ENH: (further) Doxygen documentation updates for module support

doc/Doxygen/Doxyfile

@@ -578,7 +578,7 @@ SORT_MEMBERS_CTORS_1ST = NO
 # appear in their defined order.
 # The default value is: NO.
 
-SORT_GROUP_NAMES       = NO
+SORT_GROUP_NAMES       = YES
 
 # If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be sorted by
 # fully-qualified names, including namespaces. If set to NO, the class list will

src/OpenFOAM/global/foamDoc.H

@@ -3,7 +3,7 @@
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
     \\  /    A nd           | Copyright (C) 2011-2015 OpenFOAM Foundation
-     \\/     M anipulation  |
+     \\/     M anipulation  | Copyright (C) 2016 OpenCFD Ltd.
 -------------------------------------------------------------------------------
 License
     This file is part of OpenFOAM.
@@ -56,8 +56,22 @@ License
 
 \section usingTheCode Using the code
 
+    Solvers
     - \subpage pageSolvers
+
+    Modelling
+    - \subpage pageThermophsyicalModels
+    - \subpage pageTurbulenceModelling
+    - \subpage pageLagrangianIntermediate
+
+    Boundary conditions
     - \subpage pageBoundaryConditions
+
+    Numerics
+    - \subpage pageFiniteVolumeSchemes
+    - \subpage pageMatrixSolvers
+
+    Post-processing
     - \subpage pagePostProcessing
 
 

src/OpenFOAM/matrices/lduMatrix/doc/lduMatrix.dox

@@ -0,0 +1,36 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 2016 OpenCFD Ltd.
+     \\/     M anipulation  |
+-------------------------------------------------------------------------------
+License
+    This file is part of OpenFOAM.
+
+    OpenFOAM is free software: you can redistribute it and/or modify it under
+    the terms of the GNU General Public License as published by the Free
+    Software Foundation, either version 3 of the License, or (at your option)
+    any later version.
+
+    OpenFOAM is distributed in the hope that it will be useful, but WITHOUT ANY
+    WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+    FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
+    details.
+
+    You should have received a copy of the GNU General Public License along with
+    OpenFOAM.  If not, see <http://www.gnu.org/licenses/>.
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+\page pageMatrixSolvers Matrix solvers
+
+\section secSchemes Overview
+The available matrix solvers are grouped into the following categories:
+  - \ref grpLduMatrix
+  - \ref grpLduMatrixPreconditioners
+  - \ref grpLduMatrixSmoothers
+  - \ref grpLduMatrixSolvers
+
+
+\*---------------------------------------------------------------------------*/

src/OpenFOAM/matrices/lduMatrix/doc/lduMatrixDoc.H

@@ -0,0 +1,56 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 2016 OpenCFD Ltd.
+     \\/     M anipulation  |
+-------------------------------------------------------------------------------
+License
+    This file is part of OpenFOAM.
+
+    OpenFOAM is free software: you can redistribute it and/or modify it under
+    the terms of the GNU General Public License as published by the Free
+    Software Foundation, either version 3 of the License, or (at your option)
+    any later version.
+
+    OpenFOAM is distributed in the hope that it will be useful, but WITHOUT ANY
+    WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+    FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
+    details.
+
+    You should have received a copy of the GNU General Public License along with
+    OpenFOAM.  If not, see <http://www.gnu.org/licenses/>.
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+\defgroup grpNumerics Numerics
+@{
+    This group contains numerics
+@}
+
+\defgroup grpLduMatrix Matrix manipulation and solvers
+@{
+    \ingroup grpNumerics
+    This group contains matrices
+@}
+
+\defgroup grpLduMatrixPreconditioners Preconditioners
+@{
+    \ingroup grpLduMatrix
+    This group contains matrix preconditioners
+@}
+
+\defgroup grpLduMatrixSmoothers Smoothers
+@{
+    \ingroup grpLduMatrix
+    This group contains matrix smoothers
+@}
+
+\defgroup grpLduMatrixSolvers Solvers
+@{
+    \ingroup grpLduMatrix
+    This group contains matrix solvers
+@}
+
+
+\*---------------------------------------------------------------------------*/

src/OpenFOAM/matrices/lduMatrix/preconditioners/DICPreconditioner/DICPreconditioner.H

@@ -24,6 +24,9 @@ License
 Class
     Foam::DICPreconditioner
 
+Group
+    grpLduMatrixPreconditioners
+
 Description
     Simplified diagonal-based incomplete Cholesky preconditioner for symmetric
     matrices (symmetric equivalent of DILU).  The reciprocal of the

src/OpenFOAM/matrices/lduMatrix/preconditioners/DILUPreconditioner/DILUPreconditioner.H

