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WACCM Chemistry Tutorial for Atmospheric Modeling

A tutorial outlining the chemistry preprocessor, numerical solution approach, chemical mechanisms, boundary conditions, and heterogeneous processes in the WACCM model.

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WACCM Chemistry Tutorial for Atmospheric Modeling

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  1. WACCM Chemistry Tutorial Doug Kinnison D. Marsh, S. Walters, G. Brasseur, R. Garcia, R. Roble, many more… dkin@ucar.edu 303-497-1469 8 June 2007 WACCM

  2. Tutorial Outline… Surface to 150 km (500 km) • In the Beginning… • Chemistry Preprocessor • Numerical Solution Approach • Chemical Mechanism (s) • Boundary Conditions (UB,LB) • Heterogeneous Processes • Photolysis / Heating Rates • Summary / Future Development Jarvis, “Bridging the Atmospheric Divide” Science, 293, 2218, 2001

  3. UCAR Quarterly – winter 1999 First Interactive results were show in 2003.

  4. UCAR Quarterly – winter 1999

  5. Whole Atmosphere Community Climate Model (WACCM) Model-OZone And Related chemical Tracers MOZART3 CTM Community Atmospheric Model CAM3 ACD, R. Garcia, PI WACCM CGD, B. Boville, PI TIME-GCM 0-150 km; 2.0x2.5, 66L 50-110 species HAO, R. Roble, PI Themosphere-Ionosphere-Mesosphere-Electrodynamics Processes

  6. MLT; 3-5 km Res. Need to Represent Chemical Processes at relatively fine resolution Stratosphere; 1-2 km Res. UTLS; 1 km Res. 2.8 x 2.8 Courtesy of A. Gettelman

  7. Cost of Adding Chemistry (1.9x2.5)… Courtesy of Stacy Walters

  8. Cost of Adding Chemistry… WA3/CAM = 12 WA3/GHG = 3 Courtesy of Stacy Walters

  9. Tutorial Outline… Input File • In the Beginning… • Chemistry Preprocessor • Numerical Solution Approach • Chemical Mechanism (s) • Boundary Conditions (UB,LB, In Situ) • Heterogeneous Processes • Photolysis / Heating Rates • Summary / Future Development Preprocessor Creates files specific and necessary to the chemical simulation.

  10. InputFile for Preprocessor BEGSIM output_unit_number = 7 output_file = ions.marsh.doc procout_path = ../output/ src_path = ../bkend/ procfiles_path = ../procfiles/cam/ sim_dat_path = ../output/ sim_dat_filename = ions.marsh.dat COMMENTS "This is a waccm2 simulation with:" "(1) The new advection routine Lin Rood" "(2) WACCM dynamical inputs" "(3) Strat, Meso, and Thermospheric mechanism" End COMMENTS SPECIES Solution O3, O, O1D -> O, O2, O2_1S -> O2, O2_1D -> O2 N2O, N, NO, NO2, NO3, HNO3, HO2NO2, N2O5 CH4, CH3O2, CH3OOH, CH2O, CO H2, H, OH, HO2, H2O2 CL -> Cl, CL2 -> Cl2, CLO -> ClO, OCLO -> OClO, CL2O2 -> Cl2O2 HCL -> HCl, HOCL -> HOCl, CLONO2 -> ClONO2, BRCL -> BrCl BR -> Br, BRO -> BrO, HBR -> HBr, HOBR -> HOBr, BRONO2 -> BrONO2 CH3CL -> CH3Cl, CH3BR -> CH3Br, CFC11 -> CFCl3, CFC12 -> CF2Cl2 CFC113 -> CCl2FCClF2, HCFC22 -> CHF2Cl, CCL4 -> CCl4, CH3CCL3 -> CH3CCl3 CF3BR -> CF3Br, CF2CLBR -> CF2ClBr, CO2, N2p -> N2, O2p -> O2 Np -> N, Op -> O, NOp -> NO, e, N2D -> N, H2O End Solution Fixed M, N2 End Fixed Solution classes Explicit CH4, N2O, CO, H2, CH3CL, CH3BR, CFC11, CFC12, CFC113 HCFC22, CCL4, CH3CCL3, CF3BR, CF2CLBR, CO2 End explicit Implicit O3, O, O1D, O2, O2_1S, O2_1D N, NO, NO2, OH, NO3, HNO3, HO2NO2, N2O5 CH3O2, CH3OOH, CH2O, H, HO2, H2O2, H2O CL, CL2, CLO, OCLO, CL2O2, HCL, HOCL, CLONO2, BRCL BR, BRO, HBR, HOBR, BRONO2, N2p, O2p, Np, Op, NOp, N2D, e End implicit End Solution classes

