh meshSource
             (
@@ -464,7 +499,7 @@ int main(int argc, char *argv[])
 
             for (int procITarget=0; procITarget<nProcsTarget; procITarget++)
             {
-                if 
+                if
                 (
                     !bbsTargetSet[procITarget]
                   || (
@@ -542,7 +577,7 @@ int main(int argc, char *argv[])
                 runTimeTarget
             )
         );
-        
+
         Info<< "Source mesh size: " << meshSource.nCells() << tab
             << "Target mesh size: " << meshTarget.nCells() << nl << endl;
 
diff --git a/applications/utilities/preProcessing/mapFields/setRoots.H b/applications/utilities/preProcessing/mapFields/setRoots.H
index 0d0f0f064c..dad01fb817 100644
--- a/applications/utilities/preProcessing/mapFields/setRoots.H
+++ b/applications/utilities/preProcessing/mapFields/setRoots.H
@@ -1,6 +1,7 @@
     argList::validArgs.clear();
 
     argList::validOptions.insert("source", "dir");
+    argList::validOptions.insert("sourceTime", "scalar");
 
     argList::validOptions.erase(argList::validOptions.find("parallel"));
     argList::validOptions.insert("parallelSource", "");

From 7f70974a984db93b06b0aeab0e2d39d56eb5ea11 Mon Sep 17 00:00:00 2001
From: andy <a.heather@opencfd.co.uk>
Date: Tue, 13 May 2008 16:33:58 +0100
Subject: [PATCH 2/6] added sourceTime option to mapFields (2)

---
 .../preProcessing/mapFields/setTimeIndex.H        | 15 +++++++++++++++
 1 file changed, 15 insertions(+)
 create mode 100644 applications/utilities/preProcessing/mapFields/setTimeIndex.H

diff --git a/applications/utilities/preProcessing/mapFields/setTimeIndex.H b/applications/utilities/preProcessing/mapFields/setTimeIndex.H
new file mode 100644
index 0000000000..3a36340aaf
--- /dev/null
+++ b/applications/utilities/preProcessing/mapFields/setTimeIndex.H
@@ -0,0 +1,15 @@
+    label sourceTimeIndex = 0;
+    instantList sourceTimes = runTimeSource.times();
+    if (args.options().found("sourceTime"))
+    {
+        if ((args.options()["sourceTime"]) == "latestTime")
+        {
+            sourceTimeIndex = sourceTimes.size() - 1;
+        }
+        else
+        {
+            scalar sourceTime =
+                readScalar(IStringStream(args.options()["sourceTime"])());
+            sourceTimeIndex = getTimeIndex(sourceTimes, sourceTime);
+        }
+    }

From 43a7de786200b025da6accf2c0bd5ed4573aae59 Mon Sep 17 00:00:00 2001
From: andy <a.heather@opencfd.co.uk>
Date: Wed, 14 May 2008 09:47:01 +0100
Subject: [PATCH 3/6] restoring default behaviour of mapFields re: time

---
 applications/utilities/preProcessing/mapFields/setTimeIndex.H | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/applications/utilities/preProcessing/mapFields/setTimeIndex.H b/applications/utilities/preProcessing/mapFields/setTimeIndex.H
index 3a36340aaf..20e5cde3b1 100644
--- a/applications/utilities/preProcessing/mapFields/setTimeIndex.H
+++ b/applications/utilities/preProcessing/mapFields/setTimeIndex.H
@@ -1,4 +1,4 @@
-    label sourceTimeIndex = 0;
+    label sourceTimeIndex = runTimeSource.timeIndex();
     instantList sourceTimes = runTimeSource.times();
     if (args.options().found("sourceTime"))
     {

From 238b126c6cd87a3bedef0608120c44e04493878a Mon Sep 17 00:00:00 2001
From: andy <a.heather@opencfd.co.uk>
Date: Wed, 14 May 2008 09:47:51 +0100
Subject: [PATCH 4/6] added small description line to solvers

---
 .../solvers/multiphase/lesCavitatingFoam/lesCavitatingFoam.C   | 3 ++-
 .../solvers/multiphase/rasCavitatingFoam/rasCavitatingFoam.C   | 1 +
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/applications/solvers/multiphase/lesCavitatingFoam/lesCavitatingFoam.C b/applications/solvers/multiphase/lesCavitatingFoam/lesCavitatingFoam.C
index b66186d43c..31f5b90e13 100644
--- a/applications/solvers/multiphase/lesCavitatingFoam/lesCavitatingFoam.C
+++ b/applications/solvers/multiphase/lesCavitatingFoam/lesCavitatingFoam.C
@@ -23,9 +23,10 @@ License
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 Application
-    rasCavitatingFoam
+    lesCavitatingFoam
 
 Description
+    Transient cavitation code with LES turbulence.
 
