WACCM Chemistry Tutorial Doug Kinnison D. Marsh, S. Walters, G. Brasseur, R. Garcia, R. Roble, many 8 June 2007

Tutorial Outline… 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 Surface to 150 km (500 km)

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

UCAR Quarterly – winter 1999

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

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

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

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

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 Input File Preprocessor Creates files specific and necessary to the chemical simulation.

Input File 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

Input File 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, [usr3] NO2 + NO3 + M -> N2O5 + M ; 2.e-30, 4.4, 1.4e-12,.7,.6 [usr3a] N2O5 + M -> NO2 + NO3 + M Termolecular reactions: Troe Expression 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

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

Numerical Approach System of time-dependent Ordinary Differential Eq. (1) Long-lived: Explicit Forward Euler method (e.g., N 2 O) - This system is solved via two Algorithms  t = t n +1 - t n where  t = 30 minutes Sandu et al, J. Comp. Phys., 129, , 1996.

(2) Short-lived: Implicit Backward Euler method (e.g. OH, O 3 ) - - The algebraic system for method (2) is quadradically non-linear. - - This system can be written as: - - Here G is a N i valued, non-linear vector function, where N i = # species - - Eq. 2.1 is solved via a Newton-Raphson iteration, or… (2.1) (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). Numerical Approach Cont…

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

Model Chemistry - 55 Species Mechanism Long-lived Species: (19-species) - Explicit Forward Euler Misc:CO 2, CO, CH 4, H 2 O, N 2 O, H 2, O 2 CFCs: CCl 4, CFC-11, CFC-12, CFC-113 HCFCs: HCFC-22 Chlorocarbons:CH 3 Cl, CH 3 CCl 3, Bromocarbons: CH 3 Br Halons: H-1211, H-1301 Constant Species:M, N 2 Short-lived Species: (36-species) - Implicit Backward Euler* O X : O 3, O, O( 1 D) NO X :N, N ( 2 D), NO, NO 2, NO 3, N 2 O 5, HNO 3, HO 2 NO 2 ClO X :Cl, ClO, Cl 2 O 2, OClO, HOCl, HCl, ClONO 2, Cl 2 BrO X :Br, BrO, HOBr, HBr, BrCl, BrONO 2 HO X :H, OH, HO 2, H 2 O 2 HC Species:CH 2 O, CH 3 O 2, CH 3 OOH Ions: N +, N 2 +, NO +, O +, O 2 + * Non-linear system of equations are solved using a Newton Raphson iteration technique; uses sparse matrix techniques; Sandu et al, J. Comp. Phys., 129, , Radiatively Active

Model Chemistry Species Mechanism (219 Thermal; 18 Het.; 71 photolytic) Additional Surface Source Gases (13 additional) … NHMCs:CH 3 OH, C 2 H 6, C 2 H 4, C 2 H 5 OH, CH 3 CHO C 3 H 8, C 3 H 6, CH 3 COCH 3 (Acetone) C 4 H 8 (BIGENE), C 4 H 8 O (MEK) C 5 H 8 (Isoprene), C 5 H 12 (BIGALK) C 7 H 8 (Toluene) C 10 H 16 (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.

Comparison of Mechanisms ( / 50) Ozone change in tropics RO 2 + NO -> RO + NO 2 NO 2 + hv -> NO + O O + O 2 + M -> O 3 + M Stratosphere Troposphere

Comparison of Mechanisms ( / 50) CO change in tropics Stratosphere Troposphere

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

Lower Boundary Conditions… Total Organic ChlorineCH 4, 30N CO 2, 30N Surface CO (from emission BC)

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

Upper Boundary Conditions… For most constituents in WACCM the UB is zero flux. O, O 2, H, and N mixing ratios are set using MSIS (Mass Spectrometer-Incoherent Scatter) model. CO, CO 2 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, Nitric Oxide Empirical Model (NOEM).

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

Heterogeneous Chemistry Reactions on three aerosol types (Sulfate, NAT, Water-ICE): N 2 O 5 + H 2 O => 2HNO 3 ClONO 2 + H 2 O => HOCl + HNO 3 ClONO 2 + HCl => Cl 2 + H 2 O HOCl + HCl => Cl 2 + H 2 O HOBr + HCl => BrCl + H 2 O BrONO 2 + H 2 O => HOBr + HNO 3 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 (cm 2 aerosol / cm 3 atmosphere) Units = (cm/sec) * (cm 2 /cm 3 ) = sec -1 d[N 2 O 5 ] / dt = -k [N 2 O 5 ]

Reaction Uptake Coefficient on Sulfate Aerosol (JPL-02, Sander et al.) f (T, P, H 2 SO 4 wt%, [H 2 O], [HCl], [HOCl], radius)

