Tropospheric-Chemistry

The five SuperFast rate-law helper functions migrated from GasChem.jl@8c12c048482b515fb8eb2110bf8ab4b4f4e71309 src/SuperFast.jl — the reusable builder functions the SuperFast() chemical mechanism uses to construct the rate coefficient of every gas-phase reaction. Each is migrated as its own observed-only algebraic `models` entry: rate_toppb (SuperFast.jl:6) the constant-rate / `constant_k` converter, arrh (:33) the modified-Arrhenius workhorse, arr_3rd (:64) the third-body / Troe-falloff law, rate_2HO2 (:102) the HO2+HO2 law with water-vapour enhancement, and rate_OH_CO (:142) the JPL 15-10 OH+CO law. Upstream each function returns a one-variable ReactionSystem (`@variables k(t)`); the composed builders (arr_3rd, rate_2HO2, rate_OH_CO) compose `arrh` sub-systems. This file reproduces each function's compiled rate as a topologically-ordered cascade of `type: state` algebraic equations whose named intermediates mirror the upstream Julia locals and sub-system k's verbatim, with the Arrhenius coefficients exposed as `type: parameter` (defaults taken from the representative SuperFast reaction each builder serves). All five models are purely algebraic — no time derivatives — so each rate coefficient is constant in time. Units follow the upstream's mixed CGS / ppb system (rate coefficients in 1/(s*ppb), Arrhenius pre-exponentials in cm^3/molec/s).

The five SuperFast rate-law helper functions migrated from GasChem.jl@8c12c048482b515fb8eb2110bf8ab4b4f4e71309 src/SuperFast.jl — the reusable builder functions the SuperFast() chemical mechanism uses to construct the rate coefficient of every gas-phase reaction. Each is migrated as its own observed-only algebraic `models` entry: rate_toppb (SuperFast.jl:6) the constant-rate / `constant_k` converter, arrh (:33) the modified-Arrhenius workhorse, arr_3rd (:64) the third-body / Troe-falloff law, rate_2HO2 (:102) the HO2+HO2 law with water-vapour enhancement, and rate_OH_CO (:142) the JPL 15-10 OH+CO law. Upstream each function returns a one-variable ReactionSystem (`@variables k(t)`); the composed builders (arr_3rd, rate_2HO2, rate_OH_CO) compose `arrh` sub-systems. This file reproduces each function's compiled rate as a topologically-ordered cascade of `type: state` algebraic equations whose named intermediates mirror the upstream Julia locals and sub-system k's verbatim, with the Arrhenius coefficients exposed as `type: parameter` (defaults taken from the representative SuperFast reaction each builder serves). All five models are purely algebraic — no time derivatives — so each rate coefficient is constant in time. Units follow the upstream's mixed CGS / ppb system (rate coefficients in 1/(s*ppb), Arrhenius pre-exponentials in cm^3/molec/s).

CO oxidation chemistry diagnostics from Seinfeld & Pandis (2006) Ch. 6 §6.3 Eqs. 6.9-6.18, pp. 212-219. CO oxidation is the simplest hydrocarbon-oxidation mechanism and illustrates the catalytic HOx cycling that drives tropospheric ozone production (net: CO + 2O₂ + hν → CO₂ + O₃, with OH regenerated through HO₂ + NO). This observed-only algebraic component implements six diagnostic relations: the OH loss rate L_OH (to CO, NO₂, O₃), the HO₂ loss rate L_HO2 (to NO, the HO₂ self-reaction, and O₃), the HOx radical-termination loss rate L_HOx (OH+NO₂→HNO₃ plus the HO₂ self-reaction), the high-NOx HO₂ steady-state concentration HO2_ss (Eq. 6.18), the net ozone production rate P_O3 (HO₂+NO production minus the OH+O₃ and HO₂+O₃ loss channels), and the HOx chain length (propagation rate over termination rate — the number of OH-HO₂ cycles before radical termination). Observed-only algebraic system (no time derivatives): twelve variables (six inputs CO/OH/HO₂/NO/NO₂/O₃ encoded as parameters, six outputs L_OH/L_HO2/L_HOx/HO2_ss/P_O3/chain_length as state), six rate-constant parameters (k_CO_OH, k_HO2_NO, k_HO2_HO2, k_OH_NO2, k_HO2_O3, k_OH_O3), one dimensionless stoichiometric constant (two), and six algebraic equations. Migrated from GasChem.jl@8c12c048 src/co_oxidation.jl:88 (`COOxidation` @component).

