WACCM Chemistry Tutorial

1
WACCM Chemistry Tutorial

• Doug Kinnison
• D. Marsh, S. Walters, G. Brasseur, R. Garcia, R.
  Roble, many more
• dkin_at_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
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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
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Need to Represent Chemical Processes at
relatively fine resolution
MLT 3-5 km Res.
Stratosphere 1-2 km Res.
UTLS 1 km Res.
2.8? x 2.8? Courtesy of A. Gettelman
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Cost of Adding Chemistry (1.9?x2.5?)
Courtesy of Stacy Walters
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Cost of Adding Chemistry
WA3/CAM 12 WA3/GHG 3
Courtesy of Stacy Walters
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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.
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Input File for Preprocessor
BEGSIM output_unit_number 7 output_file
ions.marsh.doc procout_path
../output/ src_path
../bkend/ procfiles_path ../procfiles/cam/ s
im_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 -gt O, O2, O2_1S -gt O2, O2_1D
-gt O2 N2O, N, NO, NO2, NO3, HNO3, HO2NO2, N2O5
CH4, CH3O2, CH3OOH, CH2O, CO H2, H, OH, HO2,
H2O2 CL -gt Cl, CL2 -gt Cl2, CLO -gt ClO, OCLO -gt
OClO, CL2O2 -gt Cl2O2 HCL -gt HCl, HOCL -gt HOCl,
CLONO2 -gt ClONO2, BRCL -gt BrCl BR -gt Br, BRO -gt
BrO, HBR -gt HBr, HOBR -gt HOBr, BRONO2 -gt BrONO2
CH3CL -gt CH3Cl, CH3BR -gt CH3Br, CFC11 -gt CFCl3,
CFC12 -gt CF2Cl2 CFC113 -gt CCl2FCClF2, HCFC22 -gt
CHF2Cl, CCL4 -gt CCl4, CH3CCL3 -gt CH3CCl3 CF3BR
-gt CF3Br, CF2CLBR -gt CF2ClBr, CO2, N2p -gt N2, O2p
-gt O2 Np -gt N, Op -gt O, NOp -gt NO, e, N2D -gt 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
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Input File for Preprocessor
Photolysis jo2_a O2 hv -gt O O1D jo2_b
O2 hv -gt 2O jo3_a O3 hv -gt O1D O2_1D
jo3_b O3 hv -gt O O2 jn2o N2O hv -gt
O1D N2 jno NO hv -gt N O jno_i NO
hv -gt NOp e jno2 NO2 hv -gt NO O
jn2o5_a N2O5 hv -gt NO2 NO3 jn2o5_b N2O5
hv -gt NO O NO3 . .
Reactions cph25,cph N2D O2 -gt NO O1D
5.e-12 cph26,cph N2D O -gt N O
4.5e-13 . NO O M -gt NO2 M
9.0e-32, 1.5,
3.0e-11, 0., 0.6 NO2 O M -gt NO3 M
2.5e-31, 1.8, 2.2e-11, .7,
0.6 NO2 O3 -gt NO3 O2
1.2e-13, -2450 usr3 NO2 NO3 M -gt
N2O5 M 2.e-30, 4.4, 1.4e-12, .7, .6
usr3a N2O5 M -gt NO2 NO3 M
bimolecular reactions Arrhenius Expression
------------------------------------------------
-------------- Sulfate aerosol reactions
--------------------------------------------------
------------ het1 N2O5 -gt 2HNO3 het2
CLONO2 -gt HOCL HNO3 het3 BRONO2 -gt HOBR
HNO3 het4 CLONO2 HCL -gt CL2 HNO3 het5
HOCL HCL -gt CL2 H2O het6 HOBR HCL -gt
BRCL H2O
Termolecular reactions Troe Expression
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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

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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 tn1 - tn where ?t 30 minutes
Sandu et al, J. Comp. Phys., 129, 101-110, 1996.
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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).
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Tutorial Outline

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

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

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Lower Boundary Conditions
Total Organic Chlorine
CH4, 30N
CO2, 30N
Surface CO (from emission BC)
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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)
• SPEs (Jackman/Marsh)

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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).

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Tutorial Outline

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

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Heterogeneous Chemistry

• Reactions on three aerosol types (Sulfate, NAT,
  Water-ICE)
• N2O5 H2O gt 2HNO3
• ClONO2 H2O gt HOCl HNO3
• ClONO2 HCl gt Cl2 H2O
• HOCl HCl gt Cl2 H2O
• HOBr HCl gt BrCl H2O
• BrONO2 H2O gt 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

