Perturbations in NO by lightning do not alter NO2 mixing ratio

fjp...@gmail.com

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Jan 9, 2023, 1:54:29 AM1/9/23

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Dear all,

I am running WRF-Chem with lightning. My goal is investigating the influence of LNOX on other chemical species.

I have built my configuration from the Exercise 4 (https://ruc.noaa.gov/wrf/wrf-chem/tutorialexercises/tutorialexercises004.html), i.e., using RACM-KPP-GOCART option. I have adapted the domain and the date/time to my case.

I am running a simulation with lightning (lightning_option=1) and another without lightning.

I can see a significant total number of lightning in the simulation with lightning. In addition, I can see high values of lnox_total in the output. I can also see notable variations in the mixing ratio of NO between the simulations with and without lightning. However, it seems like the injected LNO is not influencing other chemical species, as I cannot see any perturbation in NO2, O3, etc...

It seems to me like the chem options are not set correctly, so the chemistry is not working. What do you think? I have done many tests changing different options, but I always get the same NO2 mixing ratio in the simulations with and without lightning.

This is the complete namelist i am using (please remember I build my emissions by following Exercise 4):

&time_control
run_days = 0,
run_hours = 18,
run_minutes = 0,
run_seconds = 0,
start_year = 2018, 2019,
start_month = 10, 09,
start_day = 19, 04,
start_hour = 00, 12,
end_year = 2018, 2019,
end_month = 10, 09,
end_day = 19, 06,
end_hour = 18, 00,
interval_seconds = 10800
input_from_file = .true.,.true.,
history_interval = 30, 60,
frames_per_outfile = 1, 1,
restart = .false.,
restart_interval = 1440,
io_form_history = 2
io_form_restart = 2
io_form_input = 2
io_form_boundary = 2
iofields_filename = "/lustre/scratch-global/iaa/WRF-E_2/WRF-4.3/test/em_real/myoutfields.txt"
io_form_auxhist24 = 2
auxhist24_interval = 60
auxinput6_inname = 'wrfbiochemi_d01',
auxinput7_inname = 'wrffirechemi_d<domain>',
auxinput8_inname = 'wrfchemi_d01_2018-10-19_00:00:00',
auxinput12_inname = 'wrf_chem_input',
auxinput5_interval_m = 86400,
auxinput7_interval_m = 86400,
auxinput8_interval_m = 86400,
io_form_auxinput2 = 2,
io_form_auxinput5 = 2,
io_form_auxinput6 = 2,
io_form_auxinput7 = 2,
io_form_auxinput8 = 2,
io_form_auxinput12 = 2,
debug_level = 0,
auxinput1_inname = "met_em.d<domain>.<date>",
/
auxinput13_inname = 'wrfchemv_d<domain>',
auxinput13_interval_m = 86400,
io_form_auxinput13 = 2,
/

&domains
time_step = 30,
time_step_fract_num = 0,
time_step_fract_den = 1,
max_dom = 1,
e_we = 64, 220,
e_sn = 64, 214,
e_vert = 80, 45,
dzstretch_s = 1.1
p_top_requested = 5000,
num_metgrid_levels = 32,
num_metgrid_soil_levels = 4,
dx = 7000,
dy = 7000,
grid_id = 1, 2,
parent_id = 0, 1,
i_parent_start = 1, 53,
j_parent_start = 1, 25,
parent_grid_ratio = 1, 3,
parent_time_step_ratio = 1, 3,
feedback = 1,
smooth_option = 0
/

