Merging, fixing conflicts

applications/solvers/lagrangian/coalChemistryFoam/coalChemistryFoam.C

@@ -38,7 +38,6 @@ Description
 #include "CoalCloud.H"
 #include "psiChemistryModel.H"
 #include "chemistrySolver.H"
-#include "thermoPhysicsTypes.H"
 #include "timeActivatedExplicitCellSource.H"
 #include "radiationModel.H"
 

applications/solvers/lagrangian/coalChemistryFoam/createClouds.H

@@ -1,5 +1,5 @@
 Info<< "\nConstructing coal cloud" << endl;
-CoalCloud<gasThermoPhysics> coalParcels
+thermoCoalCloud coalParcels
 (
     "coalCloud1",
     rho,

applications/solvers/lagrangian/porousExplicitSourceReactingParcelFoam/createClouds.H

@@ -1,5 +1,5 @@
 Info<< "\nConstructing reacting cloud" << endl;
-BasicReactingCloud<icoPoly8ThermoPhysics> parcels
+icoPoly8ThermoReactingCloud parcels
 (
     "reactingCloud1",
     rho,

applications/solvers/lagrangian/porousExplicitSourceReactingParcelFoam/porousExplicitSourceReactingParcelFoam.C

@@ -46,7 +46,6 @@ Description
 #include "BasicReactingCloud.H"
 #include "rhoChemistryModel.H"
 #include "chemistrySolver.H"
-#include "thermoPhysicsTypes.H"
 #include "radiationModel.H"
 #include "porousZones.H"
 #include "timeActivatedExplicitMulticomponentPointSource.H"

applications/solvers/lagrangian/reactingParcelFoam/createClouds.H

@@ -1,5 +1,5 @@
 Info<< "\nConstructing reacting cloud" << endl;
-BasicReactingCloud<gasThermoPhysics> parcels
+thermoReactingCloud parcels
 (
     "reactingCloud1",
     rho,

applications/solvers/lagrangian/reactingParcelFoam/reactingParcelFoam.C

@@ -37,7 +37,6 @@ Description
 #include "BasicReactingCloud.H"
 #include "psiChemistryModel.H"
 #include "chemistrySolver.H"
-#include "thermoPhysicsTypes.H"
 #include "radiationModel.H"
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //

applications/utilities/mesh/generation/snappyHexMesh/snappyHexMeshDict

@@ -280,11 +280,14 @@ addLayersControls
     nBufferCellsNoExtrude 0;
 
 
-    // Overall max number of layer addition iterations
+    // Overall max number of layer addition iterations. The mesher will exit
+    // if it reaches this number of iterations; possibly with an illegal
+    // mesh.
     nLayerIter 50;
 
     // Max number of iterations after which relaxed meshQuality controls
-    // get used.
+    // get used. Up to nRelaxIter it uses the settings in meshQualityControls,
+    // after nRelaxIter it uses the values in meshQualityControls::relaxed.
     nRelaxedIter 20;
 }
 

applications/utilities/mesh/manipulation/createBaffles/createBaffles.C

@@ -125,6 +125,7 @@ label findPatchID(const polyMesh& mesh, const word& name)
 
 int main(int argc, char *argv[])
 {
+#   include "addRegionOption.H"
     argList::validArgs.append("faceZone");
     argList::validArgs.append("patch");
     argList::validOptions.insert("additionalPatches", "(patch2 .. patchN)");
@@ -134,7 +135,7 @@ int main(int argc, char *argv[])
 #   include "setRootCase.H"
 #   include "createTime.H"
     runTime.functionObjects().off();
-#   include "createMesh.H"
+#   include "createNamedMesh.H"
     const word oldInstance = mesh.pointsInstance();
 
     const polyBoundaryMesh& patches = mesh.boundaryMesh();

applications/utilities/mesh/manipulation/createPatch/createPatch.C

@@ -516,11 +516,13 @@ void syncPoints
 
 int main(int argc, char *argv[])
 {
+#   include "addRegionOption.H"
     argList::validOptions.insert("overwrite", "");
 
 #   include "setRootCase.H"
 #   include "createTime.H"
     runTime.functionObjects().off();
+#   include "createNamedPolyMesh.H"
 
     const bool overwrite = args.optionFound("overwrite");
 
@@ -532,6 +534,11 @@ int main(int argc, char *argv[])
         (
             "createPatchDict",
             runTime.system(),
+            (
+                regionName != polyMesh::defaultRegion
+              ? regionName
+              : word::null
+            ),
             runTime,
             IOobject::MUST_READ,
             IOobject::NO_WRITE,
@@ -551,7 +558,6 @@ int main(int argc, char *argv[])
     coupledPolyPatch::matchTol = tol;
 
 
-#   include "createPolyMesh.H"
     const word oldInstance = mesh.pointsInstance();
 
     const polyBoundaryMesh& patches = mesh.boundaryMesh();

applications/utilities/mesh/manipulation/setsToZones/setsToZones.C

@@ -60,6 +60,7 @@ int main(int argc, char *argv[])
 {
     argList::validOptions.insert("noFlipMap", "");
 
+#   include "addRegionOption.H"
 #   include "addTimeOptions.H"
 #   include "setRootCase.H"
 #   include "createTime.H"
@@ -77,7 +78,7 @@ int main(int argc, char *argv[])
 
     runTime.setTime(Times[startTime], startTime);
 
-#   include "createPolyMesh.H"
+#   include "createNamedPolyMesh.H"
 
     // Search for list of objects for the time of the mesh
     IOobjectList objects