@@ -24,6 +24,9 @@ License
 Class
     Foam::DILUPreconditioner
 
+Group
+    grpLduMatrixPreconditioners
+
 Description
     Simplified diagonal-based incomplete LU preconditioner for asymmetric
     matrices.  The reciprocal of the preconditioned diagonal is calculated

src/OpenFOAM/matrices/lduMatrix/preconditioners/FDICPreconditioner/FDICPreconditioner.H

@@ -24,6 +24,9 @@ License
 Class
     Foam::FDICPreconditioner
 
+Group
+    grpLduMatrixPreconditioners
+
 Description
     Faster version of the DICPreconditioner diagonal-based incomplete
     Cholesky preconditioner for symmetric matrices

src/OpenFOAM/matrices/lduMatrix/preconditioners/GAMGPreconditioner/GAMGPreconditioner.H

@@ -24,6 +24,9 @@ License
 Class
     Foam::GAMGPreconditioner
 
+Group
+    grpLduMatrixPreconditioners
+
 Description
     Geometric agglomerated algebraic multigrid preconditioner.
 

src/OpenFOAM/matrices/lduMatrix/preconditioners/diagonalPreconditioner/diagonalPreconditioner.H

@@ -24,6 +24,9 @@ License
 Class
     Foam::diagonalPreconditioner
 
+Group
+    grpLduMatrixPreconditioners
+
 Description
     Diagonal preconditioner for both symmetric and asymmetric matrices.
 

src/OpenFOAM/matrices/lduMatrix/preconditioners/noPreconditioner/noPreconditioner.H

@@ -24,6 +24,9 @@ License
 Class
     Foam::noPreconditioner
 
+Group
+    grpLduMatrixPreconditioners
+
 Description
     Null preconditioner for both symmetric and asymmetric matrices.
 

src/OpenFOAM/matrices/lduMatrix/smoothers/DIC/DICSmoother.H

@@ -24,6 +24,9 @@ License
 Class
     Foam::DICSmoother
 
+Group
+    grpLduMatrixSmoothers
+
 Description
     Simplified diagonal-based incomplete Cholesky smoother for symmetric
     matrices.

src/OpenFOAM/matrices/lduMatrix/smoothers/DICGaussSeidel/DICGaussSeidelSmoother.H

@@ -24,6 +24,9 @@ License
 Class
     Foam::DICGaussSeidelSmoother
 
+Group
+    grpLduMatrixSmoothers
+
 Description
     Combined DIC/GaussSeidel smoother for symmetric matrices in which DIC
     smoothing is followed by GaussSeidel to ensure that any "spikes" created

src/OpenFOAM/matrices/lduMatrix/smoothers/DILU/DILUSmoother.H

@@ -24,6 +24,9 @@ License
 Class
     Foam::DILUSmoother
 
+Group
+    grpLduMatrixSmoothers
+
 Description
     Simplified diagonal-based incomplete LU smoother for asymmetric matrices.
 

src/OpenFOAM/matrices/lduMatrix/smoothers/GaussSeidel/GaussSeidelSmoother.H

@@ -24,6 +24,9 @@ License
 Class
     Foam::GaussSeidelSmoother
 
+Group
+    grpLduMatrixSmoothers
+
 Description
     A lduMatrix::smoother for Gauss-Seidel
 

src/OpenFOAM/matrices/lduMatrix/smoothers/nonBlockingGaussSeidel/nonBlockingGaussSeidelSmoother.H

@@ -24,6 +24,9 @@ License
 Class
     Foam::nonBlockingGaussSeidelSmoother
 
+Group
+    grpLduMatrixSmoothers
+
 Description
     Variant of gaussSeidelSmoother that expects processor boundary
     cells to be sorted last and so can block later. Only when the

src/OpenFOAM/matrices/lduMatrix/smoothers/symGaussSeidel/symGaussSeidelSmoother.H

@@ -24,6 +24,9 @@ License
 Class
     Foam::symGaussSeidelSmoother
 
+Group
+    grpLduMatrixSmoothers
+
 Description
     A lduMatrix::smoother for symmetric Gauss-Seidel
 

src/OpenFOAM/matrices/lduMatrix/solvers/BICCG/BICCG.H

@@ -24,6 +24,9 @@ License
 Class
     Foam::BICCG
 
+Group
+    grpLduMatrixSolvers
+
 Description
     Diagonal incomplete LU preconditioned BiCG solver derived from the general
     preconditioned BiCG solver PBiCG but with the choice of preconditioner
@@ -49,7 +52,7 @@ namespace Foam
 {
 
 /*---------------------------------------------------------------------------*\
-                           Class BICCG Declaration
+                            Class BICCG Declaration
 \*---------------------------------------------------------------------------*/
 
 class BICCG
@@ -64,6 +67,7 @@ class BICCG
         //- Disallow default bitwise assignment
         void operator=(const BICCG&);
 
+
 public:
 
     //- Return the dictionary constructed from the components.
@@ -112,7 +116,6 @@ public:
     //- Destructor
     virtual ~BICCG()
     {}
-
 };
 
 

src/OpenFOAM/matrices/lduMatrix/solvers/GAMG/GAMGSolver.H

@@ -24,10 +24,13 @@ License
 Class
     Foam::GAMGSolver
 
+Group
+    grpLduMatrixSolvers
+
 Description
     Geometric agglomerated algebraic multigrid solver.
 