&dfi_control
/

&physics
mp_physics = 2, 2, 2,
progn = 0, 0, 0,
naer = 1e9,
ra_lw_physics = 1, 1, 1,
ra_sw_physics = 2, 2, 2,
radt = 30, 30, 10,
sf_sfclay_physics = 1, 1, 1,
sf_surface_physics = 2, 2, 2,
bl_pbl_physics = 1, 1, 1,
bldt = 1, 1, 0,
cu_physics = 5, 5, 0,
cugd_avedx = 1,
cudt = 1, 1, 1,
isfflx = 1,
ifsnow = 1,
icloud = 1,
surface_input_source = 1,
num_soil_layers = 4,
sf_urban_physics = 0, 0, 0,
maxiens = 1,
maxens = 3,
maxens2 = 3,
maxens3 = 16,
ensdim = 144,
cu_rad_feedback = .true.,
cu_diag = 1,
nudge_lightning = 1, 1,
nudge_light_times = 0, 0,
nudge_light_timee = 64800, 10800,
nudge_light_int = 90, 3600,
path_to_files = "/lustre/scratch-global/iaa/WRF-E_2/WRF-4.3/test/em_real/"
lightning_option = 1,
iccg_method = 3,
cldtop_adjustment = 2,
lightning_start_seconds = 0,
flashrate_factor = 1,
do_radar_ref = 1,
lightning_dt = 90
/

&fdda
/

&dynamics
hybrid_opt = 2,
w_damping = 0,
diff_opt = 2, 2,
km_opt = 4, 4,
diff_6th_opt = 0, 0,
diff_6th_factor = 0.12, 0.12,
base_temp = 290.
damp_opt = 3,
zdamp = 5000., 5000.,
dampcoef = 0.2, 0.2,
khdif = 0, 0,
kvdif = 0, 0,
non_hydrostatic = .true., .true.,
moist_adv_opt = 1, 1,
scalar_adv_opt = 1, 1,
gwd_opt = 1, 0,
/

&bdy_control
spec_bdy_width = 5,
specified = .true.
/

&grib2
/

&chem
lnox_opt = 1,
n_ic = 500,
n_cg = 500,
lnox_passive = .false.,
kemit = 1,
chem_opt = 301,
bioemdt = 1.5,
photdt = 30,
chemdt = 1.5,
io_style_emissions = 2,
emiss_opt = 5,
emiss_opt_vol = 0,
emiss_inpt_opt = 1,
emiss_ash_hgt = 20000.,
chem_in_opt = 2,
phot_opt = 3,
gas_drydep_opt = 0,
aer_drydep_opt = 0,
bio_emiss_opt = 0,
ne_area = 300,
dust_opt = 1,
dmsemis_opt = 1,
seas_opt = 1,
depo_fact = 0.25,
gas_bc_opt = 1,
gas_ic_opt = 1,
aer_bc_opt = 1,
aer_ic_opt = 1,
gaschem_onoff = 1,
aerchem_onoff = 1,
wetscav_onoff = 0,
cldchem_onoff = 0,
vertmix_onoff = 1,
chem_conv_tr = 0,
conv_tr_wetscav = 0,
conv_tr_aqchem = 0,
biomass_burn_opt = 1,
plumerisefire_frq = 30,
have_bcs_chem = .false.,
aer_ra_feedback = 0,
aer_op_opt = 0,
opt_pars_out = 0,
diagnostic_chem = 3,
/

&namelist_quilt
nio_tasks_per_group = 0,
nio_groups = 1,
/

Regards,

Javier

fjp...@gmail.com

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Jan 12, 2023, 5:34:27 AM1/12/23

to wrf-chem, fjp...@gmail.com

Hi all,

I am still having problems. Here is an update:

I can see a perturbation in NO2, O3, etc.. when I set chem_opt = 5: Carbon Bond Mechanism Z (CBM-Z), even when I am using the same emissions. I do not understand why...

I have now changed to MOZCART. I have prepared the chem. input by using mozbc, the biogenic emissions from MEGAN by using bio_emiss and the anthropogenic emissions from EDGAR-HTAP using anthro_emiss. I still have the same problem: I cannot see any perturbation produced by the injected LNO. I suspect I am introducing some error that makes the chemistry not working.

