The fundamental properties provided by the specie class hierarchy were
mole-based, i.e. provide the properties per mole whereas the fundamental
properties provided by the liquidProperties and solidProperties classes are
mass-based, i.e. per unit mass.  This inconsistency made it impossible to
instantiate the thermodynamics packages (rhoThermo, psiThermo) used by the FV
transport solvers on liquidProperties.  In order to combine VoF with film and/or
Lagrangian models it is essential that the physical propertied of the three
representations of the liquid are consistent which means that it is necessary to
instantiate the thermodynamics packages on liquidProperties.  This requires
either liquidProperties to be rewritten mole-based or the specie classes to be
rewritten mass-based.  Given that most of OpenFOAM solvers operate
mass-based (solve for mass-fractions and provide mass-fractions to sub-models it
is more consistent and efficient if the low-level thermodynamics is also
mass-based.

This commit includes all of the changes necessary for all of the thermodynamics
in OpenFOAM to operate mass-based and supports the instantiation of
thermodynamics packages on liquidProperties.

Note that most users, developers and contributors to OpenFOAM will not notice
any difference in the operation of the code except that the confusing

    nMoles     1;

entries in the thermophysicalProperties files are no longer needed or used and
have been removed in this commet.  The only substantial change to the internals
is that species thermodynamics are now "mixed" with mass rather than mole
fractions.  This is more convenient except for defining reaction equilibrium
thermodynamics for which the molar rather than mass composition is usually know.
The consequence of this can be seen in the adiabaticFlameT, equilibriumCO and
equilibriumFlameT utilities in which the species thermodynamics are
pre-multiplied by their molecular mass to effectively convert them to mole-basis
to simplify the definition of the reaction equilibrium thermodynamics, e.g. in
equilibriumCO

    // Reactants (mole-based)
    thermo FUEL(thermoData.subDict(fuelName)); FUEL *= FUEL.W();

    // Oxidant (mole-based)
    thermo O2(thermoData.subDict("O2")); O2 *= O2.W();
    thermo N2(thermoData.subDict("N2")); N2 *= N2.W();

    // Intermediates (mole-based)
    thermo H2(thermoData.subDict("H2")); H2 *= H2.W();

    // Products (mole-based)
    thermo CO2(thermoData.subDict("CO2")); CO2 *= CO2.W();
    thermo H2O(thermoData.subDict("H2O")); H2O *= H2O.W();
    thermo CO(thermoData.subDict("CO")); CO *= CO.W();

    // Product dissociation reactions

    thermo CO2BreakUp
    (
        CO2 == CO + 0.5*O2
    );

    thermo H2OBreakUp
    (
        H2O == H2 + 0.5*O2
    );

Please report any problems with this substantial but necessary rewrite of the
thermodynamic at https://bugs.openfoam.org

Henry G. Weller
CFD Direct Ltd.

functionObjects::scalarTransport: Added support for optional laminar and turbulent diffusion coefficients

Description
    Evolves a passive scalar transport equation.

    - To specify the field name set the \c field entry
    - To employ the same numerical schemes as another field set
      the \c schemesField entry,
    - A constant diffusivity may be specified with the \c D entry,

    - Alternatively if a turbulence model is available a turbulent diffusivity
      may be constructed from the laminar and turbulent viscosities using the
      optional diffusivity coefficients \c alphaD and \c alphaDt (which default
      to 1):
      \verbatim
          D = alphaD*nu + alphaDt*nut
      \endverbatim

Resolves feature request https://bugs.openfoam.org/view.php?id=2453

Resolves bug-report https://bugs.openfoam.org/view.php?id=2455

Now the interFoam and compressibleInterFoam families of solvers use the same
alphaEqn formulation and supporting all of the MULES options without
code-duplication.

The semi-implicit MULES support allows running with significantly larger
time-steps but this does reduce the interface sharpness.

Description
    Simple solidification porosity model

    This is a simple approximation to solidification where the solid phase
    is represented as a porous blockage with the drag-coefficient evaluated from

        \f[
            S = - \alpha \rho D(T) U
        \f]

    where
    \vartable
        \alpha  | Optional phase-fraction of solidifying phase
        D(T)    | User-defined drag-coefficient as function of temperature
    \endvartable

    Note that the latent heat of solidification is not included and the
    temperature is unchanged by the modelled change of phase.

