Development for v6.3.0 #249

N1ckP3rsl3y · 2024-12-18T22:04:27Z

Update SOILWAT2 to v8.1.0

- Update function calls where the name has changes and/or the argument(s) changed - SOILWAT2 no longer has `files_nc.in` - Switch the following types: RealD -> double and RealF -> float - SW_WEATHER_HIST is no longer a pointer to a pointer, but is one array of SW_WEATHER_HIST instances - SOILWAT2 now provides a function that handles the calculations/setting of weather data * Remove calculations from `rSW2_set_weather_hist()` * Store all weather data in a temporary location * Call SOILWAT2's function `SW_WTH_setWeatherValues()` to calculate/set the weather - Update names changes of and within the struct SW_PATH_INPUTS - Update the setting of `swrcp` to set `swrcpOM` and `swrcpMineralSoil`

- Update the use flag `inputsProvideSWRCp` over `site_has_swrcpMineralSoil` - New helper function to `onSet_SW_SIT_tranp()` * Move the setting of transpiration from `onSet_SW_SIT()` * Set after we read soil information

dschlaep

It seems we need a couple more rSOILWAT2 updates to reflect all SOILWAT2 changes related to SWRC parameters (separate inputs of organic and mineral ps from calculated bulk; and provide sapric depth as input) -- see more detailed comments. Thanks!

dschlaep · 2024-12-19T14:57:30Z

src/rSW_Site.c

@@ -152,18 +153,18 @@ static void onSet_SW_LYR(SEXP SW_LYR, LOG_INFO* LogInfo) {
 		imperm = p_Layers[i + j * 10];
 		soiltemp = p_Layers[i + j * 11];

-		v->width[lyrno] = dmax - dmin;
+		v->soils.width[lyrno] = dmax - dmin;


onSet_SW_LYR() should also v->soils.depths[lyrno] = dmax; as the updated SOILWAT2's SW_LYR_read()

Should onSet_SW_LYR() now also call SW_Site->n_evap_lyrs = nlayers_bsevap(SW_Site->soils.evap_coeff, SW_Site->n_layers); as the updated SOILWAT2's SW_LYR_read()?

dschlaep · 2024-12-19T15:10:43Z

src/rSW_Site.c

@@ -184,7 +185,7 @@ static SEXP onGet_SW_SWRCp(void) {
 	int i, k;
 	SW_SITE *v = &SoilWatRun.Site;
 	SEXP SWRCp, SWRCp_names, SWRCp_names_y;
-	RealD *p_SWRCp;
+	double *p_SWRCp;


onGet_SW_SWRCp() should now

copy v->soils.swrcpMineralSoil[i][k] into "p_SWRCp"

copy v->swrcpOM into new "omSWRCp"

This is because SOILWAT2 now distinguishes between SWRCp in the mineral soil swrcpMineralSoil (user inputs), SWRCp in the organic matter swrcpOM (user input) and the calculated bulk soil SWRCp swrcp. For rSOILWAT2, SWRCp (slot "SWRCp" of S4 class "swSoils") is equivalent to SWRCp in the mineral soil (user inputs) -- but we cannot rename it for backwards compatibility .... That also means that we need now to add a new slot "omSWRCp" to S4 class "swSoils" for equivalency with SOILWAT2. And similarly, S4 class "swSite" gains a new slot "depthSapric"

dschlaep · 2024-12-19T15:11:53Z

src/rSW_Site.c

+            if (isMineral) {
+                v->soils.swrcpMineralSoil[i][k] = p_SWRCp[i + (v->n_layers) * k];
+            } else {
+                v->swrcpOM[i][k] = p_SWRCp[i + (v->n_layers) * k];


onSet_SW_SWRCp() -- see longer comment for onGet_SW_SWRCp()

copy p_SWRCp into v->soils.swrcpMineralSoil

copy new "omSWRCp" into v->swrcpOM

dschlaep · 2024-12-19T15:13:02Z

src/rSW_Site.c

@@ -622,28 +636,38 @@ void onSet_SW_SIT(SEXP SW_SIT, LOG_INFO* LogInfo) {
 	strcpy(v->site_ptf_name, CHAR(STRING_ELT(swrc_flags, 1)));
 	v->site_ptf_type = encode_str2ptf(v->site_ptf_name);
 	PROTECT(has_swrcp = GET_SLOT(SW_SIT, install("has_swrcp")));
-	v->site_has_swrcp = LOGICAL(has_swrcp)[0];
+	v->inputsProvideSWRCp = LOGICAL(has_swrcp)[0];


onSet_SW_SIT() -- see longer comment for onGet_SW_SWRCp()

copy new slot "depthSapric" to v->depthSapric

dschlaep · 2024-12-19T15:14:01Z

src/rSW_Site.c

@@ -458,7 +479,7 @@ SEXP onGet_SW_SIT(void) {
 	setAttrib(swrc_flags, R_NamesSymbol, swrc_names);

