Cleanup AppLib Color functions

This is much faster and more readable.

[CL] Move creation of Phreeqc instance in the ctor

Dmitri Naumov authored 5 years ago and renchao.lu committed 5 years ago

The instance_id is used exclusively in the PhreeqcIO class.

Cleanup MaterialStateVariables in solid models

If there are no additional members in the MaterialStateVariables,
the default implementation from MechanicsBase is sufficient.

Needed to update the integrateStress return value type.

The default implementation is sufficient for classes,
which don't do anything special with
the MaterialStateVariables.

All the implementations didn't do anything useful but casting types.
I don't remember the reasons for that complex implementation
of assignment. Could be that some progress in the compilers
makes live easier now.

[PL] BC; Fix lower order element values access.

In cases when the underlying element is quadratic but the shape function
is of linear order, there is a dimension mismatch between the
NodalVectorType and the return value of the getNodalValuesOnElement.

Taking the first rows of the return matrix ensures correct dimensions.

Convert to linear mesh tests

Previously the conversion relied on the node numbering,
which is not necessary.

2D_Adaptive_dt_ThermalConvection_constviscosityStaggeredScheme
sporadically runs into the 900 s timeout on vismac05.
Increased to 1800 s.

[CL] Use ostream for all output operators.

[MatL/MPL] Check uniqueness of components and phases