Error while reading namelist chem

Any issues with running WRF Chemistry

Error while reading namelist chem

Postby mvwxfxm » Fri Jul 08, 2011 10:56 am

I am working with the WRFChem V3.2 and comparing the output data with recorded observations. I have successfuly ran the WRF using one domain, but I get this error in the real.exe when I try a new Domain:
taskid: 0 hostname: wrf1
------ ERROR while reading namelist chem ------
Namelist dfi_control not found in namelist.input. Using registry defaults for variables in dfi_control
Namelist tc not found in namelist.input. Using registry defaults for variables in tc
Namelist scm not found in namelist.input. Using registry defaults for variables in scm
Namelist fire not found in namelist.input. Using registry defaults for variables in fire
-------------- FATAL CALLED ---------------
FATAL CALLED FROM FILE: <stdin> LINE: 9543
ERRORS while reading one or more namelists from namelist.input.
-------------------------------------------
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
0 for domain 1, setting sgfdda interval and ending time to 0 for that domain.
--- NOTE: obs_nudge_opt is 0 for domain 1, setting obs nudging interval and ending time to 0 for that domain.
--- NOTE: num_soil_layers has been set to 4
WRF V3.3 MODEL
*************************************
Parent domain
ids,ide,jds,jde 1 100 1 93
ims,ime,jms,jme -4 32 -4 26
ips,ipe,jps,jpe 1 25 1 19
*************************************
DYNAMICS OPTION: Eulerian Mass Coordinate
alloc_space_field: domain 1 , 58825972 bytes allocated
med_initialdata_input: calling input_input
Timing for processing wrfinput file (stream 0) for domain 1: 0.82305 elapsed seconds.
INPUT LandUse = "USGS"
INITIALIZE THREE Noah LSM RELATED TABLES
LANDUSE TYPE = USGS FOUND 27 CATEGORIES
INPUT SOIL TEXTURE CLASSIFICATION = STAS
SOIL TEXTURE CLASSIFICATION = STAS FOUND 19 CATEGORIES

And the chem namelist itself:
&chem
kemit = 19,
chem_opt = 0, 2,
bioemdt = 30, 30,
photdt = 30, 30,
chemdt = 2.0, 2.0,
frames_per_emissfile = 36,
io_style_emissions = 1,
emiss_inpt_opt = 1, 1,
emiss_opt = 3, 3,
chem_in_opt = 1, 0,
phot_opt = 1, 1,
gas_drydep_opt = 1, 1,
aer_drydep_opt = 1, 1,
bio_emiss_opt = 1, 1,
dust_opt = 0,
dmsemis_opt = 0,
seas_opt = 0,
gas_bc_opt = 1, 1,
gas_ic_opt = 1, 1,
aer_bc_opt = 1, 1,
aer_ic_opt = 1, 1,
gaschem_onoff = 1, 1,
aerchem_onoff = 1, 1,
wetscav_onoff = 0, 0,
cldchem_onoff = 0, 0,
vertmix_onoff = 1, 1,
chem_conv_tr = 1, 1,
biomass_burn_opt = 1, 0,
plumerisefire_frq = 30, 30,
aer_ra_feedback = 0, 0,
have_bcs_chem = .false., .false.,
/

Iv tried looking over the formant and I don't see anything wrong. Anyone have a idea what is wrong?
mvwxfxm
 
Posts: 1
Joined: Thu Jul 07, 2011 12:05 pm

Re: Error while reading namelist chem

Postby imdnme » Wed Jul 13, 2011 3:51 am

Hello,

I have the same problem when trying to run real.exe, even for a single domain with no chemistry ( max_dom = 1, chem_opt = 0).

------ ERROR while reading namelist chem ------
...
FATAL CALLED FROM FILE: <stdin> LINE: 9543

Here is the &chem section of my namelist.input (located between &grib2 and &namelist_quilt; I used namelist.input.chem from WRFV3/test/em_real/ as a template)

&chem
kemit = 1,
chem_opt = 0, 0, 0, 0,
bioemdt = 30, 30, 30, 30,
photdt = 30, 30, 30, 30,
chemdt = 2., 2., 2., 2.,
frames_per_emissfile = 36,
io_style_emissions = 0,
emiss_inpt_opt = 1, 1, 1, 1,
emiss_opt = 3, 3, 3, 3,
chem_in_opt = 0, 0, 0, 0,
phot_opt = 0, 0, 0, 0,
gas_drydep_opt = 0, 0, 0, 0,
aer_drydep_opt = 0, 0, 0, 0,
bio_emiss_opt = 0, 0, 0, 0,
dust_opt = 0,
dmsemis_opt = 0,
seas_opt = 0,
gas_bc_opt = 1, 1, 1, 1,
gas_ic_opt = 1, 1, 1, 1,
aer_bc_opt = 1, 1, 1, 1,
aer_ic_opt = 1, 1, 1, 1,
gaschem_onoff = 0, 0, 0, 0,
aerchem_onoff = 0, 0, 0, 0,
wetscav_onoff = 0, 0, 0, 0,
cldchem_onoff = 0, 0, 0, 0,
vertmix_onoff = 0, 0, 0, 0,
chem_conv_tr = 0, 0, 0, 0,
biomass_burn_opt = 0, 0, 0, 0,
plumerisefire_frq = 30, 30, 30, 30,
aer_ra_feedback = 0, 0, 0, 0,
have_bcs_chem = .false., .false., .false., .false.,
imdnme
 