-  Characteristics:
+    Characteristics:
       - Requires positive definite, diagonally dominant matrix.
       - Agglomeration algorithm: selectable and optionally cached.
       - Restriction operator: summation.
@@ -65,7 +68,7 @@ namespace Foam
 {
 
 /*---------------------------------------------------------------------------*\
-                           Class GAMGSolver Declaration
+                         Class GAMGSolver Declaration
 \*---------------------------------------------------------------------------*/
 
 class GAMGSolver

src/OpenFOAM/matrices/lduMatrix/solvers/ICCG/ICCG.H

@@ -24,6 +24,9 @@ License
 Class
     Foam::ICCG
 
+Group
+    grpLduMatrixSolvers
+
 Description
     Incomplete Cholesky preconditioned CG solver derived from the general
     preconditioned CG solver PCG but with the choice of preconditioner
@@ -64,6 +67,7 @@ class ICCG
         //- Disallow default bitwise assignment
         void operator=(const ICCG&);
 
+
 public:
 
         //- Return the dictionary constructed from the components.
@@ -111,7 +115,6 @@ public:
     //- Destructor
     virtual ~ICCG()
     {}
-
 };
 
 

src/OpenFOAM/matrices/lduMatrix/solvers/PCG/PCG.H

@@ -24,6 +24,9 @@ License
 Class
     Foam::PCG
 
+Group
+    grpLduMatrixSolvers
+
 Description
     Preconditioned conjugate gradient solver for symmetric lduMatrices
     using a run-time selectable preconditioner.
@@ -44,7 +47,7 @@ namespace Foam
 {
 
 /*---------------------------------------------------------------------------*\
-                           Class PCG Declaration
+                             Class PCG Declaration
 \*---------------------------------------------------------------------------*/
 
 class PCG

src/OpenFOAM/matrices/lduMatrix/solvers/diagonalSolver/diagonalSolver.H

@@ -24,6 +24,9 @@ License
 Class
     Foam::diagonalSolver
 
+Group
+    grpLduMatrixSolvers
+
 Description
     Foam::diagonalSolver
 
@@ -43,7 +46,7 @@ namespace Foam
 {
 
 /*---------------------------------------------------------------------------*\
-                           Class diagonalSolver Declaration
+                       Class diagonalSolver Declaration
 \*---------------------------------------------------------------------------*/
 
 class diagonalSolver

src/OpenFOAM/matrices/lduMatrix/solvers/smoothSolver/smoothSolver.H

@@ -24,6 +24,9 @@ License
 Class
     Foam::smoothSolver
 
+Group
+    grpLduMatrixSolvers
+
 Description
     Iterative solver for symmetric and asymetric matrices which uses a
     run-time selected smoother e.g. GaussSeidel to converge the solution to
@@ -65,6 +68,7 @@ protected:
         //- Read the control parameters from the controlDict_
         virtual void readControls();
 
+
 public:
 
     //- Runtime type information

src/TurbulenceModels/turbulenceModels/doc/turbulenceModel.dox

@@ -0,0 +1,36 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 2016 OpenCFD Ltd.
+     \\/     M anipulation  |
+-------------------------------------------------------------------------------
+License
+    This file is part of OpenFOAM.
+
+    OpenFOAM is free software: you can redistribute it and/or modify it under
+    the terms of the GNU General Public License as published by the Free
+    Software Foundation, either version 3 of the License, or (at your option)
+    any later version.
+
+    OpenFOAM is distributed in the hope that it will be useful, but WITHOUT ANY
+    WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+    FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
+    details.
+
+    You should have received a copy of the GNU General Public License along with
+    OpenFOAM.  If not, see <http://www.gnu.org/licenses/>.
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+\page pageTurbulenceModelling Turbulence modelling
+
+\section secSchemes Overview
+The available turbulence models are grouped into the following categories:
+  - \ref grpTurbulence
+  - \ref grpRASTurbulence
+  - \ref grpDESTurbulence
+  - \ref grpLESTurbulence
+
+
+\*---------------------------------------------------------------------------*/

