the parameter in the avg nc file is empty

 Posts: 20
 Joined: Thu May 04, 2017 1:31 pm
 Location: south china sea institute of oceanography
the parameter in the avg nc file is empty
Hi, everyone, I run ROMS and got the empty results (the NaN was shown in the first step and was attached below). I used Woapisces (have been provided by Olivier Aumont. These data have been computed by a coupled NEMOPISCES global model) to compute the initial and boundary conditions of NO3 and O2.Then, I used WOA2009 ( World Ocean Atlas directory 2009 )to compute the initial and boundary conditions of temperature and salty. Then, I used coads dataset to compute forcing and boundary condition of Wind stress, Heat fluxes w3, Fresh water fluxes (evaporation  precipitation), Sea surface temperature and heat flux sensitivity to the sea surface temperature (dQdSST),Sea surface salinity,Short wave radiation, pair air pressure. the chlorophyll initial conditions was computed by using modis data in 2016,and NH4, LdetritusN, and et al were set as a constant with the time and loction in the boundary files. finally, i got a empty result and showd as below. Is there any way I can figure out what is the problem? the grid files? the water depth problem? or the parameter in the forcing file , boundary file ,and initial file are not match? or show i check some scripts to find out it?
Thank you so much for your help in advance. I have long struggled with the problem
TIMESTEP YYYYMMDD hh:mm:ss.ss KINETIC_ENRG POTEN_ENRG TOTAL_ENRG NET_VOLUME
C => (i,j,k) Cu Cv Cw Max Speed
0 00010101 00:00:00.00 0.000000E+00 1.385104E+04 1.385104E+04 6.120327E+14
(000,000,00) 0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00
DEF_HIS  creating history file, Grid 01: ocean_his.nc
WRT_HIS  wrote history fields (Index=1,1) in record = 0000001
DEF_AVG  creating average file, Grid 01: ocean_avg.nc
DEF_DIAGS  creating diagnostics file, Grid 01: ocean_dia.nc
1 00010101 00:09:00.00 NaN NaN NaN NaN
(190,001,30) 1.953902E02 7.791596E03 0.000000E+00 Infinity
Thank you so much for your help in advance. I have long struggled with the problem
TIMESTEP YYYYMMDD hh:mm:ss.ss KINETIC_ENRG POTEN_ENRG TOTAL_ENRG NET_VOLUME
C => (i,j,k) Cu Cv Cw Max Speed
0 00010101 00:00:00.00 0.000000E+00 1.385104E+04 1.385104E+04 6.120327E+14
(000,000,00) 0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00
DEF_HIS  creating history file, Grid 01: ocean_his.nc
WRT_HIS  wrote history fields (Index=1,1) in record = 0000001
DEF_AVG  creating average file, Grid 01: ocean_avg.nc
DEF_DIAGS  creating diagnostics file, Grid 01: ocean_dia.nc
1 00010101 00:09:00.00 NaN NaN NaN NaN
(190,001,30) 1.953902E02 7.791596E03 0.000000E+00 Infinity

 Posts: 20
 Joined: Thu May 04, 2017 1:31 pm
 Location: south china sea institute of oceanography
Re: the parameter in the avg nc file is empty
for Sea surface temperature and salinity in forcing files were computed by using the coads dataset (coads05) ,but the salinity and temperature in the boundary files were computed by using woapisces dataset. Would that be a problem?
Re: the parameter in the avg nc file is empty
Perhaps you should show us the ROMS output where it is reading all these files. It gives the min and max of everything, so that we can see if they are all sensible.
If you are getting NaNs, that's from the model physics, not the ecosystem stuff.
If you are getting NaNs, that's from the model physics, not the ecosystem stuff.

 Posts: 20
 Joined: Thu May 04, 2017 1:31 pm
 Location: south china sea institute of oceanography
Re: the parameter in the avg nc file is empty
Thank you so much for your reply.kate wrote:Perhaps you should show us the ROMS output where it is reading all these files. It gives the min and max of everything, so that we can see if they are all sensible.
