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Fixes identified through the 2024 fates tutorial usage #77

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3686b58
add tree damage and cohort age tracking to namelist option documentation
glemieux Sep 11, 2024
ddaeba6
attempting to link to fates-doc subsection
glemieux Sep 11, 2024
ace430d
reformat FBG and nocomp case table
glemieux Sep 11, 2024
3941815
start adding model feature table to parameter file page
glemieux Sep 12, 2024
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11 changes: 9 additions & 2 deletions docs/source/user/Namelist-Options-and-Run-Time-Modes.md
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Expand Up @@ -22,13 +22,20 @@ For more information on how to set and use these modes, click on the links in th
| use_fates_fixed_biogeog | true/false | `.false.` | Turns on/off {doc}`fixed biogeography mode <Fixed-Biogeography-Mode>` |
| use_fates_nocomp | true/false | `.false.` | Turns on/off no-competition mode |
| use_fates_sp | true/false | `.false.` | Turns on/off {doc}`satellite phenology mode <SP-(satellite-phenology)-mode>` |
| use_fates_tree_damage | true/false | `.false.` | Turns on/of {doc}`tree crown damage <fates-doc:fates_tech_note>` |
| use_fates_cohort_age_tracking | true/false | `.false.` | Enables tracking of cohort age |

For the nocomp and fixed biogeography, there are logical interactions between them, so what happens is related to the values of both switches. This logic looks like:

| | use_fixed_biogeog = true | use_fixed_biogeog = false |
| -------------------- |:-----------------:| :------: |
| **use_fates_nocomp = true** | Every PFT is given its own patch and the patch area for each PFT corresponds to the observed map | Every PFT is given its own patch and every PFT is given the same amount of patch area everywhere |
| **use_fates_nocomp = false** | Competition happens, but only between the PFTs that are allowed on a given gridcell | Competition occurs and governs the distribution of PFTs |
| **use_fates_nocomp = true** | Case A | Case B|
| **use_fates_nocomp = false** | Case C | Case D |

- Case A: Every PFT is given its own patch and the patch area for each PFT corresponds to the observed map
- Case B: Every PFT is given its own patch and every PFT is given the same amount of patch area everywhere
- Case C: Competition happens, but only between the PFTs that are allowed on a given gridcell
- Case D: Competition occurs and governs the distribution of PFTs

For namelist entries that control the soil properties, or biogeochemical cycling, please refer to the host land-model documentation. Also, compare the desired namelist entries with the defaults generated by a FATES compset. Please create issues with questions regarding incompatibilities until more comprehensive documentation becomes available.

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21 changes: 19 additions & 2 deletions docs/source/user/Notes-on-the-Parameter-File.md
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Expand Up @@ -11,7 +11,6 @@ https://github.com/NGEET/fates/tree/master/parameter_files

A short history of the changes to parameter files before they were added to version control is as follows:


Time description format is `c<YYMMDD>.cdl`

There are two ways to get the netcdf version of these files.
Expand All @@ -20,6 +19,24 @@ There are two ways to get the netcdf version of these files.

---

## Model switches

Some of the FATES model features a set via the parameter file. The following table defines the features that are switchable:


| Parameter file variable | Options | Default | Description |
| fates_allom_amode | | | |
| fates_daylength_factor_switch | | | |
| fates_hydro_htftype_node | | | |
| fates_leaf_stomatal_model | | | |
| fates_leaf_stomatal_assim_model | | | |
| fates_maintresp_leaf_model | | | |
| fates_mort_cstarvation_model | | | |
| fates_rad_model | | | |
| fates_regeneration_model | | | |

### Seed dispersal

## Old versions of the fates parameter files
(Stopped tracking post API 3)

Expand All @@ -28,4 +45,4 @@ There are two ways to get the netcdf version of these files.

[fates_params_2troppftclones.c171010.cdl (sci.1.4.0_api.3.0.0)](content/fates_params_2troppftclones.c171010.cdl) : Tue Oct 10 11:32:10 PDT 2017 (Charlie Koven/Ryan Knox), Added: fates_history_sizeclass_bin_edges, fates_history_ageclass_bin_edges, fates_dbh_repro_threshold,fates_allom_dbh_maxheight,fates_allom_d2ca_coefficient_max,fates_allom_d2ca_coefficient_max,fates_logging_coll_under_frac. Removed: fates_max_dbh, fates_allom_d2bl_slascaler. Changed values: fates_allom_d2bl1, fates_fdi_a, fates_fdi_b, fates_logging_event_code. Updated metadata: fates_logging_collateral_frac

[fates_params_2troppftclones.c170810.cdl (sci.1.3.0_api.2.0.0) ](content/fates_params_2troppftclones.c170810.cdl)
[fates_params_2troppftclones.c170810.cdl (sci.1.3.0_api.2.0.0) ](content/fates_params_2troppftclones.c170810.cdl)