Merge commit 'origin/master' into olesenm

applications/utilities/mesh/advanced/autoRefineMesh/autoRefineMesh.C

@@ -451,7 +451,7 @@ void doRefinement
     const labelHashSet& refCells,
     labelList& refLevel
 )
-{ 
+{
     label oldCells = mesh.nCells();
 
     // Multi-iteration, multi-direction topology modifier.
@@ -565,7 +565,7 @@ void subsetMesh
     // Update cutCells for removed cells.
     cutCells.updateMesh(morphMap());
 }
-    
+
 
 // Divide the cells according to status compared to surface. Constructs sets:
 // - cutCells : all cells cut by surface
@@ -877,7 +877,7 @@ int main(int argc, char *argv[])
 
 
         // Added cells from 2:1 refinement level restriction.
-        while 
+        while
         (
             limitRefinementLevel
             (
@@ -887,7 +887,8 @@ int main(int argc, char *argv[])
                 refLevel,
                 cutCells
             )
-        );
+        )
+        {}
 
 
         Info<< "    Current cells           : " << mesh.nCells() << nl
@@ -988,7 +989,8 @@ int main(int argc, char *argv[])
                 refLevel,
                 hanging
             )
-        );
+        )
+        {}
 
         doRefinement(mesh, refineDict, hanging, refLevel);
 

applications/utilities/mesh/advanced/refinementLevel/refinementLevel.C

@@ -26,12 +26,12 @@ Description
     Tries to figure out what the refinement level is on refined cartesian
     meshes. Run BEFORE snapping.
 
-    Writes 
+    Writes
     - volScalarField 'refinementLevel' with current refinement level.
     - cellSet 'refCells' which are the cells that need to be refined to satisfy
       2:1 refinement.
 
-    Works by dividing cells into volume bins. 
+    Works by dividing cells into volume bins.
 
 \*---------------------------------------------------------------------------*/
 
@@ -77,7 +77,7 @@ bool limitRefinementLevel
             }
         }
     }
-            
+
     if (refCells.size() > oldNCells)
     {
         Info<< "Added an additional " << refCells.size() - oldNCells
@@ -143,7 +143,7 @@ int main(int argc, char *argv[])
                 << lowerLimits[lowerLimits.size()-1] << " .. "
                 << upperLimits[upperLimits.size()-1] << endl;
 
-            // Create new bin.            
+            // Create new bin.
             bins.append(DynamicList<label>());
             lowerLimits.append(sortedVols[i]);
             upperLimits.append(1.1*lowerLimits[lowerLimits.size()-1]);
@@ -243,7 +243,7 @@ int main(int argc, char *argv[])
         return 1;
     }
 
-    
+
     labelIOList refLevel
     (
         IOobject
@@ -308,7 +308,7 @@ int main(int argc, char *argv[])
             bField[faceI] = postRefLevel[own];
         }
     }
-        
+
     Info<< "Determined current refinement level and writing to "
         << postRefLevel.name() << " (as volScalarField; for post processing)"
         << nl
@@ -325,7 +325,7 @@ int main(int argc, char *argv[])
     // Cells to refine
     cellSet refCells(mesh, "refCells", 100);
 
-    while 
+    while
     (
         limitRefinementLevel
         (
@@ -333,7 +333,8 @@ int main(int argc, char *argv[])
             refLevel,       // current refinement level
             refCells        // cells to refine
         )
-    );
+    )
+    {}
 
     if (refCells.size() > 0)
     {

applications/utilities/mesh/conversion/ansysToFoam/ansysToFoam.L

@@ -265,7 +265,8 @@ int main(int argc, char *argv[])
     }
 
     yyFlexLexer lexer(&ansysStream);
-    while(lexer.yylex() != 0);
+    while(lexer.yylex() != 0)
+    {}
 
