Merge remote-tracking branch 'origin/master' into develop

applications/solvers/multiphase/icoReactingMultiphaseInterFoam/phasesSystem/phasePair/phasePair/phasePair.H

@@ -22,11 +22,11 @@ License
     along with OpenFOAM.  If not, see <http://www.gnu.org/licenses/>.
 
 Class
-    Foam::phasePair description for mass transfer between a pair of
+    Foam::phasePair
-    phases. The direction of the mass transfer is from the phase
-    'from' to the phasse 'to'.
 
 Description
+    Description for mass transfer between a pair of phases. The direction of
+    the mass transfer is from the phase 'from' to the phasse 'to'.
 
 SourceFiles
     phasePair.C

bin/foamLog

@@ -241,7 +241,7 @@ getAllQueries()
     #-- Add ones from database, present in log file
     # Note: just like awk, line selected with regular expression,
     #       column with string.
-    local dbQueries=$(getDbQueryList $db)
+    local dbQueries="$(getDbQueryList $db)"
 
     for var in $dbQueries
     do

src/OpenFOAM/containers/Bits/PackedList/PackedList.H

@@ -157,7 +157,7 @@ public:
         // \code
         //     (numElem / elem_per_block)
         //   + (numElem % elem_per_block) ? 1 : 0
-        // \code
+        // \endcode
         // But avoiding the modulus operation
         static constexpr label num_blocks(label numElem)
         {
@@ -498,7 +498,6 @@ public:
             Ostream& os,
             const PackedList<Width>& list
         );
-
 };
 
 

src/OpenFOAM/db/functionObjects/functionObject/functionObject.H

@@ -32,7 +32,7 @@ Description
     field and derived quantities.  Alternatively, the same actions can be
     executed after the simulation using the \c -postProcess command-line option.
 
-    \subsection secFunctionObjects Using function objects
+    \section secFunctionObjects Using function objects
 
     FunctionObjects are selected by additional entries in the
     $FOAM_CASE/system/controlDict dictionary.  Each object is listed in the \c

src/OpenFOAM/global/fileOperations/collatedFileOperation/hostCollatedFileOperation.H

@@ -29,9 +29,9 @@ Description
 
     In parallel it will assume ranks are sorted according to hostname
     and the lowest rank per hostname will be the IO rank. The output directories
-    will get a unique name processors<N>_<low>-<high> where N is the overall
+    will get a unique name processors\<N\>_\<low\>-\<high\> where N is the
-    number of processors and low and high is the range of ranks contained
+    overall number of processors and low and high is the range of ranks
-    in the files. Each of these subsets uses its own communicator.
+    contained in the files. Each of these subsets uses its own communicator.
 
     Instead of using the hostnames the IO ranks can be assigned using the
     FOAM_IORANKS environment variable (also when running non-parallel), e.g.

src/OpenFOAM/global/fileOperations/masterUncollatedFileOperation/masterUncollatedFileOperation.H

@@ -28,8 +28,9 @@ Description
     fileOperations that performs all file operations on the master processor.
     Requires the calls to be parallel synchronised!
 
-    Limitations: - no /processor in filename
+    Limitations
-                 - no /uniform/ in the filename
+    - no /processor in filename
+    - no /uniform/ in the filename
 
     The main logic is in ::filePath which returns a
     - same path on all processors. This can either be a global file
@@ -40,12 +41,12 @@ Description
     - different path on all processors (processor0/0/p)
 
     system/controlDict:
-    filePath worldmaster: <globalRoot>/system/controlDict
+    filePath worldmaster: \<globalRoot\>/system/controlDict
              localmaster:           ,,
              slave      :           ,,
 
     processor0/uniform/time
-    filePath worldmaster: <globalRoot>/processorXXX/uniform/time
+    filePath worldmaster: \<globalRoot\>/processorXXX/uniform/time
              localmaster:           ,,
              slave      :           ,,
 

src/OpenFOAM/meshes/polyMesh/zones/ZoneMesh/ZoneMesh.H

@@ -279,6 +279,7 @@ public:
         //
         //      if (nOrig == zones.size()) { existing... } else { new... }
         //  \endcode
+        //  \param zoneName the name of the zone
         //  \param verbose report if an existing zone was selected or
         //      a new zone was created.
         //  \return non-const reference to the existing or new zone

src/OpenFOAM/primitives/functions/Function1/Table/Table.H

@@ -86,6 +86,12 @@ public:
         //- Copy constructor
         explicit Table(const Table<Type>& tbl);
 
