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.
Make use of CPU affinity to have dedicated input/output processors, as these are not scalable in WRF-Chem:
- Within namelist.wrf.blueprint:
  &namelist_quilt
  
  nio_tasks_per_group = 5 ! number of processors used for IO quilting per IO group.
  
  nio_tasks_per_group = 2 ! number of quilting groups
  
  So the number of cores = nproc_x * nproc_y + nio_groups * nio_tasks_per_group
  
  For example, 42 = 4 * 8 + 2 * 5
LC and BS have created a selection of data science scripts using Python.

Troubleshooting and errors¶

Find the errors’ first occurance, checking rsl.error, rsl.out, .e, .o, and .log files within the run folder.
You need to make sure all programs are compiled and useable, and that the paths in your config.bash point to the correct locations.
You need to ensure that your data is all available for the period you want to simulate (including meteo spin-up).
You need to ensure your namelists are correct.
If the error if related to a FORTRAN run-time error.
Check WRF FAQ’s.
Check WRF forums.
Check Google groups for:
- WRFChem.
- fire_emiss.
- anthro_emis.
- Runs.
Try increasing the debug level.
Timesteps for meteorology (time_step in namelist.wrf), chemistry (chemdt in namelist.chem), and biogenics (bioemdt in namelist.chem) need to match (careful of units).
If no error message given at the bottom of rsl.error. file:
- Potentially a violation of the CFL criterion:
  Try reducing the timestep.
  
  Try turning w_damping off.
- Potentially a memory error:
  Increase the number of cores.
  
  Increase the memory per core.

Download ECMWF meteorlogy files¶

Create an account with ECMWF.
Follow the steps.
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).

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.
- 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: SO₂ + OH -> SO₄
  
  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:

python plot_wrfchemi.py

To run with NAEI emissions¶

Follow the guide created by Ailish Graham.

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.
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:

+: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. A direct download link is here. 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:

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 and here within Chapter 2 here.

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.