Resurrect "vegetation establishment" #337
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dschlaep
commented
Jan 9, 2023
dschlaep
commented
- close Resurrect functionality to calculate and output vegetation establishment #336
- addressing #336 - note: "vegetation establishment" functionality must be activated and output turned on (see #336 for more details) - "ERROR: Input/estab.in : Layers requested (estab_lyrs) > (# transpiration layers=0)." was produced because code previously tested `estab_lyrs` before `SW_Site.n_transp_lyrs[]` was initialized -> this commit * creates new `SW_VES_init_run()` to initialize vegetation establishment parameters of each species by `_spp_init()` and checked by `_sanity_check()` -- which now are called after `SW_SIT_init_run()` that initializes soil parameters (to fix above error message); previously, they were erroneously called by `SW_VegEstab_construct()`, i.e., before soil parameters were initialized * struct `SW_VEGESTAB_INFO` gains new element `vegType` to encode to which vegetation type a species belongs; this is required to correctly check validity of `estab_lyrs` (previous code was from a time before `SOILWAT2` handled multiple vegetation types simultaneously) * accordingly, species input files with establishment parameters gain one new input line to provide associated vegetation type, and `_read_spp()` is updated to read in value of `vegType` * `_sanity_check()` now checks that `vegType` is implemented; now correctly checks `estab_lyrs` against `SW_Site.n_transp_lyrs[]` of the associated vegetation type; and error messages now include species name * `SW_VegEstab_construct()` now allocates memory for `SW_VegEstab.p_oagg[eSW_Year]->days` (which is de-allocated by `SW_VES_deconstruct()` which previously errored because it was previously erroneously never allocated)
Codecov Report
@@ Coverage Diff @@
## master #337 +/- ##
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+ Coverage 52.68% 56.16% +3.47%
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Files 20 20
Lines 3625 3657 +32
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+ Hits 1910 2054 +144
+ Misses 1715 1603 -112
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…_Estab - we expect consistent output files, i.e., no special treatment of output period for vegetation establishment results (remove restriction to yearly output if `timeStep` is not set) - `SW_OUT_read_onekey()` loses argument `period`
…ablishment parameters - existing `SW_VES_read()` reads through "estab.in" and does not read input files with species establishment parameters if the use flag is turned off - new `SW_VES_read2()` accepts two arguments that allow overriding the use flag read in from "estab.in" (e.g., to programmatically turn on/off the establishment functionality)
- previously, vegetation type inputs that were not implemented caused the fail due to `key2veg[v->vegType]`, i.e., out of bounds error -> if `vegType` is misspecified, then error message cannot translate with `key2veg` to string, i.e., create error message with just `vegType` value -> `vegType` is base0, thus any value >= NVEGTYPES is not implemented
- Organize input files for species establishment in subfolder "estab" - add `_ProjDir` to file path of each species establishment file, e.g., utilized by STEPWAT2 to locate the files relative to the SOILWAT2 directory
…point - `min_swc_estab` is calculated across the top soil layers (n = `estab_lyrs`) but previously the checks compared it against the wilting point of the most shallow soil layer only -> `min_swc_estab` is now checked against the average across `estab_lyrs` the same way as it is calculated and then utilized for establishment calculations
N1ckP3rsl3y
approved these changes
Jan 12, 2023
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