Merge pull request #391 from DrylandEcology/feature_includeOutputInTests

Feature include output code in tests

- close #85

include/SW_Model.h

@@ -30,7 +30,7 @@ extern "C" {
 /*             Global Function Declarations            */
 /* --------------------------------------------------- */
 void SW_MDL_read(SW_MODEL* SW_Model, char *InFiles[], LOG_INFO* LogInfo);
-void SW_MDL_construct(Bool newperiod[], TimeInt days_in_month[]);
+void SW_MDL_construct(SW_MODEL* SW_Model);
 void SW_MDL_deconstruct(void);
 void SW_MDL_new_year(SW_MODEL* SW_Model);
 void SW_MDL_new_day(SW_MODEL* SW_Model);

include/SW_Output.h

@@ -126,7 +126,8 @@ extern char const *styp2str[];
 /* =================================================== */
 /*             Global Function Declarations            */
 /* --------------------------------------------------- */
-void SW_OUT_init_ptrs(SW_ALL* sw);
+void SW_OUT_init_ptrs(SW_OUTPUT* SW_Output);
+void SW_GENOUT_init_ptrs(SW_GEN_OUT *GenOutput);
 void SW_OUT_construct(Bool make_soil[], Bool make_regular[],
 		SW_OUTPUT_POINTERS* SW_OutputPtrs, SW_OUTPUT* SW_Output,
 		LyrIndex n_layers, SW_GEN_OUT *GenOutput);
@@ -153,6 +154,13 @@ void SW_OUT_flush(SW_ALL* sw, SW_OUTPUT_POINTERS* SW_OutputPtrs,
 				  LOG_INFO* LogInfo);
 void _collect_values(SW_ALL* sw, SW_OUTPUT_POINTERS* SW_OutputPtrs,
 		Bool bFlush_output, TimeInt tOffset, LOG_INFO* LogInfo);
+
+void SW_OUT_close_files(SW_FILE_STATUS* SW_FileStatus, SW_GEN_OUT* GenOutput,
+						LOG_INFO* LogInfo);
+void SW_OUT_create_files(SW_FILE_STATUS* SW_FileStatus, SW_OUTPUT* SW_Output,
+	LyrIndex n_layers, char *InFiles[], SW_GEN_OUT* GenOutput,
+	LOG_INFO* LogInfo);
+
 void _echo_outputs(SW_ALL* sw);
 void _echo_all_inputs(SW_ALL* sw);
 
@@ -169,6 +177,9 @@ void SW_OUT_set_SXWrequests(OutPeriod timeSteps_SXW[][SW_OUTNPERIODS],
 		IntUS *used_OUTNPERIODS, SW_OUTPUT *SW_Output, LOG_INFO *LogInfo);
 #endif
 
+void SW_GENOUT_deepCopy(SW_GEN_OUT* dest, SW_GEN_OUT* source, SW_OUTPUT* SW_Output, LOG_INFO* LogInfo);
+
+
 
 // Functions that format the output in `sw_outstr` for printing
 /* --------------------------------------------------- */

include/SW_Output_outarray.h

@@ -57,6 +57,9 @@ extern const IntUS ncol_TimeOUT[SW_OUTNPERIODS];
 /* --------------------------------------------------- */
 void SW_OUT_set_nrow(SW_MODEL* SW_Model, Bool use_OutPeriod[],
 					           size_t nrow_OUT[]);
+
+void SW_OUT_construct_outarray(SW_GEN_OUT *GenOutput, SW_OUTPUT* SW_Output,
+									   LOG_INFO *LogInfo);
 void SW_OUT_deconstruct_outarray(SW_GEN_OUT *GenOutput);
 
 #ifdef RSOILWAT
@@ -66,11 +69,10 @@ void get_outvalleader(SW_MODEL* SW_Model, OutPeriod pd,
 
 #ifdef STEPWAT
 void do_running_agg(RealD *p, RealD *psd, size_t k, IntU n, RealD x);
-void setGlobalSTEPWAT2_OutputVariables(SW_OUTPUT* SW_Output, SW_GEN_OUT *GenOutput,
-									   LOG_INFO *LogInfo);
 #endif
 