src/finiteVolume/finiteVolume/doc/finiteVolumeSchemes.dox

@@ -0,0 +1,40 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 2016 OpenCFD Ltd.
+     \\/     M anipulation  |
+-------------------------------------------------------------------------------
+License
+    This file is part of OpenFOAM.
+
+    OpenFOAM is free software: you can redistribute it and/or modify it under
+    the terms of the GNU General Public License as published by the Free
+    Software Foundation, either version 3 of the License, or (at your option)
+    any later version.
+
+    OpenFOAM is distributed in the hope that it will be useful, but WITHOUT ANY
+    WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+    FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
+    details.
+
+    You should have received a copy of the GNU General Public License along with
+    OpenFOAM.  If not, see <http://www.gnu.org/licenses/>.
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+\page pageFiniteVolumeSchemes Numerical schemes
+
+\section secSchemes Overview
+The available numerical schemes are grouped into the following categories:
+  - \ref grpFvGradSchemes
+  - \ref grpFvSnGradSchemes
+  - \ref grpFvDivSchemes
+  - \ref grpFvLaplacianSchemes
+  - \ref grpFvDdtSchemes
+  - \ref grpFvConvectionSchemes
+  - \ref grpFvSurfaceInterpolationSchemes
+  - \ref grpFvLimitedSurfaceInterpolationSchemes
+
+
+\*---------------------------------------------------------------------------*/

src/finiteVolume/finiteVolume/doc/finiteVolumeSchemesDoc.H

@@ -25,6 +25,7 @@ License
 
 \defgroup grpFvSchemes Finite volume numerical schemes
 @{
+    \ingroup grpNumerics
     This group contains finite volume numerical schemes
 @}
 

src/fvOptions/constraints/derived/fixedTemperatureConstraint/fixedTemperatureConstraint.H

@@ -24,6 +24,9 @@ License
 Class
     Foam::fv::fixedTemperatureConstraint
 
+Group
+    grpFvOptionsConstraints
+
 Description
     Fixed temperature equation constraint
 

src/fvOptions/constraints/derived/velocityDampingConstraint/velocityDampingConstraint.H

@@ -24,6 +24,9 @@ License
 Class
     Foam::fv::velocityDampingConstraint
 
+Group
+    grpFvOptionsConstraints
+
 Description
     Constraint for velocity to dampen velocity fluctuations in
     steady simulations

src/fvOptions/constraints/general/explicitSetValue/ExplicitSetValue.H

@@ -24,6 +24,9 @@ License
 Class
     Foam::fv::explicitSetValue
 
+Group
+    grpFvOptionsConstraints
+
 Description
     Set values field values explicity.
 

src/fvOptions/corrections/limitTemperature/limitTemperature.H

@@ -24,6 +24,9 @@ License
 Class
     Foam::fv::limitTemperature
 
+Group
+    grpFvOptionsCorrections
+
 Description
     Correction for temperature to apply limits between minimum and maximum
     values

src/fvOptions/doc/fvOptionsDoc.H

@@ -0,0 +1,51 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 2016 OpenCFD Ltd.
+     \\/     M anipulation  |
+-------------------------------------------------------------------------------
+License
+    This file is part of OpenFOAM.
+
+    OpenFOAM is free software: you can redistribute it and/or modify it under
+    the terms of the GNU General Public License as published by the Free
+    Software Foundation, either version 3 of the License, or (at your option)
+    any later version.
+
+    OpenFOAM is distributed in the hope that it will be useful, but WITHOUT ANY
+    WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+    FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
+    details.
+
+    You should have received a copy of the GNU General Public License along with
+    OpenFOAM.  If not, see <http://www.gnu.org/licenses/>.
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+\defgroup grpFvOptions Finite volume Options
+@{
+    \ingroup grpNumerics
+    This group contains finite volume options
+@}
+
+\defgroup grpFvOptionsSources Sources
+@{
+    \ingroup grpFvOptions
+    This group contains finite volume sources
+@}
+
+\defgroup grpFvOptionsCorrections Corrections
+@{
+    \ingroup grpFvOptions
+    This group contains finite volume corrections
+@}
+
+\defgroup grpFvOptionsConstraints Constraints
+@{
+    \ingroup grpFvOptions
+    This group contains finite volume constraints
+@}
+
+
+\*---------------------------------------------------------------------------*/

src/fvOptions/sources/derived/actuationDiskSource/actuationDiskSource.H

@@ -24,6 +24,9 @@ License
 Class
     Foam::fv::actuationDiskSource
 
+Group
+    grpFvOptionsSources
+
 Description
     Actuation disk source
 

src/fvOptions/sources/derived/buoyancyEnergy/buoyancyEnergy.H

@@ -24,6 +24,9 @@ License
 Class
     Foam::fv::buoyancyEnergy
 
+Group
+    grpFvOptionsSources
+
 Description
     Calculates and applies the buoyancy energy source rho*(U&g) to the energy
     equation.

