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Running WRFChem ===== The i ran meteorology sucessfuly last time with the same configurations, but now with chemistry does not work. ## namelist.wps  &share wrf_core = 'ARW', max_dom = 3, start_date = '2014-08-04_00:00:00','2014-08-04_00:00:00','2014-08-04_00:00:00', end_date = '2014-08-11_00:00:00','2014-08-11_00:00:00','2014-08-11_00:00:00', interval_seconds = 21600 io_form_geogrid = 2, / &geogrid parent_id = 1, 1, 2, parent_grid_ratio = 1, 5, 5, i_parent_start = 1, 26, 57, j_parent_start = 1, 26, 59, e_we = 80, 181, 191, e_sn = 80, 181, 181, geog_data_res = 'modis_30s+2m', 'modis_30s+30s', 'modis_30s+30s', dx = 25000, dy = 25000, map_proj = 'mercator', ref_lat = -23.550391, ref_lon = -46.633949, truelat1 = -23.550391, truelat2 = -24.550, stand_lon = -39.300, geog_data_path = '/scr4/sibarra/geo/geog' / &ungrib out_format = 'WPS', prefix = 'FILE', / &metgrid fg_name = 'FILE' io_form_metgrid = 2, /  running ncl util/plotgrids_new.ncl returns the following figure. ![](https://i.imgur.com/7vk4j79.png) Now can be run the other wrf scripts:  cd geogrid ln -sf GEOGRID.TBL.ARW_CHEM GEOGRID.TBL ln -sf ungrib/Variable_Tables/Vtable.GFS Vtable ./geogrid.exe ./link_grib.csh /scr4/sibarra/met/GFS2014/GFS* ./ungrib.exe ./metgrid.exe  ## real.exe From http://www2.mmm.ucar.edu/wrf/users/docs/user_guide_V3.8/users_guide_chap4.htm#Real The real-data WRF cases are those that have the input data to the “real.exe” The WPS package delivers data that is ready to be used in the WRF system by the “real.exe” program: - The data adheres to the WRF IO API. Unless you are developing special tools, stick with the netCDF option to communicate between the WPS package and “real.exe”. - The data has already been horizontally interpolated to the correct grid-point staggering for each variable, and the winds are correctly rotated to the WRF model map projection. - 3-D meteorological data required from the WPS: pressure, u, v, temperature, relative humidity, geopotential height - Optional 3-D hydrometeor data may be provided to the real program at run-time, but these fields will not be used in the coarse-grid lateral boundary file. Fields named: QR, QC, QS, QI, QG, QH, QNI (mixing ratio for rain, cloud, snow, ice, graupel, hail, and number concentration) are eligible for input from the metgrid output files. - 3D soil data from the WPS: soil temperature, soil moisture, soil liquid (optional, depending on physics choices in the WRF model) - 2D meteorological data from the WPS: sea level pressure, surface pressure, surface u and v, surface temperature, surface relative humidity, input elevation - 2-D meteorological optional data from WPS: sea surface temperature, physical snow depth, water equivalent snow depth - 2D static data for the physical surface: terrain elevation, land use categories, soil texture categories, temporally-interpolated monthly