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

Based on Whitby, Atmos. Environ., 1978

Num

ber

Dist

ributi

onVo

lum

eD

istrib

ution

Typical Urban Conditions

Aerosol Size Distribution

Based on Whitby, Atmos. Environ., 1978

Num

ber

Dist

ributi

onVo

lum

eD

istrib

ution

Typical Urban Conditions

Aerosol Size Distribution

Based on Whitby, Atmos. Environ., 1978

Num

ber

Dist

ributi

onVo

lum

eD

istrib

ution

Typical Urban Conditions

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

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

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

CMAQ Model Components

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

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

TransportationIndustrial

ResidentialPower Plants

FireBiogenic

etc

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

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

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

CMAQ Model Components

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

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