Latest revision as of 23:23, 25 December 2018

Running the WPS

First, one must run the WRF Preprocessing System (WPS) to prepare the input data for driving WRF. The WPS configuration options are defined in the "namelist.wps" file.

Step 1: Defining model domains with geogrid

In the "geogrid" namelist record, the projection of the simulation domain is defined. As of WRF-GC version 0.1, only two sets of map projections and specified parameters are supported:

• Mercator /'mercator' (truelat1)

• Unrotated regular latitude-longitude /'lat-lon' (pole_lat, pole_lon, stand_lon)

An example of "geogrid" namelist records in the "namelist.wps" file is shown below:

       &share 
        wrf_core = 'ARW',
        max_dom = 1,
        start_date = '2015-01-01_00:00:00',
        end_date   = '2015-01-02_00:00:00',
        interval_seconds = 21600
        io_form_geogrid = 2,
       /

       &geogrid
        parent_id         =   1,   
        parent_grid_ratio =   1,   
        i_parent_start    =   1,  
        j_parent_start    =   1,  
        e_we              =  245,
        e_sn              =  181, 
        geog_data_res = 'gtopo_2m+usgs_2m+nesdis_greenfrac+2m',
        dx = 27000,
        dy = 27000,
        map_proj = 'mercator',
        ref_lat   =  35.0,
        ref_lon   =  105.0,
        truelat1  =  30.0,
        stand_lon =  105.0,
        geog_data_path = '/users/wrf/data/geog'
       /

Step 2: Downloading and extracting meteorological data from GRIB files with ungrib

For a 'real' WRF case, you need to download the meteorological data that will be used as the initial and boundary condition to drive WRF. You have a number of choices. We use the NCEP FNL reanalyses product.

Available free datasets for driving WRF

An example of "ungrib" namelist records in the "namelist.wps" file is shown below:

       &share 
        wrf_core = 'ARW',
        max_dom = 1,
        start_date = '2015-01-01_00:00:00',
        end_date   = '2015-01-02_00:00:00',
        interval_seconds = 21600
        io_form_geogrid = 2,
       /

       &ungrib
        out_format = 'WPS',
        prefix = 'FILE',
       /

Step 3: Horizontally interpolating meteorological data with metgrid

An example of "metgrid" namelist records in the "namelist.wps" file is shown below:

       &share 
        wrf_core = 'ARW',
        max_dom = 1,
        start_date = '2015-01-01_00:00:00',
        end_date   = '2015-01-02_00:00:00',
        interval_seconds = 21600
        io_form_geogrid = 2,
       /

       &metgrid
       fg_name = 'FILE'
       io_form_metgrid = 2,
       /

Preparing GEOS-Chem shared data directories

The GEOS-Chem shared data directories contain many large files necessary for the WRF-GC. Please Set up the top-level root directory for GEOS-Chem shared data, which is called ExtData. Please create the /dir/to/data/ExtData and set your directories in the "input.geos" file:

       Root data directory : /dir/to/data/ExtData

The ExtData directory structure cotains two subdirectories:

- CHEM_INPUTS: Non-emissions data for GEOS-Chem chemistry modules

• Download the CHEM_INPUTS data directories via anonymous FTP from the Harvard data directory archive (ftp.as.harvard.edu). Please refer to : Downloading GEOS-Chem source code and data

- HEMCO: Emissions inventories for the HEMCO emissions component

• Download the HEMCO data directories with a pakeage provided by GEOS-Chem Support Team. Please refer to : Downloading the HEMCO data

• Set the HEMCO data directory in the "HEMCO_Config.rc" file

       Root : /dir/to/data/ExtData/HEMCO

Emissions for WRF-GC

Preparing emission files is not required. WRF-GC uses the Harvard-NASA Emissions Component (HEMCO) with on-line regridding. Configure HEMCO refer to the "HEMCO_Config.rc" file inside the run directory for WRF. For more information on HEMCO data directories, please refer to the HEMCO wiki

