Implement Darcy Physics

[mmegally]

Current situation

See issue #616 on introducing darcy physics.

Release Notes

• Adding new equation type "darcy" to solve for pressure/flows in porous domains
  Closes Add implementation for darcy flow problem #616, Closes Tissue perfusion model #71

Code of Conduct & Contributing Guidelines

• I agree to follow the Code of Conduct and Contributing Guidelines.

[ktbolt]

@mmegally You've changed 47 files for this PR. It would be helpful to describe at a high level in #616 the implementation, how this is used (XML) and any related issues for data files, linear solver, etc.

[zasexton]

@ktbolt i think the majority of these file changes have to do with adding any new physics into the current procedural framework. Unfortunate but expected at this point in my opinion. @mmegally I'll do my review in a few hours when I have some time. From my first glance id say that you should remove the sbatch slurm scripts from the commits. These shouldn't be in the testing infrastructure. I'll give a more formal review in a bit though

[mmegally]

@ktbolt I went ahead and added a new comment to issue #616 with some details on the file change split, implementation, and XML usage. Let me know if there is anything else I can clarify. To reiterate my comment from there, 31/47 of the file changes are related to the test cases. I will also go ahead and remove the SLURMs from the test folder as zack mentioned right now

[ktbolt]

@mmegally Got it, thanks for adding the Issue comments !

[ktbolt]

@mmegally The darcy_convergence tests are not part of the CI tests so shouldn't they be stored somewhere else ?

Also rename the svFSI.xml files to solver.xml.

[codecov]

Codecov Report

❌ Patch coverage is 51.48515% with 245 lines in your changes missing coverage. Please review.
✅ Project coverage is 73.08%. Comparing base (8c2975f) to head (ae99df4).

Files with missing lines	Patch %	Lines
Code/Source/solver/darcy.cpp	0.00%	142 Missing ⚠️
Code/Source/solver/post.cpp	37.73%	33 Missing ⚠️
Code/Source/solver/set_equation_props.h	85.34%	17 Missing ⚠️
Code/Source/solver/read_files.cpp	67.74%	10 Missing ⚠️
Code/Source/solver/stokes.cpp	41.66%	7 Missing ⚠️
Code/Source/solver/eq_assem.cpp	0.00%	5 Missing ⚠️
Code/Source/solver/l_elas.cpp	54.54%	5 Missing ⚠️
Code/Source/solver/shells.cpp	66.66%	5 Missing ⚠️
Code/Source/solver/ustruct.cpp	54.54%	5 Missing ⚠️
Code/Source/solver/heats.cpp	50.00%	3 Missing ⚠️
... and 6 more

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #620      +/-   ##
==========================================
- Coverage   73.45%   73.08%   -0.37%     
==========================================
  Files         267      268       +1     
  Lines       40041    40270     +229     
  Branches     6706     6738      +32     
==========================================
+ Hits        29413    29433      +20     
- Misses      10385    10594     +209     
  Partials      243      243              

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[zasexton]

Suggested changes for Darcy equation initialization and fiber-flux reconstruction.

[michelebucelli]

Thank you @mmegally! I left a few comments.

[zasexton]

About to push some commits to this fork then we can elevate this draft to a full PR. in the meantime @mmegally can you resolve the active comments that you have addressed along with their appropriate commit tags? you've been doing a great job at fixing up the code so far :)

[zasexton]

In my opinion we only piece requiring a bit more review is the zero initialization for the 2D cases to make sure that we are not getting heap error allocations and out-of-bounds. I'll fork this branch and double-check now to make any appropriate changes, if necessary.

[michelebucelli]

Thanks! I did a second pass, I only have a few minor suggestions left.

[zasexton]

We are getting very close to closing this PR I believe. I'll make one more fork to address a comment I made about the post.cpp file for higher-order elements. Ultimately I don't think this is a show-stopper for the regular use case of this physics but we should guarantee that it produces expected values if higher-order meshes are ever used with the darcy physics.

[zasexton]

I believe this PR is in a good position to merge

[michelebucelli]

Thanks for addressing my previous comments! Just a few very minor leftovers, but otherwise approved.

[zasexton]

Great! Thanks @michelebucelli for the review. @mmegally after making a few minor edits to address the lingering comments I think you should feel free to merge this code :)