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Reaction Uptake Coefficient on Sulfate Aerosol
(JPL-02, Sander et al.)
f (T, P, H2SO4 wt, H2O, HCl, HOCl, radius)
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Sulfate Aerosol Reaction Probability Equations
JPL02
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Reaction Uptake Coefficient on NAT, ICE Aerosol
(JPL-02, Sander et al.)
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SAGEII, Lidar Data Time-series _at_47.5 N
Taken from WMO, Scientific Assessment of Ozone
Depletion, Chapter 4, 2002
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Global SAD Data Used in Model Studies.
Thomason et al., JGR, 1996
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Aerosol SAD
Agung
El Chichon
Mt Pinatubo
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Stratospheric AerosolsTypes
Carslaw et al., Rev. Geophys., 1997
Liquid (STS)
LIQUID
SOLID
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CCM Approach - Heterogeneous ProcessesConsidine,
Drdla et al., JGR, 108, 8318, 2003.
Sulfate Aerosols (H2O, H2SO4) - LBS
Rlbs 0.1 mm
k1/4VSAD? (SAD from SAGEII)
gt200 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
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T (K)86N, ZA
Denitrification
HNO3 (vmr)86N, ZA
Santee et al., MLS Aura Proposal (2007) will
evaluate the denitrification approach in WACCM3
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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!
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Courtesy of Cora Randall, CU/LASP
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86S, 43 hPa, Zonal Mean
NO2
ClONO2 HCl gt Cl2 HNO3 Cl2 hv gt 2Cl 2(Cl
O3 gt ClO O2) ClO ClO M gt Cl2O2
M Cl2O2 hv gt 2Cl O2 -------------------------
------------ 2O3 gt 3O2
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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.
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Tutorial Outline

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

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Model Chemistry - Photolytic Processes
O2 hv -gt O (3P) O(1D) dO2/dt -JO2
O2 JO2 (p) ? Fexo (?,t) x Nflux(p, ?) x ?
(?) x ? (?)
Inline (33 Bins)
LUT (67 Bins)
750 nm
121 nm
200 nm

• Nflux is based on TUV (Madronich)
• Nflux (p, ?) is function of (Col. O3 Zenith
  Angle, Albedo)
• ? x ? is function of ( T, p )

• JO2 Lyman Alpha
• JO2 SRB
• JNO SRB
• ? x ? of ?20 species
• Nflux (p, ?) is funct.(O3, O2)

CAM3 SW Heating rates
Heating and Photolysis rates
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Fexo for Solar Cycle Studies Model Input
Spectral composite courtesy of Judith Lean
(NRL) and Tom Woods (CU/LASP)
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Ion Chemistry Included in WACCM3 NOx Production

• Ion species
• N2 , O2 , N , O , NO , and e
• Photon / Photoelectron processes with O, N, O2,
  N2
• Reactions with Neutrals
• r1 O O2 -gt O2 O
• r2 O N2 -gt NO N
• r3 N2 O -gt NO N(2D)
• r4 O2 N -gt NO O
• r5 O2 NO -gt NO O2
• r6 N O2 -gt O2 N
• r7 N O2 -gt NO O
• r8 N O -gt O N
• r9 N2 O2 -gt O2 N2
• r10 O2 N2 -gt NO NO
• r11 N2 O -gt O N2

Reactions the produce NOx ra1 NO e -gt N O
(20) -gt N(2D) O
(80) ra3 N2 e -gt 2N (10)
-gt N(2D) N (90)
N(2D) O2 gt NO O
Courtesy of D. Marsh
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SPEs
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Model Chemistry - Photolytic Processes
O2 hv -gt O (3P) O(1D) dO2/dt -JO2
O2 JO2 (p) ? Fexo (?,t) x Nflux(p, ?) x ?
(?) x ? (?)
Inline (33 Bins)
LUT (67 Bins)
750 nm
121 nm
200 nm

• Nflux is based on TUV (Madronich)
• Nflux (p, ?) is function of (Col. O3 Zenith
  Angle, Albedo)
• ? x ? is function of ( T, p )

• JO2 Lyman Alpha
• JO2 SRB
• JNO SRB
• ? x ? of ?20 species
• Nflux (p, ?) is funct.(O3, O2)

CAM3 SW Heating rates
Heating and Photolysis rates
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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? (lt175 nm)
h? (lt310 nm)

O(1D)

O2
Heat
N2
O2 (1?)
M
Heat
O2 (1?)
Heat
762 nm 865 nm
O(3P)
N2 (v)
M
1.27 ?m
Heat
O2
Heat
Heat
O2
N2
CO2 (001)
O2
Heat
4.3 ?m
CO2
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Chemical Potential Heating Reactions

Mlynczak and Solomon, 1993
Plus 12 ion-neutral CPH reactions
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Heating Rate Approach (WACCM)
WACCM3 SW LUT/Parm. 121-750nm (ThermalCPH-AG)
CAM3 SW Heating, gt200nm (O3, O2, H2O)
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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
51
Bromine Chemistry
32N
Chapter 2, WMO, 2007
52
Next Major Chemistry Updates
53
Next Major Chemistry Updates
54
The End