src/fvOptions/sources/derived/buoyancyForce/buoyancyForce.H

@@ -24,6 +24,9 @@ License
 Class
     Foam::fv::buoyancyForce
 
+Group
+    grpFvOptionsSources
+
 Description
     Calculates and applies the buoyancy force rho*g to the momentum equation
     corresponding to the specified velocity field.

src/fvOptions/sources/derived/directionalPressureGradientExplicitSource/directionalPressureGradientExplicitSource.H

@@ -24,6 +24,9 @@ License
 Class
     Foam::fv::directionalPressureGradientExplicitSource
 
+Group
+    grpFvOptionsSources
+
 Description
     Creates an explicit  pressure gradient source in such a way to deflect the
     flow towards an specific direction (flowDir). Alternatively add an extra

src/fvOptions/sources/derived/effectivenessHeatExchangerSource/effectivenessHeatExchangerSource.H

@@ -24,6 +24,9 @@ License
 Class
     Foam::fv::effectivenessHeatExchangerSource
 
+Group
+    grpFvOptionsSources
+
 Description
     Heat exchanger source model, in which the heat exchanger is defined as a
     selection of cells.

src/fvOptions/sources/derived/explicitPorositySource/explicitPorositySource.H

@@ -24,6 +24,9 @@ License
 Class
     Foam::fv::explicitPorositySource
 
+Group
+    grpFvOptionsSources
+
 Description
     Explicit porosity source
 

src/fvOptions/sources/derived/meanVelocityForce/meanVelocityForce.H

@@ -24,6 +24,9 @@ License
 Class
     Foam::fv::meanVelocityForce
 
+Group
+    grpFvOptionsSources
+
 Description
     Calculates and applies the force necessary to maintain the specified mean
     velocity.

src/fvOptions/sources/derived/radialActuationDiskSource/radialActuationDiskSource.H

@@ -24,6 +24,9 @@ License
 Class
     Foam::fv::radialActuationDiskSource
 
+Group
+    grpFvOptionsSources
+
 Description
     Actuation disk source including radial thrust
 

src/fvOptions/sources/derived/rotorDiskSource/rotorDiskSource.H

@@ -24,6 +24,9 @@ License
 Class
     Foam::fv::rotorDiskSource
 
+Group
+    grpFvOptionsSources
+
 Description
     Rotor disk source
 

src/fvOptions/sources/derived/solidificationMeltingSource/solidificationMeltingSource.H

@@ -24,6 +24,9 @@ License
 Class
     Foam::fv::solidificationMeltingSource
 
+Group
+    grpFvOptionsSources
+
 Description
     This source is designed to model the effect of solidification and melting
     processes, e.g. windhield defrosting.  The phase change occurs at the

src/fvOptions/sources/derived/tabulatedAccelerationSource/tabulatedAccelerationSource.H

@@ -24,6 +24,9 @@ License
 Class
     Foam::fv::tabulatedAccelerationSource
 
+Group
+    grpFvOptionsSources
+
 Description
     Solid-body 6-DoF acceleration source
 
@@ -64,7 +67,7 @@ namespace fv
 {
 
 /*---------------------------------------------------------------------------*\
-                          Class tabulatedAccelerationSource Declaration
+                 Class tabulatedAccelerationSource Declaration
 \*---------------------------------------------------------------------------*/
 
 class tabulatedAccelerationSource
@@ -84,6 +87,7 @@ protected:
 
         dimensionedVector g0_;
 
+
 private:
 
     // Private Member Functions

src/fvOptions/sources/general/codedSource/CodedSource.H

@@ -24,6 +24,9 @@ License
 Class
     Foam::fv::codedSource
 
+Group
+    grpFvOptionsSources
+
 Description
    Constructs on-the-fly fvOption source
 

src/fvOptions/sources/general/semiImplicitSource/SemiImplicitSource.H

@@ -24,6 +24,9 @@ License
 Class
     Foam::fv::SemiImplicitSource
 
+Group
+    grpFvOptionsSources
+
 Description
     Semi-implicit source, described using an input dictionary.  The injection
     rate coefficients are specified as pairs of Su-Sp coefficients, i.e.

src/fvOptions/sources/interRegion/interRegionExplicitPorositySource/interRegionExplicitPorositySource.H

@@ -24,6 +24,9 @@ License
 Class
     Foam::fv::interRegionExplicitPorositySource
 
+Group
+    grpFvOptionsSources
+
 Description
     Inter-region explicit porosity source.
 

