v3.17.17

version used in the Pichelstorfer autoCONSTRAINT description paper
simonom · Nov 28, 2024 · fadecc4 · fadecc4
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diff --git a/.DS_Store b/.DS_Store
diff --git a/Images_for_readme/v4_to_v5_effect_example.png b/Images_for_readme/v4_to_v5_effect_example.png
diff --git a/MANIFEST.in b/MANIFEST.in
@@ -1,3 +1,2 @@
 exclude __pycache__
-exclude umansysprop
 include README.md
diff --git a/PyCHAM/.DS_Store b/PyCHAM/.DS_Store
diff --git a/PyCHAM/J_value_file_open.py b/PyCHAM/J_value_file_open.py
diff --git a/PyCHAM/ODE_solver_break_relevant_fluxes.txt b/PyCHAM/ODE_solver_break_relevant_fluxes.txt
@@ -1,6 +1,6 @@
 ##########################################################################################
 #                                                                                        											 #
-#    Copyright (C) 2018-2024 Simon O'Meara : simon.omeara@manchester.ac.uk                  				 #
+#    Copyright (C) 2018-2022 Simon O'Meara : simon.omeara@manchester.ac.uk                  				 #
 #                                                                                       											 #
 #    All Rights Reserved.                                                                									 #
 #    This file is part of PyCHAM                                                         									 #
@@ -14,46 +14,37 @@
 #    ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS       			 #
 #    FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more              				 #
 #    details.                                                                            										 #
-#                                                                #
-#    You should have received a copy of the GNU General Public License along with #
-#    PyCHAM.  If not, see <http://www.gnu.org/licenses/>.        #
-#                                                                #
+#                                                                                        											 #
+#    You should have received a copy of the GNU General Public License along with        					 #
+#    PyCHAM.  If not, see <http://www.gnu.org/licenses/>.                                 							 #
+#                                                                                        											 #
 ##########################################################################################
-# File created at 2024-11-12 13:44:01.256094 by ode_brk_err_mess
+# File created at 2022-09-08 10:23:30.769217 by ode_brk_err_mess
 
 Gas and particle-phase concentrations of water prior to solver (molecules/cm3) with size bin numbers starting at 1: 
-Gas: 1.3060546374485062e+17
-Size bin 1: 0.10987263238457909
-Size bin 2: 0.0
-Size bin 3: 0.0
-Size bin 4: 0.0
-Size bin 5: 0.0
-Size bin 6: 0.0
-Size bin 7: 4549410177626.267
-Size bin 8: 0.0
-Size bin 9: 0.0
-Size bin 10: 0.0
-Size bin 11: 0.0
-Size bin 12: 0.0
+Gas: 2.889287438226125e+17
+Size bin 1: 0.00433748478103535
+Size bin 2: 28384.67701926618
+Size bin 3: 8068035.437009814
+Size bin 4: 1468627264.573658
+Size bin 5: 221658626354.8917
+Size bin 6: 24878984351624.465
 
 Gas and particle-phase concentrations of water following solver (molecules/cm3) with size bin numbers starting at 1: 
-Gas: 1.3060546374485062e+17
-Size bin 1: -0.033106772570678664
-Size bin 2: 0.0
-Size bin 3: 0.0
-Size bin 4: 0.0
-Size bin 5: 0.0
-Size bin 6: 0.0
-Size bin 7: 4549390630339.442
-Size bin 8: 0.0
-Size bin 9: 0.0
-Size bin 10: 0.0
-Size bin 11: 0.0
-Size bin 12: 0.0
+Gas: 2.889287438226125e+17
+Size bin 1: -0.2139812572211136
+Size bin 2: 28700.498194842992
+Size bin 3: 8068254.056466927
+Size bin 4: 1468627304.7700033
+Size bin 5: 221658626358.43076
+Size bin 6: 24878984351621.285
+
+Gas-phase reaction fluxes with equation numbers starting at 1 (# molecules/cm3/s):
+Eq. 1 reac: [1.23361992e+08]
+Eq. 1 prod: [1.23361992e+08]
 
