extra spin up option

spin up can now be done over just the time period of the simulation and just over one run, i.e. without needing to iterate to reach 10 % agreement in RO2 pool value
simonom · Nov 25, 2024 · ca47c9b · ca47c9b
1 parent 04b0bdb
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diff --git a/PyCHAM/__pycache__/accom_coeff_calc.cpython-39.pyc b/PyCHAM/__pycache__/accom_coeff_calc.cpython-39.pyc
diff --git a/PyCHAM/__pycache__/cham_up.cpython-39.pyc b/PyCHAM/__pycache__/cham_up.cpython-39.pyc
diff --git a/PyCHAM/__pycache__/def_mod_var.cpython-39.pyc b/PyCHAM/__pycache__/def_mod_var.cpython-39.pyc
diff --git a/PyCHAM/__pycache__/dydt_rec.cpython-39.pyc b/PyCHAM/__pycache__/dydt_rec.cpython-39.pyc
diff --git a/PyCHAM/__pycache__/eqn_pars.cpython-39.pyc b/PyCHAM/__pycache__/eqn_pars.cpython-39.pyc
diff --git a/PyCHAM/__pycache__/gui.cpython-39.pyc b/PyCHAM/__pycache__/gui.cpython-39.pyc
diff --git a/PyCHAM/__pycache__/hyst_eq.cpython-39.pyc b/PyCHAM/__pycache__/hyst_eq.cpython-39.pyc
diff --git a/PyCHAM/__pycache__/init_conc.cpython-39.pyc b/PyCHAM/__pycache__/init_conc.cpython-39.pyc
diff --git a/PyCHAM/__pycache__/middle.cpython-39.pyc b/PyCHAM/__pycache__/middle.cpython-39.pyc
diff --git a/PyCHAM/__pycache__/mod_var_read.cpython-39.pyc b/PyCHAM/__pycache__/mod_var_read.cpython-39.pyc
diff --git a/PyCHAM/__pycache__/obs_file_open.cpython-39.pyc b/PyCHAM/__pycache__/obs_file_open.cpython-39.pyc
diff --git a/PyCHAM/__pycache__/ode_solv.cpython-39.pyc b/PyCHAM/__pycache__/ode_solv.cpython-39.pyc
diff --git a/PyCHAM/__pycache__/ode_solv_wat.cpython-39.pyc b/PyCHAM/__pycache__/ode_solv_wat.cpython-39.pyc
diff --git a/PyCHAM/__pycache__/ode_updater.cpython-39.pyc b/PyCHAM/__pycache__/ode_updater.cpython-39.pyc
diff --git a/PyCHAM/__pycache__/ode_updater_su.cpython-39.pyc b/PyCHAM/__pycache__/ode_updater_su.cpython-39.pyc
diff --git a/PyCHAM/__pycache__/partit_var.cpython-39.pyc b/PyCHAM/__pycache__/partit_var.cpython-39.pyc
diff --git a/PyCHAM/__pycache__/plotter_ct.cpython-39.pyc b/PyCHAM/__pycache__/plotter_ct.cpython-39.pyc
diff --git a/PyCHAM/__pycache__/pp_dursim.cpython-39.pyc b/PyCHAM/__pycache__/pp_dursim.cpython-39.pyc
diff --git a/PyCHAM/__pycache__/pp_intro.cpython-39.pyc b/PyCHAM/__pycache__/pp_intro.cpython-39.pyc
diff --git a/PyCHAM/__pycache__/rate_coeffs.cpython-39.pyc b/PyCHAM/__pycache__/rate_coeffs.cpython-39.pyc
diff --git a/PyCHAM/__pycache__/retr_out.cpython-39.pyc b/PyCHAM/__pycache__/retr_out.cpython-39.pyc
diff --git a/PyCHAM/cham_up.py b/PyCHAM/cham_up.py
@@ -542,7 +542,6 @@ def cham_up(sumt, Pnow,
 
