Merge pull request #565 from DrylandEcology/feature_SOILWAT2_devel_v7…

….2.0

Updates for SOILWAT2 v7.2.0

(see https://github.com/DrylandEcology/SOILWAT2/releases/tag/v7.2.0)

* Simulation output remains the same as the previous version.

* SOILWAT2 updated handling of warnings and errors (but functionality for STEPWAT2 is identical, i.e., immediate crash on error) ([SOILWAT2 issue 368](DrylandEcology/SOILWAT2#368)).

* SOILWAT2 now offers `sw_random_t` for random numbers and internalizes all uses of `pcg` ([SOILWAT2 issue 373](DrylandEcology/SOILWAT2#373)).

* Obsolete code in DEBUG_MEM* sections is removed ([SOILWAT2 issue 369](DrylandEcology/SOILWAT2#369)).

ST_colonization.c

@@ -163,28 +163,28 @@ void initColonization(char* fileName) {
     }
     if(valuesRead != 4 && valuesRead != 5) {
       Mem_Free(tempEvents);
-      LogError(&LogInfo, LOGFATAL, "Error reading colonization file:\n\tIncorrect"
+      LogError(&LogInfo, LOGERROR, "Error reading colonization file:\n\tIncorrect"
                " number of input arguments.\n\tIs it possible you put a space"
                " somewhere? Remember this file cannot contain spaces.");
       return;
     }
     if(fromCell < 0 || toCell > ((grid_Rows * grid_Cols) - 1)) {
       Mem_Free(tempEvents);
-      LogError(&LogInfo, LOGFATAL, "Error reading colonization file:"
+      LogError(&LogInfo, LOGERROR, "Error reading colonization file:"
                "\n\tInvalid cell range ( %d - %d ) specified.", fromCell, toCell);
       return;
     }
     if(startYear < 1 || startYear > SuperGlobals.runModelYears) {
       Mem_Free(tempEvents);
-      LogError(&LogInfo, LOGFATAL, "Error reading colonization file:"
+      LogError(&LogInfo, LOGERROR, "Error reading colonization file:"
                "\n\tInvalid start year (%d) specified.", startYear);
       return;
     }
     // For the species info we need to have a cell loaded.
     load_cell(toCell / grid_Cols, toCell % grid_Cols);
     if(Species_Name2Index(name) == -1) {
       Mem_Free(tempEvents);
-      LogError(&LogInfo, LOGFATAL, "Error reading colonization file:"
+      LogError(&LogInfo, LOGERROR, "Error reading colonization file:"
                "\n\tUnrecognized species name (%s).", name);
       return;
     }

ST_environs.c

@@ -16,7 +16,7 @@
 
 #include "ST_steppe.h"
 #include "ST_globals.h"
-#include "sw_src/external/pcg/pcg_basic.h"
+#include "sw_src/include/SW_Defines.h"
 #include "sw_src/include/rands.h"
 #include "sxw.h" // externs `*SXW`
 #include "sxw_funcs.h"
@@ -34,7 +34,7 @@ static void _make_disturbance( void);
 /**************************************************************/
 /**************************************************************/
 
-pcg32_random_t environs_rng;
+sw_random_t environs_rng;
 
 
 void Env_Generate( void) {

ST_functions.h

@@ -23,9 +23,9 @@
 /* =================================================== */
 /*            Externed Global Variables                */
 /* --------------------------------------------------- */
-extern pcg32_random_t environs_rng; // defined in ST_environs.c
-extern pcg32_random_t resgroups_rng; // defined in  ST_resgroups.c
-extern pcg32_random_t species_rng; // defined in ST_species.c
+extern sw_random_t environs_rng; // defined in ST_environs.c
+extern sw_random_t resgroups_rng; // defined in  ST_resgroups.c
+extern sw_random_t species_rng; // defined in ST_species.c
 
 
 

ST_grid.c

@@ -69,7 +69,7 @@ char sd_Sep;
 int grid_Cells = 0;
 Bool UseDisturbances = 0, UseSoils = 0, sd_DoOutput = 0; //these are treated like booleans
 
-pcg32_random_t grid_rng;         // Gridded mode's unique RNG.
+sw_random_t grid_rng;         // Gridded mode's unique RNG.
 