  11. InputFile for Preprocessor Photolysis [jo2_a] O2 + hv -> O + O1D [jo2_b] O2 + hv -> 2*O [jo3_a] O3 + hv -> O1D + O2_1D [jo3_b] O3 + hv -> O + O2 [jn2o] N2O + hv -> O1D + N2 [jno] NO + hv -> N + O [jno_i] NO + hv -> NOp + e [jno2] NO2 + hv -> NO + O [jn2o5_a] N2O5 + hv -> NO2 + NO3 [jn2o5_b] N2O5 + hv -> NO + O + NO3 . . Reactions… [cph25,cph] N2D + O2 -> NO + O1D ; 5.e-12 [cph26,cph] N2D + O -> N + O ; 4.5e-13 . NO + O + M -> NO2 + M ; 9.0e-32, 1.5, 3.0e-11, 0., 0.6 NO2 + O + M -> NO3 + M ; 2.5e-31, 1.8, 2.2e-11, .7, 0.6 NO2 + O3 -> NO3 + O2 ; 1.2e-13, -2450 [usr3] NO2 + NO3 + M -> N2O5 + M ; 2.e-30, 4.4, 1.4e-12, .7, .6 [usr3a] N2O5 + M -> NO2 + NO3 + M bimolecular reactions: Arrhenius Expression * -------------------------------------------------------------- * Sulfate aerosol reactions * -------------------------------------------------------------- [het1] N2O5 -> 2*HNO3 [het2] CLONO2 -> HOCL + HNO3 [het3] BRONO2 -> HOBR + HNO3 [het4] CLONO2 + HCL -> CL2 + HNO3 [het5] HOCL + HCL -> CL2 + H2O [het6] HOBR + HCL -> BRCL + H2O Termolecular reactions: Troe Expression

  12. Tutorial Outline… • In the Beginning… • Chemistry Preprocessor • Numerical Solution Approach • Chemical Mechanism (s) • Boundary Conditions (UB,LB, In Situ) • Heterogeneous Processes • Photolysis / Heating Rates • Summary / Future Development

  13. Numerical Approach • System of time-dependent Ordinary Differential Eq. - This system is solved via two Algorithms (1) Long-lived: Explicit Forward Euler method (e.g., N2O) t = tn+1 - tn where t= 30 minutes Sandu et al, J. Comp. Phys., 129, 101-110, 1996.

  14. Numerical Approach Cont… (2) Short-lived: Implicit Backward Euler method (e.g. OH, O3) • The algebraic system for method (2) is quadradically non-linear. • This system can be written as: (2.1) • Here G is a Ni valued, non-linear vector function, where Ni = # species • Eq. 2.1 is solved via a Newton-Raphson iteration, or… (2.2) - The iteration and solution of Eq. 2.2 is carried out with a sparse matrix solver - This process is terminated when the given solution variable change in relative terms is less than a prescribed value (typically 0.001). - If the iteration max is reached (10) before reaching this criterion, the timestep is cut in half and Eq. 2.2 is iterated again. The timestep can be reduced 5 times before a result is returned (good or bad).

