Model Parameters

Temperature and Pressure Example

The two main parameters are temperature (T (K)) and pressure (num_density (molecules/cm³)). We can explore what happens when we change them:

using GasChem, EarthSciMLBase
using DifferentialEquations, ModelingToolkit
using DynamicQuantities, Plots
using ModelingToolkit: t

tspan = (0.0, 60.0*60*24*4) # 4 day simulation

# Run a simulation with constant temperature and pressure.
sys = structural_simplify(GEOSChemGasPhase())
vals = ModelingToolkit.get_defaults(sys)
for k in setdiff(unknowns(sys), keys(vals))
    vals[k] = 0 # Set variables with no default to zero.
end
prob = ODEProblem(sys, vals, tspan, vals)
sol1 = solve(prob, AutoTsit5(Rosenbrock23()))

# Now, convert parameters to variables so we can change them over time.
sys2 = param_to_var(GEOSChemGasPhase(), :T, :num_density)

# Vary temperature and pressure over time.
@unpack T, num_density = sys2
@constants T_0 = 300 [unit=u"K"]
@constants t_0 = 1 [unit=u"s"]
eqs = [
    T ~ T_0 + T_0 / 1.5 * sin(2π*t/t_0/(60*60*24)),
    num_density ~ 2.7e19 - 2.5e19*t/t_0/(60*60*24*4)
]
sys2 = extend(sys2, ODESystem(eqs, t; name = :var_T))

# Run the simulation again.
sys2 = structural_simplify(sys2)
vals = ModelingToolkit.get_defaults(sys2)
for k in setdiff(unknowns(sys2), keys(vals))
    vals[k] = 0 # Set variables with no default to zero.
end
prob = ODEProblem(sys2, vals, tspan, vals)
sol2 = solve(prob, AutoTsit5(Rosenbrock23()))

# Plot the results
p1 = plot(sol1.t, sol1[sys2.O3], xticks = :none, label = "Constant T and P",
    ylabel = "Concentration (ppb)")
plot!(p1, sol2.t, sol2[sys2.O3], label = "Varying T and P")

p2 = plot(sol2.t, sol2[sys2.T], label = "T (K)", xticks = :none)
p3 = plot(
    sol2.t, sol2[sys2.num_density], label = "num_density (molec/cm³)", xlabel = "Time (s)")

plot(p1, p2, p3, layout = grid(3, 1, heights = [0.7, 0.15, 0.15]))

Model Parameter Information

Here is a list of all of the model parameters:

using GasChem, DataFrames, EarthSciMLBase, ModelingToolkit, DynamicQuantities
@variables t [unit = u"s", description = "Time"]
gc = structural_simplify(GEOSChemGasPhase())
vars = parameters(gc)
DataFrame(
    :Name => [string(Symbolics.tosymbol(v, escape = false)) for v in vars],
    :Units => [ModelingToolkit.get_unit(v) for v in vars],
    :Description => [ModelingToolkit.getdescription(v) for v in vars],
    :Default => [ModelingToolkit.getdefault(v) for v in vars])