Methane oxidation reaction-rate diagnostics from Seinfeld & Pandis (2006) Ch. 6 §6.4, Table 6.1, pp. 219-227. Methane oxidation is the archetypal VOC oxidation mechanism in the troposphere, proceeding CH₄ → CH₃O₂ → CH₃O → HCHO → HCO → CO → CO₂. This observed-only algebraic component computes the 17 individual reaction rates R1-R17 of the complete Table 6.1 mechanism (10 bimolecular, 3 termolecular, 4 photolysis reactions) plus three diagnostic aggregates: the gross ozone production rate P_O3_gross = R15 + R3 (the two peroxy-radical + NO channels), the formaldehyde production rate P_HCHO = R6 + R8, and the methane loss rate L_CH4 = R1. Each reaction rate is the product of a 298 K rate constant and the reactant concentrations (R = k·[A]·[B] bimolecular, k·[M]·[A]·[B] termolecular, j·[A] photolysis). The fate of the methylperoxy radical CH₃O₂ — the O₃-producing NO channel R3 versus the chain-terminating HO₂ channel R4 — sets the ozone yield per CH₄ oxidized and is the central NOx-regime diagnostic of the mechanism. Purely algebraic (no time derivatives): 52 variables (15 input species and 17 rate constants encoded as parameters, 20 output diagnostics as state) and 20 equations. Migrated from GasChem.jl@8c12c048 src/methane_oxidation.jl:77 (`MethaneOxidation` @component).

Full time-resolved ODE system for the methane oxidation mechanism in the polluted-continental troposphere (Seinfeld & Pandis 2006 Ch. 6 §6.4 Table 6.1, pp. 219-227). Eighteen-state stiff ODE on the methane oxidation chain CH₄ → CH₃ → CH₃O₂ → CH₃O → HCHO → HCO → CO → (CO₂) plus the supporting NOx/HOx radical chemistry that recycles OH and converts NO ↔ NO₂. The reaction network has 22 reactions: the 17 canonical Table 6.1 reactions covering the Cl-skeleton oxidation chain through HCHO and ozone-formation chemistry via the peroxy + NO channels, plus 5 auxiliary reactions (CO + OH, OH + NO₂ → HNO₃ termination, HO₂ + HO₂ → H₂O₂ termination, NO + O₃ titration, and a zero-order external OH source representing primary OH production from O(¹D) + H₂O that is implicit in the upstream model). Eight termolecular reactions (R2, R6, R13, R14, R17) and the bimolecular cross-reactions have their O₂ and M dependence folded into effective rate constants k6_eff, k13_eff and the explicit k2_0·M·O₂, k14_0·M·O₂, k17_0·M·O₂ products with M_fixed, O2_fixed parameters at fixed STP-tropospheric values (M = 2.5e25 m⁻³, O₂ = 5.25e24 m⁻³). Migrated from GasChem.jl@8c12c048 src/methane_oxidation.jl:213 (`MethaneOxidationODE` @component / @network_component → Catalyst.ode_model). The reaction-network DSL form upstream is converted to explicit ODE equations here because the migration tracker classifies this as `Model` with `variables, parameters, equations` features (not a ReactionSystem-shaped migration — those go to a separate path; see sibling superfast.esm).