  15. Tutorial Outline… • In the Beginning… • Chemistry Preprocessor • Numerical Solution Approach • Chemical Mechanism (s) • Boundary Conditions (UB,LB) • Heterogeneous Processes • Photolysis / Heating Rates • Future Development

  16. Model Chemistry - 55 Species Mechanism • Long-lived Species: (19-species) - Explicit Forward Euler • Misc: CO2, CO, CH4, H2O, N2O, H2, O2 • CFCs: CCl4, CFC-11, CFC-12, CFC-113 • HCFCs: HCFC-22 • Chlorocarbons: CH3Cl, CH3CCl3, • Bromocarbons: CH3Br • Halons: H-1211, H-1301 • Constant Species: M, N2 • Short-lived Species:(36-species) - Implicit Backward Euler* • OX: O3, O, O(1D) • NOX: N, N (2D), NO, NO2, NO3, N2O5, HNO3, HO2NO2 • ClOX: Cl, ClO, Cl2O2, OClO, HOCl, HCl, ClONO2, Cl2 • BrOX: Br, BrO, HOBr, HBr, BrCl, BrONO2 • HOX: H, OH, HO2, H2O2 • HC Species: CH2O, CH3O2, CH3OOH • Ions: N+, N2+, NO+, O+, O2+ Radiatively Active * Non-linear system of equations are solved using a Newton Raphson iteration technique; uses sparse matrix techniques; Sandu et al, J. Comp. Phys., 129, 101-110, 1996.

  17. Model Chemistry - 106 Species Mechanism(219 Thermal; 18 Het.; 71 photolytic) • Additional Surface Source Gases (13 additional) … • NHMCs: CH3OH, • C2H6, C2H4, C2H5OH, CH3CHO • C3H8, C3H6, CH3COCH3 (Acetone) • C4H8 (BIGENE), C4H8O (MEK) • C5H8 (Isoprene), C5H12 (BIGALK) • C7H8 (Toluene) • C10H16 (Terpenes) • Radicals: Approx. 45 additional species. • Includes: Detailed 3D (lat/lon/time) emission inventories of natural and anthropogenic surface sources • Dry and wet deposition of soluble species • Lightning and Aircraft production of NOx • Kinnison et al., accepted, J. Geophys. Res., 2007.

  18. Comparison of Mechanisms (106 - 50 / 50) Ozone change in tropics RO2 + NO -> RO + NO2 Stratosphere NO2 + hv -> NO + O O + O2 + M -> O3 + M Troposphere

  19. Comparison of Mechanisms (106 - 50 / 50) CO change in tropics Stratosphere Troposphere

  20. Tutorial Outline… • In the Beginning… • Chemistry Preprocessor • Numerical Solution Approach • Chemical Mechanism (s) • Boundary Conditions (UB,LB, In Situ) • Heterogeneous Processes • Photolysis / Heating Rates • Summary / Future Development

  21. Lower Boundary Conditions… Total Organic Chlorine CH4, 30N CO2, 30N Surface CO (from emission BC)

  22. In Situ Forcings Surface NO (from emission BC) • Lightning NOx • Production: Price et al., 1997 • Distribution: Pickering, 1998 • Other In situ Forcings… • Subsonic Aircraft NOx and CO is also included. Friedl et al., 1997. • Auroral NOx (based on TIME-GCM) • SPE’s (Jackman/Marsh)

  23. Upper Boundary Conditions… • For most constituents in WACCM the UB is zero flux. • O, O2, H, and N mixing ratios are set using MSIS (Mass Spectrometer-Incoherent Scatter) model. • CO, CO2 are taken from the TIME-GCM (Roble and Ridley, 1994) • NO is taken from observations using the Student Nitric Oxide Explorer satellite (SNOE; Barth et al., 2003), which has been parameterized as a function of latitude, season, phase of solar cycle in Marsh et al, 2004 - Nitric Oxide Empirical Model (NOEM).

