fixed bug affecting multiple size bins

The wrong dimension was being indexed for N_perbin when initial particle volumes were being calculated, leading to error in the ode solver. This has now been resolved.
simonom · Nov 18, 2024 · 04b0bdb · 04b0bdb
1 parent 95d164e
commit 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__/dydt_rec.cpython-39.pyc b/PyCHAM/__pycache__/dydt_rec.cpython-39.pyc
diff --git a/PyCHAM/__pycache__/eqn_interr.cpython-39.pyc b/PyCHAM/__pycache__/eqn_interr.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__/ode_solv.cpython-39.pyc b/PyCHAM/__pycache__/ode_solv.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__/part_nsd.cpython-39.pyc b/PyCHAM/__pycache__/part_nsd.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__/pp_water_equil.cpython-39.pyc b/PyCHAM/__pycache__/pp_water_equil.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__/size_distr.cpython-39.pyc b/PyCHAM/__pycache__/size_distr.cpython-39.pyc
diff --git a/PyCHAM/__pycache__/write_ode_solv.cpython-39.pyc b/PyCHAM/__pycache__/write_ode_solv.cpython-39.pyc
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 2024-11-15 17:34:41.360613
+# File Created at 2024-11-18 11:42:12.348731
 
 import numpy as np 
 

diff --git a/PyCHAM/eqn_interr.py b/PyCHAM/eqn_interr.py
@@ -275,8 +275,11 @@ def eqn_interr(num_sb, erf, err_mess, self):
 				# component and that component is organic
 				if ('[O]' in name_SMILE):
 					if ('C' in name_SMILE or 'c' in name_SMILE):
-						# if it is an alkoxy radical (rather than alkyl peroxy radical) add its index to list
-						if ('O[O]' not in name_SMILE and '[O]O' not in name_SMILE): # ensure it's not alkyl peroxy radical
+						# if it is an alkoxy radical (rather than 
+						# alkyl peroxy radical) add its index to list
+						# ensure it's not alkyl peroxy radical
+						if ('O[O]' not in name_SMILE and 
+						'[O]O' not in name_SMILE):
 							self.RO_indx.append(comp_num)			
 
 				comp_num += 1 # number of unique species
@@ -293,7 +296,8 @@ def eqn_interr(num_sb, erf, err_mess, self):
 			name_only_this_eq.append(name_only)
 
 			# store reactant index
-			# check if index already present in this reaction - i.e. component appears more than once
+			# check if index already present in this reaction - 
+			# i.e. component appears more than once
 			if (sum(rindx[eqn_step, 0:reactant_step] == int(name_indx)) > 0):
 				# get existing index of this component
 				exist_indx = (np.where(rindx[eqn_step, 0:reactant_step]==(int(name_indx))))[0]

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 2024-11-15 17:34:41.373159
+# File Created at 2024-11-18 11:42:12.349062
 
 # function for deliquescence
 def drh(TEMP):

diff --git a/PyCHAM/init_conc.py b/PyCHAM/init_conc.py
@@ -223,7 +223,7 @@ def init_conc(num_comp, init_conc, PInit,
 
 	for i in range(num_comp): # loop through all components to get molar weights
 		y_mw[i] = self.Pybel_objects[i].molwt # molecular mass (g/mol)
-
+		
 	# --------------------------------------------------------------
 	# account for water's properties
 