This is the namelist.input I am using now for MOZCART:

auxinput5_inname = '/lustre/scratch-global/iaa/WRF-E_2/ANTHRO/src/',
auxinput6_inname = '/lustre/scratch-global/iaa/WRF-E_2/megan_bio_emiss/wrfbiochemi_d01',
auxinput12_inname = 'wrf_chem_input_d01',
auxinput5_interval_m = 60,

io_form_auxinput2 = 2,
io_form_auxinput5 = 2,
io_form_auxinput6 = 2,

io_form_auxinput12 = 2,
debug_level = 0,
auxinput1_inname = "met_em.d<domain>.<date>",

force_use_old_data=T

mp_physics = 8, 2, 2,

progn = 0, 0, 0,
naer = 1e9,
ra_lw_physics = 1, 1, 1,
ra_sw_physics = 2, 2, 2,

radt = 15, 30, 10,

sf_sfclay_physics = 1, 1, 1,
sf_surface_physics = 2, 2, 2,
bl_pbl_physics = 1, 1, 1,

bldt = 0, 1, 0,

cu_physics = 5, 5, 0,
cugd_avedx = 1,

cudt = 0, 1, 1,

isfflx = 1,
ifsnow = 1,
icloud = 1,
surface_input_source = 1,
num_soil_layers = 4,
sf_urban_physics = 0, 0, 0,

mp_zero_out = 2,
mp_zero_out_thresh = 1.e-12,

maxiens = 1,
maxens = 3,
maxens2 = 3,
maxens3 = 16,
ensdim = 144,

sst_update = 0,
topo_wind = 1, 1

cu_rad_feedback = .true.,
cu_diag = 1,
nudge_lightning = 1, 1,
nudge_light_times = 0, 0,
nudge_light_timee = 64800, 10800,

nudge_light_int = 30, 3600,
path_to_files = "/lustre/scratch-global/iaa/WRF-E_2/WRF-4.3/test/em_real/"
lightning_option = 11,

iccg_method = 3,
cldtop_adjustment = 2,
lightning_start_seconds = 0,
flashrate_factor = 1,
do_radar_ref = 1,

lightning_dt = 30

/

&fdda
/

&dynamics
hybrid_opt = 2,

w_damping = 1,
diff_opt = 1, 2,

km_opt = 4, 4,
diff_6th_opt = 0, 0,

diff_6th_factor = 0.05, 0.12,
base_temp = 290.
damp_opt = 1,
zdamp = 5000., 5000.,
dampcoef = 0.15, 0.2,

khdif = 0, 0,
kvdif = 0, 0,
non_hydrostatic = .true., .true.,
moist_adv_opt = 1, 1,

scalar_adv_opt = 2, 1,

gwd_opt = 1, 0,
/

&bdy_control
spec_bdy_width = 5,

spec_zone = 1,
relax_zone = 4,
specified = .true., .false.,
nested = .false.,.true.,

/

&grib2
/

&chem
lnox_opt = 1,
n_ic = 500,
n_cg = 500,
lnox_passive = .false.,

kemit = 11,
chem_opt = 112, 112,
bioemdt = 1, 1,
photdt = 1, 1
chemdt = 1, 1,
io_style_emissions = 1,
emiss_inpt_opt = 111, 111,
emiss_opt = 8, 8,
emiss_opt_vol = 0, 0,
chem_in_opt = 1, 0,
phot_opt = 3, 3
gas_drydep_opt = 1, 1,
aer_drydep_opt = 1, 1,
bio_emiss_opt = 3, 3,
ne_area = 118,
gas_bc_opt = 112, 112,
gas_ic_opt = 112, 112,
aer_bc_opt = 112, 112,
aer_ic_opt = 112, 112,
gaschem_onoff = 1, 1,
aerchem_onoff = 1, 1,
wetscav_onoff = 1, 1,
cldchem_onoff = 0, 0,
vertmix_onoff = 1, 1,
chem_conv_tr = 1, 0,
conv_tr_wetscav = 0, 0
conv_tr_aqchem = 0, 0,
seas_opt = 0,
dust_opt = 0,
dmsemis_opt = 1,
biomass_burn_opt = 2, 2,
plumerisefire_frq = 15, 15,
scale_fire_emiss = .true., .true.,
have_bcs_chem = .false., .true.,
aer_ra_feedback = 0, 0,
aer_op_opt = 1,
opt_pars_out = 1,
!have_bcs_upper = .true., .true.,
!fixed_ubc_press = 50., 50.,
!fixed_ubc_inname = 'ubvals_b40.20th.track1_1996-2005.nc',
!emi_inname = 'wrfchemi_d<domain>_<date>'
chemdiag=0,1