 				# index for mole fraction of seed particles
 				self.seedx_tcnt = seedt_cnt
-
 				[y[num_comp:num_comp*(num_sb-self.wall_on+1)], 
 				N_perbin, _,_] = pp_dursim.pp_dursim(
 				yp0, N_perbin0, mean_radn, pconcn, lowsize, 
@@ -861,6 +860,16 @@ def cham_up(sumt, Pnow,
 	if (ic_red == 1 and bc_red == 0):
 		bc_red = 1
 
+	# if equilibrium gas-particle partitioning turned on
+	if (self.equi_gtop_partit == 1):
+		# effective saturation concentrations of 
+		# components (ug/m3)
+		# eq. 1 of O'Meara et al. (2014)
+		# doi.org/10.1039/C4CP00857J
+		self.Cstar = (10.**6*y_mw.reshape(1, -1)*
+		self.Psat_Pa/
+		(8.314*temp_now))
+
 	return(temp_now, Pnow, light_time_cnt, tnew, bc_red, update_count, 
 		Cinfl_now, seedt_cnt, Cfactor, infx_cnt, gasinj_cnt, DStar_org, y, tempt_cnt, 
 		RHt_cnt, N_perbin, x, pconcn_frac, pcontf, tot_in_res, self)
diff --git a/PyCHAM/def_mod_var.py b/PyCHAM/def_mod_var.py
@@ -149,6 +149,9 @@ def def_mod_var(caller, self): # define function
 	# known to partition inside 
 	# prop_calc.py and volat_calc.py
 	self.inorg_part_flag = 0
+	# whether (1) or not (0) to treat gas-particle paritioning as equilibrium, i.e.
+	# not dynamic partitioning
+	self.equi_gtop_partit = 0 
 
 	# gas inputs ------------------------------------------------------------
 	# chemical scheme name of components present initially
@@ -164,8 +167,10 @@ def def_mod_var(caller, self): # define function
 	self.con_infl_tf = 0 
 
 	# chemical scheme name of components with constant concentration	
-	self.const_comp = []
-	# Chemical scheme names of components injected instantaneously after start of experiment
+	self.const_comp = np.zeros((0, 0)).astype('str')
+	# times that constant concentration applies to
+	self.const_compt = np.zeros((1)).astype('float')
+	# chemical scheme names of components injected instantaneously after start of experiment
 	Compt = []
 	# times at which instantaneous injection of component(s) occur after 
 	# experiment start (s)

diff --git a/PyCHAM/dydt_rec.py b/PyCHAM/dydt_rec.py
@@ -24,7 +24,7 @@
 # changes due to gas-phase photochemistry and partitioning are included; 
 # generated in init_conc and treats loss from gas-phase as negative
 
-# File Created at 2024-11-18 11:42:12.348731
+# File Created at 2024-11-25 13:30:41.338052
 
 import numpy as np 
 

diff --git a/PyCHAM/eqn_pars.py b/PyCHAM/eqn_pars.py
@@ -122,7 +122,8 @@ def extr_mech(int_tol, num_sb, drh_str, erh_str, self):
 	# get index of components with continuous influx/concentration -----------
 	# empty array for storing index of components with constant influx
 	self.con_infl_indx = np.zeros((len(self.con_infl_nam)))
-	self.con_C_indx = np.zeros((len(self.const_comp))).astype('int')
+	self.con_C_indx = np.zeros((self.const_comp.shape[0], 
+		self.const_comp.shape[1])).astype('int')
 	delete_row_list = [] # prepare for removing rows of unrecognised components
 
 	icon = 0 # count on constant influxes
@@ -185,29 +186,38 @@ def extr_mech(int_tol, num_sb, drh_str, erh_str, self):
 		self.con_infl_nam = (self.con_infl_nam[si])
 