If you are getting NaNs, that's from the model physics, not the ecosystem stuff.
the information is:
Basin information for Grid 01:
Maximum grid stiffness ratios: rx0 = 2.309898E01 (Beckmann and Haidvogel)
rx1 = 3.380662E+00 (Haney)
Initial basin volumes: TotVolume = 6.1203271774E+14 m3
MinVolume = 1.4128306732E+05 m3
MaxVolume = 2.4265090838E+09 m3
Max/Min = 1.7174804666E+04
NL ROMS/TOMS: started timestepping: (Grid: 01 TimeSteps: 00000001  00001600)
GET_2DFLD  surface uwind component, 00010116 00:00:00.00
(Grid=01, Rec=0000001, Index=2, File: roms_frc.nc)
(Tmin= 15.0000 Tmax= 345.0000) t = 15.0000
(Min = 7.09940031E+00 Max = 2.02652608E+00) regrid = F
GET_2DFLD  surface vwind component, 00010116 00:00:00.00
(Grid=01, Rec=0000001, Index=2, File: roms_frc.nc)
(Tmin= 15.0000 Tmax= 345.0000) t = 15.0000
(Min = 8.94021906E+00 Max = 2.09216018E+00) regrid = F
GET_2DFLD  surface air pressure, 00010116 00:00:00.00
(Grid=01, Rec=0000001, Index=2, File: roms_frc.nc)
(Tmin= 15.0000 Tmax= 345.0000) t = 15.0000
(Min = 8.81692599E+02 Max = 1.02820669E+03) regrid = F
GET_2DFLD  solar shortwave radiation flux, 00010116 00:00:00.00
(Grid=01, Rec=0000001, Index=2, File: roms_frc.nc)
(Tmin= 15.0000 Tmax= 345.0000) t = 15.0000
(Min = 2.76230526E05 Max = 4.07666000E05) regrid = F
GET_2DFLD  surface air temperature, 00010116 00:00:00.00
(Grid=01, Rec=0000001, Index=2, File: roms_frc.nc)
(Tmin= 15.0000 Tmax= 345.0000) t = 15.0000
(Min = 1.01931778E+01 Max = 2.32485524E+01) regrid = F
GET_2DFLD  surface air relative humidity, 00010116 00:00:00.00
(Grid=01, Rec=0000001, Index=2, File: roms_frc.nc)
(Tmin= 15.0000 Tmax= 345.0000) t = 15.0000
(Min = 7.93226792E01 Max = 8.58040507E01) regrid = F
GET_NGFLD  temperature eastern boundary condition, 00010116 00:00:00.00
(Grid= 01, Rec=0000001, Index=1, File: roms_bry.nc)
(Tmin= 15.0000 Tmax= 345.0000) t = 15.0000
(Min = 2.07808005E+00 Max = 2.52018462E+01)
GET_NGFLD  salinity eastern boundary condition, 00010116 00:00:00.00
(Grid= 01, Rec=0000001, Index=1, File: roms_bry.nc)
(Tmin= 15.0000 Tmax= 345.0000) t = 15.0000
(Min = 3.38538422E+01 Max = 3.46242217E+01)
GET_NGFLD  nitrate eastern boundary condition, 00010116 00:00:00.00
(Grid= 01, Rec=0000001, Index=1, File: roms_bry.nc)
(Tmin= 15.0000 Tmax= 345.0000) t = 15.0000
(Min = 2.69948635E01 Max = 4.16393587E+01)
GET_NGFLD  ammonium eastern boundary condition, 00010116 00:00:00.00
(Grid= 01, Rec=0000001, Index=1, File: roms_bry.nc)
(Tmin= 15.0000 Tmax= 345.0000) t = 15.0000
(Min = 5.00000000E+00 Max = 5.00000000E+00)
GET_NGFLD  chlorophyll eastern boundary condition, 00010116 00:00:00.00
(Grid= 01, Rec=0000001, Index=1, File: roms_bry.nc)
(Tmin= 15.0000 Tmax= 345.0000) t = 15.0000