 \*---------------------------------------------------------------------------*/
 
diff --git a/applications/solvers/multiphase/rasCavitatingFoam/rasCavitatingFoam.C b/applications/solvers/multiphase/rasCavitatingFoam/rasCavitatingFoam.C
index 9ed182be37..bcc0b5441c 100644
--- a/applications/solvers/multiphase/rasCavitatingFoam/rasCavitatingFoam.C
+++ b/applications/solvers/multiphase/rasCavitatingFoam/rasCavitatingFoam.C
@@ -26,6 +26,7 @@ Application
     rasCavitatingFoam
 
 Description
+    Transient cavitation code with RAS turbulence.
 
 \*---------------------------------------------------------------------------*/
 

From aac95d1038b436cca10abf464ab59d0a5849ad58 Mon Sep 17 00:00:00 2001
From: mattijs <m.janssens@opencfd.co.uk>
Date: Wed, 14 May 2008 12:42:26 +0100
Subject: [PATCH 5/6] Handling starting from 0 or 1 on indexing

---
 .../conversion/tetgenToFoam/tetgenToFoam.C    | 169 ++++++++----------
 1 file changed, 70 insertions(+), 99 deletions(-)

diff --git a/applications/utilities/mesh/conversion/tetgenToFoam/tetgenToFoam.C b/applications/utilities/mesh/conversion/tetgenToFoam/tetgenToFoam.C
index 6ce391ad03..9155c5f563 100644
--- a/applications/utilities/mesh/conversion/tetgenToFoam/tetgenToFoam.C
+++ b/applications/utilities/mesh/conversion/tetgenToFoam/tetgenToFoam.C
@@ -56,18 +56,14 @@ NOTE:
 always. Might use some geometric check instead.
 - marked faces might not actually be boundary faces of mesh. This is not handled
 and you'll have to run without face file (-noFaceFile option)
-- default is to have indices starting at 1. Use -startAt0 if starting at 0.
-- all input is expected to be ordered.
+
 \*---------------------------------------------------------------------------*/
 
 #include "argList.H"
 #include "Time.H"
 #include "polyMesh.H"
 #include "IFstream.H"
-#include "polyPatch.H"
 #include "cellModeller.H"
-#include "ListOps.H"
-#include <fstream>
 
 using namespace Foam;
 
@@ -79,7 +75,6 @@ int main(int argc, char *argv[])
 {
     argList::validArgs.append("file prefix");
     argList::validOptions.insert("noFaceFile", "");
-    argList::validOptions.insert("startAt0", "");
 
 #   include "setRootCase.H"
 #   include "createTime.H"
@@ -87,34 +82,29 @@ int main(int argc, char *argv[])
 
     bool readFaceFile = !args.options().found("noFaceFile");
 
-    bool startAt1 = !args.options().found("startAt0");
-
     fileName prefix(args.additionalArgs()[0]);
 
     fileName nodeFile(prefix + ".node");
     fileName eleFile(prefix + ".ele");
     fileName faceFile(prefix + ".face");
 
-    Info<< "Files:" << endl
-        << "    nodes : " << nodeFile << endl
-        << "    elems : " << eleFile << endl
-        << "    faces : " << faceFile << endl
-        << endl;
-
-
-    if (readFaceFile)
+    if (!readFaceFile)
     {
-        Info<< "Reading .file for boundary information" << nl << endl;
-    }
-    if (startAt1)
-    {
-        Info<< "Numbering in files starts at 1" << nl << endl;
+        Info<< "Files:" << endl
+            << "    nodes : " << nodeFile << endl
+            << "    elems : " << eleFile << endl
+            << endl;
     }
     else
     {
-        Info<< "Numbering in files starts at 0" << nl << endl;
-    }
+        Info<< "Files:" << endl
+            << "    nodes : " << nodeFile << endl
+            << "    elems : " << eleFile << endl
+            << "    faces : " << faceFile << endl
+            << endl;
 