 /**
  * \brief The main struct of the gridded mode module.
@@ -485,7 +485,7 @@ static void _init_grid_files(void)
 		grid_directories[i] = Str_Dup(Str_TrimLeftQ(buf), &LogInfo);
 	}
 	if (i != N_GRID_DIRECTORIES)
-		LogError(&LogInfo, LOGFATAL, "Invalid files.in");
+		LogError(&LogInfo, LOGERROR, "Invalid files.in");
 
 	for (i = 0; i < N_GRID_FILES; i++)
 	{
@@ -494,7 +494,7 @@ static void _init_grid_files(void)
 		grid_files[i] = Str_Dup(Str_TrimLeftQ(buf), &LogInfo);
 	}
 	if (i != N_GRID_FILES)
-		LogError(&LogInfo, LOGFATAL, "Invalid files.in");
+		LogError(&LogInfo, LOGERROR, "Invalid files.in");
 
 	// opens the log file...
 	if (!strcmp("stdout", grid_files[GRID_FILE_LOGFILE])){
@@ -568,7 +568,7 @@ static void _init_soilwat_outputs(char* fileName) {
   int cell;
   FILE* inFile = fopen(fileName, "r");
   if(!inFile) {
-    LogError(&LogInfo, LOGFATAL, "Could not open SOILWAT2 output cells file."
+    LogError(&LogInfo, LOGERROR, "Could not open SOILWAT2 output cells file."
              "\n\tFile named \"%s\"", fileName);
   }
 
@@ -1163,11 +1163,11 @@ static void _read_disturbances_in(void)
 		}
 
 		if (num != 11)
-			LogError(&LogInfo, LOGFATAL, "Invalid %s file line %d wrong",
+			LogError(&LogInfo, LOGERROR, "Invalid %s file line %d wrong",
 					grid_files[GRID_FILE_DISTURBANCES], i + 2);
 	}
 	if (i != grid_Cells)
-		LogError(&LogInfo, LOGFATAL, "Invalid %s file wrong number of cells",
+		LogError(&LogInfo, LOGERROR, "Invalid %s file wrong number of cells",
 				grid_files[GRID_FILE_DISTURBANCES]);
 
     unload_cell();
@@ -1223,7 +1223,7 @@ static void _read_soils_in(void){
 
 	FILE* f = OpenFile(grid_files[GRID_FILE_SOILS], "r", &LogInfo);
 	if(!GetALine(f, buf)){ // Throw out the header line.
-		LogError(&LogInfo, LOGFATAL, "%s file empty.", grid_files[GRID_FILE_SOILS]);
+		LogError(&LogInfo, LOGERROR, "%s file empty.", grid_files[GRID_FILE_SOILS]);
 	}
 
 	for(i = 0; i < grid_Cells; ++i){
@@ -1232,17 +1232,17 @@ static void _read_soils_in(void){
 		load_cell(row, col);
 