/

&namelist_quilt
nio_tasks_per_group = 0,
nio_groups = 1,
/

Xin Zhang

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Jan 13, 2023, 4:27:19 AM1/13/23

to fjp...@gmail.com, wrf-chem

Hi Javier,

Could you try MOZ(C)ART with FTUV or TUV photolysis?

You can check the guide here: https://ruc.noaa.gov/wrf/wrf-chem/Users_guide.pdf

Best regards,

Xin

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Xin Zhang

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Jan 13, 2023, 4:35:30 AM1/13/23

to fjp...@gmail.com, wrf-chem

Ha, sorry I didn't see you set phot_opt to 3.

No idea why you didn't see any changes in other gases.

Maybe you can check the temporal evolution of NOx and see whether it is being chemically removed correctly.

BTW, I ran WRF-Chem with lightning NOx on/off before and everything works well.

In case you wanna check the namelists, here is the link:

https://github.com/zxdawn/Namelists

Regards,

Xin

fjpi

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Jan 13, 2023, 5:34:02 AM1/13/23

to Xin Zhang, wrf-chem

Dear Xin,

thank you for your help! Yes, I am using photolysis...

I get an error when accessing to the link you have provided.

Regards,

Javier

Xin Zhang

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Jan 13, 2023, 5:53:19 AM1/13/23

to fjpi, wrf-chem

Sorry, Javier. I forgot to make that repo public. It should be available now.

Regards,

Xin

fjpi

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Jan 13, 2023, 6:06:45 AM1/13/23

to Xin Zhang, wrf-chem

Thank you, Xin! I will take a look

fjpi

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Jan 14, 2023, 3:43:48 AM1/14/23

to Xin Zhang, wrf-chem

Dear Xin,

just a brief question. When I run real.exe to get the wrfinput and wrfbdy files before building the emissions and the initial profiles (MOZCART), should I set chem_pot = 0 or chem_pot = 112?

Thanks!

Regards,

Javier

Xin Zhang

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Jan 14, 2023, 4:38:03 AM1/14/23

to fjpi, wrf-chem

Dear Javier,

You need to set chem_opt=0 to generate wrfinput and wrfbdy first.

Then, use these files to prepare all emissions.

When you set up the emissions, you can run MOZBC with chem_opt=112 to modify wrfinput and wrfbdy automatically.

Here're the general steps: https://dreambooker.site/2017/12/10/wrf-chem-mozcart-and-wrf_tips/#/wrf-chem

Hope my old notes are useful for your question.

Best regards,

Xin

fjpi

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Jan 15, 2023, 10:58:45 PM1/15/23

to Xin Zhang, wrf-chem

Dear Xin,

thank you very much for the general steps! I will follow them to try to find my error.

Regards,

Javier

fjpi

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Jan 16, 2023, 5:54:59 AM1/16/23

to Xin Zhang, wrf-chem

Dear Xin,

your comments were very helpful to understand some points that I did not fully understand. However, I cannot see the effect of the LNO yet...

Here are some points where I still have some doubts:

1.- When I run ./real.exe with chem_opt = 0, I assume I have to set chem_in_opt = 0 as well.

2.- When I tun ./real.exe before mozbc, apart from setting chem_opt = 112, I have to set chem_in_opt =1. Am I right? If I set chem_opt = 112 & chem_in_opt =0, I get an error when running ./real.exe

Thank you!

Regards,

Javier

Xin Zhang

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Jan 16, 2023, 6:27:34 AM1/16/23

to fjpi, wrf-chem

Dear Javier,

Glad you understand the settings better now.