     Info << "Creating points" << endl;
 

applications/utilities/mesh/conversion/fluent3DMeshToFoam/fluent3DMeshToFoam.L

@@ -583,7 +583,8 @@ endOfSection               {space}")"{space}
 <readCellData>{spaceNl}{lbrac} {
         // Quickly scan to the end of the cell data block and discard
         register int c;
-        while ((c = yyinput()) != 0 && c != ')');
+        while ((c = yyinput()) != 0 && c != ')')
+        {}
     }
 
 {faceTree} {
@@ -763,7 +764,8 @@ int main(int argc, char *argv[])
 
     yyFlexLexer lexer(&fluentStream.stdStream());
 
-    while(lexer.yylex() != 0);
+    while(lexer.yylex() != 0)
+    {}
 
     Info<< "\nFINISHED LEXING\n\n";
 

applications/utilities/mesh/conversion/fluentMeshToFoam/fluentMeshToFoam.L

@@ -901,7 +901,8 @@ int main(int argc, char *argv[])
     }
 
     yyFlexLexer lexer(&fluentStream);
-    while(lexer.yylex() != 0);
+    while(lexer.yylex() != 0)
+    {}
 
     Info<< "\n\nFINISHED LEXING\n\n\n";
     // Lookup table giving number of vertices given a fluent cell type ID

applications/utilities/mesh/conversion/gambitToFoam/gambitToFoam.L

@@ -665,7 +665,8 @@ int main(int argc, char *argv[])
     }
 
     yyFlexLexer lexer(&gambitStream);
-    while(lexer.yylex() != 0);
+    while(lexer.yylex() != 0)
+    {}
 
     Info << "Finished lexing" << endl;
 

applications/utilities/mesh/manipulation/Optional/setSet/setSet.C

@@ -189,7 +189,7 @@ void writeVTK
         faceList setFaces(cellFaces.size());
         labelList faceValues(cellFaces.size());
         label setFaceI = 0;
-        
+
         forAllConstIter(Map<label>, cellFaces, iter)
         {
             setFaces[setFaceI] = mesh.faces()[iter.key()];
@@ -217,7 +217,7 @@ void writeVTK
             mesh,
             currentSet,
             mesh.time().path()/vtkName
-        );        
+        );
     }
     else
     {
@@ -331,7 +331,7 @@ bool doCommand
     // Get some size estimate for set.
     const globalMeshData& parData = mesh.globalData();
 
-    label typSize = 
+    label typSize =
         max
         (
             parData.nTotalCells(),
@@ -449,7 +449,7 @@ bool doCommand
                 }
             }
             else
-            {        
+            {
                 if (is >> sourceType)
                 {
                     autoPtr<topoSetSource> setSource
@@ -743,7 +743,7 @@ int main(int argc, char *argv[])
     else if (!read_history(historyFile))
     {
         Info<< "Successfully read history from " << historyFile << endl;
-    }        
+    }
 #endif
 
 
@@ -754,7 +754,7 @@ int main(int argc, char *argv[])
     FatalError.throwExceptions();
     FatalIOError.throwExceptions();
 
-    while (1)
+    do
     {
         string rawLine;
 

applications/utilities/parallelProcessing/reconstructParMesh/Make/options

@@ -4,5 +4,4 @@ EXE_INC = \
 
 EXE_LIBS = \
     -ldynamicMesh \
-    -lmeshTools \
+    -lmeshTools
-   

applications/utilities/postProcessing/dataConversion/foamDataToFluent/Make/options

@@ -2,5 +2,4 @@ EXE_INC = \
     -I$(LIB_SRC)/finiteVolume/lnInclude
 
 EXE_LIBS = \
-    -lfiniteVolume \
+    -lfiniteVolume
-   

applications/utilities/postProcessing/dataConversion/foamToEnsight/Make/options

@@ -4,5 +4,4 @@ EXE_INC = \
 
 EXE_LIBS = \
     -lfiniteVolume \
-    -llagrangian \
+    -llagrangian
-   

applications/utilities/postProcessing/dataConversion/foamToFieldview9/Make/options

