Chemical Initial/Boundary Conditions (IC/BC)

WRF-GC is a regional model. Boundary conditions from a global model are generally required. Initial conditions can be provided by a WRF-GC run or other global models.

You can use MOZART4-GEOS5, CAM-chem, or GEOS-Chem as input for initial/boundary conditions.

The general process is as follows:

  • Identify which data source you want to use as ic/bc.

  • Set-up WRF-GC, and run real.exe to generate wrfinput_d01 (initial conditions), and wrfbdy_d01 (boundary conditions)

  • Prepare ic/bc inputs into a netCDF format accepted by mozbc. (mozbc for WRF-GC is located here)

  • Use mozbc to add these inputs to wrfinput_d01 and/or wrfbdy_d01 files.

  • Run the WRF-GC model.

Preparing IC/BC file from global GEOS-Chem output

Details are available in the PDF getting started guide. A MATLAB script will process global GEOS-Chem outputs to netCDF files accepted by mozbc, which are then generated into WRF(-GC) initial/boundary files.

Run the GEOS-Chem standard full-chemistry simulation

We recommend running at a resolution 2 x 2.5 degree because this will provide higher resolution initial and boundary condition data to WRF-GC (which generally has higher resolution). 4 x 5 degree is also supported.

The running time must cover the WRF-GC simulation period, with at least one day preceding: e.g. if the simulation period of WRF-GC is from 2015-06-10 00:00:00 to 2015-06-20 00:00:00 (UTC), the time ranges for GEOS-Chem should be at least available from 2015-06-09 00:00:00 to 2015-06-20 00:00:00, not including necessary initialization (spin-up).

Output the netCDF diagnostic files every 6 hours (00, 06, 12, 18), including:

  1. GEOSChem.SpeciesConc.YYYYMMDD_HHIIz.nc4 (contains instantaneous SpeciesConc_?ADV?)

  2. GEOSChem.StateMet.YYYYMMDD_HHIIz.nc4 (contains Met_PS1DRY).

Using the HISTORY.rc configuration similar to follows:

  SpeciesConc.template:       '%y4%m2%d2_%h2%n2z.nc4',
  SpeciesConc.frequency:      00000000 060000
  SpeciesConc.duration:       00000000 060000
  SpeciesConc.mode:           'instantaneous'
  SpeciesConc.fields:         'SpeciesConc_?ALL?             ',
::

  StateMet.template:          '%y4%m2%d2_%h2%n2z.nc4',
  StateMet.frequency:         00000000 060000
  StateMet.duration:          00000000 060000
  StateMet.mode:              'instantaneous'
  StateMet.fields:            'Met_AD                        ',
                              'Met_AIRDEN                    ',
                              'Met_AIRVOL                    ',
                              'Met_BXHEIGHT                  ',
                              'Met_PBLTOPL                   ',
                              'Met_PBLH                      ',
                              'Met_PMID                      ',
                              'Met_PMIDDRY                   ',
                              'Met_PS1DRY                    ',
                              'Met_PS1WET                    ',
                              'Met_PS2DRY                    ',
                              'Met_PS2WET                    ',
                              'Met_PSC2WET                   ',
                              'Met_PSC2DRY                   ',
                              'Met_T                         ',
                              'Met_TO3                       ',
                              'Met_TropHt                    ',
                              'Met_TropLev                   ',
                              'Met_TropP                     ',
                              'Met_TS                        ',
::

Converting GEOS-Chem output to mozbc readable format

Use the MATLAB script convert_gcoutput_mozart_structure_selected_domain.m (available here, GNU Octave may work as well) to merge the GEOS-Chem output files and reconstruct the data structure for mozbc to read.

Run the script in the GEOS-Chem output directory (OutputDir). Modify the script before running as follows:

  1. filename_input: set the input filename as any one of the GEOS-Chem species concentration output files, e.g. GEOSChem.SpeciesConc.20150601_0000z.nc4.

  2. filename_output: set the output filename freely. If your file is too large, you may want to split the dates into separate files. In this case, the file names must end in 4-character integers, i.e., 0001.nc, 0002.nc, 0003.nc, …

  3. simulation_4_5/simulation_2_25:

If the resolution of global GEOS-Chem simulation is 2×2.5 degree, please set it as follows:

simulation_4_5               = false;
simulation_2_25              = true;

If the resolution of global GEOS-Chem simulation is 4×5 degree, please set it as follows:

simulation_4_5               = true;
simulation_2_25              = false;

  1. Set the time ranges for output file

startyr                      = 2015;
endyr                        = 2015;
startmon                     = 6;
endmon                       = 6;
startdate                    = 7;
enddate                      = 21;

  1. Set the domain for output file (needs to be larger than your WRF-GC domain). The subsetting is index-based.

For example, if the resolution of global GEOS-Chem simulation is 2x2.5, longitude indices range from 0 to 144 and correspond to longitudes 0:2.5:357.5, latitude indices range from 1 to 91 and correspond to -90:2:90. Then these indices would be set in the script as follows:

lon_left                     = 1;  % longitude of western lateral condition
lon_right                    = 73; % longitude of eastern lateral condition
lat_bottom                   = 46; % latitude of southern lateral condition
lat_upper                    = 91; % latitude of northern lateral condition

The netCDF file will be generated after running the script.

Note

If you want to use data from other year / months to run WRF-GC, you can tweak the script to read alternative GEOS-Chem output file names. The time slices in the GEOS-Chem output files is not checked by the script.

Warning

If the script is taking too long to write the netCDF output file, try splitting the file into multiple contiguous date chunks. mozbc will be able to read and automatically increment the file number, provided they end with four integer digits.

Preparing IC/BC file from CAM-chem/WACCM output

Refer to the WRF-Chem documentation.

Using mozbc

Building mozbc (only need to do once)

  1. Download a customized version of mozbc for WRF-GC’s hybrid sigma-eta grid. This is available at Xu Feng’s GitHub, fengx7/mozbc_for_WRFv3.9

git clone https://github.com/fengx7/mozbc_for_WRFv3.9.git mozbc

  1. Go to the mozbc directory downloaded and configure the environment. Set up the path to your netCDF library

export NETCDF_DIR=/path/to/netcdf/here

The content inside $NETCDF_DIR should have include, … folders that correspond to netCDF.

  1. Compile mozbc. Run ./make_mozbc.

Configuring mozbc

Edit the input configuration file ending in .inp, corresponding to the version of GEOS-Chem you are using.

Configure the paths to the WRF input in dir_wrf (wrfinput_d01, wrfbdy_d01 … - run real.exe to generate these first) and the source netCDF file for IC/BC (created in step above). Make sure the paths end in trailing slashes (/)

dir_wrf = '/my/path/to/WRF/run/'
dir_moz = '/my/path/to/source/data/for/ic-bc/'
fn_moz  = 'wrfgc_icbc_data_test1.nc'

Run mozbc:

./mozbc < input.inp

Note

If you want to change the species mapping or add new species, please modify the spc_map in the input file, e.g.: 'isoprene -> ISOP' where “isoprene” is the name of WRF-GC chemical species and “ISOP” is the name of GEOS-Chem species.

If the chemical IC/BC have been successfully written into the wrfinput_d<domain> and wrfbdy_d<domain> files, “bc_wrfchem completed successfully” will appear.