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A Brief Introduction to CMAQ. Serena H. Chung BioEarth 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:

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A brief introduction to cmaq

A Brief Introduction to CMAQ

Serena H. Chung

BioEarth Working Group 1 Seminar

May 21, 2012


Outline

Outline

  • Chemical Transport Models (CTMs)

  • CMAQ Model Components

  • CMAQ Output

  • Parallel Programming in CMAQ

  • WRF and CMAQ Linkages


Chemical transport models ctms

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

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

emission

chemical

reaction

horizontal

advection

vertical

advection

horizontal

diffusion

change in

concentration

vertical

diffusion

deposition


Chemical mechanisms

Chemical Mechanisms

HNO3

PAN

OH

hn

  • 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

DMS or VOC

O3

HNO3

NO

NO2

NO3

N2O5

O3

H2O

NO2 + Aer

RO2 or HO2

Atmospheric

Deposition

NOx (NO+NO2)

Nitrogen cycle in the troposphere is tightly

coupled to O3 & aerosol chemistry

R can be lots of stuff with carbon and hydrogen atoms


Aerosol size distribution

Aerosol Size Distribution

Typical Urban Conditions

Number

Distribution

Volume

Distribution

Based on Whitby, Atmos. Environ., 1978


Aerosol size distribution composition

Aerosol Size Distribution & Composition

Typical Urban Conditions

Number

Distribution

Volume

Distribution

Based on Whitby, Atmos. Environ., 1978


Aerosol size distribution1

Aerosol Size Distribution

Typical Urban Conditions

Number

Distribution

Volume

Distribution

Based on Whitby, Atmos. Environ., 1978


Aerosol size distribution2

Aerosol Size Distribution

Typical Urban Conditions

Number

Distribution

Volume

Distribution

Based on Whitby, Atmos. Environ., 1978


Aerosol size distribution number vs surface vs volume

2.5 mm

10 mm

Aerosol Size Distribution:Number vs Surface vs Volume

Number

  • 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.

Surface Area

Volume

Figure 7.6

Seinfeld & Pandis


Aerosol size representations

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)NmixtureNbin

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


Chemical tranport model

Chemical Tranport Model

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

    • vertical diffusion, emission, & dry deposition

    • horizontal advection

    • vertical advection

    • horizontal diffusion

    • cloud processes (includes aqueous chemistry)

    • gas-phase chemistry

    • aerosol chemistry

emission

chemical

reaction

horizontal

advection

vertical

advection

horizontal

diffusion

change in

concentration

vertical

diffusion

deposition


Horizontal discretization in cmaq

Horizontal Discretization in CMAQ

AIRPACT-3 Example:

12-km x 12-km grids in

Lambert Conformal Conic Projection

Arakawa C Grid

vi,j+1

j+1

Ci,j,s

ui+1,j

North

j

East

Dy

j-1

i-1

i

i+1

Dx


Vertical discretization in cmaq

Vertical Discretization in CMAQ

WRF Example: Terrain-Following, Hydrostatic Pressure Grid

where Ph = hydrostatic pressure

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

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

wi,k+1

Ci,k,s

ui+1,j

k+1

k

Up

East

Dh

k-1

i-1

i

i+1

Figure not to scale

Adapted from Figure 2.1 of Skamarock et al., 2008

Dx


Vertical discretization

Vertical Discretization

AIRPACT-4 Example


Cmaq grid cell in 3 dimension

CMAQ Grid Cell in 3-Dimension

wi,j,k+1

vi,j+1,k

ui+1,j,k

ui,j,k

  • Air density

  • Temperature

  • Pressure

  • Water mixing ratios (vapor, rain, snow, ice)

  • Gas- and aerosol-phase chemical species mixing ratios

vi,j/2,k

wi,j,k

Up

North

East


Why does cmaq take so long to run

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

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

CMAQ Model Components

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


Cmaq model components1

CMAQ Model Components

  • Meteorological fields from a numerical weather model

    • Usually MM5 or WRF, though other models can also be used

Meteorology

Example of Layer 1 Temperature and Wind Fields from WRF

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

http://www.atmos.washington.edu/mm5rt


Cmaq model components2

CMAQ Model Components

  • 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

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


Cmaq model components3

CMAQ Model Components

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

Transportation

Industrial

Residential

Power Plants

Fire

Biogenic

etc

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


Cmaq model components4

CMAQ Model Components

  • Initial Conditions:

  • Usually from a previous run

  • Only ~ 2-3 days for spin-up required

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


Cmaq model components5

CMAQ Model Components

  • Boundary Conditions Using:

  • “Idealized’ profile,

  • Results from a coarser, bigger domain CMAQ simulation, or

  • Results of global CTMs

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


Cmaq model components6

CMAQ Model Components

  • Photolysis Rate Calculations

  • Using look-up table for clear-sky conditions and adjusted “online” based on cloud conditions

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


Cmaq model components7

CMAQ Model Components

Solves

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


Cmaq output

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

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 distribution

CMAQ Output: Vertical Distribution

AIRPACT-4 Output for

10AM PST on Feb 23, 2011

O3 Concentation


Parallel progamming in cmaq

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

14

15

12

13

8

9

10

11

4

5

6

7

2

3

0

1


A brief introduction to cmaq

WRF-CMAQ Soft Link

Static

Geographical Data

GEOGRID

METGRID

Emission

Models

UNGRIB

Global Data

MCIP

Geographical & Large-scale

Meteorological Data

Interpolated to simulation grids

ICON

REAL

CCTM

BCON

Initial & Boundary Conditions

JPROC

WRF

Meteorological

Fields


A brief introduction to cmaq

Coupled WRF-CMAQ

Static

Geographical Data

GEOGRID

METGRID

Emission

Models

Global Data

UNGRIB

Geographical & Large-scale

Meteorological Data

Interpolated to simulation grids

MCIP

REAL

Initial & Boundary Conditions

ICON

WRF

call aqprep

call cmaq_driver

call feedback_read

CCTM

Meteorological

Fields

BCON

JPROC

Speciated Aerosol Size Distributions, &

O3 Concentrations


Wrf cmaq domains

WRF-CMAQ Domains

CMAQ_COL_DIM

delta_x

CMAQ_ROW_DIM

CMAQ Domain

5 columns

Max CMAQ Domain

5 rows

delta_y

WRF Domain

Adapted from Figure 2 of Wong et al., Geosci. Model Dev., 2012


Coupled wrf cmaq computaional performance

Coupled WRF-CMAQ Computaional Performance

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

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

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


Some resources

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


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