# Frequently Asked Questions

## Recommendations

  • Submit runs individually and quality control.

  • Check all steps in the process have run correctly.

  • Check main.bash.o has “substituting initial chemistry from restart” if do not want a cold start.

  • Manage space requirements, as run and output folders can get very large.

  • Run main.bash in 2 week chunks to fit within 48 hours.

  • Information on improving performance [here](https://github.com/wrfchem-leeds/WRFotron/issues/29).

  • A selection of data science scripts using Python [here](https://github.com/wrfchem-leeds/python-scripts).

## Anthropogenic emissions

  • Check that: - The anthro_emis input namelist (e.g., emis_edgarhtap2_mozmos.inp) has the following mappings (i.e., WRFChem variable assigned to inventory variable):

    • ORGI and ORGJ assigned to POM (particulate organic matter). - The emissions of Organic Carbon (OC) need to be converted to total particulate organic matter (POM), which includes the associated oxygen, hydrogen and other elements.

    • PM25I and PM25J assigned to OIN_PM2.5 (other inorganic matter under 2.5 $mu m$).

    • PM_10 assigned to PM2.5_10 (coarse particulate matter for 2.5-10 $mu m$).

    • These 3 inventory variables (i.e., POM, OIN_PM2.5, and PM2.5_10) have their own NetCDF files: - Ideally, these are provided directly from the emission inventory. - If not, then you can calculate them for your data offline.

    • Ensure that these files have their units attribute set to “kg m-2 s-1” ([reference](https://github.com/wrfchem-leeds/WRFotron/issues/48)). - This can be done using the following command for all emission variables within the files. For example, for the POM file for the variable emis_tot use: ncatted -O -a units,emis_tot,a,c,”kg m-2 s-1” EDGARHTAP2_MEIC2015_POM_2010.0.1x0.1.nc

  • Example for EDGARHTAP2.2/MEIC emissions using chem_opt = 202: - This inventory provided OC (organic carbon), PM2.5 (all PM2.5), and PM10 (all PM10). - First, create the required variables (save them all as new NetCDF files using the chemical names POM, OIN_PM2.5, and PM2.5_10):

    • Create POM file by multiplying OC by a scaling factor. - The scaling factor is usually in the range of 1.4-1.7 and is ideally sector-specific.

    • Create OIN_PM2.5 as equal to PM2.5 - BC - POM. - Here, you are subtracting POM, which you calculated above. - Set any negative values to 0 (as this can cause errors).

    • Create PM2.5_10 as equal PM10 - PM2.5. - Take care here to ensure subtacting PM2.5, and not just OIN_PM2.5. - Set any negative values to 0 (as this can cause errors).

    • Then, open the anthro_emis input namelist emis_edgarhtap2-meic2015_mozmos.inp. - Check that src_names has:

      • ‘POM(12)’

      • ‘OIN_PM2.5(1)’

      • ‘PM2.5_10(1)’

      • Check that emis_map has: - ‘ORGJ(a)->0.9*POM(emis_tot)’ - ‘PM25J(a)->0.9*OIN_PM2.5(emis_tot)’ - ‘PM_10(a)->PM2.5_10(emis_tot)’

  • These instructions may be different for other emission inventories and chemical mechanisms.

## Troubleshooting and errors

## Download ECMWF meteorlogy files

  • [Create an account with ECMWF](https://apps.ecmwf.int/registration/).

  • [Follow the steps](https://confluence.ecmwf.int/display/WEBAPI/Access+ECMWF+Public+Datasets).

  • Login.

  • Retrieve your key.

  • Copy the information to ~/.ecmwfapirc

  • Create a python2 environment for ecmwf-api-client (this library has not yet been updated for python 3).

    `bash conda create -n python2_ecwmf -c conda-forge ecmwf-api-client `

  • Go to the folder initial_boundary_meteo_ecmwf.

  • Edit the python scripts:

    • Both surface and pressurelevels.

    • Only need to change the date and target name.