 Wall not turned on so no gas-wall partitioning fluxes reported
 
 Gas-particle partitioning fluxes (molecules/cm3/s) for each component with negative concentrations following call to ODE solver, where a negative flux represents loss from the gas-phase and positive represents gain to the gas-phase.  For each component, flux to the smallest size bin is the first value, and flux to the largest size bin is the final value.
-H2O: [ 2.51174382e+07 -0.00000000e+00 -0.00000000e+00 -0.00000000e+00
- -0.00000000e+00 -0.00000000e+00  3.43390553e+15 -0.00000000e+00
- -0.00000000e+00 -0.00000000e+00 -0.00000000e+00 -0.00000000e+00]
+H2O: [ 4.37542801e+05 -6.32951988e+08 -4.38145478e+08 -8.05593754e+07
+ -7.09279567e+06  6.37618702e+06]
diff --git a/PyCHAM/PyCHAM_logo_transparent.png b/PyCHAM/PyCHAM_logo_transparent.png
diff --git a/PyCHAM/RO2_indices.py b/PyCHAM/RO2_indices.py
@@ -0,0 +1,86 @@
+##########################################################################################
+#                                                                                        											 #
+#    Copyright (C) 2018-2022 Simon O'Meara : simon.omeara@manchester.ac.uk                  				 #
+#                                                                                       											 #
+#    All Rights Reserved.                                                                									 #
+#    This file is part of PyCHAM                                                         									 #
+#                                                                                        											 #
+#    PyCHAM is free software: you can redistribute it and/or modify it under              						 #
+#    the terms of the GNU General Public License as published by the Free Software       					 #
+#    Foundation, either version 3 of the License, or (at your option) any later          						 #
+#    version.                                                                            										 #
+#                                                                                        											 #
+#    PyCHAM is distributed in the hope that it will be useful, but WITHOUT                						 #
+#    ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS       			 #
+#    FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more              				 #
+#    details.                                                                            										 #
+#                                                                                        											 #
+#    You should have received a copy of the GNU General Public License along with        					 #
+#    PyCHAM.  If not, see <http://www.gnu.org/licenses/>.                                 							 #
+#                                                                                        											 #
+##########################################################################################
+'''generates an array of component indices for the components that constitute a particular component type'''
+# for peroxy radicals makes a two column array, with the first column giving the index of components
+# included in the peroxy radical list and the
+# second column containing the index based on where the RO2 occurs in comp_namelist (i.e., relative
+# to all other components from the chemical scheme)
+
+import numpy as np
+
+def RO2_indices(RO2_names, self):
+
+	# inputs: -----------------------------------------------------------------------------------------
+	# self.comp_namelist - all chemical scheme names
+	# RO2_names - all RO2 (non-HOM) names
+	# self - reference to PyCHAM
+	# ---------------------------------------------------------------------------------------------------
+
+	# store the names of RO2 species which are present in the equation file
+	# get a list of INDICES of RO2 that present in the equation file 
+	# (or total species dict)
+	# empty list for RO2_indices
+	RO2_indices0 = []
+	self.RO2_indices = []
+
+	for name in RO2_names:
+
+		if (name in self.comp_namelist):
+			# get the RO2 index
+			index0 = RO2_names.index(name)
+			RO2_indices0.append(index0)
+			# get the self.comp_namelist index for this RO2 species
+			index1 = self.comp_namelist.index(name)
+			self.RO2_indices.append(index1)
+
+	# ensure elements in RO2_indices are integer (iterable)
+	RO2_indices0 = (np.asarray(RO2_indices0, dtype=int)).reshape(-1, 1)
+	self.RO2_indices = (np.asarray(self.RO2_indices, dtype=int)).reshape(-1, 1)
+	self.RO2_indices = np.hstack((RO2_indices0, self.RO2_indices))
+
+	return(self)
+
+def HOMRO2_indices(self):
+
+	# inputs: -----------------------------------------------------------------------------------------
+	# self.comp_namelist - all chemical scheme names
+	# ---------------------------------------------------------------------------------------------------
+
+	# store the names of HOMRO2 species which are present in the equation file
+	# get a list of INDICES of RO2 that present in the equation file 
+	# (or total species dict)
+	# empty list for HOMRO2 indices
+	self.HOMRO2_indices = []
+
+	cin = 0 # count on components
+	for name in self.comp_namelist: # loop through names of all components
+
+		if ('API_' in name) or ('api_' in name):
+			if ('RO2 in name'):
+				# store the HOMRO2 index
+				self.HOMRO2_indices.append(cin)
+
+		cin += 1 # count on components
+	# ensure elements in HOMRO2_indices are integer (iterable)
+	self.HOMRO2_indices = (np.asarray(self.HOMRO2_indices, dtype=int)).reshape(-1, 1)
+
+	return(self)
diff --git a/PyCHAM/__init__.py b/PyCHAM/__init__.py
@@ -1,6 +1,6 @@
 ##########################################################################################
 #                                                                                        											 #
-#    Copyright (C) 2018-2023 Simon O'Meara : simon.omeara@manchester.ac.uk                  				 #
+#    Copyright (C) 2018-2022 Simon O'Meara : simon.omeara@manchester.ac.uk                  				 #
 #                                                                                       											 #
 #    All Rights Reserved.                                                                									 #
 #    This file is part of PyCHAM                                                         									 #

diff --git a/PyCHAM/__main__.py b/PyCHAM/__main__.py
@@ -1,6 +1,6 @@
 ##########################################################################################
 #                                                                                        											 #
-#    Copyright (C) 2018-2023 Simon O'Meara : simon.omeara@manchester.ac.uk                  				 #
+#    Copyright (C) 2018-2022 Simon O'Meara : simon.omeara@manchester.ac.uk                  				 #
 #                                                                                       											 #
 #    All Rights Reserved.                                                                									 #
 #    This file is part of PyCHAM                                                         									 #

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