1. A Brief Introduction to CMAQ Serena H. Chung BioEarth Working Group 1 Seminar May 21, 2012

2. Outline Chemical Transport Models (CTMs) CMAQ Model Components CMAQ Output Parallel Programming in CMAQ WRF and CMAQ Linkages

3. Chemical Transport Models (CTMs) Transport: – Same physics as numerical weather model, but different numerical methods are needed Chemistry – Focuses on criteria pollutants which negatively affect human health Ozone (O 3 ): plant stresser  ecosystem impact Particular Matter (PM) in air quality community or aerosols in climate science community – Consists of hundreds if not thousand of chemical species – Climate impact: scatter and absorb radiation; affects cloud formation NO x (=NO + NO 2 ): most of which eventually deposits as nitrate  ecosystem impact SO 2 : forms, sulfate aerosol, contributes to acidification  ecosystem impact Mercury and other air toxics

4. Chemical Transport Model Equation Solves for species concentration C s using mass conservation equation for each grid cell and time step: Input or derived from numerical weather model (e.g., WRF, MM5)  Wind fields: u, v, w  Eddy diffusivity (turbulent diffusion) coefficients: K x =K y, K z  Temperature, Pressure, (& Radiation Fields):  To calculate reaction rates  Emissions rate can also be temperature and/or light dependent  Clouds & Precipitation:  Aqueous-phase reactions  Removal rate by wet deposition  Dry deposition velocities v d,s, where D s = v d,s C s,layer 1 change in concentration horizontal advection vertical advection horizontal diffusion vertical diffusion chemical reaction deposition emission

5. Chemical Mechanisms A chemical mechanism is a condensed set of chemical reactions – Chosen to represent conditions of interest,.e.g, O 3 in polluted environment, stratospheric O 3 Example - University of Leeds Master Chemical Mechanism – Thousands of species and >10,000 chemical reactions Options in CMAQ v5.0 – CB05: ~72 species, ~187 reactions – SAPRC99: ~88 species, ~144 reactions – SAPRC07:~150 species, ~413 reactions NONO 2 O3O3 RO 2 or HO 2 NO x (NO+NO 2 ) PAN HNO 3 OH NO 3 O3O3 HNO 3 N2O5N2O5 NO 2 + Aer H2OH2O DMS or VOC Atmospheric Deposition h ●● ● ● R can be lots of stuff with carbon and hydrogen atoms Nitrogen cycle in the troposphere is tightly coupled to O 3 & aerosol chemistry

6. Aerosol Size Distribution Based on Whitby, Atmos. Environ., 1978 Number Distribution Volume Distribution Typical Urban Conditions

7. Aerosol Size Distribution & Composition Based on Whitby, Atmos. Environ., 1978 Number Distribution Volume Distribution Typical Urban Conditions

8. Aerosol Size Distribution Based on Whitby, Atmos. Environ., 1978 Number Distribution Volume Distribution Typical Urban Conditions

9. Aerosol Size Distribution Based on Whitby, Atmos. Environ., 1978 Number Distribution Volume Distribution Typical Urban Conditions

10. Aerosol Size Distribution: Number vs Surface vs Volume Number – Affects the number of cloud droplets that form Surface Area – Affects the amount of radiation that is scatter or absorbed Volume – Portional to mass, used by the National Ambient Air Quality Standards (NAAQS) – PM 10 & PM 2.5 standards designed to distinguish coarse and fine particles. Figure 7.6 Seinfeld & Pandis Number Surface Area Volume 10  m2.5  m

11. Aerosol Size Representations No size representation, simulate only aerosol mass Use few lognormal distributions (e.g, CMAQ uses 3), each characterized by – Total particle number concentrations – Median diameter – Geometric standard deviation Use sectional bins – Track aerosol mass only, or – Track aerosol number and mass Mixtures – Internally mixed – all particles within a bin or lognormal distribution have the same chemical composition – Externally mixed – each particle contains one “species”, so species are not mixed – Combination of the two Effective number of species N eff for sectional bins with number and mass: N eff = (1 + N species ) N mixture N bin N species = ~ 20N mixture = 1-5N bin = 4-30