(Min = 5.08890706E03 Max = 2.21083747E+00)
GET_NGFLD  phytoplankton eastern boundary condition, 00010116 00:00:00.00
(Grid= 01, Rec=0000001, Index=1, File: roms_bry.nc)
(Tmin= 15.0000 Tmax= 345.0000) t = 15.0000
(Min = 2.54445353E03 Max = 1.10541874E+00)
GET_NGFLD  zooplankton eastern boundary condition, 00010116 00:00:00.00
(Grid= 01, Rec=0000001, Index=1, File: roms_bry.nc)
(Tmin= 15.0000 Tmax= 345.0000) t = 15.0000
(Min = 1.01778141E03 Max = 4.42167495E01)
GET_NGFLD  large fraction nitrogen detritus eastern boundary00010116 00:00:00.00
(Grid= 01, Rec=0000001, Index=1, File: roms_bry.nc)
(Tmin= 15.0000 Tmax= 345.0000) t = 15.0000
(Min = 6.74871588E04 Max = 1.04098397E01)
GET_NGFLD  small fraction nitrogen detritus eastern boundary00010116 00:00:00.00
(Grid= 01, Rec=0000001, Index=1, File: roms_bry.nc)
(Tmin= 15.0000 Tmax= 345.0000) t = 15.0000
(Min = 1.34974318E03 Max = 2.08196793E01)
GET_NGFLD  large fraction carbon detritus eastern boundary c00010116 00:00:00.00
(Grid= 01, Rec=0000001, Index=1, File: roms_bry.nc)
(Tmin= 15.0000 Tmax= 345.0000) t = 15.0000
(Min = 1.34974318E02 Max = 2.08196793E+00)
GET_NGFLD  small fraction carbon detritus eastern boundary c00010116 00:00:00.00
(Grid= 01, Rec=0000001, Index=1, File: roms_bry.nc)
(Tmin= 15.0000 Tmax= 345.0000) t = 15.0000
(Min = 1.34974318E02 Max = 2.08196793E+00)
GET_NGFLD  TIC eastern boundary condition, 00010116 00:00:00.00
(Grid= 01, Rec=0000001, Index=1, File: roms_bry.nc)
(Tmin= 15.0000 Tmax= 345.0000) t = 15.0000
(Min = 2.68396431E+01 Max = 4.13999324E+03)
GET_NGFLD  alkalinity eastern boundary condition, 00010116 00:00:00.00
(Grid= 01, Rec=0000001, Index=1, File: roms_bry.nc)
(Tmin= 15.0000 Tmax= 345.0000) t = 15.0000
(Min = 2.98833139E+01 Max = 4.60947700E+03)
GET_NGFLD  temperature southern boundary condition, 00010116 00:00:00.00
(Grid= 01, Rec=0000001, Index=1, File: roms_bry.nc)
(Tmin= 15.0000 Tmax= 345.0000) t = 15.0000
(Min = 2.07347797E+00 Max = 2.52018462E+01)
GET_NGFLD  salinity southern boundary condition, 00010116 00:00:00.00
(Grid= 01, Rec=0000001, Index=1, File: roms_bry.nc)
(Tmin= 15.0000 Tmax= 345.0000) t = 15.0000
(Min = 3.30676247E+01 Max = 3.46498482E+01)
GET_NGFLD  nitrate southern boundary condition, 00010116 00:00:00.00
(Grid= 01, Rec=0000001, Index=1, File: roms_bry.nc)
(Tmin= 15.0000 Tmax= 345.0000) t = 15.0000
(Min = 4.72082936E02 Max = 4.15975251E+01)
GET_NGFLD  ammonium southern boundary condition, 00010116 00:00:00.00
(Grid= 01, Rec=0000001, Index=1, File: roms_bry.nc)
(Tmin= 15.0000 Tmax= 345.0000) t = 15.0000
(Min = 5.00000000E+00 Max = 5.00000000E+00)
GET_NGFLD  chlorophyll southern boundary condition, 00010116 00:00:00.00
(Grid= 01, Rec=0000001, Index=1, File: roms_bry.nc)
(Tmin= 15.0000 Tmax= 345.0000) t = 15.0000