I always set chem_in_opt to 0 because we run mozbc to modify the wrfinput file.

See option 3, Page 19 of this Guide: https://ruc.noaa.gov/wrf/wrf-chem/wrf_tutorial_2012_brazil/Setup_run_wrf-chem.pdf

Best regards,

Xin

fjpi

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Jan 16, 2023, 9:09:59 AM1/16/23

to Xin Zhang, wrf-chem

Dear Xin,

thank you! I understand.

Firstly, I run ./real.exe with chem_in_opt=0. I get the wrfinput and the wrbdy files, I build the emissions, etc. Then, before running mozbc, I set chem_opt = 112, run ./real.exe and get this error. Do you suspect why?:

d01 2018-10-19_00:00:00 Turning off use of TROPOPAUSE level data in vertical interpolation
Max map factor in domain 1 = 1.17. Scale the dt in the model accordingly.
Using sfcprs3 to compute psfc
d01 2018-10-19_00:00:00 No average surface temperature for use with inland lakes
Assume Noah LSM input
d01 2018-10-19_00:00:00 forcing artificial silty clay loam at 1 points, out of 3969
d01 2018-10-19_00:00:00 Timing for processing 0 s.
STARTING WITH BACKGROUND CHEMISTRY
Subroutine input_chem_profile:
[drago31010015:1243849:0:1243849] Caught signal 11 (Segmentation fault: address not mapped to object at address 0x7f4e66f7f310)
==== backtrace (tid:1243849) ====
0 0x0000000000012ce0 __funlockfile() :0
1 0x0000000002591b0f __module_input_chem_data_MOD_make_chem_profile() ???:0
2 0x0000000002597746 __module_input_chem_data_MOD_input_chem_profile() ???:0
3 0x00000000004456de med_sidata_input_() ???:0
4 0x0000000000446274 MAIN__() real_em.f90:0
5 0x00000000004061d1 main() ???:0
6 0x000000000003acf3 __libc_start_main() ???:0
7 0x000000000040620e _start() ???:0
=================================

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:
#0 0x7f4eb9247cdf in ???
#1 0x2591b0f in ???
#2 0x2597745 in ???
#3 0x4456dd in ???
#4 0x446273 in ???
#5 0x4061d0 in ???
#6 0x7f4eb9693cf2 in ???
#7 0x40620d in ???
#8 0xffffffffffffffff in ???

Regards,

Javier

Xin Zhang

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Jan 17, 2023, 12:38:58 AM1/17/23

to fjpi, wrf-chem

Hi Javier,

I haven't met this issue before, but found the same one on the forum:

https://forum.mmm.ucar.edu/threads/segmentation-fault-with-real-exe-and-mozcart.10870/#post-23411

It seems related to gcc version.

The author of that post used 4.8.4 and I used 4.8.5. Could you check the gcc of your system?

Best regards,

Xin

fjpi

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Jan 17, 2023, 2:39:02 AM1/17/23

to Xin Zhang, wrf-chem

Hi Xin,

thank you again for your help!

Regarding a possible problem with the compiler, it makes sense... I am using the 11.2.0 version of gcc and the 4.3 version of WRF. Maybe I would need an older version of the compiler...

Regards,

Javier

Mary Barth

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Feb 7, 2023, 3:46:00 PM2/7/23

to fjp...@gmail.com, wrf-chem

Hello Javier,

I would first confirm that lightning is being produced by looking at flashcount and flashrate variables. Are those numbers reasonable? Or are they low? I noticed that you set cldtop_adjustment = 2, which, I believe, is recommended but I think that's more useful for severe storms like we get over the central US. Have you tested with cldtop_adjustment = 0? And just to explain, lightning_option = 11 uses the level of neutral buoyancy (which may be in wrfout too) to determine cloud top height. And flashrate is calculated from that value using an equation that is very sensitive to the cloud top height (because of the exponent). So, a LNB of 12 km changes to 10 km with cldtop_adjustment = 2, which will make a big reduction in flashrate values.