@@ -4,5 +4,4 @@ EXE_INC = \
 
 EXE_LIBS = \
     -lfiniteVolume \
-    -llagrangian \
+    -llagrangian
-   

applications/utilities/postProcessing/dataConversion/foamToVTK/Make/options

@@ -6,5 +6,5 @@ EXE_INC = \
 EXE_LIBS = \
     -lfiniteVolume \
     -llagrangian \
-    -lmeshTools \
+    -lmeshTools
-   
+

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

@@ -24,7 +24,7 @@
         -lgen -lnsl -lsocket -lw -lintl -ldl
 
 #elif defined(sgiN32) || defined(sgiN32Gcc)
- 
+
     FV_LIBS = \
         $(FV_HOME)/user/obj/iris/fv.o \
         $(FV_HOME)/user/obj/iris/fv2.o \
@@ -94,12 +94,9 @@ EXE_INC = \
     -I$(LIB_SRC)/finiteVolume/lnInclude \
     -I$(LIB_SRC)/meshTools/lnInclude \
     -I$(LIB_SRC)/browser/lnInclude \
-    -I$(FOAM_SRC)/lagrangian/basic/lnInclude \
+    -I$(FOAM_SRC)/lagrangian/basic/lnInclude
-
 
 EXE_LIBS = \
     $(FV_LIBS) \
     -lfiniteVolume \
-    -lmeshTools \
+    -lmeshTools
-   
-

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

@@ -17,4 +17,3 @@ EXE_LIBS = \
     -lspecie \
     -lcompressibleTurbulenceModels \
     -lcompressibleLESmodels
-

applications/utilities/postProcessing/miscellaneous/postChannel/Make/options

@@ -4,5 +4,4 @@ EXE_INC = \
 
 EXE_LIBS = \
     -lfiniteVolume \
-    -lsampling \
+    -lsampling
-   

applications/utilities/postProcessing/miscellaneous/ptot/Make/options

@@ -2,5 +2,4 @@ EXE_INC = \
     -I$(LIB_SRC)/finiteVolume/lnInclude
 
 EXE_LIBS = \
-    -lfiniteVolume \
+    -lfiniteVolume
-   

applications/utilities/postProcessing/miscellaneous/wdot/Make/options

@@ -2,5 +2,4 @@ EXE_INC = \
     -I$(LIB_SRC)/finiteVolume/lnInclude
 
 EXE_LIBS = \
-    -lfiniteVolume \
+    -lfiniteVolume
-   

applications/utilities/postProcessing/sampling/probeLocations/Make/options

@@ -3,7 +3,7 @@ EXE_INC = \
     -I$(LIB_SRC)/meshTools/lnInclude \
     -I$(LIB_SRC)/sampling/lnInclude \
     -I$(LIB_SRC)/triSurface/lnInclude \
-    -I$(LIB_SRC)/lagrangian/basic/lnInclude \
+    -I$(LIB_SRC)/lagrangian/basic/lnInclude
 
 EXE_LIBS = \
     -lfiniteVolume \

applications/utilities/postProcessing/sampling/sample/Make/options

@@ -3,7 +3,7 @@ EXE_INC = \
     -I$(LIB_SRC)/meshTools/lnInclude \
     -I$(LIB_SRC)/sampling/lnInclude \
     -I$(LIB_SRC)/triSurface/lnInclude \
-    -I$(LIB_SRC)/lagrangian/basic/lnInclude \
+    -I$(LIB_SRC)/lagrangian/basic/lnInclude
 
 EXE_LIBS = \
     -lfiniteVolume \

applications/utilities/postProcessing/scalarField/pPrime2/Make/options

@@ -2,5 +2,4 @@ EXE_INC = \
     -I$(LIB_SRC)/finiteVolume/lnInclude
 
 EXE_LIBS = \
-    -lfiniteVolume \
+    -lfiniteVolume
-   

applications/utilities/postProcessing/stressField/stressComponents/Make/options

@@ -6,5 +6,4 @@ EXE_INC = \
 EXE_LIBS = \
     -lfiniteVolume \
     -lincompressibleTurbulenceModels \
-    -lincompressibleTransportModels \
+    -lincompressibleTransportModels
-   

applications/utilities/postProcessing/turbulence/R/Make/options

@@ -7,5 +7,4 @@ EXE_LIBS = \
     -lfiniteVolume \
     -lincompressibleTurbulenceModels \
     -lincompressibleTransportModels \
-    -lfiniteVolume \
+    -lfiniteVolume
-   

applications/utilities/postProcessing/turbulence/createTurbulenceFields/Make/options