 	PROTECT(has_swrcp = NEW_LOGICAL(1));
-	LOGICAL(has_swrcp)[0] = v->site_has_swrcp;
+	LOGICAL(has_swrcp)[0] = v->inputsProvideSWRCp;


onGet_SW_SIT() -- see longer comment for onGet_SW_SWRCp()

copyv->depthSapric to new slot "depthSapric"

C code * Update column names to hold information for organic matter * Update the transferring of fraction organic matter between R and C * Update the setting of swrcp mineral soil to go to and from `swrcpMineralSoil` instead of `swrcp` * New function `onGet_SW_omSWRCp()` and `onSet_SW_omSWRCp()` to transfer swrcp organic matter between R and C, used to set SW_SOILS slots R code * Class `swSoils` gains new slot - omSWRCp - Add new prototype for omSWRCp - Check that slot exists and is the correct size - Add reset/setReplace method - Add slot to `sw_upgrade` method

C code * New column name "depth_sapric" * Update `onGet/Set_SW_SIT()` to transfer `depthSapric` to/from R and C R code * Add new slot "depth_sapric" to swSite * Make sure that depth_sapric is provided * Create replace/set/generic methods for "depth_sapric"

- sw_upgrade() for "swSite": new upgrade_soilLayers() to add new column "som_frac" (and set it to default values of 0) - new soilLayer_dataColumns() - fix documentation

Bugfixes for "omSWRCp" - fix onGet_SW_omSWRCp(): values were incorrectly copied; row and column names were mixed up - fix onSet_SW_SWRCp(): values were incorrectly copied; remove unused variable "isMineral" that prevented "site_has_swrcpMineralSoil" from being set correctly - fix export `swSoils_omSWRCp<-()` - fix names given to "swSoils" slot "omSWRCp": row and column names were mixed up - fix documentation New objects - sw2_list_omSWRCp: list of a matrix for each implemented SWRC with parameters for fibric and sapric peat New behavior - example code, vignette, and unit tests now set swSoils_omSWRCp() according to the selected SWRC - fix validity check for "swSoils"

- add missing variable "debug" for debug mode

- rSW_CTL_obtain_inputs() now calls onSet_SW_SOILS() before onSet_SW_SIT_transp() -- this change was needed because onSet_SW_SIT_transp() requires soil depth information that is only available after it was obtained by onSet_SW_SOILS() - see SOILWAT2 commit "Input specification of transpiration regions changed from layers to soil depth" (DrylandEcology/SOILWAT2@8c6432f)

N1ckP3rsl3y added 5 commits December 18, 2024 16:53

Prepare development for v6.3.0

ba43ea6

Update submodule SOILWAT2 to feature_nc_input

7a5af49

Update submodule

5751a4a

Update code to match latest submodule

db350c7

- Update the use flag `inputsProvideSWRCp` over `site_has_swrcpMineralSoil` - New helper function to `onSet_SW_SIT_tranp()` * Move the setting of transpiration from `onSet_SW_SIT()` * Set after we read soil information

dschlaep reviewed Dec 19, 2024

View reviewed changes

N1ckP3rsl3y and others added 10 commits December 20, 2024 16:39

Update submodule

67239c7

Set soil depths and n evap. layers when setting layer information

e8a54c0

Update .Rbuildignore

2b8b1c0

Improve sw_upgrade() for changes with v6.3.0

d3f96e3

- sw_upgrade() for "swSite": new upgrade_soilLayers() to add new column "som_frac" (and set it to default values of 0) - new soilLayer_dataColumns() - fix documentation

Update vignette with new organic matter property of soils

d1ef0fe

Fix onSet_SW_SIT_transp()

3c2e755

- add missing variable "debug" for debug mode

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Development for v6.3.0 #249

Development for v6.3.0 #249

N1ckP3rsl3y commented Dec 18, 2024

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Development for v6.3.0 #249

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