 
+
 #ifdef __cplusplus
 }
 #endif

include/SW_Output_outtext.h

@@ -26,7 +26,7 @@ extern "C" {
 /*             Global Function Declarations            */
 /* --------------------------------------------------- */
 #if defined(SOILWAT)
-void SW_OUT_create_files(SW_FILE_STATUS* SW_FileStatus, SW_OUTPUT* SW_Output,
+void SW_OUT_create_textfiles(SW_FILE_STATUS* SW_FileStatus, SW_OUTPUT* SW_Output,
 	LyrIndex n_layers, char *InFiles[], SW_GEN_OUT* GenOutput,
 	LOG_INFO* LogInfo);
 
@@ -47,7 +47,7 @@ void write_headers_to_csv(OutPeriod pd, FILE *fp_reg, FILE *fp_soil,
 void find_TXToutputSoilReg_inUse(Bool make_soil[], Bool make_regular[],
 		SW_OUTPUT* SW_Output, OutPeriod timeSteps[][SW_OUTNPERIODS],
 		IntUS used_OUTNPERIODS);
-void SW_OUT_close_files(SW_FILE_STATUS* SW_FileStatus, SW_GEN_OUT* GenOutput,
+void SW_OUT_close_textfiles(SW_FILE_STATUS* SW_FileStatus, SW_GEN_OUT* GenOutput,
 						LOG_INFO* LogInfo);
 
 

include/SW_datastructs.h

@@ -16,12 +16,12 @@
 
 
 // Array-based output:
-#if defined(RSOILWAT) || defined(STEPWAT)
+#if defined(RSOILWAT) || defined(STEPWAT) || defined(SWNETCDF)
 #define SW_OUTARRAY
 #endif
 
 // Text-based output:
-#if defined(SOILWAT) || defined(STEPWAT)
+#if (defined(SOILWAT) || defined(STEPWAT)) && !defined(SWNETCDF)
 #define SW_OUTTEXT
 #endif
 
@@ -156,6 +156,7 @@ typedef struct {
 	 * printing and summing weekly/monthly values */
 	Bool newperiod[SW_OUTNPERIODS];
 	Bool isnorth;
+	Bool doOutput; /**< Flag to indicate if output should be produced (TRUE) or not (FALSE); set to FALSE for spinup and tests */
 
     int ncSuid[2]; // First element used for domain "s", both used for "xy"
 
@@ -1007,7 +1008,7 @@ typedef struct {
 	Bool print_SW_Output;
 	char sw_outstr[MAX_LAYERS * OUTSTRLEN];
 
-	#if defined(RSOILWAT) || defined(STEPWAT)
+	#if defined(SW_OUTARRAY)
 	/** \brief A 2-dim array of pointers to output arrays.
 
 	The variable p_OUT used by rSOILWAT2 for output and by STEPWAT2 for
@@ -1170,7 +1171,7 @@ typedef struct {
 	void (*pfunc_text)(OutPeriod, SW_ALL*); /* pointer to output routine for text output */
 	#endif
 
-	#if defined(RSOILWAT)
+	#if defined(RSOILWAT) || defined(SWNETCDF)
 	void (*pfunc_mem)(OutPeriod, SW_ALL*); /* pointer to output routine for array output */
 
 	#elif defined(STEPWAT)

makefile

@@ -275,31 +275,30 @@ sources_core := \
 	$(dir_src)/SW_Flow_lib.c \
 	$(dir_src)/SW_Flow.c \
 	$(dir_src)/SW_Carbon.c \
-	$(dir_src)/SW_Domain.c
+	$(dir_src)/SW_Domain.c \
+	$(dir_src)/SW_Output.c \
+	$(dir_src)/SW_Output_get_functions.c
 
 ifdef SWNETCDF
 sources_core += $(dir_src)/SW_netCDF.c
+sources_core += $(dir_src)/SW_Output_outarray.c
+else
+sources_core += $(dir_src)/SW_Output_outtext.c
 endif
 
 sources_lib = \
 	$(sw_sources) \
-	$(sources_core) \
-	$(dir_src)/SW_Output.c \
-	$(dir_src)/SW_Output_get_functions.c
+	$(sources_core)
 objects_lib = $(sources_lib:$(dir_src)/%.c=$(dir_build_sw2)/%.o)
 