  • Qsub the .bash scripts

  • Edit pre.bash to comment out the GFS and comment in the ECMWF files

  • Ensure the date and target name correspond to those you want to run with

  • Change the number of meteorological vertical levels from 27 (GFS) to 38 (ECMWF)

  • Also, the number of meteorological soil levels from 4 (GFS):

    • To 3 for ECMWF with WRFChem4

    • To 4 for ECMWF with WRFChem3

## To run with a nest

Offline nests: - See [step-by-step guide to run with a nest document from Carly Reddington](https://github.com/wrfchem-leeds/WRFotron/blob/master/guides/Guide_to_offline_nesting_CR.pdf). - Uses ndown.exe for one-way nesting - Feedback = 0 - Parent and nest domain may drift apart

Online nests: - Turn off urban physics (i.e. sf_urban_physics = 0, 0, 0) in physics subsection of namelist.wrf. - Requires a large amount of cores, as memory intensive - Uses wrf.exe for two-way nesting - Feedback = 1 - Have an odd number for the parent_grid_ratio. - For nest 2, (e_we-s_we+1) must be one greater than an integer multiple of the parent_grid_ratio (3 or 5). - WRF will decompose each domain in the exact same way, so ensure all the domains are similar shapes (i.e. don’t have a square domain within a rectangular domain, or even a rectangular domain which is longer in the x-direction within another domain which is longer in the y-direction). - Check all namelist settings and check all required nest parameters are set (use registry to check which parameters need to be set for every domain). - All variables with dimension = max_domains or (max_dom) need to be set for the nests - Careful the domains are not too big, otherwise wrfinput won’t be created - Use same physics options and physics calling options e.g. radt/cudt

  • An exception is cumulus scheme. One may need to turn it off for a nest that has grid distance of a few kilometers or less.

  • For nest, e_we and e_sn for a parent_grid_ratio of 3 must be return a whole number when minus 1 and divide by parent_grid_ratio (3)

  • Decrease restart_interval to 720 (2/day) from 360 (4/day)

  • Tests with less than 24 hours break the coarsest domains mozbc

  • Add diurnal cycle for all domains:

    • Within MAIN_emission_processing.ncl, change to all domains.

  • Timestep:

    • Decrease propotionally

  • Radiation timestep should coincide with the finest domain resolution (1 minute per km dx), but it usually is not necessary to go below 5 minutes. All domains should use the same value, so that radiation forcing is applied at the same time for all domains.

  • Other namelist.wrf settings specific for domains < 3km res
    • &domains

      • smooth_option = 0

    • &physics

      • cugd_avedx = 3

      • smooth_option = 0

      • cu_rad_feedback = .false.

      • cu_diag = 0

      • slope_rad = 1

      • topo_shading = 1

    • &dynamics

      • non_hydrostatic = .false.

## To run with cumulus parameterisation off

Namelist.chem - cldchem_onoff = 1 - chem_conv_tr = 0 (subgrid convective transport) - conv_tr_wetscav = 0 (subgrid convective wet scavenging) - conv_tr_aqchem = 0 (subgrid convective aqueous chemistry)

Namelist.wps - Resolution < 5 km

Namelist.wrf - Resolution < 5 km - cu_physics = 0 (cumulus parameterization off) - cugd_avedx = 3 (number of grid boxes over which subsidence is spread)

Master.bash, turn off nudging - s/GRIDFDDA/0/g

## Changes for WRFChem4

Select updates for WRFChem4 - Bug fixes:

  • NOAH land surface scheme

  • Thompson microphysics scheme

  • Boundary layer and surface schemes from MYNN.

  • Chemical reaction rate constant for reaction: SO<sub>2</sub> + OH -> SO<sub>4</sub>

  • Dust < 0.46 microns contribution to AOD.

  • Dust and salt bin contributions to AOD.

  • Urban physics.

  • Fires (module_mosaic_addemiss.F).

  • glysoa not needed as no longer uses to_toa variable which has the summation error (module_mosaic_driver.F).

  • GEOGRID.TBL within WPS4/geogrid is a hard copy of the GEOGRID.TBL.ARW_CHEM including erod.