Posts: 11
Joined: Wed Jul 13, 2011 3:39 am
Location: Bulgaria

Re: Error while reading namelist chem

Postby imdnme » Wed Jul 13, 2011 4:32 am

The error disappeared when I deleted the following line:

frames_per_emissfile = 36,

It seems that for the number of timesteps in emission files there are only two options:
1) 12-h emission files ( io_style_emissions = 1,)
2) several files - one for every hour ( io_style_emissions = 2,)

I would like to make a single 72-h emission file for a tracer (chem_opt = 14), but it looks like this is not allowed and I have to split it into 6 files x 12h. Right?
imdnme
 
Posts: 11
Joined: Wed Jul 13, 2011 3:39 am
Location: Bulgaria

Re: Error while reading namelist chem

Postby ee07a2jr » Mon Nov 12, 2012 4:57 pm

Hi
I've had exactly the same problem as in the first post. I have compiled WRF CHEM 3.3.1 and am able to run real.exe and wrf.exe successfully. However, when I attempt to increase the number of domains from one to two I get the following message.

------ ERROR while reading namelist chem ------
Namelist dfi_control not found in namelist.input. Using registry defaults for variables in dfi_control
Namelist tc not found in namelist.input. Using registry defaults for variables in tc
Namelist scm not found in namelist.input. Using registry defaults for variables in scm
Namelist fire not found in namelist.input. Using registry defaults for variables in fire
-------------- FATAL CALLED ---------------
FATAL CALLED FROM FILE: <stdin> LINE: 9567
ERRORS while reading one or more namelists from namelist.input.
-------------------------------------------
Rank 0 [Mon Nov 12 20:32:10 2012] [c4-1c0s1n1] application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0


If anyone has managed to solve this problem I'd really appreciate some advice.
ee07a2jr
 
Posts: 1
Joined: Mon Nov 12, 2012 4:49 pm

Re: Error while reading namelist chem

Postby aghedo » Mon Feb 18, 2013 1:24 pm

Hi,

I found that for some reason, WRF-Chem demands you include all those namelist that were mentioned in the error message. As a default treatment, I now include the namelist listed below at the bottom of the namelist.input. For your case, you need to set the namelists: tc, dfi_control, scm, and fire.... It is okay to leave scm, fire, and tc as empty namelist.

&dfi_control
dfi_opt = 0,
dfi_nfilter = 0,
dfi_write_filtered_input = .false.,
dfi_write_dfi_history = .false.,
/

&noah_mp
/

&scm
/

&tc
/

&fire
/

&grib2
/

&diag
/

&diags
/

&logging
/


Take care,
Tutu.
aghedo
 
Posts: 2
Joined: Wed Feb 06, 2013 11:17 am

Re: Error while reading namelist chem

Postby David » Fri Jun 21, 2013 9:10 pm

Hi,

I have a similar problem with namelist.input. When i run "real. exe" appear the following message:

taskid: 0 hostname: localhost.localdomain
------ ERROR while reading namelist chem ------
-------------- FATAL CALLED ---------------
FATAL CALLED FROM FILE: <stdin> LINE: 9895
ERRORS while reading one or more namelists from namelist.input.
-------------------------------------------
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0

My namelist.input file is:

&time_control
run_days = 1,
run_hours = 0,
run_minutes = 0,
run_seconds = 0,
start_year = 2010, 2010,
start_month = 01, 01,
start_day = 1, 1,
start_hour = 0, 0,
start_minute = 00, 00,
start_second = 00, 00,
end_year = 2010, 2010,
end_month = 01, 01,
end_day = 2, 2,
end_hour = 0, 0,
end_minute = 00, 00,
end_second = 00, 00,
interval_seconds = 21600,
input_from_file = .true., .true.,
history_interval = 180, 60,
frames_per_outfile = 1000, 1000,
restart = .false.,
restart_interval = 5000,
io_form_history = 2,
io_form_restart = 2,
io_form_input = 2,
io_form_boundary = 2,
debug_level = 0,
/