src/fvOptions/sources/interRegion/interRegionHeatTransfer/constantHeatTransfer/constantHeatTransfer.H

@@ -24,6 +24,9 @@ License
 Class
     Foam::fv::constantHeatTransfer
 
+Group
+    grpFvOptionsSources
+
 Description
     Constant heat transfer model. htcConst [W/m2/K] and area/volume [1/m]
     must be provided.

src/fvOptions/sources/interRegion/interRegionHeatTransfer/interRegionHeatTransferModel/interRegionHeatTransferModel.H

@@ -24,6 +24,9 @@ License
 Class
     Foam::fv::interRegionHeatTransferModel
 
+Group
+    grpFvOptionsSources
+
 Description
     Base class for inter region heat exchange. The derived classes must
     provide the heat transfer coeffisine (htc) which is used as follows

src/fvOptions/sources/interRegion/interRegionHeatTransfer/tabulatedHeatTransfer/tabulatedHeatTransfer.H

@@ -24,6 +24,9 @@ License
 Class
     Foam::fv::tabulatedHeatTransfer
 
+Group
+    grpFvOptionsSources
+
 Description
     Tabulated heat transfer model. The heat exchange area per unit volume
     must be provided.  The 2D table returns the heat transfer coefficient

src/fvOptions/sources/interRegion/interRegionHeatTransfer/tabulatedNTUHeatTransfer/tabulatedNTUHeatTransfer.H

@@ -24,6 +24,9 @@ License
 Class
     Foam::fv::tabulatedNTUHeatTransfer
 
+Group
+    grpFvOptionsSources
+
 Description
     Tabulated heat transfer model.
 

src/fvOptions/sources/interRegion/interRegionHeatTransfer/variableHeatTransfer/variableHeatTransfer.H

@@ -24,6 +24,9 @@ License
 Class
     Foam::fv::variableHeatTransfer
 
+Group
+    grpFvOptionsSources
+
 Description
     Variable heat transfer model depending on local values. The area of contact
     between regions (area) must be provided. The Nu number is calculated as:

src/lagrangian/intermediate/doc/lagrangianIntermediate.dox

@@ -0,0 +1,41 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 2016 OpenCFD Ltd.
+     \\/     M anipulation  |
+-------------------------------------------------------------------------------
+License
+    This file is part of OpenFOAM.
+
+    OpenFOAM is free software: you can redistribute it and/or modify it under
+    the terms of the GNU General Public License as published by the Free
+    Software Foundation, either version 3 of the License, or (at your option)
+    any later version.
+
+    OpenFOAM is distributed in the hope that it will be useful, but WITHOUT ANY
+    WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+    FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
+    details.
+
+    You should have received a copy of the GNU General Public License along with
+    OpenFOAM.  If not, see <http://www.gnu.org/licenses/>.
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+\page pageLagrangianIntermediate Lagrangian modelling
+
+\section secSchemes Overview
+The available Lagrangian models are grouped into the following categories:
+  - \ref grpLagrangianIntermediateClouds
+  - \ref grpLagrangianIntermediateParcels
+  - \ref grpLagrangianIntermediateSubModels
+  - \ref grpLagrangianIntermediateKinematicSubModels
+  - \ref grpLagrangianIntermediateThermoSubModels
+  - \ref grpLagrangianIntermediateReactingSubModels
+  - \ref grpLagrangianIntermediateReactingMultiphaseSubModels
+  - \ref grpLagrangianIntermediateMPPICSubModels
+  - \ref grpLagrangianIntermediateFunctionObjects
+
+
+\*---------------------------------------------------------------------------*/

src/postProcessing/functionObjects/doc/functionObjects.dox

@@ -3,7 +3,7 @@
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
     \\  /    A nd           | Copyright (C) 2012-2014 OpenFOAM Foundation
-     \\/     M anipulation  | Copyright (C) 2015 OpenCFD Ltd.
+     \\/     M anipulation  | Copyright (C) 2015-2016 OpenCFD Ltd.
 -------------------------------------------------------------------------------
 License
     This file is part of OpenFOAM.
@@ -44,6 +44,7 @@ The current range of features comprises of:
 - \ref grpIOFunctionObjects
 - \ref grpJobControlFunctionObjects
 - \ref grpUtilitiesFunctionObjects
+- \ref grpThermophysicalFunctionObjects
 
 \linebreak
 \subsection secFieldFunctionObjectUsage Using function objects

src/postProcessing/functionObjects/utilities/reactionSensitivityAnalysis/reactionsSensitivityAnalysis.H

@@ -25,7 +25,7 @@ Class
     Foam::reactionsSensitivityAnalysis
 
 Group
-    grpUtilitiesFunctionObjects
+    grpUtilitiesFunctionObjects grpThermophysicalFunctionObjects
 