  • New defaults

    • Hybrid sigma-pressure vertical coordinate.

    • Temperature variable is now moist theta.

    • Method to compute vertical levels, smooth variation of dz.

  • Various improved options available:

    • RRTMK (ra_sw_physics = 14, ra_lw_physics = 14) improves RRTMG

## To run with WRFChem3.7.1 or WRFChem4.2 Within config.bash: - Replace all instances of 4.2 with 3.7.1, or vice-versa. - Use the appropriate geography files, being either /nobackup/WRFChem/WPSGeog3 or /nobackup/WRFChem/WPSGeog4.

Within namelist.wps.blueprint: - For the geog_data_res variable (within &geogrid), use ‘modis_30s+30s’ for WRFChem3.7.1 and use ‘default’ for WRFChem4.2.

Within namelist.wrf.blueprint: - Remove the force_use_old_data variable (within &time_control) for WRFChem3.7.1 and have it set to T for WRFChem4.2. - For the num_metgrid_soil_layers variable (within &domains), use 4 for WRFChem3.7.1 and 3 for WRFChem4.2. - For the num_soil_layers variable (within &physics), use 4 for WRFChem3.7.1 and 3 for WRFChem4.2. - For the num_land_cat variable (within &physics), use 20 for WRFChem3.7.1 and 21 for WRFChem4.2.

## To run with a diurnal cycle

Choosing the diurnal cycle: - There are several different diurnal cycles in WRF_UoM_EMIT. - They are contained in the emission_script_data*.ncl files. Whichever of these files is named emission_script_data.ncl will be the diurnal cycle that is read by MAIN_emission_processing.ncl. The current emission_script_data.ncl is a copy of emission_script_data_EU.ncl.

  • EU = European diurnal cycles based on Olivier et al 2003

  • EX = Exaggerated diurnal cycle with 99% of emissions during daytime

  • QH = Qinghua diurnal cycle

  • Change settings in MAIN_emission_processing.ncl

    • time_offset

    • oc_om_scale

  • To check if the diurnal cycle application was successful, run the following python script, which should be within WRF_UoM_EMIT, and is automatically linked to your run folder during pre.bash. Take a copy of the file from the following location if you don’t have it:

    `bash python plot_wrfchemi.py `

## To run with NAEI emissions

[Follow the guide created by Ailish Graham](https://github.com/wrfchem-leeds/WRFotron/blob/master/guides/Guide_to_NAEI_emissions_AG.pdf).

## To add (or remove) variables to wrfout files

  • First, check whether the variable is in the Registry. If it isn’t, then add it using the steps [here](https://www.climatescience.org.au/sites/default/files/WRF_gill_registry.pdf).

  • Then, if you’re running with chemistry edit the file iofields.chem, otherwise edit the file iofields.met, which are both in WRFotron.

  • There are lines of text such as:

    `bash +:h:0:ccn1,ccn2,ccn3,ccn4,ccn5,ccn6 `

  • The + is to add or - is to remove a variable.

  • The h is for the history (wrfout) stream. Can have history, restarts, or both.

  • The 0 is for the stream number. Generally, stream numbers of 10-24 are okay, and avoid 22-23.

  • Then list the variables.

## To include upper boundary conditions

  • Turn on the have_bcs_upper boolean within namelist.chem.blueprint.

  • Set the lowest pressure level where the upper boundary concentrations are overwritten: fixed_ubc_press variable, default is 50 (hPa).

  • Provide 2 data files: a climatology for tropopause levels (clim_p_trop.nc) and an input file with upper boundary conditions for gas species (fixed_ubc_inname).

    • Climatologies for 4 different time periods derived from WACCM RCP simulations are [here](https://www2.acom.ucar.edu/wrf-chem/wrf-chem-tools-community). A direct download link is [here](http://www.acom.ucar.edu/wrf-chem/UBC_inputs.tar). Within here is the clim_p_trop.nc file, along with the 4 different climatology time periods: ubvals_b40.20th.track1_1950-1959.nc, ubvals_b40.20th.track1_1980-1989.nc, ubvals_b40.20th.track1_1996-2005.nc, and ubvals_rcp4_5.2deg_2020-2029.nc where the years used to produce the climatology are specified in the file names.