+        //- Construct and return a clone
+        virtual tmp<Function1<Type>> clone() const
+        {
+            return tmp<Function1<Type>>(new Table<Type>(*this));
+        }
+
 
     //- Destructor
     virtual ~Table();

src/OpenFOAM/primitives/strings/stringOps/stringOps.H

@@ -218,10 +218,10 @@ namespace stringOps
     //  -# current directory
     //    - leading "./" : the current directory
     //  -# leading tag expansion for commonly used directories
-    //    - <etc>/        : user/group/other OpenFOAM directory
+    //    - \<etc\>/        : user/group/other OpenFOAM directory
-    //    - <case>/       : FOAM_CASE directory
+    //    - \<case\>/       : FOAM_CASE directory
-    //    - <constant>/   : FOAM_CASE/constant directory
+    //    - \<constant\>/   : FOAM_CASE/constant directory
-    //    - <system>/     : FOAM_CASE/system directory
+    //    - \<system\>/     : FOAM_CASE/system directory
     //  -# tilde expansion
     //    - leading "~/" : home directory
     //    - leading "~user" : home directory for specified user
@@ -258,10 +258,10 @@ namespace stringOps
     //  -# current directory
     //    - leading "./" : the current directory
     //  -# leading tag expansion for commonly used directories
-    //    - <etc>/        : user/group/other OpenFOAM directory
+    //    - \<etc\>/        : user/group/other OpenFOAM directory
-    //    - <case>/       : FOAM_CASE directory
+    //    - \<case\>/       : FOAM_CASE directory
-    //    - <constant>/   : FOAM_CASE/constant directory
+    //    - \<constant\>/   : FOAM_CASE/constant directory
-    //    - <system>/     : FOAM_CASE/system directory
+    //    - \<system\>/     : FOAM_CASE/system directory
     //  -# tilde expansion
     //    - leading "~/" : home directory
     //    - leading "~user" : home directory for specified user

src/atmosphericModels/kEpsilonLopesdaCosta/kEpsilonLopesdaCosta.C

@@ -3,7 +3,7 @@
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
     \\  /    A nd           | Copyright (C) 2018 OpenFOAM Foundation
-     \\/     M anipulation  |
+     \\/     M anipulation  | Copyright (C) 2018 OpenCFD Ltd.
 -------------------------------------------------------------------------------
 License
     This file is part of OpenFOAM.
@@ -50,14 +50,12 @@ void kEpsilonLopesdaCosta<BasicTurbulenceModel>::setPorosityCoefficient
 
         const scalar Cpm = readScalar(pm.dict().lookup(C.name()));
 
-        forAll(cellZoneIDs, zonei)
+        for (const label zonei : cellZoneIDs)
         {
-            const labelList& cells =
+            const labelList& cells = this->mesh_.cellZones()[zonei];
-                this->mesh_.cellZones()[cellZoneIDs[zonei]];
 
-            forAll(cells, i)
+            for (const label celli : cells)
             {
-                const label celli = cells[i];
                 C[celli] = Cpm;
             }
         }
@@ -79,15 +77,14 @@ void kEpsilonLopesdaCosta<BasicTurbulenceModel>::setCdSigma
 
         const scalar Cpm = readScalar(pm.dict().lookup(C.name()));
 