+        Info<< "Reading .face file for boundary information" << nl << endl;
+    }
 
     if (!exists(nodeFile) || !exists(eleFile))
     {
@@ -134,7 +124,7 @@ int main(int argc, char *argv[])
     }
 
 
-    std::ifstream nodeStream(nodeFile.c_str());
+    IFstream nodeStream(nodeFile);
 
     //
     // Read nodes.
@@ -145,7 +135,7 @@ int main(int argc, char *argv[])
 
     do
     {
-        std::getline(nodeStream, line);
+        nodeStream.getLine(line);
     }
     while((line.size() > 0) && (line[0] == '#'));
 
@@ -169,61 +159,60 @@ int main(int argc, char *argv[])
     //
 
     pointField points(nNodes);
+    Map<label> nodeToPoint(nNodes);
 
-    label pointI = 0;
-
-    while (nodeStream.good())
     {
-        std::getline(nodeStream, line);
+        labelList pointIndex(nNodes);
 
-        if ((line.size() > 0) && (line[0] != '#'))
+        label pointI = 0;
+
+        while (nodeStream.good())
         {
-            IStringStream nodeLine(line);
+            nodeStream.getLine(line);
 
-            label nodeI;
-            scalar x, y, z;
-            label dummy;
-
-            nodeLine >> nodeI >> x >> y >> z;
-
-            for (label i = 0; i < nNodeAttr; i++)
+            if ((line.size() > 0) && (line[0] != '#'))
             {
-                nodeLine >> dummy;
-            }
+                IStringStream nodeLine(line);
 
-            if (hasRegion)
-            {
-                nodeLine >> dummy;
-            }
+                label nodeI;
+                scalar x, y, z;
+                label dummy;
 
-            // Store point and node number.
-            if
-            (
-                 (!startAt1 && nodeI != pointI)
-              || (startAt1 && nodeI-1 != pointI)
-            )
-            {
-                FatalErrorIn(args.executable())
-                    << "point numbering not consecutive for node " << nodeI
-                    << " or numbering starts"
-                    << " at 0 or 1. Perhaps rerun w/o -startAt0 option?"
-                    << exit(FatalError);
-            }
+                nodeLine >> nodeI >> x >> y >> z;
 
-            points[pointI++] = point(x, y, z);
+                for (label i = 0; i < nNodeAttr; i++)
+                {
+                    nodeLine >> dummy;
+                }
+
+                if (hasRegion)
+                {
+                    nodeLine >> dummy;
+                }
+
+                // Store point and node number.
+                points[pointI] = point(x, y, z);
+                nodeToPoint.insert(nodeI, pointI);
+                pointI++;
+            }
+        }
+        if (pointI != nNodes)
+        {
+            FatalIOErrorIn(args.executable().c_str(), nodeStream)
+                << "Only " << pointI << " nodes present instead of " << nNodes
+                << " from header." << exit(FatalIOError);
         }
     }
 
-
     //
     // read elements
     //
 
-    std::ifstream eleStream(eleFile.c_str());
+    IFstream eleStream(eleFile);
 
     do
     {
-        std::getline(eleStream, line);
+        eleStream.getLine(line);
     }
     while((line.size() > 0) && (line[0] == '#'));
 
@@ -242,10 +231,11 @@ int main(int argc, char *argv[])
 
     if (nPtsPerTet != 4)
     {
-        FatalErrorIn(args.executable()) << "Cannot handle tets with "
+        FatalIOErrorIn(args.executable().c_str(), eleStream)
+            << "Cannot handle tets with "
             << nPtsPerTet << " points per tetrahedron in .ele file" << endl
             << "Can only handle tetrahedra with four points"
-            << exit(FatalError);
+            << exit(FatalIOError);
     }
 
     if (nElemAttr != 0)
@@ -262,39 +252,27 @@ int main(int argc, char *argv[])
     labelList tetPoints(4);
 
     cellShapeList cells(nTets);
+    label cellI = 0;
 
     while (eleStream.good())
     {
-        std::getline(eleStream, line);
+        eleStream.getLine(line);
 
         if ((line.size() > 0) && (line[0] != '#'))
         {
             IStringStream eleLine(line);
 
             label elemI;
-
             eleLine >> elemI;
 