171×4 DataFrame

Row	Name	Units	Description	Default
	String	Quantity…	String	Real
1	j_104	1.0 s⁻¹	Photolysis rate constant	0
2	j_135	1.0 s⁻¹	Photolysis rate constant	0
3	j_80	1.0 s⁻¹	Photolysis rate constant	0
4	j_87	1.0 s⁻¹	Photolysis rate constant	0
5	j_74	1.0 s⁻¹	Photolysis rate constant	0
6	j_2	1.0 s⁻¹	Photolysis rate constant	0
7	j_64	1.0 s⁻¹	Photolysis rate constant	0
8	k_cld6	1.0 s⁻¹	HMS rate constant	0
9	j_105	1.0 s⁻¹	Photolysis rate constant	0
10	j_154	1.0 s⁻¹	Photolysis rate constant	0
11	j_103	1.0 s⁻¹	Photolysis rate constant	0
12	j_21	1.0 s⁻¹	Photolysis rate constant	0
13	j_44	1.0 s⁻¹	Photolysis rate constant	0
14	j_56	1.0 s⁻¹	Photolysis rate constant	0
15	j_34	1.0 s⁻¹	Photolysis rate constant	0
16	j_112	1.0 s⁻¹	Photolysis rate constant	0
17	j_146	1.0 s⁻¹	Photolysis rate constant	0
18	j_26	1.0 s⁻¹	Photolysis rate constant	0
19	j_37	1.0 s⁻¹	Photolysis rate constant	0
20	j_117	1.0 s⁻¹	Photolysis rate constant	0
21	j_39	1.0 s⁻¹	Photolysis rate constant	0
22	k_mt1	1.0 s⁻¹	Atmospheric molecular density (i.e. pressure)	0
23	j_147	1.0 s⁻¹	Photolysis rate constant	0
24	j_120	1.0 s⁻¹	Photolysis rate constant	0
25	j_11	1.0 s⁻¹	Photolysis rate constant	0
26	j_49	1.0 s⁻¹	Photolysis rate constant	0
27	j_158	1.0 s⁻¹	Photolysis rate constant	0
28	j_141	1.0 s⁻¹	Photolysis rate constant	0
29	j_25	1.0 s⁻¹	Photolysis rate constant	0
30	j_124	1.0 s⁻¹	Photolysis rate constant	0
31	j_46	1.0 s⁻¹	Photolysis rate constant	0
32	k_cld4	1.0 s⁻¹	HMS rate constant	0
33	j_82	1.0 s⁻¹	Photolysis rate constant	0
34	j_47	1.0 s⁻¹	Photolysis rate constant	0
35	j_108	1.0 s⁻¹	Photolysis rate constant	0
36	j_81	1.0 s⁻¹	Photolysis rate constant	0
37	j_30	1.0 s⁻¹	Photolysis rate constant	0
38	j_36	1.0 s⁻¹	Photolysis rate constant	0
39	k_mt2	1.0 s⁻¹	Seasalt rate constant	0
40	j_33	1.0 s⁻¹	Photolysis rate constant	0
41	j_41	1.0 s⁻¹	Photolysis rate constant	0
42	j_17	1.0 s⁻¹	Photolysis rate constant	0
43	j_156	1.0 s⁻¹	Photolysis rate constant	0
44	j_100	1.0 s⁻¹	Photolysis rate constant	0
45	j_132	1.0 s⁻¹	Photolysis rate constant	0
46	j_99	1.0 s⁻¹	Photolysis rate constant	0
47	j_106	1.0 s⁻¹	Photolysis rate constant	0
48	j_42	1.0 s⁻¹	Photolysis rate constant	0
49	j_13	1.0 s⁻¹	Photolysis rate constant	0
50	j_9	1.0 s⁻¹	Photolysis rate constant	0
51	j_66	1.0 s⁻¹	Photolysis rate constant	0
52	j_121	1.0 s⁻¹	Photolysis rate constant	0
53	j_144	1.0 s⁻¹	Photolysis rate constant	0
54	j_77	1.0 s⁻¹	Photolysis rate constant	0
55	j_28	1.0 s⁻¹	Photolysis rate constant	0
56	j_92	1.0 s⁻¹	Photolysis rate constant	0
57	j_10	1.0 s⁻¹	Photolysis rate constant	0