diff --git a/PyCHAM/input/.DS_Store b/PyCHAM/input/.DS_Store
diff --git a/PyCHAM/input/Baker2024/MCM_PRAM_xml.xml b/PyCHAM/input/Baker2024/MCM_PRAM_xml.xml
@@ -3,14 +3,59 @@
 <species species_name="H2O" species_number="s6060">
 <smiles>O</smiles>
 </species>
-<species species_number="s6055" species_name="AMM_SUL">
-<smiles>O=S(=O)(O)O.N.N</smiles>
-</species>
-<species species_name="O" species_number="s6061">
-<smiles>[O]</smiles>
+<species species_number="s1" species_name="core">
+<smiles>NOS(O)(O)ON</smiles>
+</species>
+<species species_number="s1" species_name="core_ind">
+<smiles>CCCCCCCCCC</smiles>
+</species>
+<species species_number="s1" species_name="AMMSUL">
+<smiles>NOS(O)(O)ON</smiles>
+</species>
+<species species_number="s1" species_name="AMMChloride">
+<smiles>NCl</smiles>
+</species>
+<species species_number="s1" species_name="AMMNitrate">
+<smiles>NN(=O)(O)(O)</smiles>
+</species>
+<species species_number="s1" species_name="AMMBiSUL">
+<smiles>OS(=O)(=O)ON</smiles>
+</species>
+<species species_number="s1" species_name="C7H15CHO">
+<smiles>CCCCCCCCO</smiles>
+</species>
+<species species_number="s1" species_name="C8H17CHO">
+<smiles>CCCCCCCCCO</smiles>
+</species>
+<species species_number="s1" species_name="C9H19CHO">
+<smiles>CCCCCCCCCCO</smiles>
+</species>
+<species species_number="s1" species_name="pri_org">
+<smiles>CCCCCCCCCCCCCCCC(=O)O</smiles>
+</species>
+<species species_number="s1" species_name="pri_org_ind">
+<smiles>CCCCCCCCCCCCCCCC(=O)O</smiles>
+</species>
+<species species_number="s1" species_name="sec_org">
+<smiles>CCCCCCCCCCCCCCC</smiles>
+</species>
+<species species_number="s1" species_name="sec_org1">
+<smiles>OOCCCCCCCCCC</smiles>
+</species>
+<species species_number="s1" species_name="sec_org0">
+<smiles>OOCCCOOCCCCCCCO</smiles>
+</species>
+<species species_number="s1" species_name="sec_org-1">
+<smiles>OOCCCOOCCCOOCCCCOO</smiles>
+</species>
+<species species_number="s1" species_name="sec_org-2">
+<smiles>OOCCOOCOOCCOCOOCCCCOO</smiles>
+</species>
+<species species_number="s1" species_name="O">
+<smiles>[O]</smiles>
 </species>
 <species species_name="O2" species_number="s6062">
-<smiles>OO</smiles>
+<smiles>O=O</smiles>
 </species>
 <species species_name="C1" species_number="s6063">
 <smiles>CC</smiles>
@@ -1615,7 +1660,9 @@
 <species species_name="HYETHO2H" species_number="s520">
 <smiles>OCCOO</smiles>
 </species>
-<species species_name="NO" species_number="s521"></species>
+<species species_name="NO" species_number="s521">
+<smiles>[N]=O</smiles>
+</species>
 <species species_name="ETHOHNO3" species_number="s522">
 <smiles>OCCON(=O)=O</smiles>
 </species>

