REPORT ON POLLEN MODELING PROJECT Revised

REPORT ON POLLEN MODELING PROJECT Revised: August 28, 2014 Matthew Ladd Overview The feasibility of producing pollen concentration grids at 1 km was assessed in this project. A Linux (Ubuntu v14.04) virtual machine was used with various models were successfully compiled from source code (e.g. IOAPI, MCIP, MEGAN).

In addition

documentation for other models such as SMOKE, BEIS and CMAQ were consulted. The use of MEGAN for this purpose is not possible as the STaMPS (Simulator of the timing and magnitude of pollen season: generates daily pools of pollen available for release - i.e. emissions potential - into the atmosphere) module was only available for Southern California according to the author of MEGAN (Guenther, pers comm, 2014). MEGAN successfully produced emission rates output grids for various VOCs using the test data (already created using MM5/WRF-MCIP). There are two possible approaches for producing pollen concentration grids at 1 km however, there are issues with both approaches. The first is to have an MM5/WRFMCIP-SMOKE/BEIS-CMAQ framework according to figure 1 in Efstathiou et al. (2011). BEISv3.09 is part of SMOKE. The second is to have something like MM5/WRF/BELD3Hysplit, which should produce similar results to the first approach. Community Multiscale Air Quality Model (CMAQ) and Hysplit produce concentration grids but also estimate dispersion. MET fields for CMAQ are obtained from mesoscale meteorological models such as MM5 or WRF. MCIP is used to create input files for CMAQ. MCIP reads these MET fields simulated by WRF/MM5 then computes dry deposition velocities and other variables that CMAQ needs (but are not available in the mesoscale model) and outputs data in IOAPI format (i.e. ncf format which is basically the same as NetCDF format). format.

IOAPI is the Models-3 Input/Output Applications Programming Interface

BEIS is biogenic emissions inventory system and v3.14 is currently embedded into the sparse matrix operator kernel emissions (SMOKEv2.5) modeling system. BEIS requires land cover and MET inputs in a similar manner to MEGAN. BEIS has a 1 km vegetation database for the contiguous USA which resolves forest canopy coverage by tree species with normalized emission factors for 35 chemicals. MEGAN differs from BEIS which uses a leaf-scale emissions factor. BEIS output can be input into CMAQ. Other biogenic VOC emissions algorithms and models are BIOME3, GloBEIS2 and BEIGIS.

Challenges and limitations The first approach requires running MM5 or WRF to get output to go into MCIP, but these models are lower resolution than 1 km and require at least 2 TB of disk space for the output. MM5 requires a significant amount of geophysical data to run. I was not able to find historical output for these models and MCIP does not accept input from other models. And this framework is very complex as there are multiple models needed and this was the subject of an entire PhD thesis by Efstathiou (2009). Hourly averaged surface pollen concentrations were calculated with the CMAQ model (see table 5.1 on p.174 of Efstathiou, 2009). A spatiotemporal map coupled with a mesoscale model at 12 km resolution to develop pollen emissions rates. It should be noted that MEGAN is not mentioned in any part of the Efstathiou (2009) framework. The second approach is using either MM5 or WRF in combination with a land use emissions data product such as BELD3 and Hysplit. Hysplit runs under Windows and has a large user base, but only takes in predefined meteorological data (e.g. gridded model output such as Eta data analysis systems EDAS or MM5 output) and calculates trajectories and dispersion of air parcels. The MET variables (minimum) required by Hysplit are surface wind components (U and V), surface temperature, pressure heights of the data level and surface pressure. For example, the NAM/WRF 12 km dataset for levels between surface and 925 mb (or approx 800m MSL). In Canada there is an operational 2.5 km high resolution deterministic prediction system (HRDPS) meteorological product for our region from Environment Canada (NOTE: the 2m wind

speed forecast product is shown below) and although this is grib level 2 format, there is no way to get this into Hysplit (ARL format) as Hysplit has predefined meteorological data inputs (e.g. NARR, NAM/WRF, GFS, ECMWF, MM5, MCIP IOAPI). The ‘user entered’ option is only for single lat/lon locations on a global grid. Otherwise the default meteorological data is NARR which is only 32 km resolution and it is not a forecast but historical re-analysis data.

A 32 km resolution meteorological product may miss

important smaller scale meteorological features in Eastern Ontario and produce less reliable results. Having a very high resolution and high quality meteorological data product (at least 12 km or even 4 km) as input into Hysplit would be very important for achieving good results/output.