    Example of the solidification model specification:
    \verbatim
        type            solidification;

        solidificationCoeffs
        {
            // Solidify between 330K and 330.5K
            D table
            (
                (330.0     10000) // Solid below 330K
                (330.5     0)     // Liquid above 330.5K
            );

            // Optional phase-fraction of solidifying phase
            alpha alpha.liquid;

            // Solidification porosity is isotropic
            // use the global coordinate system
            coordinateSystem
            {
                type    cartesian;
                origin  (0 0 0);
                coordinateRotation
                {
                    type    axesRotation;
                    e1      (1 0 0);
                    e2      (0 1 0);
                }
            }
        }
    \endverbatim

Description
    Simple solidification porosity model

    This is a simple approximation to solidification where the solid phase
    is represented as a porous blockage with the drag-coefficient evaluated from

        \f[
            S = - \rho D(T) U
        \f]

    where
    \vartable
        D(T) | User-defined drag-coefficient as function of temperature
    \endvartable

    Note that the latent heat of solidification is not included and the
    temperature is unchanged by the modelled change of phase.

    Example of the solidification model specification:
    \verbatim
        type            solidification;

        solidificationCoeffs
        {
            // Solidify between 330K and 330.5K
            D table
            (
                (330.0     10000) // Solid below 330K
                (330.5     0)     // Liquid above 330.5K
            );

            // Solidification porosity is isotropic
            // use the global coordinate system
            coordinateSystem
            {
                type    cartesian;
                origin  (0 0 0);
                coordinateRotation
                {
                    type    axesRotation;
                    e1      (1 0 0);
                    e2      (0 1 0);
                }
            }
        }
    \endverbatim

Patch contributed by Timo Niemi, VTT.
Resolves patch request https://bugs.openfoam.org/view.php?id=2452

if convergence is not achieved within the maximum number of iterations.

Sometimes, particularly running in parallel, PBiCG fails to converge or diverges
without warning or obvious cause leaving a solution field containing significant
errors which can cause divergence of the application.  PBiCGStab is more robust
and does not suffer from the problems encountered with PBiCG.

Compressing and decompressing binary files introduces a significant IO overhead
without a providing significant reduction in file-size.

Patch contributed by Mattijs Janssens

Patch contributed by Mattijs Janssens

kOmegaSSTSato: Change correctNut() to correctNut(S2, F2)

Resolves bug-report https://bugs.openfoam.org/view.php?id=2450

Patch contributed by Juho Peltola, VTT
Resolves patch request https://bugs.openfoam.org/view.php?id=2446

Patch contributed by Juho Peltola, VTT.
Resolves patch request https://bugs.openfoam.org/view.php?id=2443

Patch contributed by Bruno Santos
Resolves bug-report https://bugs.openfoam.org/view.php?id=2441

Patch contributed by Bruno Santos
Resolves patch request https://bugs.openfoam.org/view.php?id=2444

Patch contributed by Bruno Santos
Resolves patch request https://bugs.openfoam.org/view.php?id=2424

Patch contributed by Timo Niemi, VTT.
Resolves bug-report https://bugs.openfoam.org/view.php?id=2442

The previous time-step compression flux is not valid/accurate on the new mesh
and it is better to re-calculate it rather than map it from the previous mesh to
the new mesh.

snappyHexMesh: Added "noRefinement" writeFlag to control the writing of cellLevel, pointLevel etc. files

By default snappyHexMesh writes files relating to the hex-splitting process into
the polyMesh directory: cellLevel level0Edge pointLevel surfaceIndex

but by setting the noRefinement flag:

writeFlags
(
    noRefinement
    .
    .
    .
);

these optional files which are generally not needed are not written.

If you run the three stages of snappyHexMesh separately or run a dynamic mesh
solver supporting refinement and unrefinement these files are needed
and "noRefinement" should not be set.

unless the blockMeshDict is in the polyMesh directory or the "-noClean" option
is specified.

This avoids problems running snappyHexMesh without first clearing files from
polyMesh which interfere with the operation of snappyHexMesh.

The files relating to the hex refinement are written out explicitly both by
snappyHexMesh and dynamicRefineFvMesh and hence should be set "NO_WRITE" rather
than "AUTO_WRITE" to avoid writing them twice.  This change corrects the
handling of the "refinementHistory" file which should not be written by
snappyHexMesh.

To run with laminar reaction rates choose the "laminar" combustion model rather
than setting "turbulentReaction no;" in the "PaSR" model.