Use const references where necessary.

Rename a the method from getNumberOfComponents() to getNumberOfGlobalComponents()
in class LocalToGlobalIndexMap.

Interface and time loop changes. Processes are in the
next commit.

Main reason for modification is the getFlux function, which for
particular processes (ComponentTransport) relies on all solutions being
available.
This modification ripples through all of the code, especially through
the boundary conditions.
Modified `applyNaturalBC`, `preTimestep`, `integrate`, and `assemble`
functions.

preTimestep now accepts a vector of solution together with
a process_id.
In postTimestep only the vector of solutions has been changed.

Pass process_id to FEM::assemble calls.

Drop dt where used together with it's updates etc.

Exemplary on SmallDeformationProcess, storage of dt
is no longer required and the assembly can be repeated
without dependency on the t/dt values.

Fixes multiple copyright messages in the doxygen docu.

ag '\\file' -L --ignore=ThirdParty *Lib |xargs  sed -i 's/\(.*\)\\copyright/\1\\file\n\1\\copyright/'

Some processes might require setup of the initial
conditions dependent variables in local assemblers.
The new interface allows such implementations.

Dmitri Naumov authored 6 years ago and Lars Bilke committed 6 years ago

The call was simply missing in the assembleWithJacobian().