UPDATE: There is meteorological model output and some re-analysis products available through the NOAA server which can be automatically converted to ARL format for use in Hysplit. The land use emissions data (biogenic emissions landuse database v 3.1 - BELD3) is only available for the USA however, there would need to be a similar data source for Canada. This may be available from Agriculture and Agri-food Canada (AAFC). Note that BELD3 provides distributions of 230 vegetation classes at 1 km resolution over the USA and uses data from the US Forest Service.

Sample output from Hysplit:

Disk space usage for models: WRF is run at resolutions of either 12 km or 4 km, with 4 days of simulation requiring ~2 TB of disk space. MCIP is run at 4km resolution and requires ~450 GB of disk space. MEGAN is run at either 1 km or 4 km resolution and requires ~1 GB at 4km resolution (in CMAQ-ready format) CMAQ is run at 4 km resolution and requires a few GB of disk space The reason for using MCIP is to have consistent meteorological (MET) and photosynthetically active radiation (PAR) output rather than “mixing and matching” MET/PAR outputs from different sources (see below). The reason for using MM5 or WRF is that MCIP is developed to process outputs from these mesoscale meteorological models and they are easily input into CMAQ or Hysplit.

MET and PAR data: PAR is available from the ECMWF ERA-Interim product (0,3,6,9,12 hrs for each month up to May 2014 at 0.7 degree resolution – there is clear sky surface PAR and PAR at surface) PAR can be estimated from: -

EPA’s BEIS pre-processor using cloud cover & pressure

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Surface observations from SURFRAD (US surface radiation network)

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Using CMAQ/MCIP code

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Using shortwave downward radiation calculated by MM5 or WRF

MET data: -

Soil moisture, soil temp, 2m temp, pressure and wind speed from HRDPS

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Soil type from MACC reanalysis (2003-2012)

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Water vapour mixing ratio from satellite data (MLS/Aura level 2 at 45 km resolution in gm/kgm, 2004 to present)

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Rain accumulation (24 hr) from ERA-Interim

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Precip adjustment (maybe precip fraction from ERA-Interim?)

Useful links: http://lar.wsu.edu/megan/ http://www.nar.ucar.edu/2012/lar/nesl/iig-simulation-pollen-release-megan.html http://www.wmo.int/pages/prog/www/DPFSERA/modelling_tools.htm http://www.cmascenter.org/cmaq/ http://glcf.umd.edu/data/par/ http://www.atmos.umd.edu/~srb/gcip/ http://www.atmos.umd.edu/~srb/gcip/hi_par.htm http://rams.atmos.colostate.edu/rams-description.html http://www2.mmm.ucar.edu/wrf/users/docs/user_guide/users_guide_chap5.html http://disc.sci.gsfc.nasa.gov/hydrology/data-holdings/nldas-parameters/photo-activeradiation http://ldas.gsfc.nasa.gov/nldas/NLDASgreen.php http://mirador.gsfc.nasa.gov/cgi-bin/mirador/collectionlist.pl?keyword=ML2H2O http://www.airqualitymodeling.org/cmaqwiki/index.php?title=CMAQv5.0.2_Readme_file https://hysplitbbs.arl.noaa.gov/viewforum.php?f=25 https://www.cmascenter.org/smoke/documentation/3.5/html/ch01.html

http://www.epa.gov/ttnchie1/emch/biogenic/ http://dd.weather.gc.ca/model_hrdps/east/grib2/12/ https://software.ecmwf.int/wiki/display/GRIB/Releases http://www.arl.noaa.gov/documents/workshop/Spring2007/HTML_Docs/index.html

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Previous Report from August 7, 2014 (with minor revisions) General notes about the computer running Linux Can do a remote desktop connection to computer with linux VM (1204-1318SMD002), start Oracle VM Virtual box to boot into linux Login using LPC user (password is Paleo2014!) User account with standard (not admin) privileges: LPC user (password is Pollen_021) Ctrl + Alt + T to open a new terminal window in linux Linux uses ‘bash’ shell by default, therefore need to switch to ‘tcsh’ shell to run ‘setenv’ commands to set up IO_API and other libraries Root user password: Egu_2018 (use command su to switch from lpc to root user privileges for installation of programs) Copying of files: cp -avr (source directory) (destination directory) Locate a file: find / -name ‘filename’

NetCDF Fortran Libraries (required by MEGAN) http://www.unidata.ucar.edu/downloads/netcdf/index.jsp