data, land sea mask, elevation of the input model’s topography - 2D static data for the projection: map factors, Coriolis, projection rotation, computational latitude - constants: domain size, grid distances, date - The WPS data may either be isobaric or some more-generalized vertical coordinate, where each column is monotonic in pressure - All 3-D meteorological data (wind, temperature, height, moisture, pressure) must have the same number of levels, and variables must have the exact same levels. For example, it is not acceptable to have more levels for temperature (for example) than height. Likewise, it is not acceptable to have an extra level for the horizontal wind components, but not for moisture.  &time_control run_days = 0, run_hours = 0, run_minutes = 0, run_seconds = 0, start_year = 2014, 2014, 2014, start_month = 08, 08, 08, start_day = 04, 04, 04, start_hour = 00, 00, 00, start_minute = 00, 00, 00, start_second = 00, 00, 00, end_year = 2014, 2014, 2014, end_month = 08, 08, 08, end_day = 11, 11, 11, end_hour = 00, 00, 00, end_minute = 00, 00, 00, end_second = 00, 00, 00, interval_seconds = 21600 input_from_file = .true.,.true.,.true., history_interval = 60, 60, 60, history_outname = "/scr4/sibarra/masp/run2/wrfout_d<domain>_<date>" frames_per_outfile = 5000, 5000, 5000, restart = .false., restart_interval = 10080, auxinput5_interval_m = 60, io_form_auxinput2 = 2, !io_form_auxinput5 = 0, io_form_history = 2 io_form_restart = 2 io_form_input = 2 io_form_boundary = 2 debug_level = 0 / &domains time_step = 150, time_step_fract_num = 0, time_step_fract_den = 1, max_dom = 3, e_we = 80, 181, 191, e_sn = 80, 181, 181, e_vert = 35, 35, 35, p_top_requested = 5000, num_metgrid_levels = 27, vert_refine_fact = 1, num_metgrid_soil_levels = 4, dx = 25000, 5000, 1000, dy = 25000, 5000, 1000, grid_id = 1, 2, 3, parent_id = 1, 1, 2, i_parent_start = 1, 26, 57, j_parent_start = 1, 26, 59, parent_grid_ratio = 1, 5, 5, parent_time_step_ratio = 1, 5, 5, feedback = 1, smooth_option = 0 / &physics mp_physics = 2, 2, 2, ra_lw_physics = 1, 1, 1, ra_sw_physics = 2, 2, 2, radt = 15, 15, 15, sf_sfclay_physics = 1, 1, 1, sf_surface_physics = 2, 2, 2, bl_pbl_physics = 1, 1, 1, bldt = 0, 0, 0, cu_physics = 5, 5, 0, cudt = 0, 0, 0, cu_diag = 1, cu_rad_feedback = .true., isfflx = 1, ifsnow = 0, icloud = 0, surface_input_source = 1, num_soil_layers = 4, num_land_cat = 20, sf_urban_physics = 1, 1, 1, / &fdda / &dynamics w_damping = 0, diff_opt = 1, 1, 1, km_opt = 4, 4, 4, diff_6th_opt = 0, 0, 0, diff_6th_factor = 0.12, 0.12, 0.12, base_temp = 290. damp_opt = 0, zdamp = 5000., 5000., 5000., dampcoef = 0.2, 0.2, 0.2 khdif = 0, 0, 0, kvdif = 0, 0, 0, non_hydrostatic = .true., .true., .true., moist_adv_opt = 1, 1, 1, scalar_adv_opt = 1, 1, 1, / &bdy_control spec_bdy_width = 5, spec_zone = 1, relax_zone = 4, specified = .true., .false.,.false., nested = .false., .true., .true., / &grib2 / &chem kemit = 1, chem_opt = 0, 0, 0, bioemdt = 30, 15, 15, photdt = 30, 15, 15, chemdt = 2., 2., 2., io_style_emissions = 1, ! 