-        forAll(cellZoneIDs, zonei)
+        for (const label zonei : cellZoneIDs)
         {
-            const labelList& cells =
+            const labelList& cells = this->mesh_.cellZones()[zonei];
-                this->mesh_.cellZones()[cellZoneIDs[zonei]];
 
             forAll(cells, i)
             {
                 const label celli = cells[i];
-                C[celli] = Cpm*Sigma[celli];
+                C[celli] = Cpm*Sigma[i];
             }
         }
     }
@@ -115,10 +112,13 @@ void kEpsilonLopesdaCosta<BasicTurbulenceModel>::setPorosityCoefficients()
                     );
 
                 setPorosityCoefficient(Cmu_, pm);
+                Cmu_.correctBoundaryConditions();
                 setPorosityCoefficient(C1_, pm);
                 setPorosityCoefficient(C2_, pm);
                 setPorosityCoefficient(sigmak_, pm);
                 setPorosityCoefficient(sigmaEps_, pm);
+                sigmak_.correctBoundaryConditions();
+                sigmaEps_.correctBoundaryConditions();
 
                 setCdSigma(CdSigma_, pm);
                 setPorosityCoefficient(betap_, pm);

src/atmosphericModels/porosityModels/powerLawLopesdaCosta/powerLawLopesdaCosta.H

@@ -22,7 +22,7 @@ License
     along with OpenFOAM.  If not, see <http://www.gnu.org/licenses/>.
 
 Class
-    Foam::powerLawLopesdaCosta
+    Foam::porosityModels::powerLawLopesdaCosta
 
 Description
     Variant of the power law porosity model with spatially varying
@@ -105,7 +105,7 @@ public:
 
 
 /*---------------------------------------------------------------------------*\
-                      Class powerLawLopesdaCosta Declaration
+                    Class powerLawLopesdaCosta Declaration
 \*---------------------------------------------------------------------------*/
 
 class powerLawLopesdaCosta

src/combustionModels/EDC/EDC.H

@@ -35,7 +35,7 @@ Description
     There are many versions and developments of the EDC model, 4 of which are
     currently supported in this implementation: v1981, v1996, v2005 and
     v2016.  The model variant is selected using the optional \c version entry in
-    the \c EDCCoeffs dictionary, \eg
+    the \c EDCCoeffs dictionary, e.g.
 
     \verbatim
         EDCCoeffs

src/dynamicMesh/motionSolvers/displacement/solidBody/multiSolidBodyMotionSolver.C

@@ -3,7 +3,7 @@
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
     \\  /    A nd           | Copyright (C) 2011-2016 OpenFOAM Foundation
-     \\/     M anipulation  |
+     \\/     M anipulation  | Copyright (C) 2018 OpenCFD Ltd.
 -------------------------------------------------------------------------------
 License
     This file is part of OpenFOAM.
@@ -117,8 +117,9 @@ Foam::multiSolidBodyMotionSolver::multiSolidBodyMotionSolver
             pointIDs_[zonei].transfer(ptIDs);
 
             Info<< "Applying solid body motion " << SBMFs_[zonei].type()
-                << " to " << pointIDs_[zonei].size() << " points of cellZone "
+                << " to "
-                << iter().keyword() << endl;
+                << returnReduce(pointIDs_[zonei].size(), sumOp<label>())
+                << " points of cellZone " << iter().keyword() << endl;
 
             zonei++;
         }

src/finiteVolume/cfdTools/general/solutionControl/loopControl/loopControl.H

@@ -45,6 +45,7 @@ Usage
             }
         }
     }
+    \endverbatim
 
     Where the loop entries comprise:
     \table

src/finiteVolume/fields/fvPatchFields/derived/turbulentDFSEMInlet/turbulentDFSEMInletFvPatchVectorField.H

@@ -45,8 +45,8 @@ Description
     except that no interpolation in time is supported.  These should be
     located in the directory:
 
-        \$FOAM_CASE/constant/boundaryData/<patchName>/points
+        \$FOAM_CASE/constant/boundaryData/\<patchName\>/points
-        \$FOAM_CASE/constant/boundaryData/<patchName>/0/\{R|U|L\}
+        \$FOAM_CASE/constant/boundaryData/\<patchName\>/0/\{R|U|L\}
 