Compiled from source code with the following configuration (nf -config --help) after installation: C compiler: GCC Fortran compiler: Gfortran Pre-processor & compiler flags: -I /usr/local/include Flags needed to compile a Fortran program: -g -O2 -I /usr/local/include OPENDAP enabled in this build: yes NetCDF-2 API is enabled: yes NetCDF-4/HDF-5 enabled: yes Fortran 90 API enabled: yes Library linking info for NetCDF: -L /usr/local/lib -lnetcdf -lnetcdf Libraries needed to link a Fortran program: -L /usr/local/lib -lnetcdff -lnetcdf -lnetcdf Install prefix: /usr/local Includedir: /usr/local/include Library version: netCDF-Fortran 4.2

IO_API libraries (required by MEGAN) List of steps to install IO_API libraries: 1. cd to /usr/local/bin 2. mkdir ‘IOAPIv3.1’ 3. tar -zxvf ‘ioapi-3.1.tar.gz’ 4. cd ioapi 5. cp Makefile.nocpl Makefile

6. gedit Makefile (see below) 7. setenv BIN Linux2_x86_64gfort or Linux2_x86_64g95 8. make dirs 9. make bins Edits to Makefile: BASEDIR = /usr/local/bin/IOAPIv3.1 INSTALL = /usr/local

CPLMODE = nocpl IOAPIDEFS = PVMINCL = /dev/null NOTE: need to be logged in as root user with tcsh shell to run setenv command

MCIP (Meteorological-Chemistry Interface Processor) (required by MEGAN) MCIP takes as inputs, mesoscale meteorological MM5 or WRF output and generates a MET file (with photo synthetically active radiation PAR and other fields) that is input into MEGAN. List of steps to install MCIP: 1. cd to /usr/local/bin 2. tar -zxvf ‘MCIPv4.2.tar.gz’ 3. gedit Makefile in the ‘src’ (source code) subdirectory then run make NETCDF = /usr/local IOAPI_ROOT = /usr/local/bin/IOAPIv3.1 PVM = /dev/null

FFLAGS = -O3 -I $(NETCDF)/include -I $(IOAPI_ROOT)/Linux2_x86_64g95

LIBS = -fopenmp -L$(IOAPI_ROOT)/Linux2_x86_64g95 -lioapi \ -L$(NETCDF)/lib -lnetcdff -lnetcdf -lnetcdf NOTE: need to be logged in as root user

Model of Emissions of Gasses and Aerosols from Nature (MEGAN) For installing MEGAN, the steps were followed exactly from the user guide (section 2.3 starting on p.6) available at http://lar.wsu.edu/megan/guides.html. Running MEGAN with the test data was successful as the output emission rates file was created and the log file indicated normal program completion.

INPUT data needed for MEGAN: MET file (with PAR & other fields: soil moisture, soil temperature, soil type, 2m temperature, pressure, water vapour mixing ratio, wind speed, 24hr rain accumulation and precipitation adjustment) LAI, PFT and EF (these were already downloaded): key variables for LAI and PFT are temperature, solar radiation, humidity, wind speed and direction, dew point temperature and soil moisture LAI – leaf area index is LAI averaged over vegetation covered surfaces (there are 46 fields - units are m2/1000m2), these are 8-day averages for the year 2008 (e.g. day 1, day 9, day 17,…,day 361) PFT – a fraction of a grid covered by a given PFT (16 plant functional types but 10 in the test data) EF – Emission factors in units of micrograms of a given compound m-2 h-2

List of steps from manual: 1. EFT, LAI and PFT csv files converted to .ncf 2. MET & PAR data files converted to .ncf & copied to subfolder ‘MGNMET’ in the INPUT folder of MEGAN (generated from MCIP with WRF or MM5 input). 3. Run the script as indicated. 4. Not sure about this step? 5. This program was not built (simply may not be needed?)

Output data file is emission rates for various compounds: List of fields: ISOP Isoprene, MYRC, SABI, LIMO, AL3CAR, OCIM, BPIN, APIN, AMTP, FARN, BCAR, OSQT, MBO, MEOH, ACTO, CO, NO, BIDER, STRESS, OTHER, D_TEMP, D_PPFD, LAT, LON, CFNO, CFNOG, SLTYP Output Netcdf file viewed using XConv:

Next steps: Since we cannot run WRF or MM5 (given our current computing setup), we need historical MET data for a specific time period (with PAR) as input to MEGAN (via MCIP), preferably a product with a very high spatial resolution for Eastern Ontario. The

manual says that land cover input data can be re-gridded for a specific model domain. After successful output of emission rates then would need to investigate programs for atmospheric dispersion (e.g. CMAQ or Hysplit).