 Description
     This function object creates four data files named:

src/thermophysicalModels/doc/thermophysicalModels.dox

@@ -0,0 +1,33 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 2016 OpenCFD Ltd.
+     \\/     M anipulation  |
+-------------------------------------------------------------------------------
+License
+    This file is part of OpenFOAM.
+
+    OpenFOAM is free software: you can redistribute it and/or modify it under
+    the terms of the GNU General Public License as published by the Free
+    Software Foundation, either version 3 of the License, or (at your option)
+    any later version.
+
+    OpenFOAM is distributed in the hope that it will be useful, but WITHOUT ANY
+    WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+    FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
+    details.
+
+    You should have received a copy of the GNU General Public License along with
+    OpenFOAM.  If not, see <http://www.gnu.org/licenses/>.
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+\page pageThermophsyicalModels Thermophsyical Models
+
+\section secSchemes Overview
+The available thermophysical models are grouped into the following categories:
+  - \ref grpThermophysicalModels
+
+
+\*---------------------------------------------------------------------------*/

src/thermophysicalModels/doc/thermophysicalModelsDoc.H

@@ -28,5 +28,11 @@ License
     This group contains thermophysical models
 @}
 
+\defgroup grpThermophysicalFunctionObjects Thermophysical function objects
+@{
+    \ingroup grpFunctionObjects
+    This group contains thermo-based function objects
+@}
+
 
 \*---------------------------------------------------------------------------*/

src/thermophysicalModels/reactionThermo/chemistryReaders/chemistryReader/chemistryReader.H

@@ -24,6 +24,9 @@ License
 Class
     Foam::chemistryReader
 
+Group
+    grpReactionThermophysicalChemistryReaders
+
 Description
     Abstract class for reading chemistry
 

src/thermophysicalModels/reactionThermo/chemistryReaders/chemkinReader/chemkinReader.H

@@ -24,6 +24,9 @@ License
 Class
     Foam::chemkinReader
 
+Group
+    grpReactionThermophysicalChemistryReaders
+
 Description
     Foam::chemkinReader
 

src/thermophysicalModels/reactionThermo/chemistryReaders/foamChemistryReader/foamChemistryReader.H

@@ -24,6 +24,9 @@ License
 Class
     Foam::foamChemistryReader
 
+Group
+    grpReactionThermophysicalChemistryReaders
+
 Description
     Chemistry reader for OpenFOAM format
 

src/thermophysicalModels/reactionThermo/derivedFvPatchFields/fixedUnburntEnthalpy/fixedUnburntEnthalpyFvPatchScalarField.H

@@ -24,6 +24,9 @@ License
 Class
     Foam::fixedUnburntEnthalpyFvPatchScalarField
 
+Group
+    grpThermoBoundaryConditions
+
 Description
     Fixed boundary condition for unburnt
 
@@ -43,7 +46,7 @@ namespace Foam
 {
 
 /*---------------------------------------------------------------------------*\
-          Class fixedUnburntEnthalpyFvPatchScalarField Declaration
+           Class fixedUnburntEnthalpyFvPatchScalarField Declaration
 \*---------------------------------------------------------------------------*/
 
 class fixedUnburntEnthalpyFvPatchScalarField

src/thermophysicalModels/reactionThermo/derivedFvPatchFields/gradientUnburntEnthalpy/gradientUnburntEnthalpyFvPatchScalarField.H

@@ -24,6 +24,9 @@ License
 Class
     Foam::gradientUnburntEnthalpyFvPatchScalarField
 
+Group
+    grpThermoBoundaryConditions
+
 Description
     gradient boundary condition for unburnt
 

src/thermophysicalModels/reactionThermo/derivedFvPatchFields/mixedUnburntEnthalpy/mixedUnburntEnthalpyFvPatchScalarField.H

@@ -24,6 +24,9 @@ License
 Class
     Foam::mixedUnburntEnthalpyFvPatchScalarField
 
+Group
+    grpThermoBoundaryConditions
+
 Description
     Mixed boundary condition for unburnt
 

