Adding SIPNET all states (snow, soil moisture, litter, wood, etc) to params$restart

[helge22a]

Description

Track water states in params$restart so that new model runs do not use default param values.

Motivation and Context

Using default param values for water states adds cyclic behavior in the model output that is not present in the data. This should help work being done by @mdietze @serbinsh @DongchenZ @Qianyuxuan

Review Time Estimate

• [ ] Immediately
• [ ] Within one week
• [ ] When possible

Types of changes

• [ ] Bug fix (non-breaking change which fixes an issue)
• [x] New feature (non-breaking change which adds functionality)
• [ ] Breaking change (fix or feature that would cause existing functionality to change)

Checklist:

• [ ] My change requires a change to the documentation.
• [ ] My name is in the list of CITATION.cff
• [ ] I have updated the CHANGELOG.md.
• [ ] I have updated the documentation accordingly.
• [ ] I have read the CONTRIBUTING document.
• [ ] I have added tests to cover my changes.
• [ ] All new and existing tests passed.

[Aariq]

This is probably a separate PR, but if for some reason you feel like doing some refactoring, a more robust alternative to the way model2netcdf works might be to use named lists. Right now it relies a lot on indexing by position which is easy to screw up by accident when adding or removing variables.

For example, instead of this ...

out <- list()
out[[1]] <- sipnet.output$npp * conversion_factor # NPP
out[[2]] <- sipnet.output$snow * 10 # SWE

...

nc_var[[1]] <- PEcAn.utils::to_ncvar("NPP", dims)
nc_var[[2]] <- PEcAn.utils::to_ncvar("SWE", dims)

...

... do this ...

out <- list(
  "NPP" = sipnet.output$npp * conversion_factor,
  "SWE" = sipnet.output$snow * 10,
...
)

nc_var <- list(
  "SWE" = PEcAn.utils::to_ncvar("SWE", dims),
  "NPP" = PEcAn.utils::to_ncvar("NPP", dims),
...
)
#order doesn't matter anymore, because you can sort them by name if you need the two lists to be in the same order
nc_var[names(out)]