(Min = 5.00979295E03 Max = 2.45184533E+00)
GET_NGFLD  phytoplankton southern boundary condition, 00010116 00:00:00.00
(Grid= 01, Rec=0000001, Index=1, File: roms_bry.nc)
(Tmin= 15.0000 Tmax= 345.0000) t = 15.0000
(Min = 2.50489647E03 Max = 1.22592267E+00)
GET_NGFLD  zooplankton southern boundary condition, 00010116 00:00:00.00
(Grid= 01, Rec=0000001, Index=1, File: roms_bry.nc)
(Tmin= 15.0000 Tmax= 345.0000) t = 15.0000
(Min = 1.00195859E03 Max = 4.90369067E01)
GET_NGFLD  large fraction nitrogen detritus southern boundar00010116 00:00:00.00
(Grid= 01, Rec=0000001, Index=1, File: roms_bry.nc)
(Tmin= 15.0000 Tmax= 345.0000) t = 15.0000
(Min = 1.18020734E04 Max = 1.03993813E01)
GET_NGFLD  small fraction nitrogen detritus southern boundar00010116 00:00:00.00
(Grid= 01, Rec=0000001, Index=1, File: roms_bry.nc)
(Tmin= 15.0000 Tmax= 345.0000) t = 15.0000
(Min = 2.36041468E04 Max = 2.07987626E01)
GET_NGFLD  large fraction carbon detritus southern boundary 00010116 00:00:00.00
(Grid= 01, Rec=0000001, Index=1, File: roms_bry.nc)
(Tmin= 15.0000 Tmax= 345.0000) t = 15.0000
(Min = 2.36041468E03 Max = 2.07987626E+00)
GET_NGFLD  small fraction carbon detritus southern boundary 00010116 00:00:00.00
(Grid= 01, Rec=0000001, Index=1, File: roms_bry.nc)
(Tmin= 15.0000 Tmax= 345.0000) t = 15.0000
(Min = 2.36041468E03 Max = 2.07987626E+00)
GET_NGFLD  TIC southern boundary condition, 00010116 00:00:00.00
(Grid= 01, Rec=0000001, Index=1, File: roms_bry.nc)
(Tmin= 15.0000 Tmax= 345.0000) t = 15.0000
(Min = 4.69368459E+00 Max = 4.13583394E+03)
GET_NGFLD  alkalinity southern boundary condition, 00010116 00:00:00.00
(Grid= 01, Rec=0000001, Index=1, File: roms_bry.nc)
(Tmin= 15.0000 Tmax= 345.0000) t = 15.0000
(Min = 5.22595810E+00 Max = 4.60484603E+03)
TIMESTEP YYYYMMDD hh:mm:ss.ss KINETIC_ENRG POTEN_ENRG TOTAL_ENRG NET_VOLUME
C => (i,j,k) Cu Cv Cw Max Speed
0 00010101 00:00:00.00 0.000000E+00 1.385104E+04 1.385104E+04 6.120327E+14
(000,000,00) 0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00
DEF_HIS  creating history file, Grid 01: ocean_his.nc
WRT_HIS  wrote history fields (Index=1,1) in record = 0000001
DEF_AVG  creating average file, Grid 01: ocean_avg.nc
DEF_DIAGS  creating diagnostics file, Grid 01: ocean_dia.nc
1 00010101 00:09:00.00 NaN NaN NaN NaN
(190,001,30) 1.953902E02 7.791596E03 0.000000E+00 Infinity

 Posts: 20
 Joined: Thu May 04, 2017 1:31 pm
 Location: south china sea institute of oceanography
Re: the parameter in the avg nc file is empty
I found the min and max value of free surface,umomentum component is zero. would that cold be a problem? the study area is 105118E;1724N.
should I use the woa or coads data to compute the free surface in the initial file.
