SIP261 Implement methane production

[Alomir]

Summary

• What: Implement methane production in SIPNET
• Motivation: Core MAGIC requirement

How was this change tested?

List steps taken to test this change, with appropriate outputs if applicable

If changes are needed for any sipnet.out files in the test/smoke subdirectories, then include output from
tools/smoke_check.py by running the commands below and pasting the output at the end of this PR. Note that
this must be run BEFORE submitting changes to any sipnet.out files.

make smoke
python tools/smoke_check.py run verbose <list tests/smoke subdirectories with changed outputs>

Run python tools/smoke_check.py help for more info.

Reproduction steps

If appropriate, list steps to reproduce the change locally

Related issues

• Fixes Implement methane production in SIPNET #261

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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[Copilot]

Pull request overview

Implements methane (CH₄) production in the SIPNET model when the anaerobic context/CLI option is enabled, including new parameters, new flux bookkeeping, output reporting, and supporting tests/docs.

Changes:

• Added methane production parameters (soilMethaneRate, litterMethaneRate) and methane flux calculation, including pool updates and mass-balance accounting.
• Populated the ch4 output column and added tracker support for timestep methane production.
• Updated model docs and extended/adjusted unit tests and test parameters to cover new anaerobic/methane dependencies.

Reviewed changes

Copilot reviewed 14 out of 15 changed files in this pull request and generated 6 comments.

Show a summary per file

File	Description
src/sipnet/state.h	Adds methane parameters, flux fields, and a methane tracker.
src/sipnet/sipnet.c	Reads new params, computes methane flux, updates pools/trackers, and outputs CH₄.
src/sipnet/balance.c	Incorporates methane into carbon outputs for balance checks.
docs/model-structure.md	Documents methane production and adds methane terms to pool ODEs.
docs/CHANGELOG.md	Adds an unreleased changelog line for methane production.
tests/smoke/russell_2/sipnet.param	Adds methane rates to smoke test parameters.
tests/sipnet/test_modeling/balance.param	Adds methane rates (and adjusts other params) for balance regression testing.
tests/sipnet/test_modeling/testMethane.c	New unit test for methane flux/pool impacts.
tests/sipnet/test_modeling/testDependencyFunctions.c	Updates context setup and adds validation checks around dependency function tests.
tests/sipnet/test_modeling/testNitrogenCycle.c	Updates context setup and adds validation checks.
tests/sipnet/test_modeling/testBalance.c	Updates context setup, adds a “no litter pool” balance scenario, and minor output handling tweaks.
tests/sipnet/test_modeling/Makefile	Adds the new methane test to the modeling test build.
tests/sipnet/test_sipnet_infrastructure/Makefile	Cleans up an additional generated artifact.
tests/sipnet/test_events_types/testEventFertilization.c	Ensures context flag dependencies are satisfied in the fertilization event test.

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[dlebauer]

Yay, this is a huge milestone!

This does not block this PR, but to consider:

Since CH4 flux from non-flooded cropland is 1) rare and 2) very very tiny or negative (we don't represent methane oxidation that consumes CH4 because it is orders of magnitude smaller than typical flooded rice emissions.

For now, I think it will be sufficient to set the new rate parameters default to 0.

We discussed having a flag that would allow methane off when n2o is on. But I don't think that is a great solution. I think having anaerobic on/off makes more sense.

To simulate CH4 from flooded rice, we can change the parameter from the default, and have this associated with the PFT.

Setting these to 0 is an unsatisfying hack, but sufficient for now. It is analogous to linking drainage rate to Rice - practical but not mechanistic. One solution would be to add time dependence to the anaerobic scheme to actually capture the development of the anoxic state. I started a discussion in Slack.