Combined atmospheric lifetime from parallel removal pathways — Seinfeld & Pandis (2006) Ch. 2 (Atmospheric Trace Constituents), Eqs. 2.7-2.9. When a trace species is removed by two independent first-order processes acting simultaneously (rate constants k_1 and k_2), the removal rates add: the inverse lifetimes (1/τ) sum while the lifetimes themselves combine harmonically. This observed-only algebraic component implements four relations: the two individual pathway lifetimes tau_1 = 1/k_1 and tau_2 = 1/k_2 (Eq. 2.6 applied per pathway), the summed inverse lifetime inverse_tau = k_1 + k_2 = 1/tau_1 + 1/tau_2 (Eqs. 2.7-2.8), and the combined lifetime tau_combined = (tau_1·tau_2)/(tau_1+tau_2) = 1/(k_1+k_2) (Eq. 2.9). The combined lifetime is always shorter than either individual pathway lifetime, and the faster (shorter-lifetime) pathway dominates: a fast removal process sets the overall atmospheric lifetime even when a slow pathway is also present; when the two pathways are equal the combined lifetime is exactly half of either. Observed-only algebraic system (no time derivatives): four state variables (tau_1, tau_2, tau_combined in s; inverse_tau in s⁻¹) computed from two rate-constant parameters (k_1, k_2 in s⁻¹) by four algebraic equations. Migrated from GasChem.jl@280ee50f src/AtmosphericLifetime.jl:204 (`MultipleRemovalLifetime` @component).

Tropospheric OH radical production from O₃ photolysis — Seinfeld & Pandis (2006) Ch. 6 §6.1 Eqs. 6.1, 6.3, 6.4, pp. 204-207. The dominant source of OH in the troposphere is O₃ photolysis below 320 nm producing electronically excited O(¹D), which either reacts with H₂O to yield two OH radicals or is collisionally quenched back to ground-state O(³P) by N₂/O₂. Implements three algebraic relations: (Eq. 6.1) O(¹D) steady-state concentration [O(¹D)] = j_O₃·[O₃] / (k₃[M] + k₄[H₂O]), (Eq. 6.4) OH yield ε_OH = 2·k₄[H₂O] / (k₃[M] + k₄[H₂O]) as the fraction of O(¹D) producing OH (the factor of 2 accounts for the 2 OH produced per O(¹D)+H₂O encounter — ε_OH ranges 0..2), (Eq. 6.3) OH production rate P_OH = j_O₃·[O₃]·ε_OH. The effective quenching rate k₃_eff = f_N₂·k₃,N₂ + f_O₂·k₃,O₂ is the air-composition-weighted average of the N₂ and O₂ quenching channels. Observed-only algebraic system (no time derivatives): six variables (three inputs O₃/H₂O/M as parameters, three outputs O₁D/ε_OH/P_OH as state) plus six rate-parameter inputs (j_O₃, k₃_N₂, k₃_O₂, k₄, f_N₂, f_O₂) and one stoichiometric constant (two=2). Migrated from GasChem.jl@8c12c048 src/oh_production.jl:88 (`OHProduction` @component).

Atmospheric lifetime against reaction with the hydroxyl radical (OH), from Seinfeld & Pandis (2006) Atmospheric Chemistry and Physics Ch. 2, Eq. 2.12: tau = 1/(k_OH*[OH]). OH is the dominant daytime oxidant of the troposphere, so the OH-reaction lifetime sets how long most reactive trace gases — methane, carbon monoxide, non-methane VOCs — persist in the atmosphere. This observed-only algebraic component implements two relations: an effective pseudo-first-order loss rate constant k_eff = k_OH*OH_conc (the second-order reaction X + OH collapsed onto the approximately constant ambient OH), and the lifetime tau_OH = 1/k_eff. The lifetime is jointly controlled by the species' intrinsic reactivity (k_OH, spanning four-plus decades across tropospheric trace gases) and the ambient oxidising capacity ([OH], varying with season, latitude and pollution): a species may persist for years in clean remote air and only hours in a polluted daytime plume. Purely algebraic system (no time derivatives): four variables — one parameter k_OH, one input OH_conc encoded as a parameter, two outputs k_eff and tau_OH as state — and two equations. Migrated from GasChem.jl@280ee50f src/AtmosphericLifetime.jl:264 (`OHReactionLifetime` @component).