  24. Tutorial Outline… • In the Beginning… • Chemistry Preprocessor • Numerical Solution Approach • Chemical Mechanism (s) • Boundary Conditions (UB,LB) • Heterogeneous Processes • Photolysis / Heating Rates • Future Development

  25. Heterogeneous Chemistry • Reactions on three aerosol types (Sulfate, NAT, Water-ICE): • N2O5 + H2O => 2HNO3 • ClONO2 + H2O => HOCl + HNO3 • ClONO2 + HCl => Cl2 + H2O • HOCl + HCl => Cl2 + H2O • HOBr + HCl => BrCl + H2O • BrONO2 + H2O => HOBr + HNO3 • Rate Constants Approach: • K = 1/4 V * SAD *  • V = mean speed (kinetic theory of gases) •  = reaction probability (# gas molecules absorbed / # gas collisions at surface) SAD = aerosol surface area density (cm2 aerosol / cm3 atmosphere) Units = (cm/sec) * (cm2/cm3) = sec-1 • d[N2O5] / dt = -k [N2O5]

  26. Reaction Uptake Coefficient on Sulfate Aerosol (JPL-02, Sander et al.) f (T, P, H2SO4 wt%, [H2O], [HCl], [HOCl], radius)

  27. Sulfate Aerosol Reaction Probability Equations: JPL02

  28. Reaction Uptake Coefficient on NAT, ICE Aerosol (JPL-02, Sander et al.)

  29. SAGEII, Lidar Data Time-series @47.5 N Taken from WMO, Scientific Assessment of Ozone Depletion, Chapter 4, 2002

  30. Global SAD Data Used in Model Studies. Thomason et al., JGR, 1996

  31. Aerosol SAD El Chichon Mt Pinatubo Agung

  32. Solid (NAT) Fahey et al., Science, 2001 NASA SOLVE Mission Carslaw et al., Rev. Geophys., 1997 Stratospheric AerosolsTypes: Liquid (STS) LIQUID SOLID

  33. CCM Approach - HeterogeneousProcessesConsidine,+Drdla et al., JGR, 108, 8318, 2003. Sulfate Aerosols (H2O, H2SO4) - LBS Rlbs = 0.1 mm k=1/4*V*SAD*(SAD from SAGEII) >200 K Sulfate Aerosols (H2O, HNO3, H2SO4) - STS Rsts = 0.5 mm Thermo. Model (Tabazadeh) ? Nitric Acid Hydrate (H2O, HNO3) – NAT RNAT= 6.5 mm; 2.3(-4) cm-3 188 K (Tsat) ICE (H2O, with NAT Coating) 185 K (Tnuc) Rice= 10-30 mm

  34. T (K)86N, ZA Denitrification HNO3 (vmr)86N, ZA Santee et al., MLS Aura Proposal (2007) will evaluate the denitrification approach in WACCM3

  35. H2O SH- Dehydration POAMIII, 1998 WACCM3 (sampled like POAMIII) Mid-latitude Air Mid-latitude Air Mid-latitude Air Mid-latitude Air Altitude (km) Descent Descent Descent Descent Altitude (km) Dehydration Dehydration Dehydration Dehydration Day of Year Day of Year WMO 2002, Figure 3-19, Nedoluha et al., 2000. Dehydration derived in prognostic H2O Routines in CAM3!

  36. Courtesy of Cora Randall, CU/LASP

  37. 86S, 43 hPa, Zonal Mean NO2 ClONO2 + HCl +> Cl2 + HNO3 Cl2 + hv => 2Cl 2(Cl + O3 => ClO + O2) ClO + ClO + M => Cl2O2 + M Cl2O2 + hv => 2Cl + O2 ------------------------------------- 2O3 => 3O2

  38. JCl2O2 Caveat… New Cl2O2 cross sections from Pope, Hansen, Bayes, Friedl, and Sander, J. Phys. Chem. A., 2007… “For conditions representative of the polar vortex (solar zenith angle of 86, 20km, and O3 and T profiles measured in March 2000) calculated photolysis rates are a factor of six lower than the current NASA recommendation. This large discrepancy calls into question the completeness of present atmospheric models of polar ozone depletion.”