NLM: GET_STATE  Read state initial conditions, 00010101 00:00:00.00
(Grid 01, t = 0.0000, File: roms_ini.nc, Rec=0001, Index=1)
 freesurface
(Min = 0.00000000E+00 Max = 0.00000000E+00)
 vertically integrated umomentum component
(Min = 0.00000000E+00 Max = 0.00000000E+00)
 vertically integrated vmomentum component
(Min = 0.00000000E+00 Max = 0.00000000E+00)
 umomentum component
(Min = 0.00000000E+00 Max = 0.00000000E+00)
 vmomentum component
(Min = 0.00000000E+00 Max = 0.00000000E+00)
 potential temperature
(Min = 2.06699248E+00 Max = 2.52018462E+01)
 salinity
(Min = 3.21682034E+01 Max = 3.46627592E+01)
 nitrate concentration
(Min = 1.47846501E+00 Max = 4.17511299E+01)
 ammonium concentration
(Min = 1.84808126E02 Max = 5.21889124E01)
 chlorophyll concentration
(Min = 0.00000000E+00 Max = 1.49550091E+01)
 phytoplankton concentration
(Min = 0.00000000E+00 Max = 7.47750454E+00)
 zooplankton concentration
(Min = 0.00000000E+00 Max = 2.99100181E+00)
 large fraction nitrogen detritus concentration
(Min = 3.69616252E03 Max = 1.04377825E01)
 small fraction nitrogen detritus concentration
(Min = 7.39232503E03 Max = 2.08755649E01)
 large fraction carbon detritus concentration
(Min = 7.39232503E02 Max = 2.08755649E+00)
 small fraction carbon detritus concentration
(Min = 7.39232503E02 Max = 2.08755649E+00)
 total inorganic carbon
(Min = 1.98850000E+03 Max = 1.98850000E+03)
 total alkalinity
(Min = 2.21400000E+03 Max = 2.21400000E+03)
GET_NGFLD  tidal period
(Grid = 01, Min = 4.30819210E+04 Max = 2.38071599E+06)
GET_2DFLD  tidal elevation amplitude
(Grid = 01, Min = 5.60665872E06 Max = 1.40909152E+01)
GET_2DFLD  tidal elevation phase angle
(Grid = 01, Min = 4.78313257E07 Max = 6.28318512E+00)
should I use the woa or coads data to compute the free surface in the initial file.
NLM: GET_STATE  Read state initial conditions, 00010101 00:00:00.00
(Grid 01, t = 0.0000, File: roms_ini.nc, Rec=0001, Index=1)
 freesurface
(Min = 0.00000000E+00 Max = 0.00000000E+00)
 vertically integrated umomentum component
(Min = 0.00000000E+00 Max = 0.00000000E+00)
 vertically integrated vmomentum component
(Min = 0.00000000E+00 Max = 0.00000000E+00)
 umomentum component
(Min = 0.00000000E+00 Max = 0.00000000E+00)
 vmomentum component
(Min = 0.00000000E+00 Max = 0.00000000E+00)
 potential temperature
(Min = 2.06699248E+00 Max = 2.52018462E+01)
 salinity
(Min = 3.21682034E+01 Max = 3.46627592E+01)
 nitrate concentration
(Min = 1.47846501E+00 Max = 4.17511299E+01)
 ammonium concentration
(Min = 1.84808126E02 Max = 5.21889124E01)
 chlorophyll concentration
(Min = 0.00000000E+00 Max = 1.49550091E+01)
 phytoplankton concentration
(Min = 0.00000000E+00 Max = 7.47750454E+00)
 zooplankton concentration
(Min = 0.00000000E+00 Max = 2.99100181E+00)
 large fraction nitrogen detritus concentration
(Min = 3.69616252E03 Max = 1.04377825E01)
 small fraction nitrogen detritus concentration
(Min = 7.39232503E03 Max = 2.08755649E01)
 large fraction carbon detritus concentration
(Min = 7.39232503E02 Max = 2.08755649E+00)
 small fraction carbon detritus concentration
(Min = 7.39232503E02 Max = 2.08755649E+00)
 total inorganic carbon
(Min = 1.98850000E+03 Max = 1.98850000E+03)
 total alkalinity
(Min = 2.21400000E+03 Max = 2.21400000E+03)
GET_NGFLD  tidal period
(Grid = 01, Min = 4.30819210E+04 Max = 2.38071599E+06)
GET_2DFLD  tidal elevation amplitude
(Grid = 01, Min = 5.60665872E06 Max = 1.40909152E+01)
GET_2DFLD  tidal elevation phase angle
(Grid = 01, Min = 4.78313257E07 Max = 6.28318512E+00)
Re: the parameter in the avg nc file is empty
You had said you were applying the stresses from COADS, but yet the model is reading winds, air pressure and the rest. This looks odd:
in that all the winds are negative. I would ask the model to write out surface fluxes and stresses to see if those look reasonable. I would try a much shorter timestep to see if you can get it to run long enough to output some useful fields so you can figure out where in the domain it is going bad.
I would not worry about starting from rest. The model spins up to match the density fields pretty quickly.
