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

This hack will be removed when the rewrite of the parcel thermodynamics is complete.

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.

Resolves bug-report http://www.openfoam.org/mantisbt/view.php?id=1552

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

Resolves bug-report http://openfoam.org/mantisbt/view.php?id=1548

Resolves bug report http://www.openfoam.org/mantisbt/view.php?id=1450

Proposed resolution of http://www.openfoam.org/mantisbt/view.php?id=1509

off-centre coefficient and the coefficient for the implicit part

Resolves issues with probes and findRefCell for meshes in which all cell face-pyramids are positive.