src/thermophysicalModels/reactionThermo/doc/reactionThermoDoc.H

@@ -0,0 +1,43 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 2016 OpenCFD Ltd.
+     \\/     M anipulation  |
+-------------------------------------------------------------------------------
+License
+    This file is part of OpenFOAM.
+
+    OpenFOAM is free software: you can redistribute it and/or modify it under
+    the terms of the GNU General Public License as published by the Free
+    Software Foundation, either version 3 of the License, or (at your option)
+    any later version.
+
+    OpenFOAM is distributed in the hope that it will be useful, but WITHOUT ANY
+    WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+    FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
+    details.
+
+    You should have received a copy of the GNU General Public License along with
+    OpenFOAM.  If not, see <http://www.gnu.org/licenses/>.
+
+\defgroup grpReactionThermophysicalModels Reaction thermophysical models
+@{
+    \ingroup grpThermophysicalModels
+    This group contains reaction thermophysical models
+@}
+
+\defgroup grpReactionThermophysicalMixtures Mixtures
+@{
+    \ingroup grpReactionThermophysicalModels
+    This group contains reaction mixtures
+@}
+
+\defgroup grpReactionThermophysicalChemistryReaders Chemistry readers
+@{
+    \ingroup grpReactionThermophysicalModels
+    This group contains chemistry readers
+@}
+
+
+\*---------------------------------------------------------------------------*/

src/thermophysicalModels/reactionThermo/functionObjects/moleFractions/moleFractions.H

@@ -24,6 +24,9 @@ License
 Class
     Foam::moleFractions
 
+Group
+    grpThermophysicalFunctionObjects
+
 Description
     This function object calculates mole-fraction fields from the mass-fraction
     fields of the psi/rhoReactionThermo and caches them for output and further

src/thermophysicalModels/reactionThermo/mixtures/SpecieMixture/SpecieMixture.H

@@ -24,6 +24,9 @@ License
 Class
     Foam::SpecieMixture
 
+Group
+    grpReactionThermophysicalMixtures
+
 Description
     Foam::SpecieMixture
 

src/thermophysicalModels/reactionThermo/mixtures/basicCombustionMixture/basicCombustionMixture.H

@@ -24,6 +24,9 @@ License
 Class
     Foam::basicCombustionMixture
 
+Group
+    grpReactionThermophysicalMixtures
+
 Description
     Specialization of the basicSpecieMixture for combustion.
 

src/thermophysicalModels/reactionThermo/mixtures/basicMultiComponentMixture/basicMultiComponentMixture.H

@@ -24,6 +24,9 @@ License
 Class
     Foam::basicMultiComponentMixture
 
+Group
+    grpReactionThermophysicalMixtures
+
 Description
     Multi-component mixture.
 

src/thermophysicalModels/reactionThermo/mixtures/basicSpecieMixture/basicSpecieMixture.H

@@ -24,6 +24,9 @@ License
 Class
     Foam::basicSpecieMixture
 
+Group
+    grpReactionThermophysicalMixtures
+
 Description
     Specialization of basicMultiComponentMixture for a mixture consisting
     of a number for molecular species.

src/thermophysicalModels/reactionThermo/mixtures/egrMixture/egrMixture.H

@@ -24,6 +24,9 @@ License
 Class
     Foam::egrMixture
 
+Group
+    grpReactionThermophysicalMixtures
+
 Description
     Foam::egrMixture
 

src/thermophysicalModels/reactionThermo/mixtures/homogeneousMixture/homogeneousMixture.H

@@ -24,6 +24,9 @@ License
 Class
     Foam::homogeneousMixture
 
+Group
+    grpReactionThermophysicalMixtures
+
 Description
     Foam::homogeneousMixture
 

src/thermophysicalModels/reactionThermo/mixtures/inhomogeneousMixture/inhomogeneousMixture.H

@@ -24,6 +24,9 @@ License
 Class
     Foam::inhomogeneousMixture
 
+Group
+    grpReactionThermophysicalMixtures
+
 Description
     Foam::inhomogeneousMixture
 

src/thermophysicalModels/reactionThermo/mixtures/multiComponentMixture/multiComponentMixture.H

@@ -24,6 +24,9 @@ License
 Class
     Foam::multiComponentMixture
 
+Group
+    grpReactionThermophysicalMixtures
+
 Description
     Foam::multiComponentMixture
 

src/thermophysicalModels/reactionThermo/mixtures/reactingMixture/reactingMixture.H

@@ -24,6 +24,9 @@ License
 Class
     Foam::reactingMixture
 
+Group
+    grpReactionThermophysicalMixtures
+
 Description
     Foam::reactingMixture
 

src/thermophysicalModels/reactionThermo/mixtures/singleStepReactingMixture/singleStepReactingMixture.H

@@ -24,6 +24,9 @@ License
 Class
     Foam::singleStepReactingMixture
 
+Group
+    grpReactionThermophysicalMixtures
+
 Description
     Single step reacting mixture
 

src/thermophysicalModels/reactionThermo/mixtures/veryInhomogeneousMixture/veryInhomogeneousMixture.H

@@ -24,6 +24,9 @@ License
 Class
     Foam::veryInhomogeneousMixture
 
+Group
+    grpReactionThermophysicalMixtures
+
 Description
     Foam::veryInhomogeneousMixture