 		if(!GetALine(f, buf)){
-			LogError(&LogInfo, LOGFATAL, "Too few lines in %s", grid_files[GRID_FILE_SOILS]);
+			LogError(&LogInfo, LOGERROR, "Too few lines in %s", grid_files[GRID_FILE_SOILS]);
 		}
 		lineReadReturnValue = _read_soil_line(buf, &tempSoil, 0);
 		if (lineReadReturnValue == SOIL_READ_FAILURE){
-			LogError(&LogInfo, LOGFATAL, "Error reading %s file.", grid_files[GRID_FILE_SOILS]);
+			LogError(&LogInfo, LOGERROR, "Error reading %s file.", grid_files[GRID_FILE_SOILS]);
 		}
 		/* If _read_soil_line didnt return SUCCESS or FAILURE,
 		   it returned a cell number to copy. */
 		else if (lineReadReturnValue != SOIL_READ_SUCCESS){
 			if(lineReadReturnValue > i){
-				LogError(&LogInfo, LOGFATAL, "%s: Attempted to copy values that have not been read yet.\n"
+				LogError(&LogInfo, LOGERROR, "%s: Attempted to copy values that have not been read yet.\n"
 				                          "\tIf you want to copy a soil make sure you define the layers"
 										  "the FIRST time you use it.", grid_files[GRID_FILE_SOILS]);
 			}
@@ -1253,11 +1253,11 @@ static void _read_soils_in(void){
 		else {
 			for(j = 1; j < tempSoil.num_layers; ++j){
 				if(!GetALine(f, buf)){
-					LogError(&LogInfo, LOGFATAL, "Too few lines in %s", grid_files[GRID_FILE_SOILS]);
+					LogError(&LogInfo, LOGERROR, "Too few lines in %s", grid_files[GRID_FILE_SOILS]);
 				}
 				lineReadReturnValue = _read_soil_line(buf, &tempSoil, j);
 				if(lineReadReturnValue != SOIL_READ_SUCCESS){
-					LogError(&LogInfo, LOGFATAL, "Different behavior is specified between layers %d and %d of"
+					LogError(&LogInfo, LOGERROR, "Different behavior is specified between layers %d and %d of"
 					                          " cell %d in file %s. (Perhaps you specified a cell to copy in one"
 											  " but not the other?)", j, j+1, i, grid_files[GRID_FILE_SOILS]);
 				}
@@ -1310,7 +1310,7 @@ static int _read_soil_line(char* buf, SoilType* destination, int layer){
 
 	if(cellNum > grid_Cells){
 		LogError(
-			&LogInfo, LOGFATAL,
+			&LogInfo, LOGERROR,
 			"%s: cell number (id=%d) is larger than number of cells in grid (n=%d).",
 			grid_files[GRID_FILE_SOILS], cellNum, grid_Cells
 		);
@@ -1324,7 +1324,7 @@ static int _read_soil_line(char* buf, SoilType* destination, int layer){
 
 		if(cellToCopy > grid_Cells){
 			LogError(
-				&LogInfo, LOGFATAL,
+				&LogInfo, LOGERROR,
 				"%s: cell to copy (id=%d) not present in grid (n=%d).",
 				grid_files[GRID_FILE_SOILS], cellToCopy, grid_Cells
 			);
@@ -1340,7 +1340,7 @@ static int _read_soil_line(char* buf, SoilType* destination, int layer){
 	if(entriesRead == 16) {
 		if(layerRead > destination->num_layers){
 			LogError(
-				&LogInfo, LOGFATAL,
+				&LogInfo, LOGERROR,
 				"%s: cell %d has too many soil layers (%d for max=%d).",
 				grid_files[GRID_FILE_SOILS], cellNum, layerRead, destination->num_layers
 			);
@@ -1437,7 +1437,7 @@ static void _read_spinup_species(void)
 		copy_cell_col = copy_cell % grid_Cols;
 
 		if (num != 3)
-			LogError(&LogInfo, LOGFATAL, "Invalid %s file", grid_files[GRID_FILE_SPINUP_SPECIES]);
+			LogError(&LogInfo, LOGERROR, "Invalid %s file", grid_files[GRID_FILE_SPINUP_SPECIES]);
 
 		int stringIndex = _get_value_index(buf, ',', 3); //gets us the index of the string that is right after what we just parsed in
 
@@ -1452,7 +1452,7 @@ static void _read_spinup_species(void)
 			continue;
 		}
 		else if (do_copy == 1)
-			LogError(&LogInfo, LOGFATAL,
+			LogError(&LogInfo, LOGERROR,
 					"Invalid %s file line %d invalid copy_cell attempt",
 					grid_files[GRID_FILE_SPINUP_SPECIES], i + 2);
 