I would be plotting RAINC (and RAINNC) to confirm that there's convective precipitation.

I suggest setting lightning_dt = 60 seconds because your chemistry is operating at chemdt=1 minute.

I also see that you have nudge_lightning active. Unfortunately I don't know if that is affecting your results.

I suggest setting bioemdt and photdt = 15 minutes as they don't change substantially during the 15 minute period.

With lnox_passive = .false., I think you should still be getting the LNOx tracer output. Are you? If not, you should turn on the tracer option: tracer_opt = 4 and add tracer_adv_opt = 2, (also set moist_adv_opt = 2 and add chem_adv_opt = 2). This tracer option is set in the namelist.input under the dynamics namelist and not the chemistry namelist.

Hope these comments help,
Mary

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fjpi

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Feb 8, 2023, 1:31:44 AM2/8/23

to Mary Barth, wrf-chem

Hi Mary,

Thank you very much for your suggestions. They are very useful.

Regarding the problem with the "non-interacting" LNOX, I discovered this is caused by an error when running ./real with chem_opt=112. I still do not know the cause. Xin suggested it could be a problem related with my compiler. I cannot use MOZCART yet.

Anyway, I changed to chem_opt=5 (CBMZ), where everything seems to be right. I think this chemical mechanism can be good enough to estimate the chemical influence of LNOx.

Regarding your comment:

"I suggest setting lightning_dt = 60 seconds because your chemistry is operating at chemdt=1 minute."

I agree. However, I would like to understand this better. If I check lightning_dt < chemdt, is the LNOx still interacting with other species correctly?

Regarding the lightning option, I have now modified the lightning subroutine based on the nudging of A. Fierro. Now, I read lightning measurements instead of calculating lightning frequency. I have modified the code to inject LNOx according to the nudged lightning. This is working well.

Thanks!

Regards,

Javier

衣清

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May 1, 2025, 2:06:46 AMMay 1

to wrf-chem, fjp...@gmail.com, wrf-chem, Mary Barth

I have the same problem as you. After running, it shows that there are emissions of LNOX_CG\LNOX_IC. But they do not participate in the chemical reaction.

The final NO2 emissions are not affected by turning on and off the lightning module. The following are my namelist parameters.

I am using wrfchem4.2 and the mozcart boundary field made by the mozbc tool using waccm data. I use gdas for meteorological data. I suspect that it is caused by my wrfchem version. I am trying to use wrfchem4.5 to see if the same problem will occur.

&time_control
start_year = 2022,
start_month = 06,
start_day = 23,
start_hour = 00,
start_minute = 00,
start_second = 00,
end_year = 2022,
end_month = 06,
end_day = 27,
end_hour = 00,
end_minute = 00,
end_second = 00,
interval_seconds = 21600,
input_from_file = .true.,
history_interval = 60,
frames_per_outfile = 24,
restart = .false.,
restart_interval = 7200,
io_form_history = 2,
io_form_restart = 2,
io_form_input = 2,
io_form_boundary = 2,
debug_level = 0,

force_use_old_data = .true.,
auxinput5_interval = 3600,
auxinput5_inname = 'wrfchemi_<hour>z_d<domain>',
auxinput6_inname = 'wrfbiochemi_d<domain>',

io_form_auxinput5 = 2,
io_form_auxinput6 = 2,

/

&domains
time_step = 10,

time_step_fract_num = 0,
time_step_fract_den = 1,
max_dom = 1,

e_we = 101,
e_sn = 101,
e_vert = 51,
p_top_requested = 5000,
num_metgrid_levels = 34,
num_metgrid_soil_levels = 4,
dx = 10000,
dy = 10000,
grid_id = 1,
parent_id = 1,
i_parent_start = 1,
j_parent_start = 1,
parent_grid_ratio = 1,
parent_time_step_ratio = 1,
feedback = 1,
smooth_option = 0,
nproc_x = 6,
nproc_y = 4,