 
 Usage

src/functionObjects/field/CourantNo/CourantNo.H

@@ -49,7 +49,7 @@ Usage
         type         | Type name: CourantNo    | yes         |
         rho          | Name of density field   | no          | rho
         field        | Name of flux field      | no          | phi
-        result       | Name of Courant number field | no     | <function name>
+        result       | Name of Courant number field | no     | \<function name\>
         log          | Log to standard output  | no          | yes
     \endtable
 

src/functionObjects/field/DESModelRegions/DESModelRegions.H

@@ -51,7 +51,7 @@ Usage
     \table
         Property     | Description             | Required    | Default value
         type         | type name: DESModelRegions| yes       |
-        resultName   | Name of DES indicator field | no      | <function name>
+        resultName   | Name of DES indicator field | no      | \<function name\>
         log          | log to standard output  | no          | yes
     \endtable
 

src/functionObjects/field/PecletNo/PecletNo.H

@@ -47,7 +47,7 @@ Usage
         type         | type name: Peclet       | yes         |
         phi          | Name of flux field      | no          | phi
         rho          | Name of density field   | no          | rho
-        result       | Name of Peclet field    | no          | <function name>
+        result       | Name of Peclet field    | no          | \<function name\>
         log          | Log to standard output  | no          | yes
     \endtable
 

src/functionObjects/field/Q/Q.H

@@ -56,7 +56,7 @@ Usage
         Property     | Description             | Required    | Default value
         type         | type name: Q            | yes         |
         U            | Name of velocity field  | no          | U
-        result       | Name of Q field         | no          | <function name>
+        result       | Name of Q field         | no          | \<function name\>
         log          | Log to standard output  | no          | yes
     \endtable
 

src/functionObjects/field/blendingFactor/blendingFactor.H

@@ -42,7 +42,7 @@ Description
     The factor is a face-based quantity, which is converted to a cell-based
     quantity by assigning the minimum blending factor for any cell face.
 
-    An indicator (volume) field, named <functionObjectName>:<fieldName>, is
+    An indicator (volume) field, named \<functionObjectName\>:\<fieldName\>, is
     generated that is set to (1 - f), i.e. values of:
     - 0 represent scheme1 as active, and
     - 1 represent scheme2 as active.

src/functionObjects/field/fluxSummary/fluxSummary.H

@@ -71,7 +71,7 @@ Usage
     - surface
     - surfaceAndDirection
 
-    Output data is written to files of the form \<timeDir\>/<faceZoneName>.dat
+    Output data is written to files of the form \<timeDir\>/\<faceZoneName\>.dat
 
 See also
     Foam::functionObjects::fvMeshFunctionObject

src/functionObjects/field/mapFields/mapFields.H

@@ -53,7 +53,7 @@ Usage
         type         | Type name: mapFields       | yes       |
         mapRegion    | Name of region to map to   | yes       |
         mapMethod    | Mapping method             | yes       |
-        patchMapMethod | Patch mapping method     | no        | <auto>
+        patchMapMethod | Patch mapping method     | no        | \<auto\>
         consistent   | Mapping meshes have consistent boundaries | yes |
         fields       | List of field names to map | yes       |
         log          | Log to standard output     | no        | yes

src/functionObjects/field/reference/reference.H

@@ -67,8 +67,8 @@ Usage
         Property     | Description             | Required | Default value
         type         | Type name: reference    | yes      |
         field        | Name of field           | yes      |
-        result       | Name of result field    | no       | reference(<field>)
+        result       | Name of result field    | no       | reference(\<field\>)
-        position     | Position to sample      | no       | <not used>
+        position     | Position to sample      | no       | \<not used\>
         scale        | Scale value             | no       | 1
         offset       | Offset value            | no       | zero
         log          | Log to standard output  | no       | yes

src/functionObjects/field/stabilityBlendingFactor/stabilityBlendingFactor.H

@@ -63,7 +63,7 @@ Description
                     ),
                     1.0
                 )
-        \f[
+        \f]
 
