GENER Tweaks

HSP2/GENER.py

@@ -27,9 +27,11 @@ def __init__(self, segment: str, copies: Dict, geners: Dict, ddlinks: Dict, ddge
             if link.SVOL == 'COPY': 
                 copy = copies[link.SVOLNO]
                 ts = copy.get_ts(link.SMEMN,link.SMEMSB1)
+                if link.MFACTOR != 1: ts *= link.MFACTOR
             elif link.SVOL == 'GENER':
                 gener = geners[link.SVOLNO]
                 ts = gener.get_ts()
+                if link.MFACTOR != 1: ts *= link.MFACTOR
             else:
                 raise NotImplementedError(f"Invalid SVOL. GENER module does not currently support reading TimeSeries for '{link.SVOL}'")
 

HSP2/PLANK_Class.py

@@ -690,7 +690,7 @@ def simulate(self, tw, phval, co2, tss, OXRX, NUTRX, iphyto, izoo, iorn, iorp, i
 			#	sestonic algae growth & respiration
 			#-----------------------------------------------------------
 			if self.PHYFG == 1:   # simulate phytoplankton, phyrx only called here
-				(po4,no3,tam,dox,self.orn,self.orp,self.orc,bod,self.phyto,self.limphy,self.co2,self.phycla,
+				(po4,no3,tam,dox,self.orn,self.orp,self.orc,bod,self.phyto,self.limphy,self.pyco2,self.phycla,
 				dophy,bodphy,tamphy,no3phy,po4phy,phdth,phgro,ornphy,orpphy,orcphy) \
 					= self.phyrx(self.phylit,tw,self.talgrl,self.talgrh,self.talgrm,self.malgr,self.cmmp, \
 							self.cmmnp,NUTRX.TAMFG,self.AMRFG,self.NSFG,self.cmmn,self.cmmlt,self.delt60, \
@@ -716,7 +716,7 @@ def simulate(self, tw, phval, co2, tss, OXRX, NUTRX, iphyto, izoo, iorn, iorp, i
 				#	zooplankton growth & death:
 				#-----------------------------------------------------------
 				if self.ZOOFG == 1:    # simulate zooplankton, zorx only called here
-					(dox,bod,self.zoo,self.orn,self.orp,self.orc,tam,no3,po4,zeat,zco2,dozoo,bodzoo,nitzoo,po4zoo,zgro,zdth,zorn,zorp,zorc) \
+					(dox,bod,self.zoo,self.orn,self.orp,self.orc,tam,no3,po4,zeat,self.zoco2,dozoo,bodzoo,nitzoo,po4zoo,zgro,zdth,zorn,zorp,zorc) \
 						= self.zorx(self.zfil20,self.tczfil,tw,self.phyto,self.mzoeat,self.zexdel,self.cvpb, \
 							self.zres20,self.tczres,NUTRX.anaer,self.zomass,NUTRX.TAMFG,self.refr, \
 							self.ZFOOD,self.zd,self.oxzd,self.cvbn,self.cvbp,self.cvbc,self.cvnrbo,self.cvbo, \

HSP2/RQUAL.py

@@ -6,7 +6,7 @@
 import logging
 import numpy as np
 from numpy import where, zeros, array, float64
-from numba import types
+from numba import types, njit
 from numba.typed import Dict
 
 from HSP2.utilities  import make_numba_dict, initm
@@ -27,9 +27,6 @@
 def rqual(store, siminfo, uci, uci_oxrx, uci_nutrx, uci_plank, uci_phcarb, ts):
 	''' Simulate constituents involved in biochemical transformations'''
 
-	#ERRMSGS =('')
-	#errors = zeros(len(ERRMSGS), dtype=np.int32)
-
 	# simulation information:
 	delt60 = siminfo['delt'] / 60  # delt60 - simulation time interval in hours
 	simlen = siminfo['steps']
@@ -157,22 +154,42 @@ def rqual(store, siminfo, uci, uci_oxrx, uci_nutrx, uci_plank, uci_phcarb, ts):
 	# initialize & run integerated WQ simulation:
 	#---------------------------------------------------------------------
 
+	(err_oxrx, err_nutrx, err_plank, err_phcarb) \
+		= _rqual_run(siminfo_, ui, ui_oxrx, ui_nutrx, ui_plank, ui_phcarb, ts)
+
+	#---------------------------------------------------------------------
+	# compile errors & return:
+	#---------------------------------------------------------------------
+
+	(errors, ERRMSGS) = _compile_errors(NUTFG, PLKFG, PHFG, err_oxrx, err_nutrx, err_plank, err_phcarb)
+
+	return errors, ERRMSGS
+
+
+@njit(cache=True)
+def _rqual_run(siminfo_, ui, ui_oxrx, ui_nutrx, ui_plank, ui_phcarb, ts):
+
 	# initialize WQ simulation:
 	RQUAL = RQUAL_Class(siminfo_, ui, ui_oxrx, ui_nutrx, ui_plank, ui_phcarb, ts)
 