58	j_7	1.0 s⁻¹	Photolysis rate constant	0
59	j_54	1.0 s⁻¹	Photolysis rate constant	0
60	k_mt5	1.0 s⁻¹	Seasalt rate constant	0
61	j_91	1.0 s⁻¹	Photolysis rate constant	0
62	k_cld2	1.0 s⁻¹	Cloud rate constant	0
63	j_71	1.0 s⁻¹	Photolysis rate constant	0
64	j_16	1.0 s⁻¹	Photolysis rate constant	0
65	j_86	1.0 s⁻¹	Photolysis rate constant	0
66	j_40	1.0 s⁻¹	Photolysis rate constant	0
67	j_22	1.0 s⁻¹	Photolysis rate constant	0
68	j_29	1.0 s⁻¹	Photolysis rate constant	0
69	j_6	1.0 s⁻¹	Photolysis rate constant	0
70	j_98	1.0 s⁻¹	Photolysis rate constant	0
71	j_45	1.0 s⁻¹	Photolysis rate constant	0
72	j_95	1.0 s⁻¹	Photolysis rate constant	0
73	j_123	1.0 s⁻¹	Photolysis rate constant	0
74	j_129	1.0 s⁻¹	Photolysis rate constant	0
75	j_63	1.0 s⁻¹	Photolysis rate constant	0
76	j_43	1.0 s⁻¹	Photolysis rate constant	0
77	j_55	1.0 s⁻¹	Photolysis rate constant	0
78	j_119	1.0 s⁻¹	Photolysis rate constant	0
79	j_131	1.0 s⁻¹	Photolysis rate constant	0
80	j_164	1.0 s⁻¹	Photolysis rate constant	0
81	j_94	1.0 s⁻¹	Photolysis rate constant	0
82	j_150	1.0 s⁻¹	Photolysis rate constant	0
83	j_137	1.0 s⁻¹	Photolysis rate constant	0
84	j_125	1.0 s⁻¹	Photolysis rate constant	0
85	j_148	1.0 s⁻¹	Photolysis rate constant	0
86	j_110	1.0 s⁻¹	Photolysis rate constant	0
87	j_20	1.0 s⁻¹	Photolysis rate constant	0
88	j_111	1.0 s⁻¹	Photolysis rate constant	0
89	j_51	1.0 s⁻¹	Photolysis rate constant	0
90	j_1	1.0 s⁻¹	Photolysis rate constant	0
91	j_69	1.0 s⁻¹	Photolysis rate constant	0
92	j_70	1.0 s⁻¹	Photolysis rate constant	0
93	j_89	1.0 s⁻¹	Photolysis rate constant	0
94	j_59	1.0 s⁻¹	Photolysis rate constant	0
95	j_155	1.0 s⁻¹	Photolysis rate constant	0
96	j_18	1.0 s⁻¹	Photolysis rate constant	0
97	j_160	1.0 s⁻¹	Photolysis rate constant	0
98	j_138	1.0 s⁻¹	Photolysis rate constant	0
99	j_62	1.0 s⁻¹	Photolysis rate constant	0
100	j_79	1.0 s⁻¹	Photolysis rate constant	0
101	j_88	1.0 s⁻¹	Photolysis rate constant	0
102	j_143	1.0 s⁻¹	Photolysis rate constant	0
103	j_149	1.0 s⁻¹	Photolysis rate constant	0
104	j_48	1.0 s⁻¹	Photolysis rate constant	0
105	j_130	1.0 s⁻¹	Photolysis rate constant	0
106	j_65	1.0 s⁻¹	Photolysis rate constant	0
107	j_75	1.0 s⁻¹	Photolysis rate constant	0
108	j_153	1.0 s⁻¹	Photolysis rate constant	0
109	j_14	1.0 s⁻¹	Photolysis rate constant	0
110	k_cld3	1.0 s⁻¹	Cloud rate constant	0
111	j_23	1.0 s⁻¹	Photolysis rate constant	0
112	j_136	1.0 s⁻¹	Photolysis rate constant	0
113	j_157	1.0 s⁻¹	Photolysis rate constant	0
114	j_145	1.0 s⁻¹	Photolysis rate constant	0
115	j_68	1.0 s⁻¹	Photolysis rate constant	0