     For option 2, the following relation is used:
         \f[
@@ -78,7 +78,7 @@ Description
                     ),
                     1.0
                 )
-        \f[
+        \f]
     Note that  magGradCC is equal to 3 for ortoghonal meshes
 
     For option 3 a PID control is used in order to control residual
@@ -89,14 +89,14 @@ Description
                 P*residual
               + I*residualIntegral
               + D*residualDifferential
-        \f[
+        \f]
 
         where P, I and D are user inputs
 
     The following relation is used:
     \f[
         fRes = (factor - meanRes)/(maxRes*meanRes);
-    \f[
+    \f]
 
         where:
             meanRes = average(residual)
@@ -120,7 +120,7 @@ Description
                 ),
                 1.0
             )
-        \f[
+        \f]
     Note that faceWeights for a orthogonal mesh is 0.5.
 
 
@@ -138,7 +138,7 @@ Description
                 ),
                 1.0
             )
-        \f[
+        \f]
 
 
     For option 6 , the following relation is used:
@@ -275,8 +275,7 @@ Usage
         tolerance    | Tolerance for number of blended cells | no | 0.001
         field        | Name of field to evaluate | yes       |
         result    | Name of surface field to be used in the localBlended scheme
-        | yes
+        | yes |
-
     \endtable
 
     The 'log' flag true write the number of cells on each scheme, plus it

src/functionObjects/solvers/scalarTransport/scalarTransport.H

@@ -48,6 +48,7 @@ Description
 Usage
     Example of function object specification to solve a scalar transport
     equation:
+    \verbatim
     functions
     {
         scalar1

src/overset/include/setCellMask.H

@@ -21,13 +21,9 @@ License
     You should have received a copy of the GNU General Public License
     along with OpenFOAM.  If not, see <http://www.gnu.org/licenses/>.
 
-Class
-
 Description
     Sets blocked cells mask field
 
-SourceFiles
-
 \*---------------------------------------------------------------------------*/
 
 {

src/overset/include/setInterpolatedCells.H

@@ -21,13 +21,9 @@ License
     You should have received a copy of the GNU General Public License
     along with OpenFOAM.  If not, see <http://www.gnu.org/licenses/>.
 
-Class
-
 Description
     Sets blocked cells mask field
 
-SourceFiles
-
 \*---------------------------------------------------------------------------*/
 
 {

src/transportModels/incompressible/viscosityModels/BirdCarreau/BirdCarreau.C

@@ -87,7 +87,7 @@ Foam::viscosityModels::BirdCarreau::BirdCarreau
     (
         IOobject
         (
-            "nu",
+            name,
             U_.time().timeName(),
             U_.db(),
             IOobject::NO_READ,

src/transportModels/incompressible/viscosityModels/Casson/Casson.C

@@ -92,7 +92,7 @@ Foam::viscosityModels::Casson::Casson
     (
         IOobject
         (
-            "nu",
+            name,
             U_.time().timeName(),
             U_.db(),
             IOobject::NO_READ,

wmake/scripts/have_kahip

@@ -83,10 +83,10 @@ have_kahip()
         # FOAM_EXT_LIBBIN is allowed to be unset
         library=$(findFirstFile \
             $FOAM_EXT_LIBBIN/$library \
-            $METIS_ARCH_PATH/lib/$static \
+            $KAHIP_ARCH_PATH/lib/$static \
-            $METIS_ARCH_PATH/lib/$library \
+            $KAHIP_ARCH_PATH/lib/$library \
-            $METIS_ARCH_PATH/lib$WM_COMPILER_LIB_ARCH/$static \
+            $KAHIP_ARCH_PATH/lib$WM_COMPILER_LIB_ARCH/$static \
-            $METIS_ARCH_PATH/lib$WM_COMPILER_LIB_ARCH/$library \
+            $KAHIP_ARCH_PATH/lib$WM_COMPILER_LIB_ARCH/$library \
         )
     elif isSystem "$KAHIP_ARCH_PATH"
     then