Make code run with "vegetation establishment" activated

- 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)

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_VegEstab.c

@@ -45,6 +45,7 @@
 #include "SW_Model.h" // externs SW_Model
 #include "SW_SoilWater.h" // externs SW_Soilwat
 #include "SW_Weather.h"  // externs SW_Weather
+#include "SW_VegProd.h" // externs `key2veg[]`
 #include "SW_VegEstab.h"
 
 
@@ -130,7 +131,7 @@ void SW_VES_deconstruct(void)
 		// De-allocate days and parameters
 		if (SW_VegEstab.count > 0)
 		{
-			if (!isnull(SW_VegEstab.p_oagg[pd]->days)) {
+			if (pd > eSW_Day && !isnull(SW_VegEstab.p_oagg[pd]->days)) {
 				Mem_Free(SW_VegEstab.p_oagg[eSW_Year]->days);
 			}
 
@@ -190,27 +191,44 @@ void SW_VES_read(void) {
 	CloseFile(&f);
 
 	SW_VegEstab_construct();
-
-	if (EchoInits)
-		_echo_VegEstab();
 }
 
 /**
-@brief Construct SW_VegEstab variable
+@brief Construct SW_VegEstab output variables
 */
 void SW_VegEstab_construct(void)
 {
+	if (SW_VegEstab.count > 0) {
+		SW_VegEstab.p_oagg[eSW_Year]->days = (TimeInt *) Mem_Calloc(
+			SW_VegEstab.count, sizeof(TimeInt), "SW_VegEstab_construct()");
+
+		SW_VegEstab.p_accu[eSW_Year]->days = (TimeInt *) Mem_Calloc(
+			SW_VegEstab.count, sizeof(TimeInt), "SW_VegEstab_construct()");
+	}
+}
+
+
+/**
+	@brief Initialization and checks of species establishment parameters
+
+	This works correctly only after
+		* species establishment parameters are read from file by `SW_VES_read()`
+		* soil layers are initialized by `SW_SIT_init_run()`
+*/
+void SW_VES_init_run(void) {
 	IntU i;
 
-	for (i = 0; i < SW_VegEstab.count; i++)
+	for (i = 0; i < SW_VegEstab.count; i++) {
 		_spp_init(i);
+	}
 
-	if (SW_VegEstab.count > 0) {
-		SW_VegEstab.p_accu[eSW_Year]->days = (TimeInt *) Mem_Calloc(
-			SW_VegEstab.count, sizeof(TimeInt), "SW_VegEstab_construct()");
+	if (EchoInits) {
+		_echo_VegEstab();
 	}
 }
 
+
+
 /**
 @brief Check that each count coincides with a day of the year.
 */
@@ -327,7 +345,7 @@ static void _zero_state(unsigned int sppnum) {
 static void _read_spp(const char *infile) {
 	/* =================================================== */
 	SW_VEGESTAB_INFO *v;
-	const int nitems = 15;
+	const int nitems = 16;
 	FILE *f;
 	int lineno = 0;
 	char name[80]; /* only allow 4 char sppnames */
@@ -347,45 +365,48 @@ static void _read_spp(const char *infile) {
 			strcpy(name, inbuf);
 			break;
 		case 1:
-			v->estab_lyrs = atoi(inbuf);
+			v->vegType = atoi(inbuf);
 			break;
 		case 2:
-			v->bars[SW_GERM_BARS] = fabs(atof(inbuf));
+			v->estab_lyrs = atoi(inbuf);
 			break;
 		case 3:
-			v->bars[SW_ESTAB_BARS] = fabs(atof(inbuf));
+			v->bars[SW_GERM_BARS] = fabs(atof(inbuf));
 			break;
 		case 4:
-			v->min_pregerm_days = atoi(inbuf);
+			v->bars[SW_ESTAB_BARS] = fabs(atof(inbuf));
 			break;
 		case 5:
-			v->max_pregerm_days = atoi(inbuf);
+			v->min_pregerm_days = atoi(inbuf);
 			break;
 		case 6:
-			v->min_wetdays_for_germ = atoi(inbuf);
+			v->max_pregerm_days = atoi(inbuf);
 			break;
 		case 7:
-			v->max_drydays_postgerm = atoi(inbuf);
+			v->min_wetdays_for_germ = atoi(inbuf);
 			break;
 		case 8:
-			v->min_wetdays_for_estab = atoi(inbuf);
+			v->max_drydays_postgerm = atoi(inbuf);
 			break;
 		case 9:
-			v->min_days_germ2estab = atoi(inbuf);
+			v->min_wetdays_for_estab = atoi(inbuf);
 			break;
 		case 10:
-			v->max_days_germ2estab = atoi(inbuf);
+			v->min_days_germ2estab = atoi(inbuf);
 			break;
 		case 11:
-			v->min_temp_germ = atof(inbuf);
+			v->max_days_germ2estab = atoi(inbuf);
 			break;
 		case 12:
-			v->max_temp_germ = atof(inbuf);
+			v->min_temp_germ = atof(inbuf);
 			break;
 		case 13:
-			v->min_temp_estab = atof(inbuf);
+			v->max_temp_germ = atof(inbuf);
 			break;
 		case 14:
+			v->min_temp_estab = atof(inbuf);
+			break;
+		case 15:
 			v->max_temp_estab = atof(inbuf);
 			break;
 		}
@@ -443,33 +464,78 @@ static void _sanity_check(unsigned int sppnum) {
 	/* =================================================== */
 	SW_LAYER_INFO **lyr = SW_Site.lyr;
 	SW_VEGESTAB_INFO *v = SW_VegEstab.parms[sppnum];
-	LyrIndex min_transp_lyrs;
-	int k;
 