Preparing chemical initial/boundary condition data

Chemical initial and boundary condition data are used output from global simulation MOZART-4/GEOS-5 similar to WRF-Chem. Please download the data from :

• https://www.acom.ucar.edu/wrf-chem/mozart.shtml

The Mozart data are processed by the WRF-Chem processor called mozbc. Please download the mozbc utility, including instructions and input files from :

• https://www.acom.ucar.edu/wrf-chem/download.shtml

Running WRF-GC

To configure WRF-GC, you need to edit three files inside the WRF run directory.

- HEMCO_Config.rc (Please refer to: GEOS-Chem Input Files)

• HEMCO_Config.rc file contains a set of switches to enable and disable emission inventories, such as:

      # ExtNr ExtName           on/off  Species
      0       Base              : on    *
          --> HEMCO_RESTART     :       false
          --> AEIC              :       true
          --> BIOFUEL           :       true
      ... etc not shown here ...

• Errors with HEMCO component when running a simulation are output into a log file called "HEMCO.log".

- input.geos (Please refer to : GEOS-Chem Input Files)

• Simulation Menu (except Root data directory) and Timestep Menu in input.geos can be safely ignored. You can configure the timestepping and operators using the WRF configuration namelist.

• Other Menus in "input.geos" can be safely ignored.

- namelist.input

• The WRF-GC model configuration options are determined in the "namelist.input" file. Please edit the "namelist.input" file to match your case.

• For WRF-GC chemistry powered by GEOS-Chem, choose chem_opt = 233.

• Cumulus Parameterization schemes (cu_physics) supported by WRF-GC v0.1 are New-Tiedtke scheme (recommended) and Zhang-McFarlene scheme.

• Microphysics schemes (mp_physics) supported by WRF-GC v0.1 are New Thompson et al. scheme, and Morrison Double-Monment scheme (recommended).

• You can configure processes by GEOS-Chem using the following switches in the "namelist.input" file.

• Convection: gc_do_convection
• Emissions: gc_do_hemco
• Turbulence/PBL mixing: gc_do_pblmix
• Chemistry: gc_do_chemistry
• Dry deposition: gc_do_drydep
• Wet deposition: gc_do_wetdep

The following "namelist.input" file has been tested. Options that are specific to your case have been highlighted in bold. We suggect that do not change the default of "&dynamics" and "&bdy_control" in the "namelist.input" file. (Please refer to : Description of Namelist Variables)

        &time_control
        run_days                            = 1,
        run_hours                           = 0,
        run_minutes                         = 0,
        run_seconds                         = 0,
        start_year                          = 2015,
        start_month                         = 01,
        start_day                           = 01,
        start_hour                          = 00,
        start_minute                        = 00,
        start_second                        = 00,
        end_year                            = 2015,
        end_month                           = 01,
        end_day                             = 02,
        end_hour                            = 00,
        end_minute                          = 00,
        end_second                          = 00,
        interval_seconds                    = 21600,
        input_from_file                     = .true.,
        history_interval                    = 60,
        frames_per_outfile                  = 1,
        restart                             = .false.,
        restart_interval                    = 0,
        io_form_history                     = 2,
        io_form_restart                     = 2,
        io_form_input                       = 2,
        io_form_boundary                    = 2,
        debug_level                         = 0,

        auxinput5_inname                    = 'wrfchemi_d<domain>_<date>',
        auxinput6_inname                    = 'wrfbiochemi_d<domain>',
        auxinput7_inname                    = 'wrffirechemi_d<domain>_<date>',
        auxinput8_inname                    = 'wrfchemi_gocart_bg_d<domain>',
        auxinput12_inname                   = 'wrf_chem_input',
        auxinput13_inname                   = 'wrfchemv_d<domain>',
        auxinput5_interval_m                = 60,
        auxinput7_interval_m                = 60,
        auxinput8_interval_m                = 14400, 14400,
        auxinput13_interval_m               = 14400, 14400,

        io_form_auxinput2                   = 2,
        io_form_auxinput5                   = 0,
        io_form_auxinput6                   = 0,
        io_form_auxinput7                   = 0,
        io_form_auxinput8                   = 0,
        io_form_auxinput12                  = 0,
        io_form_auxinput13                  = 0,
        /