 	# components with constant concentration
-	for i in range (len(self.const_comp)):
-		try:
-			# index of where constant concentration components occur in list 
-			# of components
-			self.con_C_indx[i] = self.comp_namelist.index(self.const_comp[i])
-		except:
-			# if water then we know it will be the next 
-			# component to
-			# be appended to the component list
-			if (self.const_comp[i] == 'H2O'):
-				self.con_C_indx[i] = len(
-					self.comp_namelist)
-			else: # if not water
-				erf = 1 # raise error
-				err_mess = str('''Error: constant 
-				concentration 
-				component with name ''' + 
-				str(self.const_comp[i]) + ''' 
-				has not been identified in the 
-				chemical scheme, 
-				please check it is present and the 
-				chemical scheme markers are correct''')	
-
+	for i in range(self.const_comp.shape[0]):
+		for it in range(self.const_comp.shape[1]):
+			try:
+				# index of where constant concentration components occur in list 
+				# of components
+				self.con_C_indx[i, it] = self.comp_namelist.index(
+					self.const_comp[i, it])
+
+			except:
+				# if a component doesn't appear at a given time then provide
+				# a marker for no component
+				if (self.const_comp[i, it] == ''):
+					self.con_C_indx[i, it] = -1e6
+					continue	
+
+				# if water then we know it will be the next 
+				# component to
+				# be appended to the component list
+				if (self.const_comp[i, it] == 'H2O'):
+					self.con_C_indx[i] = len(
+						self.comp_namelist)
+				else: # if not water
+					erf = 1 # raise error
+					err_mess = str('''Error: constant 
+					concentration 
+					component with name ''' + 
+					str(self.const_comp[i]) + ''' 
+					has not been identified in the 
+					chemical scheme, 
+					please check it is present and the 
+					chemical scheme markers are correct''')	
+
 	# -------------------------------------------------------------
 	# check if water in continuous influx components 
 	if ('H2O' in self.con_infl_nam):

diff --git a/PyCHAM/err_log.txt b/PyCHAM/err_log.txt
@@ -1 +1 @@
-/Users/user/Documents/GitHub/PyCHAM/PyCHAM/output/mcmAP_scheme/20Nov_0900_0959_Base
+/Users/user/Documents/GitHub/PyCHAM/PyCHAM/output/AP_BZ_MCM_PRAMAP_autoAPRAMBZ_scheme/method_ex_dynpart_1.e-8zpc_1e3inttol_RO2pool
diff --git a/PyCHAM/gui.py b/PyCHAM/gui.py
@@ -1343,7 +1343,8 @@ def SECtab(self): # more detailed plotting tab definition
 		# drop down button to select units for change tendencies
 		self.b220e = QComboBox(self)
 		self.b220e.addItem('Molar Mass (g/mol)')
-		self.b220e.addItem('Pure component saturation vapour pressure at starting temperature of simulation (Pa)')
+		self.b220e.addItem(str('Pure component saturation vapour pressure at ' +
+			'starting temperature of simulation (Pa)'))
 		self.b220e.addItem('Pure component saturation vapour pressure at 298.15 K (Pa)')
 		self.SEClayout.addWidget(self.b220e, 8, 2, 1, 1)
 
@@ -3503,7 +3504,6 @@ def on_click220c(self):
 	def on_click220d(self):
 
 		self.dir_path = self.l201.text() # name of folder with results
-
 		# get name of single component
 		self.mm_comp_name = self.e218c.text().strip()
 

diff --git a/PyCHAM/hyst_eq.py b/PyCHAM/hyst_eq.py
@@ -21,7 +21,7 @@
 ##########################################################################################
 '''solution of deliquescence and efflorescence RH, generated by eqn_pars.py in fully functioning mode, or by ui_check.py in testing mode'''
 # module to estimate deliquescence and efflorescence relative humidity as a function of temperature
-# File Created at 2024-11-18 11:42:12.349062
+# File Created at 2024-11-25 13:30:41.256636
 
 # function for deliquescence
 def drh(TEMP):

diff --git a/PyCHAM/input/.DS_Store b/PyCHAM/input/.DS_Store
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		/Users/user/Documents/GitHub/PyCHAM/PyCHAM/output/mcmAP_scheme/20Nov_0900_0959_Base
		/Users/user/Documents/GitHub/PyCHAM/PyCHAM/output/AP_BZ_MCM_PRAMAP_autoAPRAMBZ_scheme/method_ex_dynpart_1.e-8zpc_1e3inttol_RO2pool