  • Copy the climatology files over to each run folder by adding the following to the bottom of pre.bash:

    `bash msg "bringing over upper boundary condition files" cp /nobackup/${USER}/where_you_place_these_files/{clim_p_trop.nc,ubvals_b40.20th.track1_1996-2005.nc} . `

  • More information is [here](https://www2.acom.ucar.edu/sites/default/files/wrf-chem/8A_2_Barth_WRFWorkshop_11.pdf) and within Chapter 2 [here](https://github.com/wrfchem-leeds/WRFotron/blob/master/guides/MOZCART_UsersGuide.pdf).

## To run with the chemistry option T1-MOZCART (chem_opt = 114)

  • Replace the contents of mozbc.inp with that from mozbc.inp.blueprint_114_mz4.

  • Delete ONIT from boundary condition input file (i.e. moz0001.nc), as this is not currently in our version of WRFChem.

  • Delete N2O from boundary condition input file (i.e. moz0001.nc), as this is not in the MOZBC netcdf file.

  • Make the following changes to namelist.chem.blueprint: - cldchem_onoff = 0, was previously 1. - biomass_burn_opt = 4, was previously 2.

  • Make the following change to namelist.wrf.blueprint: - auxinput6_inname = ‘wrfbiochemi_d<domain>’, ! biogenic emission filename, was previously ‘wrfbiochemi_d<domain>_<date>’.

  • More information is [here](https://github.com/wrfchem-leeds/WRFotron/blob/master/guides/T1-MOZCART-UsersGuide-27April2018.pdf).

## Benchmarking and Testing

  • Run together automatically by submitting . benchmark_and_test.bash.

  • This runs short (48 hour) simulations per season over the default domain and evaluates against either the China measurements or from OpenAQ.

  • To select which measurement set the model is evaluated against, set the corresponding Boolean in benchmark.py.

  • They run from the output directory, and can both be run manually using qsub benchmark.bash and qsub tests.bash.

  • To discuss these further and suggest improvements, see the discussions for them: [Benchmarks](https://github.com/wrfchem-leeds/WRFotron/discussions/34) and [Tests](https://github.com/wrfchem-leeds/WRFotron/discussions/33).

## Run WRFChem for long-term scenarios (Climate WRF)

## To change the MOZBC boundary conditions - Change the data reference in [pre.bash](https://github.com/wrfchem-leeds/WRFotron/blob/master/pre.bash#L201-L208). - Change mozbc.inp to be a copy of the corresponding MOZBC blueprint in the namelists folder, e.g., to use WACCM instead of MZ4 make [mozbc.inp](https://github.com/wrfchem-leeds/WRFotron/blob/master/mozbc.inp) a copy of [mozbc.inp.blueprint_202_waccm](https://github.com/wrfchem-leeds/WRFotron/blob/master/namelists/mozbc.inp.blueprint_202_waccm).

## Heterogeneous chemistry with chem_opt = 202 - Follow instructions [here](https://github.com/wrfchem-leeds/WRFotron/tree/master/guides/heterogeneous_chem_WRFChem_guide.pdf).

## Misc.

  • To see details of all the variables, see the registry files e.g. for chemistry: WRFChem{version}/Registry/registry.chem

  • To see the equations used for your mechanism, see the file: WRFChem{version}/chem/KPP/mechanisms/{mechanism}/{mechanism}.eqn

  • To see the variable mappings between the mechanism and WRFChem (which can have different names), see the file: WRFChem{version}/chem/KPP/mechanisms/{mechanism}/{mechanism}.equiv

  • To see the rate constants used per equation, see the file (note, that these match the equations in sequential order e.g., the final rate constant for equation 346 matches to equation {S060}): WRFChem{version}/chem/KPP/mechanisms/{mechanism}/{mechanism}_Rates.f90