@@ -1462,7 +1462,7 @@ static void _read_spinup_species(void)
 		{
 			num = sscanf(&buf[stringIndex], "%d,", &seeds_Avail);
 			if (num != 1){
-				LogError(&LogInfo, LOGFATAL, "Invalid %s file line %d invalid species input",
+				LogError(&LogInfo, LOGERROR, "Invalid %s file line %d invalid species input",
 						 grid_files[GRID_FILE_SPINUP_SPECIES], i + 2);
 			}
 
@@ -1479,7 +1479,7 @@ static void _read_spinup_species(void)
 	}
 
 	if (i != grid_Cells)
-		LogError(&LogInfo, LOGFATAL, "Invalid %s file, not enough cells",
+		LogError(&LogInfo, LOGERROR, "Invalid %s file, not enough cells",
 				grid_files[GRID_FILE_SPINUP_SPECIES]);
 
 	if(!isAnyCellOnForSpinup){
@@ -1535,13 +1535,13 @@ static void _read_grid_setup(void)
     GetALine(f, buf);
     i = sscanf(buf, "%d %d", &grid_Rows, &grid_Cols);
     if (i != 2)
-        LogError(&LogInfo, LOGFATAL,
+        LogError(&LogInfo, LOGERROR,
                  "Invalid grid setup file (rows/cols line wrong)");
 
     grid_Cells = grid_Cols * grid_Rows;
 
     if (grid_Cells > MAX_CELLS)
-        LogError(&LogInfo, LOGFATAL,
+        LogError(&LogInfo, LOGERROR,
                  "Number of cells in grid exceeds MAX_CELLS defined in ST_defines.h");
 
     /* Allocate the 2d array of cells now that we know how many we need */
@@ -1550,48 +1550,48 @@ static void _read_grid_setup(void)
     GetALine(f, buf);
     i = sscanf(buf, "%u", &UseDisturbances);
     if (i != 1)
-        LogError(&LogInfo, LOGFATAL,
+        LogError(&LogInfo, LOGERROR,
                  "Invalid grid setup file (disturbances line wrong)");
 
     GetALine(f, buf);
     i = sscanf(buf, "%u", &UseSoils);
     if (i != 1)
-        LogError(&LogInfo, LOGFATAL, "Invalid grid setup file (soils line wrong)");
+        LogError(&LogInfo, LOGERROR, "Invalid grid setup file (soils line wrong)");
 
     GetALine(f, buf);
     i = sscanf(buf, "%d", &j);
     if (i != 1)
-        LogError(&LogInfo, LOGFATAL,
+        LogError(&LogInfo, LOGERROR,
                  "Invalid grid setup file (seed dispersal line wrong)");
     UseSeedDispersal = itob(j);
 
 	GetALine(f, buf);
 	i = sscanf(buf, "%d", &shouldSpinup);
 	if(i < 1){
-		LogError(&LogInfo, LOGFATAL, "Invalid grid setup file (Spinup line wrong)");
+		LogError(&LogInfo, LOGERROR, "Invalid grid setup file (Spinup line wrong)");
 	}
 
 	GetALine(f, buf);
 	i = sscanf(buf, "%hd", &SuperGlobals.runSpinupYears);
 	if(i < 1){
-		LogError(&LogInfo, LOGFATAL, "Invalid grid setup file (Spinup years line wrong)");
+		LogError(&LogInfo, LOGERROR, "Invalid grid setup file (Spinup years line wrong)");
 	}
 
 	GetALine(f, buf);
 	i = sscanf(buf, "%u", &writeIndividualFiles);
 	if(i < 1){
-		LogError(&LogInfo, LOGFATAL, "Invalid grid setup file (Individual output line wrong)");
+		LogError(&LogInfo, LOGERROR, "Invalid grid setup file (Individual output line wrong)");
 	}
 
