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.

Resolves bug-report https://bugs.openfoam.org/view.php?id=2428

Resolves bug-report https://bugs.openfoam.org/view.php?id=2438

Patch contributed by Bruno Santos
Resolves bug-report https://bugs.openfoam.org/view.php?id=2437

Resolves bug-report https://bugs.openfoam.org/view.php?id=2436

Avoids slight phase-fraction unboundedness at entertainment BCs and improved
robustness.

Additionally the phase-fractions in the multi-phase (rather than two-phase)
solvers are adjusted to avoid the slow growth of inconsistency ("drift") caused
by solving for all of the phase-fractions rather than deriving one from the
others.

tutorials/combustion/reactingFoam/laminar/counterFlowFlame2D_GRI_TDAC: Added deltaT to TDAC controls

Patch contributed by zhulianhua
Resolves bug-report https://bugs.openfoam.org/view.php?id=2427

Starting from an negative initial temperature causes non-convergence and a
misleading error, now a specific message is generated.

e.g.

fieldMinMax fieldMinMax write:
    min(T) = 291 in cell 255535 at location (-0.262546 -0.538933 1.00574) on processor 9
    max(T) = 336.298 in cell 419031 at location (1.7468 0.758405 8.10989) on processor 1
    min(mag(U)) = 0 in cell 14990 at location (-0.0824383 1.68479 1.5349) on processor 0
    max(mag(U)) = 652.341 in cell 218284 at location (0.609849 0.167247 1.00091) on processor 12

Patch contributed by Bruno Santos
Resolves bug-report https://bugs.openfoam.org/view.php?id=2431

Patch contributed by Karl Meredith, FM Global.

Patch contributed by Bruno Santos
Resolves patch request https://bugs.openfoam.org/view.php?id=2423

Patch provided by Bruno Santos
Resolves patch request https://bugs.openfoam.org/view.php?id=2425

New reactingFoam tutorial counterFlowFlame2DLTS_GRI_TDAC demonstrates this new
functionality.

Additionally the ISAT table growth algorithm has been further optimized
providing an overall speedup of between 15% and 38% for the tests run so far.

Updates to TDAC and ISAT provided by Francesco Contino.

Implementation updated and integrated into OpenFOAM-dev by
Henry G. Weller, CFD Direct Ltd with the help of Francesco Contino.

Original code providing all algorithms for chemistry reduction and
tabulation contributed by Francesco Contino, Tommaso Lucchini, Gianluca
D’Errico, Hervé Jeanmart, Nicolas Bourgeois and Stéphane Backaert.

e.g. in tutorials/heatTransfer/buoyantSimpleFoam/externalCoupledCavity/0/T

    hot
    {
        type            externalCoupledTemperature;
        commsDir        "${FOAM_CASE}/comms";
        file            "data";
        initByExternal  yes;
        log             true;
        value           uniform 307.75; // 34.6 degC
    }

Previously both 'file' and 'fileName' were used inconsistently in different
classes and given that there is no confusion or ambiguity introduced by using
the simpler 'file' rather than 'fileName' this change simplifies the use and
maintenance of OpenFOAM.

e.g.

motorBike
{
    type triSurfaceMesh;
    file "motorBike.obj";
}

Based on patch provided by Mattijs Janssens
Resolves part of bug-report https://bugs.openfoam.org/view.php?id=2396

Resolves bug-report https://bugs.openfoam.org/view.php?id=2422

Patch contributed by Bruno Santos
Resolves patch request https://bugs.openfoam.org/view.php?id=2238

Patch contributed by Bruno Santos
Resolves patch request https://bugs.openfoam.org/view.php?id=2411

Patch contributed by Bruno Santos
Resolves patch request https://bugs.openfoam.org/view.php?id=2410

Patch contributed by Bruno Santos
Resolves patch request https://bugs.openfoam.org/view.php?id=2409

Patch contributed by Bruno Santos
Resolves bug-report https://bugs.openfoam.org/view.php?id=2408

Based on patch contributed by Kevin Nordin-Bates
Resolves bug-report https://bugs.openfoam.org/view.php?id=2401

e.g. in the reactingFoam/laminar/counterFlowFlame2DLTS tutorial:

PIMPLE
{
    momentumPredictor no;
    nOuterCorrectors  1;
    nCorrectors     1;
    nNonOrthogonalCorrectors 0;

    maxDeltaT       1e-2;
    maxCo           1;
    alphaTemp       0.05;
    alphaY          0.05;
    Yref
    {
        O2          0.1;
        ".*"        1;
    }
    rDeltaTSmoothingCoeff 1;
    rDeltaTDampingCoeff 1;
}

will limit the LTS time-step according to the rate of consumption of 'O2'
normalized by the reference mass-fraction of 0.1 and all other species
normalized by the reference mass-fraction of 1.  Additionally the time-step
factor of 'alphaY' is applied to all species.  Only the species specified in the
'Yref' sub-dictionary are included in the LTS limiter and if 'alphaY' is omitted
or set to 1 the reaction rates are not included in the LTS limiter.

Resolves bug-report https://bugs.openfoam.org/view.php?id=2398