Ozone Production Efficiency (OPE) diagnostic from Seinfeld & Pandis (2006) Ch. 6 §6.3 Eqs. 6.21-6.24, pp. 212-219. OPE = Δ[O₃]/Δ[NOx] is the number of ozone molecules produced per molecule of NOx consumed — a central diagnostic for the NOx-VOC-O₃ regime structure of tropospheric photochemistry. This observed-only algebraic component implements three relations: gross ozone production rate P_O3 = k_HO2_NO·[HO₂]·[NO] + k_RO2_NO·[RO₂]·[NO] (the two peroxy-radical + NO channels — each peroxy+NO reaction makes an NO₂ whose photolysis yields an O₃), NOx loss rate L_NOx = k_OH_NO2·[OH]·[NO₂] (the OH + NO₂ + M → HNO₃ termination, the dominant daytime NOx sink), and OPE = P_O3 / L_NOx. High OPE (low-NOx, NOx-limited regime) means each NOx molecule cycles through many O₃-producing reactions before it is lost as nitric acid; low OPE (high-NOx, VOC-limited regime) means NOx is removed before it can drive much O₃ production. Observed-only algebraic system (no time derivatives): eight variables (five inputs OH/HO₂/RO₂/NO/NO₂ encoded as parameters, three outputs P_O3/L_NOx/OPE as state) plus three rate-constant parameters (k_HO2_NO, k_RO2_NO, k_OH_NO2) and three algebraic equations. Migrated from GasChem.jl@280ee50f src/co_oxidation.jl:183 (`OzoneProductionEfficiency` @component).

Photostationary-state diagnostic for the NO-NO₂-O₃ Leighton cycle — Seinfeld & Pandis (2006) Ch. 6 §6.2, Eqs. 6.6-6.7, pp. 207-212. Computes the photostationary-state parameter Φ = j_NO2·[NO₂] / (k_NO+O₃·[NO]·[O₃]) and its deviation from unity Φ_deviation = Φ - 1. Φ = 1 is the exact Leighton photostationary state (pure NO-NO₂-O₃ cycling, zero net ozone production); Φ > 1 indicates additional oxidants (peroxy radicals HO₂/RO₂ converting NO→NO₂ and producing ozone), Φ < 1 indicates net ozone loss. This observed-only algebraic component is the simplified companion to NOxPhotochemistry (the full Eqs. 6.5-6.8 diagnostic): five variables (three inputs NO/NO₂/O₃ encoded as parameters, two outputs Φ/Φ_deviation as state), two rate parameters (j_NO2, k_NO_O3) plus the dimensionless unity constant `one`, and two algebraic equations. No time derivatives. Migrated from GasChem.jl@8c12c048 src/nox_photochemistry.jl:145 (`PhotostationaryState` @component).

The five SuperFast rate-law helper functions migrated from GasChem.jl@8c12c048482b515fb8eb2110bf8ab4b4f4e71309 src/SuperFast.jl — the reusable builder functions the SuperFast() chemical mechanism uses to construct the rate coefficient of every gas-phase reaction. Each is migrated as its own observed-only algebraic `models` entry: rate_toppb (SuperFast.jl:6) the constant-rate / `constant_k` converter, arrh (:33) the modified-Arrhenius workhorse, arr_3rd (:64) the third-body / Troe-falloff law, rate_2HO2 (:102) the HO2+HO2 law with water-vapour enhancement, and rate_OH_CO (:142) the JPL 15-10 OH+CO law. Upstream each function returns a one-variable ReactionSystem (`@variables k(t)`); the composed builders (arr_3rd, rate_2HO2, rate_OH_CO) compose `arrh` sub-systems. This file reproduces each function's compiled rate as a topologically-ordered cascade of `type: state` algebraic equations whose named intermediates mirror the upstream Julia locals and sub-system k's verbatim, with the Arrhenius coefficients exposed as `type: parameter` (defaults taken from the representative SuperFast reaction each builder serves). All five models are purely algebraic — no time derivatives — so each rate coefficient is constant in time. Units follow the upstream's mixed CGS / ppb system (rate coefficients in 1/(s*ppb), Arrhenius pre-exponentials in cm^3/molec/s).