        &domains
        time_step                           = 120,  
        time_step_fract_num                 = 0,
        time_step_fract_den                 = 1,
        max_dom                             = 1,
        e_we                                = 245,
        e_sn                                = 181,
        s_we                                =  1,
        s_sn                                =  1, 
        e_vert                              = 50, 
        p_top_requested                     = 1000,
        num_metgrid_levels                  = 27,
        num_metgrid_soil_levels             = 4,
        dx                                  = 27000,
        dy                                  = 27000,
        grid_id                             = 1,
        parent_id                           = 1,
        i_parent_start                      = 1,
        j_parent_start                      = 1,
        parent_grid_ratio                   = 1,
        parent_time_step_ratio              = 1,
        feedback                            = 0,
        smooth_option                       = 0
        /

        &physics
        mp_physics                          = 10,
        ra_lw_physics                       = 4,
        ra_sw_physics                       = 4,
        radt                                = 15,
        sf_sfclay_physics                   = 1, 
        sf_surface_physics                  = 2, 
        sf_urban_physics                    = 0, 
        bl_pbl_physics                      = 1, 
        bldt                                = 0, 
        cu_physics                          = 16, 
        cudt                                = 0, 
        cu_diag                             = 1,  
        isfflx                              = 1,
        ifsnow                              = 1,
        icloud                              = 1,
        surface_input_source                = 1,
        num_soil_layers                     = 4,
        num_land_cat                        = 24,
        progn                               = 0,
        cu_rad_feedback                     = .true.,
        /

        &dynamics
        w_damping                           = 1,
        diff_opt                            = 1,
        km_opt                              = 4,
        diff_6th_opt                        = 0,
        diff_6th_factor                     = 0.12,
        base_temp                           = 290.,
        damp_opt                            = 0,
        zdamp                               = 5000.,
        dampcoef                            = 0.01,
        khdif                               = 0,
        kvdif                               = 0,
        non_hydrostatic                     = .true.,
        moist_adv_opt                       = 2,
        scalar_adv_opt                      = 2,
        hybrid_opt                          = 2,
        /

        &bdy_control
        spec_bdy_width                      = 5,
        spec_zone                           = 1,
        relax_zone                          = 4,
        specified                           = .true.,
        nested                              = .false.,
        /

        &chem
        kemit                               = 1,
        chem_opt                            = 233,
        chemdt                              = 10,
        gc_do_convection                    = 1,
        gc_do_pblmix                        = 1,
        gc_do_hemco                         = 1,
        gc_do_drydep                        = 1,
        gc_do_wetdep                        = 1,
        gc_do_chemistry                     = 1,
        have_bcs_chem                       = .false.,
        ne_area                             = 150,
        /

       &namelist_quilt
       nio_tasks_per_group = 0,
       nio_groups = 1,
       /

To run the initialization program, type

       ./real.exe

To run WRF-GC, use the distributed-memory parallel version of WRF's wrf.exe, like -

       mpirun -np 6 ./wrf.exe

To monitor output from WRF&GEOS-Chem, you can tail the "rsl.out.0000" file:

       tail -f rsl.out.0000

Output from WRF&GEOS-Chem are unified into the WRF output format (NetCDF Classic) files named "wrfout_d01_2015-01-01_00:00:00".

Notes

Running WRF-GC is largely similar to running WRF-Chem, thus we invite you to navigate the WRF-Chem User's Guide to familiarize with the workflow and diagnostic tools available at your disposal.