-            if (startAt1)
-            {
-                --elemI;
-            }
-
             for (label i = 0; i < 4; i++)
             {
                 label nodeI;
-
                 eleLine >> nodeI;
-
-                if (startAt1)
-                {
-                    --nodeI;
-                }
-
-                tetPoints[i] = nodeI;
+                tetPoints[i] = nodeToPoint[nodeI];
             }
 
-            cells[elemI] = cellShape(tet, tetPoints);
+            cells[cellI++] = cellShape(tet, tetPoints);
 
             // Skip attributes
             for (label i = 0; i < nElemAttr; i++)
@@ -321,11 +299,11 @@ int main(int argc, char *argv[])
         // read boundary faces
         //
 
-        std::ifstream faceStream(faceFile.c_str());
+        IFstream faceStream(faceFile);
 
         do
         {
-            std::getline(faceStream, line);
+            faceStream.getLine(line);
         }
         while((line.size() > 0) && (line[0] == '#'));
 
@@ -344,10 +322,11 @@ int main(int argc, char *argv[])
 
         if (nFaceAttr != 1)
         {
-            FatalErrorIn(args.executable()) << "Expect boundary markers to be"
+            FatalIOErrorIn(args.executable().c_str(), faceStream)
+                << "Expect boundary markers to be"
                 << " present in .face file." << endl
                 << "This is the second number in the header which is now:"
-                << nFaceAttr << exit(FatalError);
+                << nFaceAttr << exit(FatalIOError);
         }
 
         // List of Foam vertices per boundary face
@@ -357,6 +336,8 @@ int main(int argc, char *argv[])
         boundaryPatch.setSize(nFaces);
         boundaryPatch = -1;
 
+        label faceI = 0;
+
         // Region to patch conversion
         Map<label> regionToPatch;
 
@@ -364,35 +345,23 @@ int main(int argc, char *argv[])
 
         while (faceStream.good())
         {
-            std::getline(faceStream, line);
+            faceStream.getLine(line);
 
             if ((line.size() > 0) && (line[0] != '#'))
             {
                 IStringStream faceLine(line);
 
-                label faceI, dummy, region;
+                label tetGenFaceI, dummy, region;
 
-                faceLine >> faceI;
-
-                if (startAt1)
-                {
-                    --faceI;
-                }
+                faceLine >> tetGenFaceI;
 
                 // Read face and reverse orientation (Foam needs outwards
                 // pointing)
                 for (label i = 0; i < 3; i++)
                 {
                     label nodeI;
-
                     faceLine >> nodeI;
-
-                    if (startAt1)
-                    {
-                        --nodeI;
-                    }
-
-                    f[2-i] = nodeI;
+                    f[2-i] = nodeToPoint[nodeI];
                 }
 
                 boundaryFaces[faceI] = f;
@@ -431,6 +400,8 @@ int main(int argc, char *argv[])
                         faceLine >> dummy;
                     }
                 }
+
+                faceI++;
             }
         }
 

From 202212497f7fa5b7a3163daa989a668379f79f32 Mon Sep 17 00:00:00 2001
From: andy <a.heather@opencfd.co.uk>
Date: Thu, 15 May 2008 12:46:02 +0100
Subject: [PATCH 6/6] correcting buondary conditions for tutorial case

---
 .../simplifiedSiwek/constant/polyMesh/blockMeshDict           | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tutorials/rhoTurbTwinParcelFoam/simplifiedSiwek/constant/polyMesh/blockMeshDict b/tutorials/rhoTurbTwinParcelFoam/simplifiedSiwek/constant/polyMesh/blockMeshDict
index 26ea6f0982..04869c9a15 100644
--- a/tutorials/rhoTurbTwinParcelFoam/simplifiedSiwek/constant/polyMesh/blockMeshDict
+++ b/tutorials/rhoTurbTwinParcelFoam/simplifiedSiwek/constant/polyMesh/blockMeshDict
@@ -57,11 +57,11 @@ edges
 
 patches
 (
-    patch top
+    wall top
     (
         (13 15 14 12)
     )
-    patch bottom
+    wall bottom
     (
         (0 1 5 4)
         (1 8 10 5)