GeometricField: Renamed internalField() -> primitiveField() and dimensionedInternalField() -> internalField()

These new names are more consistent and logical because:

primitiveField():
primitiveFieldRef():
    Provides low-level access to the Field<Type> (primitive field)
    without dimension or mesh-consistency checking.  This should only be
    used in the low-level functions where dimensional consistency is
    ensured by careful programming and computational efficiency is
    paramount.

internalField():
internalFieldRef():
    Provides access to the DimensionedField<Type, GeoMesh> of values on
    the internal mesh-type for which the GeometricField is defined and
    supports dimension and checking and mesh-consistency checking.

In order to simplify expressions involving dimensioned internal field it
is preferable to use a simpler access convention.  Given that
GeometricField is derived from DimensionedField it is simply a matter of
de-referencing this underlying type unlike the boundary field which is
peripheral information.  For consistency with the new convention in
"tmp"  "dimensionedInteralFieldRef()" has been renamed "ref()".

CrankNicolsonDdtScheme: Use the new GeometricField constructor from DimensionedField and boundary FieldField

Non-const access to the internal field now obtained from a specifically
named access function consistent with the new names for non-canst access
to the boundary field boundaryFieldRef() and dimensioned internal field
dimensionedInternalFieldRef().

See also commit a4e2afa4

functionObjectFile provides basic directory, file and formatting functions
functionObjectFiles provides multi-file cache

Resolves bug-report http://www.openfoam.org/mantisbt/view.php?id=2075

Resolves bug-report http://www.openfoam.org/mantisbt/view.php?id=2074

functionObjects/field/histogram: New functionObject to write the volume-weighted histogram of a volScalarField

e.g.
    pressureHistogram
    {
        type            histogram;

        functionObjectLibs ("libfieldFunctionObjects.so");

        field           p;
        nBins           100;
        min             -5;
        max             5;
        setFormat       gnuplot;
    }

provides optional control for solving the pyrolysis region.

Patch contributed by Karl Meredith, FMGlobal.

When the GeometricBoundaryField template class was originally written it
was a separate class in the Foam namespace rather than a sub-class of
GeometricField as it is now.  Without loss of clarity and simplifying
code which access the boundary field of GeometricFields it is better
that GeometricBoundaryField be renamed Boundary for consistency with the
new naming convention for the type of the dimensioned internal field:
Internal, see commit a25a449c

This is a very simple text substitution change which can be applied to
any code which compiles with the OpenFOAM-dev libraries.

Given that the type of the dimensioned internal field is encapsulated in
the GeometricField class the name need not include "Field"; the type
name is "Internal" so

volScalarField::DimensionedInternalField -> volScalarField::Internal

In addition to the ".dimensionedInternalField()" access function the
simpler "()" de-reference operator is also provided to greatly simplify
FV equation source term expressions which need not evaluate boundary
conditions.  To demonstrate this kEpsilon.C has been updated to use
dimensioned internal field expressions in the k and epsilon equation
source terms.

both of which return the dimensionedInternalField for volFields only.

These will be useful in FV equation source term expressions which need
not evaluate boundary conditions.

This reverts commit 73fe45cd.

See also commit a4e2afa4

Resolves bug-report http://openfoam.org/mantisbt/view.php?id=2068

wmake/rules/linux.*Icc: Remove -xHost option which causes surfaceFeatureExtract to fail for some cases

Resolves bug-report http://www.openfoam.org/mantisbt/view.php?id=1938

Because C++ does not support overloading based on the return-type there
is a problem defining both const and non-const member functions which
are resolved based on the const-ness of the object for which they are
called rather than the intent of the programmer declared via the
const-ness of the returned type.  The issue for the "boundaryField()"
member function is that the non-const version increments the
event-counter and checks the state of the stored old-time fields in case
the returned value is altered whereas the const version has no
side-effects and simply returns the reference.  If the the non-const
function is called within the patch-loop the event-counter may overflow.
To resolve this it in necessary to avoid calling the non-const form of
"boundaryField()" if the results is not altered and cache the reference
outside the patch-loop when mutation of the patch fields is needed.

The...

Resolved bug-report http://openfoam.org/mantisbt/view.php?id=2065

There is a need to specify const or non-const access to a non-const
object which is not currently possible with the "boundaryField()" access
function the const-ness of the return of which is defined by the
const-ness of the object for which it is called.  For consistency with
the latest "tmp" storage class in which non-const access is obtained
with the "ref()" function it is proposed to replace the non-const form
of "boundaryField()" with "boundaryFieldRef()".

Thanks to Mattijs Janssens for starting the process of migration to
"boundaryFieldRef()" and providing a patch for the OpenFOAM and
finiteVolume libraries.

This condition creates a zero-dimensional model of an enclosed volume of
gas upstream of the inlet. The pressure that the boundary condition
exerts on the inlet boundary is dependent on the thermodynamic state of
the upstream volume.  The upstream plenum density and temperature are
time-stepped along with the rest of the simulation, and momentum is
neglected. The plenum is supplied with a user specified mass flow and
temperature.

The result is a boundary condition which blends between a pressure inlet
condition condition and a fixed mass flow. The smaller the plenum
volume, the quicker the pressure responds to a deviation from the supply
mass flow, and the closer the model approximates a fixed mass flow. As
the plenum size increases, the model becomes more similar to a specified
pressure.

The expansion from the plenum to the inlet boundary is controlled by an
area ratio and a discharge coefficient. The area ratio can be used to
represent further acceleration between a sub-grid blockage such as fins.
The discharge coefficient represents a fractional deviation from an
ideal expansion process.

This condition is useful for simulating unsteady internal flow problems
for which both a mass flow boundary is unrealistic, and a pressure
boundary is susceptible to flow reversal. It was developed for use in
simulating confined combustion.

tutorials/compressible/rhoPimpleFoam/laminar/helmholtzResonance:
    helmholtz resonance tutorial case for plenum pressure boundary

This development was contributed by Will Bainbridge

Also added the new prghTotalHydrostaticPressure p_rgh BC which uses the
hydrostatic pressure field as the reference state for the far-field
which provides much more accurate entrainment is large open domains
typical of many fire simulations.

The hydrostatic field solution is controlled by the optional entries in
the fvSolution.PIMPLE dictionary, e.g.

    hydrostaticInitialization yes;
    nHydrostaticCorrectors 5;

and the solver must also be specified for the hydrostatic p_rgh field
ph_rgh e.g.

    ph_rgh
    {
        $p_rgh;
    }

Suitable boundary conditions for ph_rgh cannot always be derived from
those for p_rgh and so the ph_rgh is read to provide them.

To avoid accuracy issues with IO, restart and post-processing the p_rgh
and ph_rgh the option to specify a suitable reference pressure is
provided via the optional pRef file in the constant directory, e.g.

    dimensions      [1 -1 -2 0 0 0 0];
    value           101325;

which is used in the relationship between p_rgh and p:

    p = p_rgh + rho*gh + pRef;

Note that if pRef is specified all pressure BC specifications in the
p_rgh and ph_rgh files are relative to the reference to avoid round-off
errors.

For examples of suitable BCs for p_rgh and ph_rgh for a range of
fireFoam cases please study the tutorials in
tutorials/combustion/fireFoam/les which have all been updated.

Henry G. Weller
CFD Direct Ltd.

Patch contributed by Juho Peltola, VTT

The new JohnsonJacksonSchaefferFrictionalStress model is included and
the LBend tutorial case to demonstrate the need for the changes to the
frictional stress models.

Resolves bug-report http://www.openfoam.org/mantisbt/view.php?id=2058