a brief introduction to cmaq serena h. chung bioearth working group 1 seminar may 21, 2012

A Brief Introduction to CMAQ

Serena H. ChungBioEarth Working Group 1 Seminar

May 21, 2012

Outline

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

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 (O3): 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

• NOx (=NO + NO2): most of which eventually deposits as nitrate ecosystem impact

• SO2 : forms, sulfate aerosol, contributes to acidification ecosystem impact

• Mercury and other air toxics

Chemical Transport Model Equation

• Solves for species concentration Cs 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: Kx=Ky, Kz

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 vd,s, where Ds = vd,s Cs,layer 1

change in concentration

horizontal advection

vertical advection

horizontaldiffusion

vertical diffusion

chemical reaction

deposition

emission

Chemical Mechanisms• A chemical mechanism is a condensed set of chemical reactions

– Chosen to represent conditions of interest, .e.g, O3 in polluted environment, stratospheric O3

• 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

NO NO2

O3

RO2 or HO2

NOx (NO+NO2)

PAN

HNO3

OH

NO3

O3 HNO3

N2O5

NO2 + Aer H2O

DMS or VOC

AtmosphericDeposition

hn

● ●

●

●

R can be lots of stuff with carbon and hydrogen atoms

Nitrogen cycle in the troposphere is tightly

coupled to O3 & aerosol chemistry

Aerosol Size Distribution

Based on Whitby, Atmos. Environ., 1978

Num

ber

Dist

ributi

onVo

lum

eD

istrib

ution

Typical Urban Conditions

Aerosol Size Distribution & Composition


Num

ber

Dist

ributi

onVo

lum

eD

istrib

ution


Aerosol Size Distribution


Num

ber

Dist

ributi

onVo

lum

eD

istrib

ution


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)

– PM10 & PM2.5 standards designed to distinguish coarse and fine particles.

Figure 7.6Seinfeld & Pandis

Number

Surface Area

Volume

10 mm2.5 mm

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 Neff for sectional bins with number and mass: Neff = (1 + Nspecies) Nmixture Nbin

Nspecies = ~ 20 Nmixture = 1-5 Nbin = 4-30

Chemical Tranport Model

• Operator splitting -- the equation is split into parts and solved separately:

1) vertical diffusion, emission, & dry deposition 2) horizontal advection3) vertical advection 4) horizontal diffusion5) cloud processes (includes aqueous chemistry)6) gas-phase chemistry7) aerosol chemistry

change in concentration

horizontal advection

vertical advection

horizontaldiffusion

vertical diffusion

chemical reaction

deposition

emission

Horizontal Discretization in CMAQ

Dx

Dy

East

North

i i+1i-1

j+1

j-1

j

Ci,j,s ui+1,j

vi,j+1

Arakawa C Grid

AIRPACT-3 Example:12-km x 12-km grids in

Lambert Conformal Conic Projection

Vertical Discretization in CMAQ

Dx

Dh

East

Up

i i+1i-1

k+1

k-1

k

Ci,k,sui+1,j

wi,k+1

WRF Example: Terrain-Following, Hydrostatic Pressure Grid

Figure not to scaleAdapted from Figure 2.1 of Skamarock et al., 2008

Pressure at model top: pht ~ 10,000 Pa (~ 15 km)

~30-40 levels with first layer height at ~ 40 m

where Ph = hydrostatic pressure

Vertical Discretization AIRPACT-4 Example

CMAQ Grid Cell in 3-Dimension

wi,j,k

wi,j,k+1

ui,j,k

ui+1,j,k

vi,j/2,k

vi,j+1,k

East

NorthUp

• Air density• Temperature• Pressure• Water mixing ratios

(vapor, rain, snow, ice)• Gas- and aerosol-phase

chemical species mixing ratios

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 ~ 109

Figure from Gustafason et al. (2005) (http://www.mmm.ucar.edu/wrf/users/workshop/WS2005/presentations/sessions8/4-Gustafson.pdf

Model Time Steps

• WRF: – Physics: recommendation is 6 seconds per km of Dx, i.e., 72 seconds for 12-km x 12-km grids

– Radiation: recommendation is 1 minute per km of Dx, 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

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



• 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



Emissions: Various models/processors, e.g.,

TransportationIndustrial

ResidentialPower Plants

FireBiogenic

etc



Initial Conditions:• Usually from a previous run• Only ~ 2-3 days for spin-up

required



Boundary Conditions Using:• “Idealized’ profile, • Results from a coarser,

bigger domain CMAQ simulation, or

• Results of global CTMs



Photolysis Rate Calculations• Using look-up table for

clear-sky conditions and adjusted “online” based on cloud conditions



Solves

CMAQ Output

• Hourly, 3-dimensional concentrations (.e.g, parts per billion or mg 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

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)

CMAQ Output: Vertical DistributionAIRPACT-4 Output for

10AM PST on Feb 23, 2011O3 Concentation

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

0 1 2

4

3

65 7

8 9 10 11

12 13 14 15

WRF-CMAQ Soft Link

Meteorological Fields

Static Geographical Data

Global Data

Geographical & Large-scale Meteorological Data

Interpolated to simulation grids

Initial & Boundary Conditions

METGRIDGEOGRID

UNGRIB

REAL

WRF

MCIP

ICON

BCON

JPROC

CCTM

EmissionModels

Coupled WRF-CMAQ

Meteorological Fields

Static Geographical Data

Global Data

Geographical & Large-scale Meteorological Data

Interpolated to simulation grids

Initial & Boundary Conditions

METGRIDGEOGRID

UNGRIB

REAL

WRF

call aqprepcall cmaq_driver

call feedback_read

MCIP

ICON

BCON

JPROC

CCTM

EmissionModels

Speciated Aerosol Size

Distributions, &O3

Concentrations

WRF-CMAQ Domains

WRF Domain

Max CMAQ Domain

CMAQ Domain5 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

Coupled WRF-CMAQ Computaional Performance

Execution timeCAM RRTMG

WRF only MCIP Offline CMAQLoose couple system, Total time

0:19:590:02:311:18:28

1:40:58

0:18:500:02:311:19:051:40:26

Coupling system w/o feedback and call frequency ratio 5:1 1:41:12 1:48:59Coupling system w/ feedback and call frequency ratio 5:1 1:43:39 2:54:25

Table 1 of Wong et al., Geosci. Model Dev., 2012

Processor

configuration

CAM RRTMGw/o

feedbackspeedup w/

feedbackspeedup w/o

feedbackSpeedup w/ feedback speedup

4x8 2:05:06 2:08:21 2:13:17 3:19:258x8 1:19:46 1.57 1:21:57 1.57 1:24:12 1.58 1:58:21 1.68

8x16 0:55:28 2.26 0:55:12 2.33 0:56:38 2.35 1:14:14 2.69

Table 2 of Wong et al., Geosci. Model Dev., 2012

Based on 24-hour simulations for a 12-km eastern US domain

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

http://www.mmm.ucar.edu/wrf/users/

http://cmascenter.org/

http://cmascenter.org/

a brief introduction to cmaq serena h. chung bioearth working group 1 seminar may 21, 2012

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