Miscellaneous bugfixes and cleanup

[brbass]

Summary

• Removes the old, non-functional volume calculation from SPH and requests Voronoi cells from RK instead.
• Adds missing includes across several files.
• Moves NodeIteratorBase stream operators from the inline header to the source file.
• Fixes the Johnson-Cook damage model to avoid circular dependencies
• Adds parallel GenerateRatioSphere in 2D.
• Includes material internal energy in the generic node distribution.

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ToDo :

• Annotate RELEASE_NOTES.md with notable changes.
• Create LLNLSpheral PR pointing at this branch. (PR#)
• LLNLSpheral PR has passed all tests.

[mcfadden8]

build_fail.txt

Hi @brbass - Our CI is reporting a build failure (attached snippet). Have you seen this before?

[brbass]

build_fail.txt

Hi @brbass - Our CI is reporting a build failure (attached snippet). Have you seen this before?

Fixed! I think it is probably a difference of compilers since this warning didn't cause an error in my local build.

[jmikeowen]

We have some CI builds enforcing warnings as errors just to keep things clean, so that's probably the difference.

[jmikeowen]

Why remove these dependencies? I believe this policy does depend on both the flaws and plastic strain -- was there a circular dependency resulting?

Also as an aside the JC damage and strength are not well tested, so be cautious using them.

[brbass]

#303

[jmikeowen]

This one is a C++ question for me: the SPH class does not have an initializeProblemDependencies method, but it's ancestor (SPHBase) does. What happens by calling the SPH:: declaration here?

[brbass]

If there is no SPH::declaration, then it will call SPHBase::declaration. But if there is an SPH::declaration in the future, this will call that instead. Seems like an awful bug to track down, so this is just being nice to our future selves.

[mcfadden8]

Hi @brbass, we are hopeful to get this into our next release. I'm ready to take any changes you might have in response to the questions/comments raised in this PR. If no changes are required, please let me know that as well.

Thanks!

[brbass]

Hi @brbass, we are hopeful to get this into our next release. I'm ready to take any changes you might have in response to the questions/comments raised in this PR. If no changes are required, please let me know that as well.

Thanks!

Responded to all! Feel free to merge whenever you guys think it is ready.