Updates for URIS valve with nonzero valve velocity and improved nonlinear convergence

[hanzhao2020]

Current situation

• The URIS code has stagnated nonlinear convergence for FSI problems #448.
• The current implementation only considers zero valve velocity.
• The scaffold surface in the aortic valve model is not considered.

Release Notes

• Resolves #448 by implementing explicit geometric coupling for FSI problems. At each time step, the fluid-structure equation is first solved until convergence, and then the mesh motion equation is solved.
• The valve velocity is computed from the input mesh motion and added to the resistive penalty term.
• The code is updated to consider the fixed aortic valve scaffold surface.

Testing

• The new code is covered by tests.

Code of Conduct & Contributing Guidelines

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

[codecov]

Codecov Report

❌ Patch coverage is 58.59155% with 147 lines in your changes missing coverage. Please review.
✅ Project coverage is 67.56%. Comparing base (869da67) to head (0560c0f).

Files with missing lines	Patch %	Lines
Code/Source/solver/uris.cpp	46.47%	91 Missing ⚠️
Code/Source/solver/fluid.cpp	65.57%	21 Missing ⚠️
Code/Source/solver/distribute.cpp	64.28%	10 Missing ⚠️
Code/Source/solver/vtk_xml.cpp	62.96%	10 Missing ⚠️
Code/Source/solver/fsi.cpp	69.23%	8 Missing ⚠️
Code/Source/solver/pic.cpp	76.92%	6 Missing ⚠️
Code/Source/solver/initialize.cpp	88.88%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #505      +/-   ##
==========================================
- Coverage   67.70%   67.56%   -0.15%     
==========================================
  Files         168      168              
  Lines       32752    33010     +258     
  Branches     5750     5819      +69     
==========================================
+ Hits        22176    22304     +128     
- Misses      10439    10568     +129     
- Partials      137      138       +1     

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[ktbolt]

@hanzhao2020 The GitHub Issue #448 has not been updated in three months and now all of a sudden there is a PR with changes to like 14 files.

How can other Team members understand the details of what the problem was and the fix ? Merging the PR and closing the Issue makes it look like the problem was never solved. I've seen developers spend two weeks trying to understand what changes were made to the code and never really understanding why the changes were made.

[hanzhao2020]

@ktbolt Thanks for this concern. The issue was not updated while I was investigating it. If it helps, I can break this PR into multiple PRs to make them easier to understand, and each PR addresses a separate issue. Or any other suggestions are appreciated.

[ktbolt]

@hanzhao2020 Issues are important because they provide a history of what code was changed and why. Each Issue has a link to the PR which provides the details of code changes but a high-level description provides a context in which to understand those changes.

For example: why was quadratic transition between RIS valve open and close thickness needed ?

The reason we do all of this is to be able to maintain and extend the code after people leave. If a year from now there are problems with the URIS code then we need to understand how to fix it.

[hanzhao2020]

@ktbolt Thank you for the clarification. I agree that issues should document the reasoning behind the code change. I can close this PR first and create/update the corresponding issues to capture these changes, then open separate PRs for these issues. Does this plan sound good to you?

[ktbolt]

@hanzhao2020 Sounds good, thank you !