116	k_mt3	1.0 s⁻¹	Seasalt rate constant	0
117	j_15	1.0 s⁻¹	Photolysis rate constant	0
118	j_113	1.0 s⁻¹	Photolysis rate constant	0
119	k_mt6	1.0 s⁻¹	Seasalt rate constant	0
120	j_118	1.0 s⁻¹	Photolysis rate constant	0
121	j_152	1.0 s⁻¹	Photolysis rate constant	0
122	j_12	1.0 s⁻¹	Photolysis rate constant	0
123	j_128	1.0 s⁻¹	Photolysis rate constant	0
124	j_114	1.0 s⁻¹	Photolysis rate constant	0
125	k_cld5	1.0 s⁻¹	HMS rate constant	0
126	j_126	1.0 s⁻¹	Photolysis rate constant	0
127	j_107	1.0 s⁻¹	Photolysis rate constant	0
128	j_96	1.0 s⁻¹	Photolysis rate constant	0
129	j_19	1.0 s⁻¹	Photolysis rate constant	0
130	j_85	1.0 s⁻¹	Photolysis rate constant	0
131	j_8	1.0 s⁻¹	Photolysis rate constant	0
132	j_165	1.0 s⁻¹	Photolysis rate constant	0
133	k_cld1	1.0 s⁻¹	Cloud rate constant	0
134	j_3	1.0 s⁻¹	Photolysis rate constant	0
135	j_76	1.0 s⁻¹	Photolysis rate constant	0
136	j_27	1.0 s⁻¹	Photolysis rate constant	0
137	j_38	1.0 s⁻¹	Photolysis rate constant	0
138	j_83	1.0 s⁻¹	Photolysis rate constant	0
139	j_162	1.0 s⁻¹	Photolysis rate constant	0
140	num_density	1.0	Number density of air (The units should be molecules/cm^3 but the equations here treat it as unitless).	2.7e19
141	j_127	1.0 s⁻¹	Photolysis rate constant	0
142	T	1.0 K	Temperature	298.15
143	k_mt4	1.0 s⁻¹	Seasalt rate constant	0
144	j_84	1.0 s⁻¹	Photolysis rate constant	0
145	j_161	1.0 s⁻¹	Photolysis rate constant	0
146	j_73	1.0 s⁻¹	Photolysis rate constant	0
147	j_97	1.0 s⁻¹	Photolysis rate constant	0
148	j_50	1.0 s⁻¹	Photolysis rate constant	0
149	j_61	1.0 s⁻¹	Photolysis rate constant	0
150	j_109	1.0 s⁻¹	Photolysis rate constant	0
151	j_140	1.0 s⁻¹	Photolysis rate constant	0
152	j_93	1.0 s⁻¹	Photolysis rate constant	0
153	j_122	1.0 s⁻¹	Photolysis rate constant	0
154	j_78	1.0 s⁻¹	Photolysis rate constant	0
155	j_159	1.0 s⁻¹	Photolysis rate constant	0
156	j_31	1.0 s⁻¹	Photolysis rate constant	0
157	j_115	1.0 s⁻¹	Photolysis rate constant	0
158	j_139	1.0 s⁻¹	Photolysis rate constant	0
159	j_163	1.0 s⁻¹	Photolysis rate constant	0
160	j_72	1.0 s⁻¹	Photolysis rate constant	0
161	j_116	1.0 s⁻¹	Photolysis rate constant	0
162	j_134	1.0 s⁻¹	Photolysis rate constant	0
163	j_90	1.0 s⁻¹	Photolysis rate constant	0
164	j_151	1.0 s⁻¹	Photolysis rate constant	0
165	j_133	1.0 s⁻¹	Photolysis rate constant	0
166	j_53	1.0 s⁻¹	Photolysis rate constant	0
167	j_24	1.0 s⁻¹	Photolysis rate constant	0
168	j_101	1.0 s⁻¹	Photolysis rate constant	0
169	j_142	1.0 s⁻¹	Photolysis rate constant	0
170	j_166	1.0 s⁻¹	Photolysis rate constant	0
171	j_32	1.0 s⁻¹	Photolysis rate constant	0