&domains
time_step = 54,
time_step_fract_num = 0,
time_step_fract_den = 1,
max_dom = 2,
e_we = 100, 91,
e_sn = 76, 61,
e_vert = 28, 28,
p_top_requested = 5000,
num_metgrid_levels = 27,
num_metgrid_soil_levels = 4,
dx = 9000, 3000,
dy = 9000, 3000,
grid_id = 1, 2,
parent_id = 1, 1,
i_parent_start = 1, 58,
j_parent_start = 1, 30,
parent_grid_ratio = 1, 3,
parent_time_step_ratio = 1, 3,
feedback = 1,
smooth_option = 0,
/

&physics
mp_physics = 3, 3,
ra_lw_physics = 1, 1,
ra_sw_physics = 1, 1,
radt = 30, 30,
sf_sfclay_physics = 1, 1,
sf_surface_physics = 2, 2,
bl_pbl_physics = 1, 1,
bldt = 0, 0,
cu_physics = 1, 1,
cudt = 5, 5,
isfflx = 1,
ifsnow = 0,
icloud = 1,
surface_input_source = 1,
num_soil_layers = 4,
sf_urban_physics = 0, 0,
maxiens = 1,
maxens = 3,
maxens2 = 3,
maxens3 = 16,
ensdim = 144,
/

&fdda
/

&dynamics
w_damping = 0,
diff_opt = 1,
km_opt = 4,
diff_6th_opt = 0, 0,
diff_6th_factor = 0.12, 0.12,
base_temp = 290.,
damp_opt = 0,
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,
/

&fire
ifire = 0,
/

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

&grib2
/

&scm
/

&chem
kemit = 18,
chem_opt = 17, 17,
bioemdt = 30, 30,
photdt = 30, 30,
chemdt = 2.0, 2.0,
frames_per_emissfile = 36,
io_style_emissions = 0,
emiss_inpt_opt = 0, 0,
emiss_opt = 17, 17,
emiss_opt_vol = 0, 0,
chem_in_opt = 0, 0,
phot_opt = 1, 1,
gas_drydep_opt = 1, 1,
aer_drydep_opt = 1, 1,
bio_emiss_opt = 17, 17,
dust_opt = 0,
dmsemis_opt = 0,
seas_opt = 1,
gas_bc_opt = 16, 16,
gas_ic_opt = 16, 16,
aer_bc_opt = 1, 1,
aer_ic_opt = 1, 1,
gaschem_onoff = 1, 1,
aerchem_onoff = 1, 1,
wetscav_onoff = 1, 1,
cldchem_onoff = 1, 1,
vertmix_onoff = 1, 1,
chem_conv_tr = 1, 1,
cu_diag = 1, 1,
biomass_burn_opt = 5, 5,
plumerisefire_frq = 30, 30,
aer_ra_feedback = 1, 1,
have_bcs_chem = .false., .false.,
vprm_opt = “VPRM_TABLE_TROPICS”,
wpeat = 0.05,
wflood = 0.19,
term_opt = "CH4_termite_NW",
wflood = 0.19,
/

&dfi_control
dfi_opt = 0,
dfi_nfilter = 0,
dfi_write_filtered_input = .false.,
dfi_write_dfi_history = .false.,
/

&namelist_quilt
nio_tasks_per_group = 0,
nio_groups = 1,
/

&noah_mp
/

&tc
/


&diag
/

&diags
/

&logging
/

Please help me.

Thanks in advance.

David.
David
 
Posts: 9
Joined: Wed Apr 17, 2013 8:55 pm

Re: Error while reading namelist chem

Postby Farnoosh » Sat Sep 14, 2013 6:04 am

Hi every body,
I faced the simillar problem :

Error while reading namelist chem
-------------- FATAL CALLED ---------------
Errors while reading one or more namelists from namelist.input.
-------------------------------------------
wrf_abort


could any body solve this?

please give me a guide.
cheers.

Farnoosh.
Farnoosh
 
Posts: 2
Joined: Tue Jul 09, 2013 5:49 am

Re: Error while reading namelist chem

Postby WRFstudy » Fri Mar 24, 2017 10:25 am

imdnme wrote:The error disappeared when I deleted the following line:

frames_per_emissfile = 36,

It seems that for the number of timesteps in emission files there are only two options:
1) 12-h emission files ( io_style_emissions = 1,)
2) several files - one for every hour ( io_style_emissions = 2,)

I would like to make a single 72-h emission file for a tracer (chem_opt = 14), but it looks like this is not allowed and I have to split it into 6 files x 12h. Right?


if you want to use the first day' emissions only but not the later days,how would you do ?Thanks for your help!
WRFstudy
 
Posts: 3
Joined: Sun Dec 25, 2016 9:34 pm


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