/

&physics
mp_physics = 8,

progn = 0,
naer = 1e9,
ra_lw_physics = 4,
ra_sw_physics = 4,
radt = 15,
sf_sfclay_physics = 1,
sf_surface_physics = 2,
bl_pbl_physics = 5,
mfshconv = 0,
bldt = 0,
cu_physics = 5,
cu_diag = 1,
cudt = 5,
ishallow = 0,
isfflx = 1,
ifsnow = 0,
icloud = 0,
surface_input_source = 3,
num_soil_layers = 4,
num_land_cat = 28,
sf_urban_physics = 0,
mp_zero_out = 2,

maxiens = 1,
maxens = 3,
maxens2 = 3,
maxens3 = 16,
ensdim = 144,

cu_rad_feedback = .false.,
topo_wind = 1,
usemonalb = .true.,
tmn_update = 1,
sst_update = 0,
sst_skin = 0,

lightning_option = 11,
iccg_method = 1,
iccg_prescribed_num = 4,
iccg_prescribed_den = 1,

lightning_dt = 10,
lightning_start_seconds = 600,
flashrate_factor = 1.0,
cellcount_method = 1,
cldtop_adjustment = 2,

do_radar_ref = 1,
/

&fdda
/

&dynamics
w_damping = 1,
diff_opt = 2,
km_opt = 4,
base_temp = 290.,
damp_opt = 0,
zdamp = 5000.,
dampcoef = 0.2,
khdif = 0,
kvdif = 0,
non_hydrostatic = .true.,
moist_adv_opt = 1,
scalar_adv_opt = 1,
tracer_opt = 4,

/

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

nested = .false.,
/

&grib2
/

&chem

kemit = 1,
chem_opt = 112,
chem_in_opt = 0,
bio_emiss_opt = 3,
photdt = 10,
chemdt = 10,

io_style_emissions = 1,
emiss_inpt_opt = 111,

emiss_opt = 7,
phot_opt = 3,
gas_drydep_opt = 1,
aer_drydep_opt = 0,
ne_area = 200,
biomass_burn_opt = 3,
plumerisefire_frq = 60,
dust_opt = 0,
dmsemis_opt = 0,
seas_opt = 0,

gas_bc_opt = 1,
gas_ic_opt = 1,

aer_bc_opt = 0,
aer_ic_opt = 0,

gaschem_onoff = 1,
aerchem_onoff = 1,
wetscav_onoff = 0,
cldchem_onoff = 0,
vertmix_onoff = 1,

chem_conv_tr = 1,
aer_ra_feedback = 0,
have_bcs_chem = .true.,

lnox_opt = 2,
N_IC = 200,
N_CG = 200,
lnox_passive = .false.,

/

&namelist_quilt
nio_tasks_per_group = 2,
nio_groups = 1,
/

Mary Barth

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May 1, 2025, 11:33:47 AMMay 1

to 衣清, wrf-chem, fjp...@gmail.com

Hi there,

Have you looked at the lightning output to see how much lightning flashes are produced?

There should be IC_FLASHCOUNT and CG_FLASHCOUNT in the output file. Check the User's Guide for information about these variables as they are an accumulated flash count during the simulation.

- Mary

^--^--^--^--^--^--^--^--^--^--^--^--^--^--^-^--^--^--^-^--^

Mary Barth

Senior Scientist

phone: 303-497-8186 email: bar...@ucar.edu

NSF - National Center for Atmospheric Research

P.O. Box 3000

Boulder, CO 80307

^--^--^--^--^--^--^--^--^--^--^--^--^--^--^-^--^--^--^-^--^

衣清

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May 1, 2025, 12:32:10 PMMay 1

to wrf-chem, Mary Barth, wrf-chem, fjp...@gmail.com, 衣清

Thanks for the reply, my previous mistake was because I opened the tracer_opt= 4, when I turn off the tracer option, LNOX can participate in the chemical reaction normally.

衣清

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May 2, 2025, 3:51:08 PMMay 2

to wrf-chem, 衣清, Mary Barth, wrf-chem, fjp...@gmail.com

Hello, the previous problem is still not solved. I turned off the tracer setting and updated the wrfchem version to wrfchem4.5.

