mixtureKEpsilon: Changed bounded non-conservative transport flux to be volumetric rather than mass-based
Avoids numerical problems caused by large density gradients, particularly around the interface.
Allows the use of higher-order differencing for km and epsilonm

Also changed internalDegreesOfFreedom to be an integer type

Allows the specification of a reference height, for example the height
of the free-surface in a VoF simulation, which reduces the range of p_rgh.

hRef is a uniformDimensionedScalarField specified via the constant/hRef
file, equivalent to the way in which g is specified, so that it can be
looked-up from the database.  For example see the constant/hRef file in
the DTCHull LTSInterFoam and interDyMFoam cases.

Avoids unnecessary increases in precision during intermediate steps for
cases with adjustable time-step which may require very high precision to
represent the time name.

Add check for round-off error causing time reversal
Resolves bug-report http://www.openfoam.org/mantisbt/view.php?id=815

Resolves bug-report http://www.openfoam.org/mantisbt/view.php?id=1568

Revert changes in tutorial to correspond to the version in OpenFOAM-2.1.x
Resolves bug-report http://openfoam.org/mantisbt/view.php?id=1207

This approach simply accumulates data outside the range of the bins into
the first or last bin which may be OK for small motions.  For larger
motions it may be better if the bins are updated or operate in a
coordinate system attached to the body for solid-body motion.
Resolves bug-report http://www.openfoam.org/mantisbt/view.php?id=1560

Provided by Bruno Santos
Also some general cleaning and update of comment.
Resolves bug-report http://www.openfoam.org/mantisbt/view.php?id=1167

Resolves bug-report http://www.openfoam.org/mantisbt/view.php?id=815

Changes based on patches from and discussions with Bruno Santos
Resolves bug-report http://www.openfoam.org/mantisbt/view.php?id=815

Added the pressure dependent part of the entropy from the equation of
state to that returned by the thermo entropy function.

TODO: Add entropy defect to the PengRobinsonGas::s(p, T) function.

Resolves bug-report http://www.openfoam.org/mantisbt/view.php?id=1411

between liquid and solid mixture composition and the specie lists
defined in the thermodynamics package.

Note this does not change the current limitation that both liquid and
solid mixtures contain ALL the corresponding phase species defined in
the thermodynamics package.  However, missing species are included
automatically during construction of phaseProperties.

lagrangian: Replace dummy "notImplemented" functions with abstract functions making base classes abstract
Make clone functions const and abstract in abstract base classes
Change copy constructors to take const argument
Make private data mutable where necessary

No species specified: indicates phase is not present
Some species specified: missing entries assumed to have 0 mass-fraction

Resolves bug-report http://www.openfoam.org/mantisbt/view.php?id=1347

Resolves bug-report http://www.openfoam.org/mantisbt/view.php?id=1443

Resolves bug-report http://www.openfoam.org/mantisbt/view.php?id=1524

Resolves bug-report http://www.openfoam.org/mantisbt/view.php?id=1556

Ensures consistency between the mixture thermodynamics and composition specifications for the parcels.
Simpler more efficient implementation.
Resolves bug-report http://www.openfoam.org/mantisbt/view.php?id=1395
as well as other consistency issues not yet reported.

The implementation now correspond to the definitions in the readily
available reference:

http://personalpages.manchester.ac.uk/staff/david.d.apsley/specturb.pdf

in which a large number of linear and non-linear models are presented in
a clean and consistent manner.  This has made re-implementation and
checking far easier than working from the original references which anyway
are no longer available for the LienCubicKE and ShihQuadraticKE models.

Also use the innerSqr function where appropriate

which takes the inner product of a symmTensor with itself and returns a symmTensor