[GeoMechanicsApplication] Split the calculation of the inputs for the utility functions for element matrices and the calling of the functions

[rfaasse]

As a developer I would like to split the calculation of inputs and calling of functions, such that I can refactor the functions to calculate the relevant matrices for the entire element at once, instead of for each integration point individually.

Background
The created utility functions CalculatePermeabilityMatrix, CalculateCouplingMatrix and CalculateCompressibilityMatrix currently calculate the contribution of a single integration point in the element. This should change to calculate the matrix contributions of all integration points at once.

This means the utility functions need to get their inputs for all integration points at once (in form of a list/vector). This issue aims to create these lists to enable that refactor step later on. Note this means that the utility function signatures will not be changed in this issue.

Acceptance criteria
In all places where the CalculatePermeabilityMatrix, CalculateCouplingMatrix and CalculateCompressibilityMatrix are called, the input lists should be calculated in a separate loop.

Successor #12320