@@ -6,4 +6,4 @@ EXE_INC = \
 EXE_LIBS = \
     -lfiniteVolume \
     -lincompressibleTurbulenceModels \
-    -lincompressibleTransportModels \
+    -lincompressibleTransportModels

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

@@ -8,4 +8,3 @@ EXE_LIBS = \
     -lfiniteVolume \
     -lbasicThermophysicalModels \
     -lspecie
-

applications/utilities/postProcessing/velocityField/streamFunction/Make/options

@@ -2,5 +2,4 @@ EXE_INC = \
     -I$(LIB_SRC)/finiteVolume/lnInclude
 
 EXE_LIBS = \
-    -lfiniteVolume \
+    -lfiniteVolume
-   

applications/utilities/postProcessing/wall/wallGradU/Make/options

@@ -6,5 +6,4 @@ EXE_INC = \
 EXE_LIBS = \
     -lincompressibleTurbulenceModels \
     -lincompressibleTransportModels \
-    -lfiniteVolume \
+    -lfiniteVolume
-   

applications/utilities/postProcessing/wall/wallHeatFlux/Make/options

@@ -10,5 +10,4 @@ EXE_LIBS = \
     -lcombustionThermophysicalModels \
     -lfiniteVolume \
     -lspecie \
-    -lbasicThermophysicalModels \
+    -lbasicThermophysicalModels
-   

applications/utilities/postProcessing/wall/wallShearStress/Make/options

@@ -6,5 +6,4 @@ EXE_INC = \
 EXE_LIBS = \
     -lincompressibleTurbulenceModels \
     -lincompressibleTransportModels \
-    -lfiniteVolume \
+    -lfiniteVolume
-   

applications/utilities/postProcessing/wall/yPlusLES/Make/options

@@ -7,5 +7,4 @@ EXE_INC = \
 EXE_LIBS = \
     -lincompressibleLESmodels \
     -lincompressibleTransportModels \
-    -lfiniteVolume \
+    -lfiniteVolume
-   

applications/utilities/postProcessing/wall/yPlusRAS/Make/options

@@ -6,5 +6,4 @@ EXE_INC = \
 EXE_LIBS = \
     -lincompressibleTurbulenceModels \
     -lincompressibleTransportModels \
-    -lfiniteVolume \
+    -lfiniteVolume
-   

applications/utilities/surface/surfaceCoarsen/bunnylod/progmesh.C

@@ -7,7 +7,7 @@
  *  See the header file progmesh.h for a description of this module
  */
 
-#include <stdio.h>  
+#include <stdio.h>
 #include <math.h>
 #include <stdlib.h>
 #include <assert.h>
@@ -151,11 +151,11 @@ void Vertex::RemoveIfNonNeighbor(Vertex *n) {
 
 
 float ComputeEdgeCollapseCost(Vertex *u,Vertex *v) {
-	// if we collapse edge uv by moving u to v then how 
+	// if we collapse edge uv by moving u to v then how
 	// much different will the model change, i.e. how much "error".
 	// Texture, vertex normal, and border vertex code was removed
 	// to keep this demo as simple as possible.
-	// The method of determining cost was designed in order 
+	// The method of determining cost was designed in order
 	// to exploit small and coplanar regions for
 	// effective polygon reduction.
 	// Is is possible to add some checks here to see if "folds"
@@ -173,7 +173,7 @@ float ComputeEdgeCollapseCost(Vertex *u,Vertex *v) {
 			sides.Add(u->face[i]);
 		}
 	}
-	// use the triangle facing most away from the sides 
+	// use the triangle facing most away from the sides
 	// to determine our curvature term
 	for(i=0;i<u->face.num;i++) {
 		float mincurv=1; // curve for face i and closer side to it
@@ -184,7 +184,7 @@ float ComputeEdgeCollapseCost(Vertex *u,Vertex *v) {
 		}
 		curvature = max(curvature,mincurv);
 	}
-	// the more coplanar the lower the curvature term   
+	// the more coplanar the lower the curvature term
 	return edgelength * curvature;
 }
 