The five SuperFast rate-law helper functions migrated from GasChem.jl@8c12c048482b515fb8eb2110bf8ab4b4f4e71309 src/SuperFast.jl — the reusable builder functions the SuperFast() chemical mechanism uses to construct the rate coefficient of every gas-phase reaction. Each is migrated as its own observed-only algebraic `models` entry: rate_toppb (SuperFast.jl:6) the constant-rate / `constant_k` converter, arrh (:33) the modified-Arrhenius workhorse, arr_3rd (:64) the third-body / Troe-falloff law, rate_2HO2 (:102) the HO2+HO2 law with water-vapour enhancement, and rate_OH_CO (:142) the JPL 15-10 OH+CO law. Upstream each function returns a one-variable ReactionSystem (`@variables k(t)`); the composed builders (arr_3rd, rate_2HO2, rate_OH_CO) compose `arrh` sub-systems. This file reproduces each function's compiled rate as a topologically-ordered cascade of `type: state` algebraic equations whose named intermediates mirror the upstream Julia locals and sub-system k's verbatim, with the Arrhenius coefficients exposed as `type: parameter` (defaults taken from the representative SuperFast reaction each builder serves). All five models are purely algebraic — no time derivatives — so each rate coefficient is constant in time. Units follow the upstream's mixed CGS / ppb system (rate coefficients in 1/(s*ppb), Arrhenius pre-exponentials in cm^3/molec/s).

The five SuperFast rate-law helper functions migrated from GasChem.jl@8c12c048482b515fb8eb2110bf8ab4b4f4e71309 src/SuperFast.jl — the reusable builder functions the SuperFast() chemical mechanism uses to construct the rate coefficient of every gas-phase reaction. Each is migrated as its own observed-only algebraic `models` entry: rate_toppb (SuperFast.jl:6) the constant-rate / `constant_k` converter, arrh (:33) the modified-Arrhenius workhorse, arr_3rd (:64) the third-body / Troe-falloff law, rate_2HO2 (:102) the HO2+HO2 law with water-vapour enhancement, and rate_OH_CO (:142) the JPL 15-10 OH+CO law. Upstream each function returns a one-variable ReactionSystem (`@variables k(t)`); the composed builders (arr_3rd, rate_2HO2, rate_OH_CO) compose `arrh` sub-systems. This file reproduces each function's compiled rate as a topologically-ordered cascade of `type: state` algebraic equations whose named intermediates mirror the upstream Julia locals and sub-system k's verbatim, with the Arrhenius coefficients exposed as `type: parameter` (defaults taken from the representative SuperFast reaction each builder serves). All five models are purely algebraic — no time derivatives — so each rate coefficient is constant in time. Units follow the upstream's mixed CGS / ppb system (rate coefficients in 1/(s*ppb), Arrhenius pre-exponentials in cm^3/molec/s).

Parameters-preset model representing typical remote/background tropospheric conditions with low NOx. Migrated from GasChem.jl@8c12c048 src/combined_system.jl:261 (`RemoteConditions` @component). Eleven species concentrations are declared as parameters in SI units (m⁻³); the model exposes them as algebraic outputs (`*_out`) so a parent system or test harness can read presets without depending on MTK parameter-introspection APIs. Based on Seinfeld & Pandis Chapter 6 background conditions: ~30 ppb O₃, ~10 ppt NO, ~20 ppt NO₂, ~80 ppb CO.