 
-# SOILWAT2-standalone
-sources_bin := $(dir_src)/SW_Main.c $(dir_src)/SW_Output_outtext.c
+# Code for SOILWAT2-standalone program
+sources_bin := $(dir_src)/SW_Main.c
 objects_bin := $(sources_bin:$(dir_src)/%.c=$(dir_build_sw2)/%.o)
 
 
-# Unfortunately, we currently cannot include 'SW_Output.c' because
-#  - cannot increment expression of enum type (e.g., OutKey, OutPeriod)
-#  - assigning to 'OutKey' from incompatible type 'int'
-# ==> instead, we use 'SW_Output_mock.c' which provides mock versions of the
-# public functions (but will result in some compiler warnings)
-sources_lib_test := $(sources_core) $(dir_src)/SW_Output_mock.c
+# Code for SOILWAT2-test library (include all source code)
+sources_lib_test := $(sources_core)
 objects_lib_test := $(sources_lib_test:$(dir_src)/%.c=$(dir_build_test)/%.o)
 
 

src/SW_Control.c

@@ -93,7 +93,7 @@ static void _end_day(SW_ALL* sw, SW_OUTPUT_POINTERS* SW_OutputPtrs,
                      LOG_INFO* LogInfo) {
   int localTOffset = 1; // tOffset is one when called from this function
 
-  if ( !sw->Model.SW_SpinUp.spinup ) {
+  if ( sw->Model.doOutput ) {
     _collect_values(sw, SW_OutputPtrs, swFALSE, localTOffset, LogInfo);
       if(LogInfo->stopRun) {
           return; // Exit function prematurely due to error
@@ -168,6 +168,11 @@ void SW_ALL_deepCopy(SW_ALL* source, SW_ALL* dest, LOG_INFO* LogInfo)
     }
 
     SW_VegEstab_alloc_outptrs(&dest->VegEstab, LogInfo);
+    if(LogInfo->stopRun) {
+        return; // Exit function prematurely due to error
+    }
+
+    SW_GENOUT_deepCopy(&dest->GenOutput, &source->GenOutput, dest->Output, LogInfo);
 }
 
 
@@ -314,7 +319,8 @@ void SW_CTL_init_ptrs(SW_ALL* sw) {
   SW_MKV_init_ptrs(&sw->Markov);
   SW_VES_init_ptrs(&sw->VegEstab);
   SW_VPD_init_ptrs(&sw->VegProd);
-  SW_OUT_init_ptrs(sw);
+  SW_OUT_init_ptrs(sw->Output);
+  SW_GENOUT_init_ptrs(&sw->GenOutput);
   SW_SWC_init_ptrs(&sw->SoilWat);
 }
 
@@ -428,7 +434,7 @@ void SW_CTL_setup_domain(unsigned long userSUID,
  */
 void SW_CTL_setup_model(SW_ALL* sw, SW_OUTPUT_POINTERS* SW_OutputPtrs,
                         LOG_INFO* LogInfo) {
-	SW_MDL_construct(sw->Model.newperiod, sw->Model.days_in_month);
+	SW_MDL_construct(&sw->Model);
 	SW_WTH_construct(&sw->Weather);
 
 	// delay SW_MKV_construct() until we know from inputs whether we need it
@@ -586,7 +592,7 @@ void SW_CTL_run_current_year(SW_ALL* sw, SW_OUTPUT_POINTERS* SW_OutputPtrs,
   #ifdef SWDEBUG
   if (debug) swprintf("'SW_CTL_run_current_year': flush output\n");
   #endif
-  if ( !sw->Model.SW_SpinUp.spinup ) {
+  if ( sw->Model.doOutput ) {
     SW_OUT_flush(sw, SW_OutputPtrs, LogInfo);
   }
 
@@ -628,6 +634,7 @@ void SW_CTL_run_spinup(SW_ALL* sw, LOG_INFO* LogInfo) {
     scope = sw->Model.SW_SpinUp.scope,
     finalyr = sw->Model.startyr + scope - 1,
     *years;
+  Bool prev_doOut = sw->Model.doOutput;
 
     years = ( TimeInt* )Mem_Malloc( sizeof( TimeInt ) * duration, "SW_CTL_run_spinup()", LogInfo );
     if(LogInfo->stopRun) {
@@ -637,7 +644,7 @@ void SW_CTL_run_spinup(SW_ALL* sw, LOG_INFO* LogInfo) {
   #ifdef SWDEBUG
   int debug = 0;
   #endif
-  
+
   switch ( mode ) {
     case 2:
       // initialize structured array
@@ -680,6 +687,8 @@ void SW_CTL_run_spinup(SW_ALL* sw, LOG_INFO* LogInfo) {
 
   sw->Model.startyr = years[0]; // set startyr for spinup
 
+  sw->Model.doOutput = swFALSE; // turn output temporarily off
+
   for (yrIdx = 0; yrIdx < duration; yrIdx++) {
     *cur_yr = years[ yrIdx ];
 
