Use consistent way to compute the deformation gradient

[amgebauer]

We are now using F=I+grad_u for every shape of the solid elements to compute the deformation gradient.

For the previously failing contact tests, I adapted the coordinates such that the two bodies are not in contact in the initial configuration (avoiding a singularity arising when computing the exact deformation gradient).

Draft for now since there might be some tests that fail due to tolerances.

Closes #70

[Copilot]

Pull request overview

This PR standardizes the deformation gradient computation across all solid element shapes to consistently use F = I + grad_u (incremental formulation). Previously, hex8 elements used F = (X+u)^T * dN/dX^T (total formulation) while other element types used the incremental approach. To accommodate this change, contact test node coordinates were adjusted by adding a small offset (1e-16) to prevent initial contact singularities.

Key changes:

• Unified deformation gradient calculation method across all element types
• Modified contact test geometries to avoid numerical issues with the new formulation
• Updated reference values in multiple test files to reflect the new computational approach

Reviewed changes

Copilot reviewed 12 out of 12 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
src/solid_3D_ele/4C_solid_3D_ele_calc_lib.hpp	Removed conditional logic for hex8 elements; all elements now use F = I + grad_u formulation
tests/input_files/contact3D_nitsche_hex8_sym_coulomb.4C.yaml	Adjusted node coordinates by adding 1e-16 offset to z-coordinates for nodes 1-125 to avoid initial contact
tests/input_files/contact3D_nitsche_hex8_sym_coulomb_new_struc.4C.yaml	Same coordinate adjustment as above for consistency
tests/input_files/ssti_mono_3D_6hex8_elch_s2i_butlervolmerthermo_cycling.4C.yaml	Updated expected displacement and scalar field values due to deformation gradient calculation change
tests/input_files/ssti_mono_3D_6hex8_elch_s2i_butlervolmerthermo_BGS-AMG_3x3.4C.yaml	Updated expected scalar field value
tests/input_files/ssti_mono_3D_3hex8_elch_s2i_butlervolmerthermo_growthlaw.4C.yaml	Updated expected displacement value
tests/input_files/ssi_mono_3D_hex8_elch_s2i_butlervolmercapacity_BGS-AMG_4x4.4C.yaml	Updated multiple expected scalar field values
tests/input_files/ssi_mono_3D_hex8_elch_s2i_butlervolmer_grain_boundary_meshtying_BGS-AMG_5x5.4C.yaml	Updated displacement and scalar field values
tests/input_files/ssi_mono_3D_2blocks_hex8_nonmatching_nitsche_contact_scatra_s2i_linearperm.4C.yaml	Updated scalar and displacement values; standardized number format to scientific notation
tests/input_files/ssi_mono_3D_2blocks_hex8_nonmatching_nitsche_contact_scatra_s2i_constperm_BGS-AMG_3x3.4C.yaml	Updated multiple scalar and displacement values
tests/input_files/ssi_mono_3D_2blocks_hex8_nonmatching_nitsche_contact_scatra_s2i_constperm_BGS-AMG_2x2.4C.yaml	Updated multiple scalar and displacement values
tests/input_files/ssi_mono_3D_2blocks_hex8_nonmatching_nitsche_contact_scatra_s2i_constperm.4C.yaml	Updated multiple scalar and displacement values; standardized number format

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[rjoussen]

Does this mean contact simulations are no longer expected to work if the interfaces match exactly at the beginning?