Merge pull request #337 from DrylandEcology/feature_vegestab

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"

NEWS.md

@@ -1,3 +1,19 @@
+# SOILWAT2 v6.7.0
+* This version produces exactly the same simulation output
+  as the previous release under default values
+  (i.e., vegetation establishment is turned off).
+
+* 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.
+
+## Changes to inputs
+* New input via `"<species>.estab"` sets the vegetation type of
+  a species establishment parameters'.
+
 
 # SOILWAT2 v6.6.0
 * Random number generators now produce sequences that can be exactly reproduced.

SW_Control.c

@@ -160,7 +160,7 @@ void SW_CTL_init_run(void) {
 	SW_PET_init_run();
 	SW_SKY_init_run();
 	SW_SIT_init_run();
-	// SW_VES_init_run() not needed
+	SW_VES_init_run(); // must run after `SW_SIT_init_run()`
 	SW_VPD_init_run();
 	SW_FLW_init_run();
 	SW_ST_init_run();

SW_Control.h

@@ -18,6 +18,8 @@
 #ifndef SW_CONTROL_H
 #define SW_CONTROL_H
 
+#include "generic.h" // for `Bool`, `swTRUE`, `swFALSE`
+
 #ifdef __cplusplus
 extern "C" {
 #endif

SW_Output.c

@@ -1946,8 +1946,7 @@ void SW_OUT_new_year(void)
 
 
 
-int SW_OUT_read_onekey(OutKey k, OutSum sumtype, char period[], int first,
-	int last, char msg[])
+int SW_OUT_read_onekey(OutKey k, OutSum sumtype, int first, int last, char msg[])
 {
 	int res = 0; // return value indicating type of message if any
 
@@ -1987,11 +1986,6 @@ int SW_OUT_read_onekey(OutKey k, OutSum sumtype, char period[], int first,
 		SW_Output[k].sumtype = eSW_Sum;
 		first = 1;
 		last = 366;
-		#ifndef RSOILWAT
-		strcpy(period, "YR");
-		#else
-		if (period) {} // avoid `-Wunused-parameter`
-		#endif
 
 	} else if ((k == eSW_AllVeg || k == eSW_ET || k == eSW_AllWthr || k == eSW_AllH2O))
 	{
@@ -2159,10 +2153,13 @@ void SW_OUT_read(void)
 		#endif
 
 		// Fill information into `SW_Output[k]`
-		msg_type = SW_OUT_read_onekey(k,
+		msg_type = SW_OUT_read_onekey(
+			k,
 			str2stype(Str_ToUpper(sumtype, upsum)),
-			period, first, !Str_CompareI("END", (char *)last) ? 366 : atoi(last),
-			msg);
+			first,
+			!Str_CompareI("END", (char *)last) ? 366 : atoi(last),
+			msg
+		);
 
 		if (msg_type != 0) {
 			if (msg_type > 0) {

SW_Output.h

@@ -247,8 +247,7 @@ void SW_OUT_deconstruct(Bool full_reset);
 void SW_OUT_set_ncol(void);
 void SW_OUT_set_colnames(void);
 void SW_OUT_new_year(void);
-int SW_OUT_read_onekey(OutKey k, OutSum sumtype, char period[], int first,
-	int last, char msg[]);
+int SW_OUT_read_onekey(OutKey k, OutSum sumtype, int first, int last, char msg[]);
 void SW_OUT_read(void);
 void SW_OUT_sum_today(ObjType otyp);
 void SW_OUT_write_today(void);