Improve ElementSubdomainModifier moving boundary and reinitialization

[Wendy-Ji]

This pull request addresses several problems with ElementSubdomainModifier. The biggest changes in this PR are:

• The creation of the ElementSubdomainModifierBase to contain all the code for changing subdomain, modifying sidesets/nodesets, and reinitialization (ElementSubdomainModifier now only determines which elements are changing subdomain, and their previous and new subdomain IDs)
• Greater control over the changing sidesets/nodesets using the moving_boundaries and moving_boundary_subdomain_pairs parameters (moving_boundary_name and complement_moving_boundary_name are replaced by these)
• Control over which changed elements are reinitialized using the reinitialize_subdomains and old_subdomain_reinitialized parameters (apply_initial_conditions is replaced by these)

This fixes:

• The moving_boundary_name was not updating correctly and the complement_moving_boundary_name was being used instead. This redundancy has been removed, and the ability to choose which 'side' of the moving boundary to use is still retained
• An adaptivity file (*-s0*.e) file was being output at every time step even where there were no subdomain changes. meshChanged() is now only called when at least one element changes its subdomain.
• Segmentation fault for particular scenarios when running in parallel has been fixed

This adds:

• moving_boundary_subdomain_pairs gives greater control over the updates of the boundary. This is based on which pairs of subdomains elements are between (only applies to elements that change subdomain ID). External element sides can now also be added to the boundary.
• Reinitialization of variables and auxvariables was previously all or nothing for elements that changed subdomains. Now user can control whether reinitialization occurs depending on the old and new subdomain IDs
• Reinitialization of material properties always occurred previously. Now they reinitialize on the same elements as the variables and auxvariables do

refs #25736

@hugary1995 Continues some of the work from #26254

[moosebuild]

Job Documentation on 352a2d3 wanted to post the following:

View the site here

This comment will be updated on new commits.

[moosebuild]

Job Coverage on 352a2d3 wanted to post the following:

Framework coverage

	0ef472	#27965 352a2d
	Total	Total	+/-	New
Rate	85.03%	85.05%	+0.02%	96.32%
Hits	105219	105254	+35	314
Misses	18526	18506	-20	12

Diff coverage report

Full coverage report

Modules coverage

Coverage did not change

Full coverage reports

Reports

• framework
• chemical_reactions
• combined
• contact
• electromagnetics
• external_petsc_solver
• fluid_properties
• fsi
• functional_expansion_tools
• geochemistry
• heat_transfer
• level_set
• misc
• navier_stokes
• optimization
• peridynamics
• phase_field
• porous_flow
• ray_tracing
• rdg
• reactor
• richards
• scalar_transport
• solid_mechanics
• solid_properties
• stochastic_tools
• thermal_hydraulics
• xfem

This comment will be updated on new commits.

[Wendy-Ji]

Hello, this PR will cause some errors when testing malamute and racoon as the parameters have been changed for CoupledVarThresholdElementSubdomainModifier. I have made PRs to patch these. Thank you.

idaholab/malamute#160
hugary1995/raccoon#171

[hugary1995]

#28314 resulted in some conflicts in this PR. I resolved the conflicts (hopefully correctly) and force pushed to your branch. @Wendy-Ji let me know if I missed anything. I'm still reviewing this PR.

[hugary1995]

I have some really minor comments. There are some files that need to be restored -- I will take care of them.

[hugary1995]

Since I am not an independent reviewer as I authored part of ElementSubdomainModifierBase.h/.C, we will need at least one approval from either @dewenyushu or @GiudGiud .

[dewenyushu]

Excited to see this code improvement. Very well coded and documented. I just have a few comments.

[GiudGiud]

Will be tomorrow, got too busy

[GiudGiud]

looks good

[GiudGiud]

@Wendy-Ji if you could update your malamute patch please. If you don't have time please just give me write access and I'll finish it up

[Wendy-Ji]

@Wendy-Ji if you could update your malamute patch please. If you don't have time please just give me write access and I'll finish it up

The PR is still under review, but I think everything in the patch is up to date now. I've given you write access in case there's something else I've missed