Reduced Complexity Mode: Fixed Biogeography

This pre-release introduces a reduced complexity mode for FATES. It updates the FATES side to implement the transfer of the PFT area fields into FATES, and prevents plants establishing outside of areas where they are not specified in the surface dataset. The PFTs still compete, hence this is Fixed Biogeography WITH competition

Circular dependencies fix, hydro refactor, size/age mortality enhancement

This release includes all updates to the code since the last release at tag sci.1.27.3_api.7.3.0. The major updates include: refactoring FatesInterfaceMod into two separate modules to remove circular dependencies that was holding up a fix for E3SM; the addition of new capability in mortality of cohorts by size and age; a refactor of the hydraulics code that now results in regression tests passing; an update to grass phenology that allows grasses to drop stem in cold and drought conditions, and updates to SPITFIRE resulting in less ignitions, less area burn, and lower fire intensity to more acceptable behavior. This release also initiates the minting of a Zenodo DOI for the repository.
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Conversion of modules from public by default to private by default

All modules are now private by default so that developers must now explicitly declare variables/types/procedures to by public as necessary. This change has been adopted to help mitigate potential involuntary or erroneous access to data particularly when importing other modules. Relevant discussion in issue #502 and PR #539.

Removed Erroneous Tree LAI/SAI Calls

This set of changes removed unnecessary calls to calculate plant LAI and SAI during the main driver call. These calls also erroneously did not pre-compute crown area, leading to temporarily over-inflated in-crown leaf areas. This addresses issue #540.

Updated Parameter File

This release contains updates to the fates parameter file. This includes the following changes:

1. Increased precision of all real numbers from single to double precision
2. Removal of out-dated "fates-pft_used" parameter
3. Removal of single element 1d vectors, which are now scalars
4. fates_seed_rain is now fates_seed_suppl
5. q10 parameters for frozen (fates_q10_froz) and non-frozen (fates_q10_mr) soils are now exclusively in the fates parameter file
6. fire parameters have been given a "fire" prefix: fates_fire_FBD, fates_fire_low_moisture_Coeff, fates_fire_low_moisture_Slope, fates_fire_mid_moisture, fates_fire_mid_moisture_Coeff, fates_fire_mid_moisture_Slope, fates_fire_min_moisture, fates_fire_SAV
7. logging_export_frac has been added which adds an efficiency term to trunk exporting
8. maximum conductivity for root surfaces (fates_hydr_kmax_rsurf) is now fates_hydr_kmax_rsurf1, and the "out-of-root-direction" on the same surface is now fates_hydr_kmax_rsurf2
9. parameters have been sorted in alphabetical order
10. sorting scripts have been debugged and updated

Updates to Root Surface Conductivity and Minimum Stomatal Conductance

This set of changes contains updates to the FATES-HYDRO code that allows for separate specification of the root-to-soil direction of maximum hydraulic conductivity at the root surface. It also makes the calculations of minimum stomatal conductance during photosynthesis more consistent across different contexts. These changes were made by Chonggang Xu.

Refactor of fire code vector indices, fixes to logging

This set of changes contains a set of updates to the fire code, which makes the indexing of litter pools match indexing in relevant non-fire vectors of the code. This set also contains important bug fixes in the logging module.

Note that index changes in the fire code will impact users, in that the values in the parameter files have not changed order for the following variables: fates_FBD, fates_low_moisture_Coeff, fates_low_moisture_Slope, fates_max_decomp, fates_mid_moisture, fates_mid_moisture_Coeff, fates_mid_moisture_Slope, fates_min_moisture and fates_SAV. Specifically, index 1 of the parameters has now been moved to the last position, and the other positions have been moved to lower positions. See differences here: https://github.com/NGEET/fates/pull/523/files#diff-a236898dbb7848d5cfdf2610b0ba32c0R1124

Phenology Refactor

This release contains a refactor of the phenology timing code. These changes are all site-level changes to how leaf drop and leaf flushing is signaled. This includes a combination of code cleaning and some bug fixes.

Seed rain bug fix, refactor to dbh resets

This is a minor bug fix release. This adds carbon balance tracking to external seed rain, and refactors a call to reset dbh to occur outside of the parteh structure, thus allowing us to not include its effect in dbh growth diagnostics.

Consolidation of default parameter file into 12 pfts

This release contains a consolidated default parameter file with 12 pfts. Bug fixes were also implemented to get tests passing with the biodiversity inherent in 12 vs 1 pfts.