  39. Tutorial Outline… • In the Beginning… • Chemistry Preprocessor • Numerical Solution Approach • Chemical Mechanism (s) • Boundary Conditions (UB,LB) • Heterogeneous Processes • Photolysis / Heating Rates • Future Development

  40. EUV (23 Bins) 0.05 nm 121 nm Model Chemistry - Photolytic Processes O2 + hv -> O (3P) + O(1D); d[O2]/dt = -JO2 [O2] JO2(p)= Fexo (,t) x Nflux(p, )x()x() Inline (33 Bins) LUT (67 Bins) 121 nm 750 nm 200 nm • JO2 Lyman Alpha • JO2 SRB • JNO SRB •  x of 20 species • Nflux (p, ) is funct.(O3, O2) • Nflux is based on TUV (Madronich) • Nflux (p, )is function of (Col. O3; Zenith Angle, Albedo) •  x  is function of ( T, p ) CAM3 SW Heating rates Heating and Photolysis rates

  41. Fexo for Solar Cycle Studies: Model Input Spectral composite courtesy of: Judith Lean (NRL) and Tom Woods (CU/LASP)

  42. Ion species: N2+ , O2+ , N+ , O+ , NO+ , and e Photon / Photoelectron processes with O, N, O2, N2 Reactions with Neutrals: r1: O+ + O2 -> O2+ + O r2: O+ + N2 -> NO+ + N r3: N2+ + O -> NO+ + N(2D) r4: O2+ + N -> NO+ + O r5: O2+ + NO -> NO+ + O2 r6: N+ + O2 -> O2+ + N r7: N+ + O2 -> NO+ + O r8: N+ + O -> O+ + N r9: N2+ + O2 -> O2+ + N2 r10: O2+ + N2 -> NO+ + NO r11: N2+ + O -> O+ + N2 Ion Chemistry Included in WACCM3: NOx Production Reactions the produce NOx ra1: NO+ + e -> N + O (20%) -> N(2D) + O (80%) ra3: N2+ + e -> 2N (10%) -> N(2D) + N (90%) N(2D) + O2 => NO + O Courtesy of D. Marsh

  43. SPE’s

  44. EUV (23 Bins) 0.05 nm 121 nm Model Chemistry - Photolytic Processes O2 + hv -> O (3P) + O(1D); d[O2]/dt = -JO2 [O2] JO2(p)= Fexo (,t) x Nflux(p, )x()x() Inline (33 Bins) LUT (67 Bins) 121 nm 750 nm 200 nm • JO2 Lyman Alpha • JO2 SRB • JNO SRB •  x of 20 species • Nflux (p, ) is funct.(O3, O2) • Nflux is based on TUV (Madronich) • Nflux (p, )is function of (Col. O3; Zenith Angle, Albedo) •  x  is function of ( T, p ) CAM3 SW Heating rates Heating and Photolysis rates

  45. Heating Rate Approach Solar Energy, h Atomic and Molecular Internal Energy Translational Energy Chemical Potential Energy Radiative Loss

  46. Heating Rate Approach Cont… O3 O2 +h (<175 nm) + h (<310 nm) O(1D) + +O2 Heat +N2 O2 (1) +M Heat O2 (1) Heat 762 nm 865 nm N2 (v) O(3P) +M 1.27 m Heat O2 Heat Heat O2 N2 CO2 (001) O2 Heat 4.3 m CO2

  47. Chemical Potential Heating Reactions Mlynczak and Solomon, 1993 Plus 12 ion-neutral CPH reactions

  48. Heating Rate Approach (WACCM) WACCM3 SW LUT/Parm. 121-750nm (Thermal+CPH-AG) CAM3 SW Heating, >200nm (O3, O2, H2O)

  49. Tutorial Outline… • In the Beginning… • Chemistry Preprocessor • Numerical Solution Approach • Chemical Mechanism (s) • Boundary Conditions (UB,LB, In Situ) • Heterogeneous Processes • Photolysis / Heating Rates • Summary /Future Development

  50. Next Major Chemistry Updates

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