-	min_transp_lyrs = SW_Site.n_transp_lyrs[SW_TREES];
-	ForEachVegType(k) {
-		min_transp_lyrs = min(min_transp_lyrs, SW_Site.n_transp_lyrs[k]);
+
+	if (v->vegType > NVEGTYPES) {
+		LogError(
+			logfp,
+			LOGFATAL,
+			"%s (%s) : Specified vegetation type (%s [%d]) is not implemented.",
+			MyFileName,
+			v->sppname,
+			key2veg[v->vegType],
+			v->vegType
+		);
 	}
 
-	if (v->estab_lyrs > min_transp_lyrs) {
-		LogError(logfp, LOGFATAL, "%s : Layers requested (estab_lyrs) > (# transpiration layers=%d).", MyFileName, min_transp_lyrs);
+	if (v->estab_lyrs > SW_Site.n_transp_lyrs[v->vegType]) {
+		LogError(
+			logfp,
+			LOGFATAL,
+			"%s (%s) : Layers requested (estab_lyrs = %d) > "
+			"(# transpiration layers = %d).",
+			MyFileName,
+			v->sppname,
+			v->estab_lyrs,
+			SW_Site.n_transp_lyrs[v->vegType]
+		);
 	}
 
 	if (v->min_pregerm_days > v->max_pregerm_days) {
-		LogError(logfp, LOGFATAL, "%s : First day of germination > last day of germination.", MyFileName);
+		LogError(
+			logfp,
+			LOGFATAL,
+			"%s (%s) : First day of germination > last day of germination.",
+			MyFileName,
+			v->sppname
+		);
 	}
 
 	if (v->min_wetdays_for_estab > v->max_days_germ2estab) {
-		LogError(logfp, LOGFATAL, "%s : Minimum wetdays after germination (%d) > maximum days allowed for establishment (%d).", MyFileName, v->min_wetdays_for_estab,
-				v->max_days_germ2estab);
+		LogError(
+			logfp,
+			LOGFATAL,
+			"%s (%s) : Minimum wetdays after germination (%d) > "
+			"maximum days allowed for establishment (%d).",
+			MyFileName,
+			v->sppname,
+			v->min_wetdays_for_estab,
+			v->max_days_germ2estab
+		);
 	}
 
 	if (v->min_swc_germ < lyr[0]->swcBulk_wiltpt) {
-		LogError(logfp, LOGFATAL, "%s : Minimum swc for germination (%.4f) < wiltpoint (%.4f)", MyFileName, v->min_swc_germ, lyr[0]->swcBulk_wiltpt);
+		LogError(
+			logfp,
+			LOGFATAL,
+			"%s (%s) : Minimum swc for germination (%.4f) < wiltpoint (%.4f)",
+			MyFileName,
+			v->sppname,
+			v->min_swc_germ,
+			lyr[0]->swcBulk_wiltpt
+		);
 	}
 
 	if (v->min_swc_estab < lyr[0]->swcBulk_wiltpt) {
-		LogError(logfp, LOGFATAL, "%s : Minimum swc for establishment (%.4f) < wiltpoint (%.4f)", MyFileName, v->min_swc_estab, lyr[0]->swcBulk_wiltpt);
+		LogError(
+			logfp,
+			LOGFATAL,
+			"%s (%s) : Minimum swc for establishment (%.4f) < wiltpoint (%.4f)",
+			MyFileName,
+			v->sppname,
+			v->min_swc_estab,
+			lyr[0]->swcBulk_wiltpt
+		);
 	}
 
 }
@@ -512,7 +578,8 @@ void _echo_VegEstab(void) {
 
 	strcpy(outstr, errstr);
 	for (i = 0; i < SW_VegEstab.count; i++) {
-		sprintf(errstr, "Species: %s\n----------------\n"
+		sprintf(
+				errstr, "Species: %s (vegetation type %s [%d])\n----------------\n"
 				"Germination parameters:\n"
 				"\tMinimum SWP (bars)  : -%.4f\n"
 				"\tMinimum SWC (cm/cm) : %.4f\n"
@@ -522,9 +589,18 @@ void _echo_VegEstab(void) {
 				"\tFirst possible day  : %d\n"
 				"\tLast  possible day  : %d\n"
 				"\tMinimum consecutive wet days (after first possible day): %d\n",
-				v[i]->sppname, v[i]->bars[SW_GERM_BARS], v[i]->min_swc_germ / lyr[0]->width,
-				v[i]->min_swc_germ, v[i]->min_temp_germ, v[i]->max_temp_germ,
-				v[i]->min_pregerm_days, v[i]->max_pregerm_days, v[i]->min_wetdays_for_germ);
+				v[i]->sppname,
+				key2veg[v[i]->vegType],
+				v[i]->vegType,
+				v[i]->bars[SW_GERM_BARS],
+				v[i]->min_swc_germ / lyr[0]->width,
+				v[i]->min_swc_germ,
+				v[i]->min_temp_germ,
+				v[i]->max_temp_germ,
+				v[i]->min_pregerm_days,
+				v[i]->max_pregerm_days,
+				v[i]->min_wetdays_for_germ
+			);
 