 	GetALine(f, buf);
 	if (sscanf(buf, "%u", &recordDispersalEvents) != 1) {
-		LogError(&LogInfo, LOGFATAL,
+		LogError(&LogInfo, LOGERROR,
 				"Invalid %s file: seed dispersal events output line\n", grid_files[GRID_FILE_SETUP]);
     }
 
 	GetALine(f, buf);
 	if (sscanf(buf, "%d", &outputSDData) != 1) {
-		LogError(&LogInfo, LOGFATAL, "Invalid grid setup file (Seed Dispersal Data Output\n");
+		LogError(&LogInfo, LOGERROR, "Invalid grid setup file (Seed Dispersal Data Output\n");
 	}
 
     CloseFile(&f, &LogInfo);
@@ -2002,7 +2002,7 @@ static void _separateSOILWAT2DailyOutput(char* fileName, int* cellNumbers) {
   FILE* inFile = fopen(fileName, "r");
 
   if(!inFile) {
-    LogError(&LogInfo, LOGFATAL, "Issue while separating SOILWAT2 output.\n\tFile"
+    LogError(&LogInfo, LOGERROR, "Issue while separating SOILWAT2 output.\n\tFile"
              "\"%s\" not found.", fileName);
   }
 
@@ -2066,7 +2066,7 @@ static void _separateSOILWAT2MonthlyOutput(char* fileName, int* cellNumbers) {
   FILE* inFile = fopen(fileName, "r");
 
   if(!inFile) {
-    LogError(&LogInfo, LOGFATAL, "Issue while separating SOILWAT2 output.\n\tFile"
+    LogError(&LogInfo, LOGERROR, "Issue while separating SOILWAT2 output.\n\tFile"
              "\"%s\" not found.", fileName);
   }
 
@@ -2128,7 +2128,7 @@ static void _separateSOILWAT2YearlyOutput(char* fileName, int* cellNumbers) {
   FILE* inFile = fopen(fileName, "r");
 
   if(!inFile) {
-    LogError(&LogInfo, LOGFATAL, "Issue while separating SOILWAT2 output.\n\tFile"
+    LogError(&LogInfo, LOGERROR, "Issue while separating SOILWAT2 output.\n\tFile"
              "\"%s\" not found.", fileName);
   }
 

ST_grid.h

@@ -17,7 +17,7 @@
 /******** These modules are necessary to compile ST_grid.c ********/
 #include "ST_stats.h"
 #include "ST_defines.h"
-#include "sw_src/external/pcg/pcg_basic.h"
+#include "sw_src/include/SW_Defines.h"
 #include "sxw_vars.h"
 #include "sw_src/include/SW_Site.h"
 #include "sw_src/include/SW_SoilWater.h"
@@ -306,7 +306,7 @@ typedef enum
 /* =================================================== */
 /*            Externed Global Variables                */
 /* --------------------------------------------------- */
-extern pcg32_random_t grid_rng;
+extern sw_random_t grid_rng;
 extern CellType** gridCells;
 extern int grid_Rows;
 extern int grid_Cols;

ST_indivs.c

@@ -460,7 +460,7 @@ void _delete (IndivType *ndv)
 
   if ((s->est_count > 0 && s->IndvHead == NULL)
      || (s->est_count == 0 && s->IndvHead != NULL))
-     LogError(&LogInfo, LOGFATAL,
+     LogError(&LogInfo, LOGERROR,
               "PGMR: Indiv Count out of sync in _delete()");
 
   Mem_Free(ndv);
@@ -489,7 +489,7 @@ void Indiv_SortSize( const byte sorttype,
     case SORT_A: cmpfunc = Indiv_CompSize_A; break;
     case SORT_D: cmpfunc = Indiv_CompSize_D; break;
     default:
-      LogError(&LogInfo, LOGFATAL,
+      LogError(&LogInfo, LOGERROR,
              "Invalid sort mode in Indiv_SortSize");
   }