I also installed the tuv module and set phot_opt = 4. I also checked that there is indeed lightning excitation, and lnox_cg and lnox_ic are generated, but these generated lnox do not participate in atmospheric chemical reactions.

When I compared the results of turning on and off the lightning module, I found that the final no2 production did not change.

Can you help me check if there is an error in my namelist setting?

time_step = 60,

time_step_fract_num = 0,
time_step_fract_den = 1,
max_dom = 1,
e_we = 101,
e_sn = 101,
e_vert = 51,
p_top_requested = 5000,
num_metgrid_levels = 34,
num_metgrid_soil_levels = 4,
dx = 10000,
dy = 10000,
grid_id = 1,
parent_id = 1,
i_parent_start = 1,
j_parent_start = 1,
parent_grid_ratio = 1,
parent_time_step_ratio = 1,
feedback = 1,
smooth_option = 0,

nproc_x = 10,
nproc_y = 10,

lightning_dt = 60,
lightning_start_seconds = 600,
flashrate_factor = 3,

cellcount_method = 1,
cldtop_adjustment = 2,

do_radar_ref = 1,
/

&fdda
/

&dynamics
w_damping = 1,
diff_opt = 2,
km_opt = 4,
base_temp = 290.,
damp_opt = 0,
zdamp = 5000.,
dampcoef = 0.2,
khdif = 0,
kvdif = 0,
non_hydrostatic = .true.,
moist_adv_opt = 1,
scalar_adv_opt = 1,

tracer_opt = 0,

/

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

nested = .false.,
/

&grib2
/

&chem

kemit = 1,
chem_opt = 112,
chem_in_opt = 0,
bio_emiss_opt = 3,

photdt = 60,
chemdt = 60,

io_style_emissions = 1,
emiss_inpt_opt = 111,

emiss_opt = 8,
phot_opt = 4,

gas_drydep_opt = 1,
aer_drydep_opt = 0,
ne_area = 200,
biomass_burn_opt = 3,
plumerisefire_frq = 60,
dust_opt = 0,
dmsemis_opt = 0,
seas_opt = 0,
gas_bc_opt = 1,
gas_ic_opt = 1,
aer_bc_opt = 0,
aer_ic_opt = 0,
gaschem_onoff = 1,
aerchem_onoff = 1,
wetscav_onoff = 0,
cldchem_onoff = 0,
vertmix_onoff = 1,
chem_conv_tr = 1,
aer_ra_feedback = 0,
have_bcs_chem = .true.,

lnox_opt = 2,
N_IC = 200,

N_CG = 500,

lnox_passive = .false.,

/

&namelist_quilt
nio_tasks_per_group = 2,
nio_groups = 1,
/

Mary Barth

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May 2, 2025, 6:08:08 PMMay 2

to 衣清, wrf-chem, fjp...@gmail.com

Hi there,

Which lightning_option are you using?

At dx=10km, I'd suggest using the settings for parameterized convection:

lightning_option = 11

lnox_option = 1

What are the mixing ratios of LNOX_IC and LNOX_CG?

- Mary

^--^--^--^--^--^--^--^--^--^--^--^--^--^--^-^--^--^--^-^--^

Mary Barth

Senior Scientist

phone: 303-497-8186 email: bar...@ucar.edu

NSF - National Center for Atmospheric Research

P.O. Box 3000

Boulder, CO 80307

^--^--^--^--^--^--^--^--^--^--^--^--^--^--^-^--^--^--^-^--^

衣清

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May 3, 2025, 2:39:32 PMMay 3

to wrf-chem, Mary Barth, wrf-chem, fjp...@gmail.com, 衣清

Thank you for your reply.

My problem has been solved perfectly. After my inspection, I found that the kpp part of my wrfchem was not compiled normally, resulting in kpp not participating in the mozcart calculation process.

After I recompiled tuv and kpp, lnox can participate in atmospheric chemical reactions normally.

Thank you again for your patient reply.

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