Sulfate Aerosol Reaction Probability Equations: JPL02

Reaction Uptake Coefficient on NAT, ICE Aerosol (JPL-02, Sander et al.) ReactionNATWater-Ice N 2 O5 + H 2 O => 2 HNO ClONO 2 + H 2 O => HNO 3 + HOCl ClONO 2 + HCl => HNO 3 + Cl HOCl + HCl => H 2 O + Cl BrONO 2 + H 2 O => HNO 3 + HOBr HOBr + HCl => BrCl + H 2 O -0.3

SAGEII, Lidar Data N Taken from WMO, Scientific Assessment of Ozone Depletion, Chapter 4, 2002

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

Aerosol SAD Agung El Chichon Mt Pinatubo

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

CCM Approach - Heterogeneous Processes Considine, +Drdla et al., JGR, 108, 8318, >200 K Sulfate Aerosols (H 2 O, H 2 SO 4 ) - LBS R lbs = 0.1  m Sulfate Aerosols (H 2 O, HNO 3, H 2 SO 4 ) - STS R sts = 0.5  m Nitric Acid Hydrate (H 2 O, HNO 3 ) – NAT R NAT = 6.5  m; 2.3(-4) cm-3 k=1/4*V*SAD*  (SAD from SAGEII) Thermo. Model (Tabazadeh) ICE (H 2 O, with NAT Coating) R ice =  m  188 K (T sat ) 185 K (T nuc )

T (K) 86N, ZA HNO 3 (vmr) 86N, ZA Denitrification Santee et al., MLS Aura Proposal (2007) will evaluate the denitrification approach in WACCM3

H 2 O SH- Dehydration POAMIII, 1998WACCM3 (sampled like POAMIII) Descent Mid-latitude Air Dehydration WMO 2002, Figure 3-19, Nedoluha et al., Descent Mid-latitude Air Dehydration Descent Mid-latitude Air Dehydration Descent Mid-latitude Air Dehydration Altitude (km) Day of Year Dehydration derived in prognostic H 2 O Routines in CAM3!

Courtesy of Cora Randall, CU/LASP

86S, 43 hPa, Zonal Mean ClONO 2 + HCl +> Cl 2 + HNO3 Cl 2 + hv => 2Cl 2(Cl + O 3 => ClO + O 2 ) ClO + ClO + M => Cl 2 O 2 + M Cl 2 O 2 + hv => 2Cl + O O 3 => 3O 2 NO2

JCl 2 O 2 Caveat… New Cl 2 O 2 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 O 3 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.”

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

Model Chemistry - Photolytic Processes 750 nm N flux is based on TUV (Madronich) N flux (p, ) is function of (Col. O 3 ; Zenith Angle, Albedo)  x  is function of ( T, p ) Inline (33 Bins)LUT (67 Bins) O 2 + hv -> O ( 3 P) + O( 1 D); d[O 2 ]/dt = -J O2 [O 2 ] J O2 ( p ) =  F exo (,t ) x N flux ( p, ) x  ( ) x  ( ) 200 nm CAM3 SW Heating rates 121 nm JO 2 Lyman Alpha JO 2 SRB JNO SRB  x  of  20 species N flux (p, ) is funct.(O 3, O 2 ) Heating and Photolysis rates 121 nm EUV (23 Bins) 0.05 nm

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

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

SPE’s

Model Chemistry - Photolytic Processes 750 nm N flux is based on TUV (Madronich) N flux (p, ) is function of (Col. O 3 ; Zenith Angle, Albedo)  x  is function of ( T, p ) Inline (33 Bins)LUT (67 Bins) O 2 + hv -> O ( 3 P) + O( 1 D); d[O 2 ]/dt = -J O2 [O 2 ] J O2 ( p ) =  F exo (,t ) x N flux ( p, ) x  ( ) x  ( ) 200 nm CAM3 SW Heating rates 121 nm JO 2 Lyman Alpha JO 2 SRB JNO SRB  x  of  20 species N flux (p, ) is funct.(O 3, O 2 ) Heating and Photolysis rates 121 nm EUV (23 Bins) 0.05 nm

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

Heating Rate Approach Cont… O3O3 O( 1 D) O 2 ( 1  ) + h (<310 nm) O 2 ( 1  ) + O( 3 P)N 2 (v) N2N2 CO 2 (001) CO 2 O2O2 Heat O2O2 4.3  m 1.27  m 762 nm 865 nm O2O2 + h (<175 nm) +N 2 +O 2 O2O2 Heat +M

