Resurrect functionality to calculate and output vegetation establishment #336
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dschlaep
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Jan 9, 2023
- 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)
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With 087242a, output is produced in columns
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This was referenced Jan 9, 2023
dschlaep
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Jan 13, 2023
Resurrect "vegetation establishment" Functionality to calculate and output establishment/recruitment of species now works again and is now covered by tests (issue #336, @dschlaep). Note that this functionality assesses yearly the chances of species to recruit/establish based on simulated daily conditions; however, establishment/recruitment outcomes are not utilized to inform the simulation. - The functionality is activated by 1. activating it in "Inputs/estab.in"; default is 0 ("off") 2. listing at least one species input file with establishment parameters (default includes "bouteloua.estab" and "bromus.estab") 3. providing the listed species input files with establishment parameters (defaults include "bouteloua.estab" and "bromus.estab") 4. turning on output for key "ESTABL" in "Inputs/outsetup.in"; default is "off"
dschlaep
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Jan 13, 2023
- SOILWAT2's "vegetation establishment" module works again (also as part of STEPWAT2); see DrylandEcology/SOILWAT2#336 - note: these are calculations are made on simulated SOILWAT2's conditions and do not inform simulations (no feedback) - input files with species establishment parameters "<species>.estab" now organized in a subfolder within SOILWAT2's inputs - new input parameter "vegetation type" that associates a species with one of SOILWAT2's simulated vegetation types - notes * SOILWAT2's "establishment" is calculated under the following conditions: (i) there are input files with species establishment parameters; (ii) at least one of those files is correctly listed in `"estab.in"` and the input flag in `"estab.in"` is on * these establishment results are included in the output files only if `"ESTABL"` is turned on in `"outsetup.in"` * default values: calculations are turned off and output is turned off
dschlaep
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Jan 14, 2023
Updates for SOILWAT2 (v6.7.0): fix its "vegetation establishment" - SOILWAT2's "vegetation establishment" module works again (also as part of STEPWAT2); see DrylandEcology/SOILWAT2#336 - note: these are calculations are made on simulated SOILWAT2's conditions and do not inform simulations (no feedback) - input files with species establishment parameters "<species>.estab" now organized in a subfolder within SOILWAT2's inputs - new input parameter "vegetation type" that associates a species with one of SOILWAT2's simulated vegetation types - notes * SOILWAT2's "establishment" is calculated under the following conditions: (i) there are input files with species establishment parameters; (ii) at least one of those files is correctly listed in `"estab.in"` and the input flag in `"estab.in"` is on * these establishment results are included in the output files only if `"ESTABL"` is turned on in `"outsetup.in"` * default values: calculations are turned off and output is turned off
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Historically, SOILWAT2 was capable to calculate days when conditions where favorable for "establishment" of species according to several parameters; the module is called "VegEstab". It has been unused for many years.
The functionality is activated by
The latest release
v6.0.0, with activated establishment and output turned on, produces a run-time error:The text was updated successfully, but these errors were encountered: