to avoid problems when writing "nComponents"

consistency with UList/List and so that functions which take a UPtrList
argument can also be called for PtrList.

Resolves bug-report http://www.openfoam.org/mantisbt/view.php?id=2080
Patch contributed by Mattijs Janssens

functionObjects: Moved into the functionObjects namespace and rationalized and simplified failable construction

Rather than requiring each functionObject to handle failed construction
internally (using the active_ flag) the static member function "viable"
is provided which returns true if construction of the functionObject is
likely to be successful.  Failed construction is then handled by the
wrapper-class which constructs the functionObject,
e.g. "OutputFilterFunctionObject".

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()".

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 22f4ad32

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

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

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 4a57b9be

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 3cfc54ba.

See also commit 22f4ad32

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 most straight forward way of resolving this problem is to name the
const and non-const forms of the member functions differently e.g. the
non-const form could be named:

    mutableBoundaryField()
    mutBoundaryField()
    nonConstBoundaryField()
    boundaryFieldRef()

Given that in C++ a reference is non-const unless specified as const:
"T&" vs "const T&" the logical convention would be

    boundaryFieldRef()
    boundaryFieldConstRef()

and given that the const form which is more commonly used is it could
simply be named "boundaryField()" then the logical convention is

    GeometricBoundaryField& boundaryFieldRef();

    inline const GeometricBoundaryField& boundaryField() const;

This is also consistent with the new "tmp" class for which non-const
access to the stored object is obtained using the ".ref()" member function.

This new convention for non-const access to the components of
GeometricField will be applied to "dimensionedInternalField()" and "internalField()" in the
future, i.e. "dimensionedInternalFieldRef()" and "internalFieldRef()".

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.

Resolves bug-report http://www.openfoam.org/mantisbt/view.php?id=2060

Now the calculation of the 2nd-invariant is more efficient and
accumulates less round-off error.

Particularly useful for lists of dictionaries.

See also http://www.openfoam.org/mantisbt/view.php?id=2036

Using method based on
http://ntrs.nasa.gov/archive/nasa/casi.ntrs.nasa.gov/20070017872.pdf
but simplified for the case where the quaternions are similar.

inline Foam::vector Foam::septernion::transformPoint(const vector& v) const
{
    return r().transform(v - t());
}

Now there is a 1:1 correspondence between septernion and
spatialTransform and a septernion constructor from spatialTransform
provided.

Additionally "septernion::transform" has been renamed
"septernion::transformPoint" to clarify that it transforms coordinate
points rather than displacements or other relative vectors.

    //- Return the unit quaternion (versor) from the given vector
    //  (w = sqrt(1 - |sqr(v)|))
    static inline quaternion unit(const vector& v);