Chemical Potential Heating Reactions Chemical ReactionsKJ/mole O + O 3 => 2O O + O + M => O 2 + M O + OH => H + O O + HO 2 => OH + O H + O 2 + M => HO 2 + M O + O 2 + M => O 3 + M H + O 3 => OH + O HO 2 + NO => NO 2 + OH HO 2 + O 3 => OH + 2O HO 2 + HO 2 => H 2 O 2 + O OH + O 3 => HO 2 + O NO + O 3 => NO 2 + O NO 2 + O => NO + O OH + HO 2 => H 2 O + O H + HO 2 => H 2 + O Mlynczak and Solomon, 1993 Chemical ReactionsKJ/mole O ( 1 D) + O 2 => O + O 2 ( 1  ) O ( 1 D) + N 2 => O + N Chemical ReactionsKJ/mole O 2 ( 1  ) + O => O 2 ( 1  ) + O O 2 ( 1  ) + O 2 => O 2 ( 1  ) + O O 2 ( 1  ) + N 2 => O 2 ( 1  ) + N O 2 ( 1  ) + O 3 => O 2 ( 1  ) + O O 2 ( 1  )+ O => O 2 + O O 2 ( 1  )+ O 2 => 2O O 2 ( 1  )+N 2 => O 2 + N Chemical ReactionsKJ/mole N ( 2 D) + O 2 => NO + O( 1 D) N ( 2 D) + O => N + O N + O 2 => NO + O N + NO => N 2 + O Plus 12 ion-neutral CPH reactions

Heating Rate Approach (WACCM) WACCM3 SW LUT/Parm nm (Thermal+CPH-AG) CAM3 SW Heating, >200nm (O 3, O 2, H 2 O)

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

Next Major Chemistry Updates TopicContactAction/Comments Completion Date Mechanism D. Kinnison J. Orlando, J.F. Lamarque, R. Salawitch Add Halon 2402 to Middle Atmosphere Add Halon 2402 to Middle Atmosphere Implement a Whole Atm Mechanism (w/NMHC’s; will not include short- lived Org-Br) Implement a Whole Atm Mechanism (w/NMHC’s; will not include short- lived Org-Br) Add Short-lived Org Bromine species Add Short-lived Org Bromine species Fall 2007 Fall 2007 Gas-phase Reactions D. Kinnison Update to JPL06 Update to JPL06 Fall 2007 Fall 2007 Photolysis D. Kinnison S. Walters Update to JPL06 Update to JPL06 JCl 2 O 2 cross sections? JCl 2 O 2 cross sections? Add temperature dependence to wavelengths < 200nm. Add temperature dependence to wavelengths < 200nm. Extend reference atmosphere profile in STUV (>140km) Extend reference atmosphere profile in STUV (>140km) Speed up? Reduce memory imprint? Speed up? Reduce memory imprint? Photochemical Benchmark. Photochemical Benchmark. Fall 2007 Fall 2007

Bromine Chemistry… Chapter 2, WMO, N

Next Major Chemistry Updates TopicContactAction/Comments Completion Date Mechanism D. Kinnison J. Orlando, J.F. Lamarque, R. Salawitch Add Halon 2402 to Middle Atmosphere Add Halon 2402 to Middle Atmosphere Implement a Whole Atm Mechanism (w/NMHC’s; will not include short- lived Org-Br) Implement a Whole Atm Mechanism (w/NMHC’s; will not include short- lived Org-Br) Add Short-lived Org Bromine species Add Short-lived Org Bromine species Fall 2007 Fall 2007 Gas-phase Reactions D. Kinnison Update to JPL06 Update to JPL06 Fall 2007 Fall 2007 Photolysis D. Kinnison S. Walters Update to JPL06 Update to JPL06 JCl 2 O 2 cross sections? JCl 2 O 2 cross sections? Add temperature dependence to wavelengths < 200nm. Add temperature dependence to wavelengths < 200nm. Extend reference atmosphere profile in STUV (>140km) Extend reference atmosphere profile in STUV (>140km) Speed up? Reduce memory imprint? Speed up? Reduce memory imprint? Photochemical Benchmark. Photochemical Benchmark. Fall 2007 Fall 2007

Next Major Chemistry Updates TopicContactAction/Comments Completion Date Lower Boundary Condition D. Kinnison S. Walters Use finer temporal resolution observations for REF1; Get from SPARC CCMVal Use finer temporal resolution observations for REF1; Get from SPARC CCMVal Summer 2007 Summer 2007 Update Sulfate SAD D. Kinnison S. Tilmes A. Gettelman Update to SPARC SAD data; better in polar region Update to SPARC SAD data; better in polar region Derive Heating rates from SAD Derive Heating rates from SAD Done Done Evaluate Radical Chemistry D. Kinnison R. Salawitch Use PSS model. Use PSS model. Compare Odd-Ox rates to balloon data. Compare Odd-Ox rates to balloon data. ? Evaluate Polar de-NOy D. Kinnison, M. Santee Compare denitrification in WACCM3 to Aura MLS data. Compare denitrification in WACCM3 to Aura MLS data. Move setting routine out of chemistry? Move setting routine out of chemistry? ? Stratospheric Temperatures R. Garcia, F. Sassi, J. Richter Improvements in Temperature representation in WACCM3 Improvements in Temperature representation in WACCM3 GW Tuning GW Tuning ?

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