12. Chemical Tranport Model Operator splitting -- the equation is split into parts and solved separately: 1)vertical diffusion, emission, & dry deposition 2)horizontal advection 3)vertical advection 4)horizontal diffusion 5)cloud processes (includes aqueous chemistry) 6)gas-phase chemistry 7)aerosol chemistry change in concentration horizontal advection vertical advection horizontal diffusion vertical diffusion chemical reaction deposition emission

13. Horizontal Discretization in CMAQ xx yy East North i i+1 i-1 j+1 j-1 j C i,j,s u i+1,j v i,j+1 Arakawa C Grid AIRPACT-3 Example: 12-km x 12-km grids in Lambert Conformal Conic Projection

14. Vertical Discretization in CMAQ xx  East Up i i+1 i-1 k+1 k-1 k C i,k,s u i+1,j w i,k+1 WRF Example: Terrain-Following, Hydrostatic Pressure Grid Figure not to scale Adapted from Figure 2.1 of Skamarock et al., 2008 Pressure at model top: p ht ~ 10,000 Pa (~ 15 km) ~30-40 levels with first layer height at ~ 40 m where P h = hydrostatic pressure

15. Vertical Discretization AIRPACT-4 Example

16. CMAQ Grid Cell in 3-Dimension w i,j,k w i,j,k+1 u i,j,k u i+1,j,k v i,j/2,k v i,j+1,k East North Up Air density Temperature Pressure Water mixing ratios (vapor, rain, snow, ice) Gas- and aerosol-phase chemical species mixing ratios

17. Why does CMAQ take so long to run? The nature of chemical transport models: – Gas phase: ~ 100 chemical species – Particle phase: ~20 species, 3-16 size bins  effectively ~60-320 species minimum ODEs governing the chemical reactions: – Nonlinear – Stiff -- eigenvalues of Jacobian : negative; min/max ratio is ~ 10 9 Figure from Gustafason et al. (2005) (http://www.mmm.ucar.edu/wrf/users/workshop/WS2005 /presentations/sessions8/4-Gustafson.pdf

18. Model Time Steps WRF: – Physics: recommendation is 6 seconds per km of  x, i.e., 72 seconds for 12-km x 12-km grids – Radiation: recommendation is 1 minute per km of  x, i.e., 12 minutes for 12-km x 12-km grids CMAQ: – Synchronization between all processes: ~ 1-3 min – Adaptive time step within each process

19. CMAQ Model Components http://www.airqualitymodeling.org/cmaqwiki/index.php?title=File:Figure5-1.png

20. CMAQ Model Components http://www.airqualitymodeling.org/cmaqwiki/index.php?title=File:Figure5-1.png Meteorology Meteorological fields from a numerical weather model Usually MM5 or WRF, though other models can also be used http://www.atmos.washington.edu/mm5rt Example of Layer 1 Temperature and Wind Fields from WRF

21. CMAQ Model Components http://www.airqualitymodeling.org/cmaqwiki/index.php?title=File:Figure5-1.png Converts WRF or MM5 output files into CMAQ- ready files Calculates/diagnoses parameters not provided by WRF (e.g., Monin-Obukhov length) Calculates dry deposition velocities (depends on land- use type and turbulence characteristics) Keeps the same horizontal grid cell size Collapses WRF layers into fewer layers if desired

22. CMAQ Model Components http://www.airqualitymodeling.org/cmaqwiki/index.php?title=File:Figure5-1.png Emissions: Various models/processors, e.g., Transportation Industrial Residential Power Plants Fire Biogenic etc

23. CMAQ Model Components http://www.airqualitymodeling.org/cmaqwiki/index.php?title=File:Figure5-1.png Initial Conditions: Usually from a previous run Only ~ 2-3 days for spin-up required

24. CMAQ Model Components http://www.airqualitymodeling.org/cmaqwiki/index.php?title=File:Figure5-1.png Boundary Conditions Using: “Idealized’ profile, Results from a coarser, bigger domain CMAQ simulation, or Results of global CTMs

25. CMAQ Model Components http://www.airqualitymodeling.org/cmaqwiki/index.php?title=File:Figure5-1.png Photolysis Rate Calculations Using look-up table for clear-sky conditions and adjusted “online” based on cloud conditions