diff --git a/PyCHAM/input/auto_call_test/MCM_PRAM_xml.xml b/PyCHAM/input/auto_call_test/MCM_PRAM_xml.xml
@@ -3,11 +3,101 @@
 <species species_name="H2O" species_number="s6060">
 <smiles>O</smiles>
 </species>
-<species species_number="s6055" species_name="AMM_SUL">
-<smiles>O=S(=O)(O)O.N.N</smiles>
+<species species_number="s1" species_name="core">
+<smiles>NOS(O)(O)ON</smiles>
+</species>
+<species species_number="s1" species_name="core_ind">
+<smiles>CCCCCCCCCC</smiles>
+</species>
+<species species_number="s1" species_name="AMMSUL">
+<smiles>NOS(O)(O)ON</smiles>
+</species>
+<species species_number="s1" species_name="AMMChloride">
+<smiles>NCl</smiles>
+</species>
+<species species_number="s1" species_name="AMMNitrate">
+<smiles>NN(=O)(O)(O)</smiles>
+</species>
+<species species_number="s1" species_name="AMMBiSUL">
+<smiles>OS(=O)(=O)ON</smiles>
+</species>
+<species species_number="s1" species_name="C7H15CHO">
+<smiles>CCCCCCCCO</smiles>
+</species>
+<species species_number="s1" species_name="C8H17CHO">
+<smiles>CCCCCCCCCO</smiles>
+</species>
+<species species_number="s1" species_name="C9H19CHO">
+<smiles>CCCCCCCCCCO</smiles>
+</species>
+<species species_number="s1" species_name="pri_org">
+<smiles>CCCCCCCCCCCCCCCC(=O)O</smiles>
+</species>
+<species species_number="s1" species_name="pri_org_ind">
+<smiles>CCCCCCCCCCCCCCCC(=O)O</smiles>
+</species>
+<species species_number="s1" species_name="sec_org">
+<smiles>CCCCCCCCCCCCCCC</smiles>
+</species>
+<species species_number="s1" species_name="sec_org1">
+<smiles>OOCCCCCCCCCC</smiles>
+</species>
+<species species_number="s1" species_name="sec_org0">
+<smiles>OOCCCOOCCCCCCCO</smiles>
+</species>
+<species species_number="s1" species_name="sec_org-1">
+<smiles>OOCCCOOCCCOOCCCCOO</smiles>
+</species>
+<species species_number="s1" species_name="sec_org-2">
+<smiles>OOCCOOCOOCCOCOOCCCCOO</smiles>
+</species>
+<species species_number="s1" species_name="O">
+<smiles>[O]</smiles>
+</species>
+<species species_name="O2" species_number="s6062">
+<smiles>O=O</smiles>
+</species>
+<species species_name="C1" species_number="s6063">
+<smiles>CC</smiles>
 </species>
-<species species_name="O" species_number="s6061">
-<smiles>[O]</smiles>
+<species species_name="C2" species_number="s6064">
+<smiles>CCCC</smiles>
+</species>
+<species species_name="C3" species_number="s6065">
+<smiles>CCCCCC</smiles>
+</species>
+<species species_name="C4" species_number="s6066">
+<smiles>CCCCCCCC</smiles>
+</species>
+<species species_name="C5" species_number="s6067">
+<smiles>CCCCCCCCCC</smiles>
+</species>
+<species species_name="C6" species_number="s6068">
+<smiles>CCCCCCCCCCCC</smiles>
+</species>
+<species species_name="C7" species_number="s6069">
+<smiles>CCCCCCCCCCCCCC</smiles>
+</species>
+<species species_name="C8" species_number="s6070">
+<smiles>CCCCCCCCCCCCCCCC</smiles>
+</species>
+<species species_name="C9" species_number="s6071">
+<smiles>CCCCCCCCCCCCCCCCCC</smiles>
+</species>
+<species species_name="C10" species_number="s6072">
+<smiles>CCCCCCCCCCCCCCCCCCCC</smiles>
+</species>
+<species species_name="C11" species_number="s6073">
+<smiles>CCCCCCCCCCCCCCCCCCCCCC</smiles>
+</species>
+<species species_name="C12" species_number="s6074">
+<smiles>CCCCCCCCCCCCCCCCCCCCCCCC</smiles>
+</species>
+<species species_name="C13" species_number="s6075">
+<smiles>CCCCCCCCCCCCCCCCCCCCCCCCCC</smiles>
+</species>
+<species species_name="C14" species_number="s6076">
+<smiles>CCCCCCCCCCCCCCCCCCCCCCCCCCCC</smiles>
 </species>
 <species species_name="CH3OH" species_number="s1">
 <smiles>OC</smiles>
@@ -1570,7 +1660,9 @@
 <species species_name="HYETHO2H" species_number="s520">
 <smiles>OCCOO</smiles>
 </species>
-<species species_name="NO" species_number="s521"></species>
+<species species_name="NO" species_number="s521">
+<smiles>[N]=O</smiles>
+</species>
 <species species_name="ETHOHNO3" species_number="s522">
 <smiles>OCCON(=O)=O</smiles>
 </species>

diff --git a/PyCHAM/input/nus/MCM_PRAM_xml.xml → ...M/input/neg_conc_example/MCM_PRAM_xml.xml b/PyCHAM/input/nus/MCM_PRAM_xml.xml → ...M/input/neg_conc_example/MCM_PRAM_xml.xml
@@ -55,7 +55,7 @@
 <smiles>[O]</smiles>
 </species>
 <species species_name="O2" species_number="s6062">
-<smiles>OO</smiles>
+<smiles>O=O</smiles>
 </species>
 <species species_name="C1" species_number="s6063">
 <smiles>CC</smiles>
@@ -1660,7 +1660,9 @@
 <species species_name="HYETHO2H" species_number="s520">
 <smiles>OCCOO</smiles>
 </species>
-<species species_name="NO" species_number="s521"></species>
+<species species_name="NO" species_number="s521">
+<smiles>[N]=O</smiles>
+</species>
 <species species_name="ETHOHNO3" species_number="s522">
 <smiles>OCCON(=O)=O</smiles>
 </species>