Added stand_alone to init() and init_discharge, and edited to allocat…

…e Q differently depending on if stand alon emode or not. Seeing discrepancies between master stand_alone results and current stand_alone results. Differences exist before these edits.

include/topmodel.h

@@ -38,11 +38,11 @@ extern void init_water_balance(
 				double **deficit_local, double **deficit_root_zone, 
 				double *sbar, double *bal);
 
-extern void init_discharge_array(int *num_delay, double *Q0, double area, 
+extern void init_discharge_array(int stand_alone, int *num_delay, double *Q0, double area, 
 			int *num_time_delay_histo_ords, double **time_delay_histogram,
                         double **Q);
 
-extern void init(FILE *in_param_fptr, FILE *output_fptr, char *subcat,
+extern void init(FILE *in_param_fptr, FILE *output_fptr, char *subcat, int stand_alone,
 	      int num_channels, int num_topodex_values, int yes_print_output,
 	      double area, double **time_delay_histogram,
 	      double *cum_dist_area_with_dist, double dt, 

src/bmi_topmodel.c

@@ -302,9 +302,8 @@ int init_config(const char* config_file, topmodel_model* model)
         &model->cum_dist_area_with_dist,&model->tl,&model->dist_from_outlet);
 
     fclose(model->subcat_fptr);
-
-
-    init(model->params_fptr,model->output_fptr,model->subcat,model->num_channels,model->num_topodex_values,
+
+    init(model->params_fptr,model->output_fptr,model->subcat,model->stand_alone, model->num_channels, model->num_topodex_values,
         model->yes_print_output,model->area,&model->time_delay_histogram,model->cum_dist_area_with_dist,
         model->dt,model->tl,model->dist_from_outlet,&model->num_time_delay_histo_ords,&model->num_delay,
 	&model->szm,&model->t0,&model->chv,&model->rv,&model->td, &model->srmax,
@@ -473,6 +472,7 @@ static int Update_until (Bmi *self, double t)
 
 static int Finalize (Bmi *self)
 {
+
     if (self){
         topmodel_model* model = (topmodel_model *)(self->data);
 
@@ -494,9 +494,9 @@ static int Finalize (Bmi *self)
             // framework-controlled mode.
             //-----------------------------------------------------------
             if (model->stand_alone == TRUE){
-                results(model->output_fptr,model->out_hyd_fptr,model->nstep, 
+	        results(model->output_fptr,model->out_hyd_fptr,model->nstep, 
                 model->Qobs, model->Q, model->yes_print_output);                 
-            }
+	    }
         }    
 
         if( model->Q != NULL )
@@ -1045,7 +1045,7 @@ static int Set_value (Bmi *self, const char *name, void *array)
                   &topmodel->num_delay, &topmodel->time_delay_histogram);
         free(tch);
         // Reinitialise discharge array
-        init_discharge_array(&topmodel->num_delay, &topmodel->Q0, topmodel->area, 
+        init_discharge_array(topmodel->stand_alone, &topmodel->num_delay, &topmodel->Q0, topmodel->area, 
 				&topmodel->num_time_delay_histo_ords, &topmodel->time_delay_histogram, 
 				&topmodel->Q);	
     }

src/topmodel.c

@@ -142,8 +142,6 @@ extern void topmod(FILE *output_fptr, int nstep, int num_topodex_values,
 /* BMI Adaption: 
   current_time_step, *sump, *sumae, *sumq, stand_alone
   added as function input parameters */
-//shift Q array to align current time step
-shift_Q(Q, num_delay + num_time_delay_histo_ords);
 
 double ex[num_topodex_values+1]; //+1 to maintin 1 based array indexing
 //NJF TODO consider warning on all program limits here since this is essentially
@@ -175,8 +173,15 @@ if(yes_print_output==TRUE && current_time_step==1)
 /* BMI Adaption: Set iteration to bmi's current_time_step (standalone) or 1 (framework)
   Counter++ is handled by bmi's update()*/
 
-if (stand_alone == TRUE)it=current_time_step;
-else it=1;  
+if (stand_alone == TRUE) {
+	it=current_time_step;
+}
+else {
+        it=1; 
+        //shift Q array to align current time step
+        shift_Q(Q, num_delay + num_time_delay_histo_ords);
+}
+
 
 *qof=0.0;
 *quz=0.0;
@@ -718,6 +723,7 @@ extern void calc_time_delay_histogram(int num_channels, double area,
 
 /** 
  * Function to (re)initialize discharge array
+ * @params[in] stand_alone, int, 0 for running with ngen and 1 for running in stand alone mode
  * @params[in] num_delay, pointer of type int, number of time steps lag (delay) in channel within 
  * 	catchment to outlet. Output from calc_time_delay_histogram
  * @params[in] Q0, pointer of type double, initial subsurface flow per unit area
@@ -730,18 +736,20 @@ extern void calc_time_delay_histogram(int num_channels, double area,
  *
  * @params[out] Q, pointer of type double and length num_delay+num_time_delay_histo_ords, simulated discharge
  */
-
-extern void init_discharge_array(int *num_delay, double *Q0, double area, 
+extern void init_discharge_array(int stand_alone, int *num_delay, double *Q0, double area, 
 			int *num_time_delay_histo_ords, double **time_delay_histogram,
                         double **Q)
 {
-    //if Q is already allocated, need to free and re-compute the required size
-    if(*Q != NULL){
-      free(*Q);
-      *Q = NULL;
+    // if not in stand alone mode, then reallocate Q
+    if(stand_alone != TRUE) {
+      // if Q is already allocated, need to free and re-compute the required size
+      if(*Q != NULL){
+        free(*Q);
+        *Q = NULL;
+      }
+      //*Q = calloc(*num_delay + *num_time_delay_histo_ords + 1, sizeof(double));
+      d_alloc(Q, *num_delay + *num_time_delay_histo_ords);
     }
-    //*Q = calloc(*num_delay + *num_time_delay_histo_ords + 1, sizeof(double));
-    d_alloc(Q, *num_delay + *num_time_delay_histo_ords);
 
     // declare local variables
     double sum;
@@ -841,6 +849,7 @@ extern void init_water_balance(
  * @params[in] in_param_fptr, FILE pointer, file with parameters (e.g., params.dat)
  * @params[in] output_fptr, FILE pointer, file to which output will be written (e.g., topmod-cat.out)
  * @params[in] subcat, pointer of type char, name of subcatchment, read in from in_param_fptr file
+ * @params[in] stand_alone, int, 0 for running with ngen and 1 for running in stand alone mode
  * @params[in] num_channels, int, defined in subcat.dat file
  * @params[in] num_topodex_values, int, number of topodex histogram values 
  * 	(i.e., number of A/TANB ordinates)
@@ -902,7 +911,7 @@ extern void init_water_balance(
  * @params[out] bal, pointer of type double, residual of water balance 
  * 
  */
-extern void init(FILE *in_param_fptr, FILE *output_fptr, char *subcat,
+extern void init(FILE *in_param_fptr, FILE *output_fptr, char *subcat, int stand_alone,
 	      int num_channels, int num_topodex_values, int yes_print_output,
 	      double area, double **time_delay_histogram,
 	      double *cum_dist_area_with_dist, double dt, 
@@ -974,7 +983,7 @@ if(yes_print_output==TRUE)
 
 
 // Reinitialise discharge array
-init_discharge_array(num_delay, Q0, area, 
+init_discharge_array(stand_alone, num_delay, Q0, area, 
 			num_time_delay_histo_ords, time_delay_histogram, 
 			Q);