26. CMAQ Model Components http://www.airqualitymodeling.org/cmaqwiki/index.php?title=File:Figure5-1.png Solves

27. CMAQ Output Hourly, 3-dimensional concentrations (.e.g, parts per billion or  g m -3 ) of chemical species Hourly accumulated wet and dry deposition (.e.g, kg ha -1 hr -1 ) for relevant species netCDF files – same as WRF, but different conventions for date/time – read/write easier with use of Models-3 I/O API library Examples: – http://lar.wsu.edu/airpact – http://lar.wsu.edu/airpact/gmap/testC.html

28. CMAQ Output : AIRPACT Example Lots of stuff at: – AIRPACT-3: http://lar.wsu.edu/airpact – AIRPACT-4: http://lar.wsu.edu/airpact/gmap/testC.html 12-km, Surface-Layer, Hourly Concentrations of Secondary Organic Aerosl (SOA)

29. CMAQ Output: Vertical Distribution AIRPACT-4 Output for 10AM PST on Feb 23, 2011 O 3 Concentation

30. Parallel Progamming in CMAQ Distributed Memory using Message Passing Interface (MPI) ( WRF supports OpenMP and MPI) Divide and conquer by horizontal domain decomposition – Similar to WRF, but specifics are different For I/O, each processor gets the data for its subdomain by extracting the data from the full domain. However, only one processor is responsible for writing to the output data files; thus, gathering full domain data is required before writing 01 2 4 3 657 8 91011 1213 1415

31. WRF-CMAQ Soft Link Meteorological Fields Static Geographical Data Static Geographical Data Global Data Geographical & Large-scale Meteorological Data Interpolated to simulation grids Geographical & Large-scale Meteorological Data Interpolated to simulation grids Initial & Boundary Conditions METGRID GEOGRID UNGRIB REAL WRF MCIP ICON BCON JPROC CCTM Emission Models Emission Models

32. Coupled WRF-CMAQ Meteorological Fields Static Geographical Data Static Geographical Data Global Data Geographical & Large-scale Meteorological Data Interpolated to simulation grids Geographical & Large-scale Meteorological Data Interpolated to simulation grids Initial & Boundary Conditions METGRID GEOGRID UNGRIB REAL WRF call aqprep call cmaq_driver call feedback_read WRF call aqprep call cmaq_driver call feedback_read MCIP ICON BCON JPROC CCTM Emission Models Emission Models Speciated Aerosol Size Distributions, & O 3 Concentrations

33. WRF-CMAQ Domains WRF Domain Max CMAQ Domain CMAQ Domain 5 columns 5 rows delta_x delta_y CMAQ_COL_DIM CMAQ_ROW_DIM Adapted from Figure 2 of Wong et al., Geosci. Model Dev., 2012

34. Coupled WRF-CMAQ Computaional Performance Execution time CAMRRTMG WRF only MCIP Offline CMAQ Loose couple system, Total time 0:19:59 0:02:31 1:18:28 1:40:58 0:18:50 0:02:31 1:19:05 1:40:26 Coupling system w/o feedback and call frequency ratio 5:11:41:121:48:59 Coupling system w/ feedback and call frequency ratio 5:11:43:392:54:25 Table 1 of Wong et al., Geosci. Model Dev., 2012 Processor configuration CAMRRTMG w/o feedback speedupw/ feedback speedupw/o feedback Speedupw/ feedback speedup 4x82:05:062:08:212:13:173:19:25 8x81:19:461.571:21:571.571:24:121.581:58:211.68 8x160:55:282.260:55:122.330:56:382.351:14:142.69 Table 2 of Wong et al., Geosci. Model Dev., 2012 Based on 24-hour simulations for a 12-km eastern US domain

35. Some resources http://cmaq-model.org http://cmascenter.org/ Seinfeld, J.H. and S.N. Pandis, Atmospheric Chemistry and Physics: From Air Pollution to Climate Change, John Wiley & Sons, 2006. Jacob, D.J., Introduction to Atmospheric Chemistry, Princeton University Press, 1999. Jacobson, M.Z., Fundamentals of Atmospheric Modeling, Cambridge University Press, 1999