@@ -193,7 +193,7 @@ void ComputeEdgeCostAtVertex(Vertex *v) {
 	// from vertex v.  Since we are only interested in reducing
 	// the object by selecting the min cost edge at each step, we
 	// only cache the cost of the least cost edge at this vertex
-	// (in member variable collapse) as well as the value of the 
+	// (in member variable collapse) as well as the value of the
 	// cost (in member variable objdist).
 	if(v->neighbor.num==0) {
 		// v doesn't have neighbors so it costs nothing to collapse
@@ -247,7 +247,7 @@ void Collapse(Vertex *u,Vertex *v){
 	for(i=u->face.num-1;i>=0;i--) {
 		u->face[i]->ReplaceVertex(u,v);
 	}
-	delete u; 
+	delete u;
 	// recompute the edge collapse costs for neighboring vertices
 	for(i=0;i<tmp.num;i++) {
 		ComputeEdgeCostAtVertex(tmp[i]);
@@ -256,15 +256,15 @@ void Collapse(Vertex *u,Vertex *v){
 
 void AddVertex(List<Vector> &vert){
 	for(int i=0;i<vert.num;i++) {
-		Vertex *v = new Vertex(vert[i],i);
+		new Vertex(vert[i],i);
 	}
 }
 void AddFaces(List<tridata> &tri){
 	for(int i=0;i<tri.num;i++) {
-		Triangle *t=new Triangle(
+		new Triangle(
-					      vertices[tri[i].v[0]],
+            vertices[tri[i].v[0]],
-					      vertices[tri[i].v[1]],
+            vertices[tri[i].v[1]],
-					      vertices[tri[i].v[2]] );
+            vertices[tri[i].v[2]] );
 	}
 }
 
@@ -284,7 +284,7 @@ Vertex *MinimumCostEdge(){
 	return mn;
 }
 
-void ProgressiveMesh(List<Vector> &vert, List<tridata> &tri, 
+void ProgressiveMesh(List<Vector> &vert, List<tridata> &tri,
                      List<int> &map, List<int> &permutation)
 {
 	AddVertex(vert);  // put input data into our data structures

bin/doxyScr

@@ -131,7 +131,8 @@ s/^    //
 
 /SourceFiles/,/^[ ]*$/{
 s?SourceFiles?@par Source files\
-<ul>?
+<ul>\
+  <li><a href="%filePath%">%fileName%</a></li>?
 s?^[ ]*$?</ul>\
 ?
 s? *\([a-zA-Z0-9]*\.[a-zA-Z]*\)?  <li><a href="%dirName%/\1">\1</a></li>?

src/thermophysicalModels/specie/reaction/Reactions/Reaction/Reaction.H

@@ -81,6 +81,10 @@ public:
             scalar exponent;
 
             specieCoeffs()
+            :
+                index(-1),
+                stoichCoeff(0),
+                exponent(1)
             {}
 
             specieCoeffs(const speciesTable& species, Istream& is);
@@ -157,7 +161,7 @@ public:
         {
             const speciesTable& species_;
             const HashPtrTable<ReactionThermo>& thermoDatabase_;
-        
+
         public:
 
             iNew
@@ -257,7 +261,7 @@ public:
                 const scalar T,
                 const scalar p,
                 const scalarField& c
-            ) const;            
+            ) const;
 
             //- Reverse rate constant from the given forward rate constant
             virtual scalar kr