version: "1.0.0"
name: Chapman-NOx
# Based on the canonical MICM Chapman config:
#   ~/EarthSystem/MUSICA/configs/v1/chapman/config.yaml
# with three NOx reactions added on top.
#
# ARRHENIUS rate form (MICM v1):
#   k = A * (T/D)^B * exp(C/T) * (1 + E*P)
# Every reaction must provide D (reference T in K) and E (pressure
# coefficient in 1/Pa) or the defaults bite you — leaving D unset
# silently makes (T/D)^B very wrong for stratospheric T.
#
# Rate constants in SI (mol/m^3 basis). cgs values in comments.

species:
  - name: M
    is third body: true
    __description: Third-body molecule.
  - name: O2
    # Do not mark as CONSTANT tracer — the canonical MICM Chapman
    # config treats O2 as a regular species integrated by the solver.
    # MICM reads [O2] from MPAS state each step via
    # MICM_from_chemistry, so a uniform 0.2095 VMR seed is preserved.
    __molar mass: 0.032
    __long name: molecular_oxygen
    __do advect: true
    __initial concentration: 0.0
  - name: O
    __absolute tolerance: 1e-10
    __molar mass: 0.016
    __long name: atomic_oxygen_3P
    __do advect: true
    __initial concentration: 0.0
  - name: O1D
    __absolute tolerance: 1e-10
    __molar mass: 0.016
    __long name: atomic_oxygen_1D
    __do advect: true
    __initial concentration: 0.0
  - name: O3
    __absolute tolerance: 1e-10
    __molar mass: 0.048
    __long name: ozone
    __atoms: 3
    __do advect: true
    __initial concentration: 0.0
  - name: NO
    __absolute tolerance: 1e-10
    __molar mass: 0.030
    __long name: nitric_oxide
    __do advect: true
    __initial concentration: 0.0
  - name: NO2
    __absolute tolerance: 1e-10
    __molar mass: 0.046
    __long name: nitrogen_dioxide
    __do advect: true
    __initial concentration: 0.0

phases:
  - name: gas
    species:
      - M
      - O
      - O2
      - O3
      - O1D
      - NO
      - NO2

reactions:
  # ----- Chapman cycle (values copied from MUSICA/configs/v1/chapman) -----

  - type: PHOTOLYSIS
    gas phase: gas
    reactants:
      - species name: O2
    products:
      - species name: O
        coefficient: 2
    name: jO2

  - type: ARRHENIUS
    # O + O2 + M -> O3 + M    (JPL: k0 = 6.0e-34 (T/300)^-2.4, termolecular)
    gas phase: gas
    reactants:
      - species name: O
        coefficient: 1
      - species name: O2
        coefficient: 1
      - species name: M
        coefficient: 1
    products:
      - species name: O3
        coefficient: 1
      - species name: M
        coefficient: 1
    A: 217.59707599952029
    B: -2.4
    C: 0
    D: 300
    E: 0
    name: R2

  - type: PHOTOLYSIS
    gas phase: gas
    reactants:
      - species name: O3
        coefficient: 1
    products:
      - species name: O
        coefficient: 1
      - species name: O2
        coefficient: 1
    name: jO3_O

  - type: ARRHENIUS
    # O + O3 -> 2 O2    (JPL: k = 8.0e-12 exp(-2060/T))
    gas phase: gas
    reactants:
      - species name: O
        coefficient: 1
      - species name: O3
        coefficient: 1
    products:
      - species name: O2
        coefficient: 2
    A: 4817712.608
    B: 0
    C: -2059.0316582998285
    D: 300
    E: 0
    name: R4

  - type: PHOTOLYSIS
    gas phase: gas
    reactants:
      - species name: O3
        coefficient: 1
    products:
      - species name: O1D
        coefficient: 1
      - species name: O2
        coefficient: 1
    name: jO3_O1D

  - type: ARRHENIUS
    # O1D + M -> O + M    (approximate combined O1D+N2 and O1D+O2 quenching)
    gas phase: gas
    reactants:
      - species name: O1D
        coefficient: 1
      - species name: M
        coefficient: 1
    products:
      - species name: O
        coefficient: 1
      - species name: M
        coefficient: 1
    A: 14223365.93
    B: 0
    C: 90.0
    D: 300
    E: 0
    name: R6

  - type: ARRHENIUS
    # O1D + O3 -> 2 O2    (JPL: k = 1.2e-10)
    gas phase: gas
    reactants:
      - species name: O1D
        coefficient: 1
      - species name: O3
        coefficient: 1
    products:
      - species name: O2
        coefficient: 2
    A: 7.22e7
    B: 0
    C: 0
    D: 300
    E: 0
    name: R7

  # ----- NOx catalytic O3 destruction -----

  - type: ARRHENIUS
    # NO + O3 -> NO2 + O2    (JPL: k = 3.0e-12 exp(-1500/T); existing lnox_o3
    # value A=1.084e6 preserved)
    gas phase: gas
    reactants:
      - species name: NO
        coefficient: 1
      - species name: O3
        coefficient: 1
    products:
      - species name: NO2
        coefficient: 1
      - species name: O2
        coefficient: 1
    A: 1.084e6
    B: 0
    C: -1370.0
    D: 300
    E: 0
    name: R_NO_O3

  - type: ARRHENIUS
    # NO2 + O -> NO + O2    (JPL: k = 5.1e-12 exp(+210/T))
    gas phase: gas
    reactants:
      - species name: NO2
        coefficient: 1
      - species name: O
        coefficient: 1
    products:
      - species name: NO
        coefficient: 1
      - species name: O2
        coefficient: 1
    A: 3.07e6
    B: 0
    C: 210.0
    D: 300
    E: 0
    name: R_NO2_O

  - type: PHOTOLYSIS
    gas phase: gas
    reactants:
      - species name: NO2
        coefficient: 1
    products:
      - species name: NO
        coefficient: 1
      - species name: O
        coefficient: 1
    name: jNO2