2 cuando se lee modelar todo el periodo emiss_inpt_opt = 1, 1, 1, emiss_opt = 2, 3, 3, chem_in_opt = 0, 0, 0, phot_opt = 2, 2, 2, gas_drydep_opt = 0, 1, 1, aer_drydep_opt = 0, 1, 1, bio_emiss_opt = 1, 1, 1, dust_opt = 0, dmsemis_opt = 0, seas_opt = 2, gas_bc_opt = 1, 1, 1, gas_ic_opt = 1, 1, 1, aer_bc_opt = 1, 1, 1, aer_ic_opt = 1, 1, 1, aer_op_opt = 1, 0, 0, ! opt_pars_out = 1, 0, 0, gaschem_onoff = 1, 1, 1, aerchem_onoff = 1, 1, 1, wetscav_onoff = 0, 0, 0, cldchem_onoff = 0, 0, 0, vertmix_onoff = 1, 1, 1, chem_conv_tr = 1, 1, 1, biomass_burn_opt = 0, 0, 1, ! plumerisefire_frq = 30, 30, 30, aer_ra_feedback = 0, 0, 0 have_bcs_chem = .true., .false., .false., / &namelist_quilt nio_tasks_per_group = 0, nio_groups = 1, /  Then  ln -sf ../../../WPS/met_em* . ssh noh4 mpirun -machinefile /scr4/sibarra/host2 -np 32 ./real.exe & tail -f rsl.error.0000  After real were generated al three wrfinputs for d01, d02 and d03. So now it is a good idea to generate the wrfchemi input files. Some of the results are ![NO](https://i.imgur.com/QgMyuOE.png) ![CO](https://i.imgur.com/zjS4Nu0.png) ![ALD](https://i.imgur.com/PdVLBMC.png) ## wrf.exe After ./real.exe was ran sucessfully, it is time to run ./wrf.exe. Nevertheless, it can be used the same namelist.input. That is because, the namelist.input in this case has max_dom=3, and the strategy here will be to simulate first the domain 3 and 2, the bigger domains.  &time_control run_days = 0, run_hours = 0, run_minutes = 0, run_seconds = 0, start_year = 2014, 2014, 2014, start_month = 08, 08, 08, start_day = 04, 04, 04, start_hour = 00, 00, 00, start_minute = 00, 00, 00, start_second = 00, 00, 00, end_year = 2014, 2014, 2014, end_month = 08, 08, 08, end_day = 11, 11, 11, end_hour = 00, 00, 00, end_minute = 00, 00, 00, end_second = 00, 00, 00, interval_seconds = 21600 input_from_file = .true.,.true.,.true., history_interval = 60, 60, 60, history_outname = "/scr4/sibarra/masp/run2/wrfout_d<domain>_<date>" frames_per_outfile = 5000, 5000, 5000, restart = .false., restart_interval = 10080, auxinput5_interval_m = 60, io_form_auxinput2 = 2, !io_form_auxinput5 = 0, io_form_history = 2 io_form_restart = 2 io_form_input = 2 io_form_boundary = 2 debug_level = 0 / &domains time_step = 150, time_step_fract_num = 0, time_step_fract_den = 1, max_dom = 2, e_we = 80, 181, 191, e_sn = 80, 181, 181, e_vert = 35, 35, 35, p_top_requested = 5000, num_metgrid_levels = 27, vert_refine_fact = 1, num_metgrid_soil_levels = 4, dx = 25000, 5000, 1000, dy = 25000, 5000, 1000, grid_id = 1, 2, 3, parent_id = 1, 1, 2, i_parent_start = 1, 26, 57, j_parent_start = 1, 26, 59, parent_grid_ratio = 1, 5, 5, parent_time_step_ratio = 1, 5, 5, feedback = 1, smooth_option = 0 / &physics mp_physics = 2, 2, 2, ra_lw_physics = 1, 1, 1, ra_sw_physics = 2, 2, 2, radt = 15, 15, 15, sf_sfclay_physics = 1, 1, 1, sf_surface_physics = 2, 2, 2, bl_pbl_physics = 1, 1, 1, bldt = 0, 0, 0, cu_physics = 5, 5, 0, cudt = 0, 0, 0, cu_diag = 1, cu_rad_feedback = .true., isfflx = 1, ifsnow = 0, icloud = 0, surface_input_source = 1, num_soil_layers = 4, num_land_cat = 20, sf_urban_physics = 1, 1, 1, / &fdda / &dynamics w_damping = 0, diff_opt = 1, 1, 1, km_opt = 4, 4, 4, diff_6th_opt = 0, 0, 0, diff_6th_factor = 0.12, 0.12, 0.12, base_temp = 290. damp_opt = 0, zdamp = 5000., 5000., 5000., dampcoef = 0.2, 0.2, 0.2 khdif = 0, 0, 0, kvdif = 0, 0, 0, non_hydrostatic = .true., .true., .true., moist_adv_opt = 1, 1, 1, scalar_adv_opt = 1, 1, 1, / &bdy_control spec_bdy_width = 5, spec_zone = 1, relax_zone = 4, specified = .true., .false.,.false., nested = .false., .true., .true., / &grib2 / &chem kemit = 1, chem_opt = 0, 0, 0, bioemdt = 30, 15, 15, photdt = 30, 15, 15, chemdt = 2., 2., 2., io_style_emissions = 1, ! 2 cuando se lee modelar todo el periodo emiss_inpt_opt = 1, 1, 1, emiss_opt = 2, 3, 3, chem_in_opt = 0, 0, 0, phot_opt = 2, 2, 2, gas_drydep_opt = 0, 1, 1, aer_drydep_opt = 0, 1, 1, bio_emiss_opt = 1, 1, 1, dust_opt = 0, dmsemis_opt = 0, seas_opt = 2, gas_bc_opt = 1, 1, 1, gas_ic_opt = 1, 1, 1, aer_bc_opt = 1, 1, 1, aer_ic_opt = 1, 1, 1, aer_op_opt = 1, 0, 0, ! opt_pars_out = 1, 0, 0, gaschem_onoff = 1, 1, 1, aerchem_onoff = 1, 1, 1, wetscav_onoff = 0, 0, 0, cldchem_onoff = 0, 0, 0, vertmix_onoff = 1, 1, 1, chem_conv_tr = 1, 1, 1, biomass_burn_opt = 0, 0, 1, ! plumerisefire_frq = 30, 30, 30, aer_ra_feedback = 0, 0, 0 have_bcs_chem = .true., .false., .false., / &namelist_quilt nio_tasks_per_group = 0, nio_groups = 1, /  The changes from the previous namelist are: max_dom=2  ssh noh4 mpirun -machinefile /scr4/sibarra/host2 -np 32 ./wrf.exe & tail -f rsl.error.0000  ## ndow.exe before running ./ndow.exe there are important changes to do at the namelist.input. Timestep should changes from 150 to 6, interval_seconds = 3600, max_dom=2, and change e_we, e_sn. In summary, delete the first column. also:  mv wrfinput_d03 wrfndi_d02 rm wrfinput_d01 | rm wrfinput_d02 ln -sf /scr4/sibarra/masp/run2/wrfout_d02_2014-08-04_00\:00\:00 wrfout_d01_2014-08-00_00\:00\:00 mpirun -machinefile /scr4/sibarra/host2 -np 32 ./ndown.exe &  Because the inputs are wrfndi_d02 and wrfout_d01.... **./down.exe** returns wrfinput and wrfbdy d02.  &time_control run_days = 0, run_hours = 0, run_minutes = 0, run_seconds = 0, start_year = 2014, 2014, 2014, start_month = 08, 08, 08, start_day = 04, 04, 04, start_hour = 00, 00, 00, start_minute = 00, 00, 00, start_second = 00, 00, 00, end_year = 2014, 2014, 2014, end_month = 08, 08, 08, end_day = 11, 11, 11, end_hour = 00, 00, 00, end_minute = 00, 00, 00, end_second = 00, 00, 00, interval_seconds = 21600 input_from_file = .true.,.true.,.true., history_interval = 60, 60, 60, history_outname = "/scr4/sibarra/masp/run2/wrfout_d<domain>_<date>" frames_per_outfile = 5000, 5000, 5000, restart = .false., restart_interval = 10080, auxinput5_interval_m = 60, io_form_auxinput2 = 2, !io_form_auxinput5 = 0, io_form_history = 2 io_form_restart = 2 io_form_input = 2 io_form_boundary = 2 debug_level = 0 / &domains time_step = 6, time_step_fract_num = 0, time_step_fract_den = 1, max_dom = 2, e_we = 181, 191, e_sn = 181, 181, e_vert = 35, 35, p_top_requested = 5000, num_metgrid_levels = 27, vert_refine_fact = 1, num_metgrid_soil_levels = 4, dx = 5000, 1000, dy = 5000, 1000, grid_id = 2, 3, parent_id = 1, 2, i_parent_start = 26, 57, j_parent_start = 26, 59, parent_grid_ratio = 5, 5, parent_time_step_ratio = 5, 5, feedback = 1, smooth_option = 0 / &physics mp_physics = 2, 2, 2, ra_lw_physics = 1, 1, 1, ra_sw_physics = 2, 2, 2, radt = 15, 15, 15, sf_sfclay_physics = 1, 1, 1, sf_surface_physics = 2, 2, 2, bl_pbl_physics = 1, 1, 1, bldt = 0, 0, 0, cu_physics = 5, 5, 0, cudt = 0, 0, 0, cu_diag = 1, cu_rad_feedback = .true., isfflx = 1, ifsnow = 0, icloud = 0, surface_input_source = 1, num_soil_layers = 4, num_land_cat = 20, sf_urban_physics = 1, 1, 1, / &fdda / &dynamics w_damping = 0, diff_opt = 1, 1, 1, km_opt = 4, 4, 4, diff_6th_opt = 0, 0, 0, diff_6th_factor = 0.12, 0.12, 0.12, base_temp = 290. damp_opt = 0, zdamp = 5000., 5000., 5000., dampcoef = 0.2, 0.2, 0.2 khdif = 0, 0, 0, kvdif = 0, 0, 0, non_hydrostatic = .true., .true., .true., moist_adv_opt = 1, 1, 1, scalar_adv_opt = 1, 1, 1, / &bdy_control spec_bdy_width = 5, spec_zone = 1, relax_zone = 4, specified = .true., .false.,.false., nested = .false., .true., .true., / &grib2 / &chem kemit = 1, chem_opt = 0, 0, 0, bioemdt = 30, 15, 15, photdt = 30, 15, 15, chemdt = 2., 2., 2., io_style_emissions = 1, ! 2 cuando se lee modelar todo el periodo emiss_inpt_opt = 1, 1, 1, emiss_opt = 2, 3, 3, chem_in_opt = 0, 0, 0, phot_opt = 2, 2, 2, gas_drydep_opt = 0, 1, 1, aer_drydep_opt = 0, 1, 1, bio_emiss_opt = 1, 1, 1, dust_opt = 0, dmsemis_opt = 0, seas_opt = 2, gas_bc_opt = 1, 1, 1, gas_ic_opt = 1, 1, 1, aer_bc_opt = 1, 1, 1, aer_ic_opt = 1, 1, 1, aer_op_opt = 1, 0, 0, ! opt_pars_out = 1, 0, 0, gaschem_onoff = 1, 1, 1, aerchem_onoff = 1, 1, 1, wetscav_onoff = 0, 0, 0, cldchem_onoff = 0, 0, 0, vertmix_onoff = 1, 1, 1, chem_conv_tr = 1, 1, 1, biomass_burn_opt = 0, 0, 1, ! plumerisefire_frq = 30, 30, 30, aer_ra_feedback = 0, 0, 0 have_bcs_chem = .true., .false., .false., / &namelist_quilt nio_tasks_per_group = 0, nio_groups = 1, /  Once ./ndown.exe was ran, outputs must change names:  mv wrfinput_d02 wrfinput_d01 | mv wrfbdy_d02 wrfbdy_d01  It is also important to change name or remove wrfout_d01...  