SIP333 Refactor Nitrogen

[Alomir]

Summary

• What: Refactor code in sipnet
• Motivation: See ticket

How was this change tested?

This change should have no functional impact; all smoke and unit tests continue to pass without modification (other than access to moved code for unit tests).

Related issues

• Fixes Refactor nitrogen out of sipnet.c #333

Checklist

• Related issues are listed above. PRs without an approved, related issue may not get reviewed.
• PR title has the issue number in it ("[#] <concise description of proposed change>")
• Tests added/updated for new features (if applicable)
• Documentation updated (if applicable)
• docs/CHANGELOG.md updated with noteworthy changes
• Code formatted with clang-format (run git clang-format if needed)

---

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[Alomir]

Note that (once I remembered the new files) the current state of the code refactor passes all tests.

Remaining is to do the part that will actually help add other limit checks (looking at you, leaf-on) - splitting calcNFixationAndUptakeFluxes into the calculate part (into nitrogen.c) and the limit check part (into limitations.c). Also, I may take the opportunity to add some utility to nitrogen.h that up-coming leaf-on checks would want. Might leave that until the next step, though.

[github-actions]

Cpp-Linter Report ⚠️

Some files did not pass the configured checks!

clang-tidy (v19.1.1) reports: 2 concern(s)

• tests/sipnet/test_modeling/testDependencyFunctions.c:174:26: error: [clang-diagnostic-implicit-function-declaration]

  call to undeclared function 'calcSoilCN'; ISO C99 and later do not support implicit function declarations

    174 |   status |= checkCNRatio(calcSoilCN(), 7.5, "Soil C:N ratio");
        |                          ^

• tests/sipnet/test_modeling/testDependencyFunctions.c:175:26: error: [clang-diagnostic-implicit-function-declaration]

  call to undeclared function 'calcLitterCN'; ISO C99 and later do not support implicit function declarations

    175 |   status |= checkCNRatio(calcLitterCN(), 5.0, "Litter C:N ratio");
        |                          ^

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