[NL] Update apply known solutions for Newton.

Dmitri Naumov authored 8 years ago and Dmitri Naumov committed 8 years ago

Now more similar to the Picard implementation doing
all the boundaries at once.

Make FileFinder general

Change shape vector to a row vector

Added finalizeAssembly(x) to avoid PETSc errors in the vector copying

[NL] Unify unsigned type usage in shape functions.

The elements' dimensions (DIM and NPOINTS) are declared
'unsigned' is the MeshLib (MeshElement::dimension and
MeshElement::n_all_nodes) and should be of the same
type for the shape functions.

Removing circular dependency with XmlLutReader

use new data holder lut class as input for file reader and input for vtk and removed circular dependency

move createGroundwaterFlowProcess() to a separate file