rm wrfout_d01_2014-08-00_00\:00\:00  In this case, this file comes form a symbolic link ln -sf ... ## ./wrf.exe  &time_control run_days = 0, run_hours = 0, run_minutes = 0, run_seconds = 0, start_year = 2014, start_month = 08, start_day = 04, start_hour = 00, start_minute = 00, start_second = 00, end_year = 2014, end_month = 08, end_day = 11, end_hour = 00, end_minute = 00, end_second = 00, interval_seconds = 21600 input_from_file = .true.,.true.,.true., history_interval = 60, history_outname = "/scr4/sibarra/masp/run2/1km/wrfout_d<domain>_<date>" frames_per_outfile = 5000, restart = .false., restart_interval = 10080, auxinput5_interval_m = 60, io_form_auxinput2 = 2, ! io_form_auxinput5 = 11, io_form_history = 2 io_form_restart = 2 io_form_input = 2 io_form_boundary = 2 debug_level = 0 / &domains time_step = 3, time_step_fract_num = 0, time_step_fract_den = 1, max_dom = 1, e_we = 191, e_sn = 181, e_vert = 35, p_top_requested = 5000, num_metgrid_levels = 27, vert_refine_fact = 1, num_metgrid_soil_levels = 4, dx = 1000, dy = 1000, grid_id = 3, parent_id = 2, i_parent_start = 57, j_parent_start = 59, parent_grid_ratio = 5, parent_time_step_ratio = 5, feedback = 1, smooth_option = 0 / &physics mp_physics = 2, ra_lw_physics = 1, ra_sw_physics = 2, radt = 15, sf_sfclay_physics = 1, sf_surface_physics = 2, bl_pbl_physics = 1, bldt = 0, cu_physics = 0, cudt = 0, cu_diag = 1, cu_rad_feedback = .true., isfflx = 1, ifsnow = 0, icloud = 0, surface_input_source = 1, num_soil_layers = 4, num_land_cat = 20, sf_urban_physics = 1, / &fdda / &dynamics w_damping = 0, diff_opt = 1, km_opt = 4, diff_6th_opt = 0, diff_6th_factor = 0.12, base_temp = 290. damp_opt = 0, zdamp = 5000., dampcoef = 0.2 khdif = 0, kvdif = 0, non_hydrostatic = .true., .true., .true., moist_adv_opt = 1, scalar_adv_opt = 1, / &bdy_control spec_bdy_width = 5, spec_zone = 1, relax_zone = 4, specified = .true., .false.,.false., nested = .false., .true., .true., / &grib2 / &chem kemit = 1, chem_opt = 1, bioemdt = 15, photdt = 15, chemdt = 2., io_style_emissions = 2, emiss_inpt_opt = 1, emiss_opt = 2, chem_in_opt = 1, phot_opt = 2, gas_drydep_opt = 1, aer_drydep_opt = 0, bio_emiss_opt = 0, dust_opt = 0, dmsemis_opt = 0, seas_opt = 0, gas_bc_opt = 1, gas_ic_opt = 1, aer_bc_opt = 1, aer_ic_opt = 1, aer_op_opt = 0, ! opt_pars_out = 0, gaschem_onoff = 1, aerchem_onoff = 1, wetscav_onoff = 0, cldchem_onoff = 0, vertmix_onoff = 1, chem_conv_tr = 0, biomass_burn_opt = 0, aer_ra_feedback = 0 have_bcs_chem = .false., .false., .false., / &namelist_quilt nio_tasks_per_group = 0, nio_groups = 1, /  Before run the model, it is good idea to check the files in the folder: ![](https://i.imgur.com/tLqCwon.png) Important files: - wrfbdy_d01 - wrfchemi_d01_2014_08_00_00:00:00 - wrfndi_d02 - wrfinput_d01 Then, just run the model  mpirun -machinefile /scr4/sibarra/host2 -np 32 ./wrf.exe & tail -f rsl.error.0000  So far, the results look very low. CO ![CO (ppm)](https://i.imgur.com/MsC6L7G.png) O$_3$ ![O3 (ppm)](https://i.imgur.com/UAOx6Ix.png) It seems that is not reading the emissiosn data, however, the terminal says that emissions data i been read correctly (i believe). ![emis](https://i.imgur.com/6bRNcJM.png)