 		sprintf(errstr, "Establishment parameters:\n"
 				"\tNumber of layers affecting successful establishment: %d\n"

SW_VegEstab.h

@@ -45,6 +45,7 @@ typedef struct {
 	/* THESE VARIABLES DO NOT CHANGE DURING THE NORMAL MODEL RUN */
 	char sppFileName[MAX_FILENAMESIZE]; /* Store the file Name and Path, Mostly for Rsoilwat */
 	char sppname[MAX_SPECIESNAMELEN + 1]; /* one set of parms per species */
+	unsigned int vegType; /**< Vegetation type of species (see "Indices to vegetation types") */
 	TimeInt min_pregerm_days, /* first possible day of germination */
 			max_pregerm_days, /* last possible day of germination */
 			min_wetdays_for_germ, 	/* number of consecutive days top layer must be */
@@ -75,7 +76,7 @@ typedef struct {
 
 typedef struct {
 	TimeInt *days;	/* only output the day of estab for each species in the input */
-					/* this array is allocated via SW_VES_Init() */
+					/* this array is allocated via `SW_VegEstab_construct()` */
 					/* each day in the array corresponds to the ordered species list */
 } SW_VEGESTAB_OUTPUTS;
 
@@ -102,7 +103,7 @@ extern SW_VEGESTAB SW_VegEstab;
 void SW_VES_read(void);
 void SW_VES_construct(void);
 void SW_VES_deconstruct(void);
-void SW_VES_init(void);
+void SW_VES_init_run(void);
 void SW_VegEstab_construct(void);
 void SW_VES_checkestab(void);
 void SW_VES_new_year(void);

testing/Input/bouteloua.estab

@@ -1,18 +1,19 @@
-bogr	# 4-char name of species
+bogr # 4-char name of species
+3    # Vegetation type of species (0, trees; 1, shrubs; 2, forbs; 3 grasses)
 # soil layer parameters
 2    # number of layers affecting establishment
 10.  # SWP (bars) requirement for germination (top layer)
 15.  # SWP (bars) requirement for establishment (average of top layers)
 # timing parameters in days
 60   # first possible day of germination
-180  # last possible day of germination 
+180  # last possible day of germination
 2    # min number of consecutive "wet" days for germination to occur
-40    # max number of consecutive "dry" days after germination allowing estab 
+40    # max number of consecutive "dry" days after germination allowing estab
 5    # min number of consecutive "wet" days after germination before establishment
-15   # min number of days between germination and establishment 
-75   # max number of days between germination and establishment 
+15   # min number of days between germination and establishment
+75   # max number of days between germination and establishment
 # temperature parameters in C
-5.  # min temp threshold for germination 
-20.  # max temp threshold for germination  
-0.  # min temp threshold for establishment 
-20.  # max temp threshold for establishment  
+5.  # min temp threshold for germination
+20.  # max temp threshold for germination
+0.  # min temp threshold for establishment
+20.  # max temp threshold for establishment

testing/Input/bromus.estab

@@ -1,4 +1,5 @@
 brte # 4-char name of species
+3    # Vegetation type of species (0, trees; 1, shrubs; 2, forbs; 3 grasses)
 # soil layer parameters
 3    # number of layers affecting establishment - 45 cm Harris and Hulbert
 10.  # SWP (bars) requirement for germination (top layer) - Harris
@@ -7,12 +8,12 @@ brte # 4-char name of species
 200   # first possible day of germination - Hulbert and Harris
 365  # last possible day of germination  - Hulbert
 6    # min number of consecutive "wet" days for germination to occur  - Hurlbert and Harris
-45    # max number of consecutive "dry" days after germination allowing estab - Harris (longtime) 
+45    # max number of consecutive "dry" days after germination allowing estab - Harris (longtime)
 6    # min number of consecutive "wet" days after germination before establishment - Harris
 15   # min number of days between germination and establishment  - Hulbert
 90   # max number of days between germination and establishment - Harris and Hulbert
 # temperature parameters in C
 10.  # min temp threshold for germination - Hulbert and Harris
 30.  # max temp threshold for germination - Hulbert and Harris
 3.  # min temp threshold for establishment - Harris
-30.  # max temp threshold for establishment - Harris and Hulbert  
+30.  # max temp threshold for establishment - Harris and Hulbert