 	# run WQ simulation:
 	RQUAL.simulate(ts)
 
-	#---------------------------------------------------------------------
-	# compile errors & return:
-	#---------------------------------------------------------------------
-	errlen_oxr = len(RQUAL.OXRX.errors)
+	# return error data:
+	#TO-DO! - return PHCARB errors once implemented
+	errors_PHCARB = zeros(2, dtype=np.int64)
+
+	return RQUAL.OXRX.errors, RQUAL.NUTRX.errors, RQUAL.PLANK.errors, errors_PHCARB
+
+def _compile_errors(NUTFG, PLKFG, PHFG, err_oxrx, err_nutrx, err_plank, err_phcarb):
+
+	errlen_oxr = len(err_oxrx)
 	errlen_ntr = 0;	errlen_plk = 0;	errlen_phc = 0
 
 	if NUTFG == 1: 
-		errlen_ntr = len(RQUAL.NUTRX.errors)
+		errlen_ntr = len(err_nutrx)
 		if PLKFG == 1:
-			errlen_plk += len(RQUAL.PLANK.errors)	
+			errlen_plk += len(err_plank)
 			if PHFG == 1:
 				#errlen_phc += len(RQUAL.PHCARB.errors)
 				pass
@@ -185,22 +202,22 @@ def rqual(store, siminfo, uci, uci_oxrx, uci_nutrx, uci_plank, uci_phcarb, ts):
 	ierr = -1
 	for i in range(errlen_oxr):
 		ierr += 1
-		errors[ierr] = RQUAL.OXRX.errors[i]
+		errors[ierr] = err_oxrx[i]
 		ERRMSGS += (ERRMSGS_oxrx[i],)
 
 	for i in range(errlen_ntr):
 		ierr += 1
-		errors[ierr] = RQUAL.NUTRX.errors[i]
+		errors[ierr] = err_nutrx[i]
 		ERRMSGS += (ERRMSGS_nutrx[i],)
 
 	for i in range(errlen_plk):
 		ierr += 1
-		errors[ierr] = RQUAL.PLANK.errors[i]
+		errors[ierr] = err_plank[i]
 		ERRMSGS += (ERRMSGS_plank[i],)
 
 	for i in range(errlen_phc):
 		ierr += 1
-		errors[ierr] = RQUAL.PHCARB.errors[i]
+		errors[ierr] = err_phcarb[i]
 		ERRMSGS += (ERRMSGS_phcarb[i],)
 
 	return errors, ERRMSGS

HSP2/main.py

@@ -45,12 +45,16 @@ def main(hdfname, saveall=False, jupyterlab=True):
         # main processing loop
         msg(1, f'Simulation Start: {start}, Stop: {stop}')
         for _, operation, segment, delt in opseq.itertuples():
+            msg(2, f'{operation} {segment} DELT(minutes): {delt}')
+
             if operation == 'COPY':
                 copy_instances[segment] = activities[operation](store, siminfo, ddext_sources[(operation,segment)]) 
             elif operation == 'GENER':
-                gener_instances[segment] = activities[operation](segment, copy_instances, gener_instances, ddlinks, ddgener) 
+                try:
+                    gener_instances[segment] = activities[operation](segment, copy_instances, gener_instances, ddlinks, ddgener) 
+                except NotImplementedError as e:
+                    print(f"GENER '{segment}' encountered unsupported feature during initialization and may not function correctly. Unsupported feature: '{e}'")
             else:
-                msg(2, f'{operation} {segment} DELT(minutes): {delt}')
                 siminfo['delt']      = delt
                 siminfo['tindex']    = date_range(start, stop, freq=Minute(delt))[1:]
                 siminfo['steps']     = len(siminfo['tindex'])
@@ -239,7 +243,11 @@ def get_uci(store):
                         siminfo['units'] = int(temp['Units'])
             elif module == 'LINKS':
                 for row in store[path].fillna('').itertuples():
-                    ddlinks[f'{row.TVOLNO}{row.TOPFST}'].append(row)
+                    if row.TVOLNO != '':
+                        ddlinks[f'{row.TVOLNO}'].append(row)
+                    else:
+                        ddlinks[f'{row.TOPFST}'].append(row)
+
             elif module == 'MASS_LINKS':
                 for row in store[path].replace('na','').itertuples():
                     ddmasslinks[row.MLNO].append(row)
@@ -418,9 +426,8 @@ def get_gener_timeseries(ts: Dict, gener_instances: Dict, ddlinks: List) -> Dict
         if link.SVOL == 'GENER':
             gener = gener_instances[link.SVOLNO]
             series = gener.get_ts()
-            if link.MFACTOR != 1: 
-                series *= link.MFACTOR
-            ts[f'{link.TMEMN}{link.TMEMSB1}{link.TMEMSB2}'] = series
+            ts[f'{link.TMEMN}{link.TMEMSB1} {link.TMEMSB2}'.rstrip()] = series
+
     return ts