@@ -689,15 +698,16 @@ void SW_CTL_run_spinup(SW_ALL* sw, LOG_INFO* LogInfo) {
 
     SW_CTL_run_current_year(sw, NULL, LogInfo);
     if(LogInfo->stopRun) {
-        free( years );
-        return; // Exit function prematurely due to error
+        goto reSet; // Exit function prematurely due to error
     }
   }
 
-  sw->Model.startyr = startyr; // reset startyr to original value
-
-  free( years );
+  reSet: {
+      sw->Model.startyr = startyr; // reset startyr to original value
+      sw->Model.doOutput = prev_doOut; // reset doOutput to original value
 
+      free( years );
+  }
 }
 
 
@@ -890,14 +900,13 @@ void SW_CTL_run_sw(SW_ALL* sw_template, SW_DOMAIN* SW_Domain, unsigned long ncSu
 
     if ( SW_Domain->SW_SpinUp.spinup ) {
       SW_CTL_run_spinup(&local_sw, LogInfo );
-      local_sw.Model.SW_SpinUp.spinup = swFALSE;
     }
 
     SW_CTL_main(&local_sw, SW_OutputPtrs, LogInfo);
 
     // Clear local instance of SW_ALL
     freeMem: {
-        SW_CTL_clear_model(swFALSE, &local_sw);
+        SW_CTL_clear_model(swTRUE, &local_sw);
     }
 
     (void) SW_Domain;

src/SW_Main.c

@@ -32,7 +32,6 @@
 #include "include/SW_Site.h"
 #include "include/SW_Weather.h"
 #include "include/SW_Output.h"
-#include "include/SW_Output_outtext.h"
 #include "include/SW_Main_lib.h"
 #include "include/SW_Domain.h"
 #include "include/SW_Model.h"

src/SW_Model.c

@@ -60,11 +60,10 @@ const TimeInt _notime = 0xffff; /* init value for _prev* */
 /**
 @brief MDL constructor for global variables.
 
-@param[out] newperiod newperiod[] Specifies when a new day/week/month/year
-	has started
-@param[out] days_in_month[] Number of days per month for "current" year
+@param[in,out] SW_Model Struct of type SW_MODEL holding basic time information
+	about the simulation
 */
-void SW_MDL_construct(Bool newperiod[], TimeInt days_in_month[]) {
+void SW_MDL_construct(SW_MODEL* SW_Model) {
 	/* =================================================== */
 	/* note that an initializer that is called during
 	 * execution (better called clean() or something)
@@ -73,13 +72,16 @@ void SW_MDL_construct(Bool newperiod[], TimeInt days_in_month[]) {
 	 */
 	OutPeriod pd;
 
-	Time_init_model(days_in_month); // values of time are correct only after Time_new_year()
+	Time_init_model(SW_Model->days_in_month); // values of time are correct only after Time_new_year()
 
 	ForEachOutPeriod(pd)
 	{
-		newperiod[pd] = swFALSE;
+		SW_Model->newperiod[pd] = swFALSE;
 	}
-	newperiod[eSW_Day] = swTRUE; // every day is a new day
+	SW_Model->newperiod[eSW_Day] = swTRUE; // every day is a new day
+
+	SW_Model->addtl_yr = 0;
+	SW_Model->doOutput = swTRUE;
 }
 
 /**
@@ -126,7 +128,6 @@ void SW_MDL_read(SW_MODEL* SW_Model, char *InFiles[], LOG_INFO* LogInfo) {
 	 but if hemisphere occurs first, skip checking for the rest
 	 and assume they're not there.
 	 */
-    SW_Model->addtl_yr = 0;
 	lineno = 0;
 	while (GetALine(f, inbuf, MAX_FILENAMESIZE)) {
 		switch(lineno) {