Code: Select all
GET_2DFLD  surface uwind component, 00010116 00:00:00.00
(Grid=01, Rec=0000001, Index=2, File: roms_frc.nc)
(Tmin= 15.0000 Tmax= 345.0000) t = 15.0000
(Min = 7.09940031E+00 Max = 2.02652608E+00) regrid = F
GET_2DFLD  surface vwind component, 00010116 00:00:00.00
(Grid=01, Rec=0000001, Index=2, File: roms_frc.nc)
(Tmin= 15.0000 Tmax= 345.0000) t = 15.0000
(Min = 8.94021906E+00 Max = 2.09216018E+00) regrid = F
I would not worry about starting from rest. The model spins up to match the density fields pretty quickly.

 Posts: 20
 Joined: Thu May 04, 2017 1:31 pm
 Location: south china sea institute of oceanography
Re: the parameter in the avg nc file is empty
thx,I really appreciated the suggestions you gave. it is important clue for me who only have biological background.kate wrote:You had said you were applying the stresses from COADS, but yet the model is reading winds, air pressure and the rest. This looks odd:
in that all the winds are negative. I would ask the model to write out surface fluxes and stresses to see if those look reasonable. I would try a much shorter timestep to see if you can get it to run long enough to output some useful fields so you can figure out where in the domain it is going bad.
I changed the timestep.
Code: Select all
100 ntimes Number of timesteps for 3D equations.
90.000 dt Timestep size (s) for 3D equations.
5 ndtfast Number of timesteps for 2D equations between
Code: Select all
T Hout(idUsms) Write out surface Umomentum stress.
T Hout(idVsms) Write out surface Vmomentum stress.
Code: Select all
DEF_DIAGS  creating diagnostics file, Grid 01: data2/ocean_dia.nc
1 00010101 00:01:30.00 2.119091E03 1.022561E+02 1.022582E+02 4.712932E+11
(001,202,30) 1.451571E01 2.060904E03 0.000000E+00 1.980366E+00
2 00010101 00:03:00.00 3.008514E03 1.022790E+02 1.022820E+02 4.711565E+11
(001,198,30) 1.850742E01 1.725912E04 3.389906E+01 2.188908E+00
3 00010101 00:04:30.00 4.848609E03 1.023024E+02 1.023072E+02 4.710154E+11
(002,204,30)
the parameter only at first time step existed in the avg.nc file. I attached the nc file here.
I will try to turnoff the biological mode part and check the forcing, grid files again.
 Attachments

 ocean_dia.nc
 (14.49 MiB) Downloaded 79 times
Re: the parameter in the avg nc file is empty
Your surface heat flux looks bizarre to the south there.

 Posts: 20
 Joined: Thu May 04, 2017 1:31 pm
 Location: south china sea institute of oceanography
Re: the parameter in the avg nc file is empty
i did my best to figure out why latent,sensible,and shlux is so wield in history file "roms_his.nc" (results were attached below). however, I have no clue. "lwrad" seems ok in history file(roms_his.nc).kate wrote:Your surface heat flux looks bizarre to the south there.
I go back to check the forcing file (roms_frc.nc) which I used "coads" and "NCEP/NCAR Reanalysis Monthly Means" data (attached below).

 Posts: 20
 Joined: Thu May 04, 2017 1:31 pm
 Location: south china sea institute of oceanography
Re: the parameter in the avg nc file is empty
here is dQdSST,"latent",lward,pair,sensible,shflux,sst in forcing file, roms_frc.nckate wrote:Your surface heat flux looks bizarre to the south there.

 Posts: 20
 Joined: Thu May 04, 2017 1:31 pm
 Location: south china sea institute of oceanography
Re: the parameter in the avg nc file is empty
parameters in restart file"rst.nc" look normal.
paramters in bry.nc "boundary condition files" look normal except NH4 is a constant .
it is only one effective value in my region (the region is too small), and this value was obtained from coads data. acutally, i set the value of TIC,alkalinity by myself. NO3 which from coads data was multiplied by a different factor to get TIC,alkalinity, and so on.
paramters in bry.nc "boundary condition files" look normal except NH4 is a constant .
it is only one effective value in my region (the region is too small), and this value was obtained from coads data. acutally, i set the value of TIC,alkalinity by myself. NO3 which from coads data was multiplied by a different factor to get TIC,alkalinity, and so on.