the parameter in the avg nc file is empty

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chaoyu1985
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Joined: Thu May 04, 2017 1:31 pm
Location: south china sea institute of oceanography

the parameter in the avg nc file is empty

#1 Post by chaoyu1985 » Mon Sep 04, 2017 3:13 am

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 NEMO-PISCES 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
TIME-STEP YYYY-MM-DD hh:mm:ss.ss KINETIC_ENRG POTEN_ENRG TOTAL_ENRG NET_VOLUME
C => (i,j,k) Cu Cv Cw Max Speed

0 0001-01-01 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 0001-01-01 00:09:00.00 NaN NaN NaN NaN
(190,001,30) 1.953902E-02 7.791596E-03 0.000000E+00 Infinity

chaoyu1985
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

#2 Post by chaoyu1985 » Mon Sep 04, 2017 3:18 am

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?

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kate
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Re: the parameter in the avg nc file is empty

#3 Post by kate » Mon Sep 04, 2017 6:56 am

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.

chaoyu1985
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

#4 Post by chaoyu1985 » Mon Sep 04, 2017 8:16 am

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.
Thank you so much for your reply.
the information is:

Basin information for Grid 01:

Maximum grid stiffness ratios: rx0 = 2.309898E-01 (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 time-stepping: (Grid: 01 TimeSteps: 00000001 - 00001600)

GET_2DFLD - surface u-wind component, 0001-01-16 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 v-wind component, 0001-01-16 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, 0001-01-16 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, 0001-01-16 00:00:00.00
(Grid=01, Rec=0000001, Index=2, File: roms_frc.nc)
(Tmin= 15.0000 Tmax= 345.0000) t = 15.0000
(Min = 2.76230526E-05 Max = 4.07666000E-05) regrid = F
GET_2DFLD - surface air temperature, 0001-01-16 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, 0001-01-16 00:00:00.00
(Grid=01, Rec=0000001, Index=2, File: roms_frc.nc)
(Tmin= 15.0000 Tmax= 345.0000) t = 15.0000
(Min = 7.93226792E-01 Max = 8.58040507E-01) regrid = F
GET_NGFLD - temperature eastern boundary condition, 0001-01-16 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, 0001-01-16 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, 0001-01-16 00:00:00.00
(Grid= 01, Rec=0000001, Index=1, File: roms_bry.nc)
(Tmin= 15.0000 Tmax= 345.0000) t = 15.0000
(Min = 2.69948635E-01 Max = 4.16393587E+01)
GET_NGFLD - ammonium eastern boundary condition, 0001-01-16 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, 0001-01-16 00:00:00.00
(Grid= 01, Rec=0000001, Index=1, File: roms_bry.nc)
(Tmin= 15.0000 Tmax= 345.0000) t = 15.0000
(Min = 5.08890706E-03 Max = 2.21083747E+00)
GET_NGFLD - phytoplankton eastern boundary condition, 0001-01-16 00:00:00.00
(Grid= 01, Rec=0000001, Index=1, File: roms_bry.nc)
(Tmin= 15.0000 Tmax= 345.0000) t = 15.0000
(Min = 2.54445353E-03 Max = 1.10541874E+00)
GET_NGFLD - zooplankton eastern boundary condition, 0001-01-16 00:00:00.00
(Grid= 01, Rec=0000001, Index=1, File: roms_bry.nc)
(Tmin= 15.0000 Tmax= 345.0000) t = 15.0000
(Min = 1.01778141E-03 Max = 4.42167495E-01)
GET_NGFLD - large fraction nitrogen detritus eastern boundary0001-01-16 00:00:00.00
(Grid= 01, Rec=0000001, Index=1, File: roms_bry.nc)
(Tmin= 15.0000 Tmax= 345.0000) t = 15.0000
(Min = 6.74871588E-04 Max = 1.04098397E-01)
GET_NGFLD - small fraction nitrogen detritus eastern boundary0001-01-16 00:00:00.00
(Grid= 01, Rec=0000001, Index=1, File: roms_bry.nc)
(Tmin= 15.0000 Tmax= 345.0000) t = 15.0000
(Min = 1.34974318E-03 Max = 2.08196793E-01)
GET_NGFLD - large fraction carbon detritus eastern boundary c0001-01-16 00:00:00.00
(Grid= 01, Rec=0000001, Index=1, File: roms_bry.nc)
(Tmin= 15.0000 Tmax= 345.0000) t = 15.0000
(Min = 1.34974318E-02 Max = 2.08196793E+00)
GET_NGFLD - small fraction carbon detritus eastern boundary c0001-01-16 00:00:00.00
(Grid= 01, Rec=0000001, Index=1, File: roms_bry.nc)
(Tmin= 15.0000 Tmax= 345.0000) t = 15.0000
(Min = 1.34974318E-02 Max = 2.08196793E+00)
GET_NGFLD - TIC eastern boundary condition, 0001-01-16 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, 0001-01-16 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, 0001-01-16 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, 0001-01-16 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, 0001-01-16 00:00:00.00
(Grid= 01, Rec=0000001, Index=1, File: roms_bry.nc)
(Tmin= 15.0000 Tmax= 345.0000) t = 15.0000
(Min = -4.72082936E-02 Max = 4.15975251E+01)
GET_NGFLD - ammonium southern boundary condition, 0001-01-16 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, 0001-01-16 00:00:00.00
(Grid= 01, Rec=0000001, Index=1, File: roms_bry.nc)
(Tmin= 15.0000 Tmax= 345.0000) t = 15.0000
(Min = 5.00979295E-03 Max = 2.45184533E+00)
GET_NGFLD - phytoplankton southern boundary condition, 0001-01-16 00:00:00.00
(Grid= 01, Rec=0000001, Index=1, File: roms_bry.nc)
(Tmin= 15.0000 Tmax= 345.0000) t = 15.0000
(Min = 2.50489647E-03 Max = 1.22592267E+00)
GET_NGFLD - zooplankton southern boundary condition, 0001-01-16 00:00:00.00
(Grid= 01, Rec=0000001, Index=1, File: roms_bry.nc)
(Tmin= 15.0000 Tmax= 345.0000) t = 15.0000
(Min = 1.00195859E-03 Max = 4.90369067E-01)
GET_NGFLD - large fraction nitrogen detritus southern boundar0001-01-16 00:00:00.00
(Grid= 01, Rec=0000001, Index=1, File: roms_bry.nc)
(Tmin= 15.0000 Tmax= 345.0000) t = 15.0000
(Min = -1.18020734E-04 Max = 1.03993813E-01)
GET_NGFLD - small fraction nitrogen detritus southern boundar0001-01-16 00:00:00.00
(Grid= 01, Rec=0000001, Index=1, File: roms_bry.nc)
(Tmin= 15.0000 Tmax= 345.0000) t = 15.0000
(Min = -2.36041468E-04 Max = 2.07987626E-01)
GET_NGFLD - large fraction carbon detritus southern boundary 0001-01-16 00:00:00.00
(Grid= 01, Rec=0000001, Index=1, File: roms_bry.nc)
(Tmin= 15.0000 Tmax= 345.0000) t = 15.0000
(Min = -2.36041468E-03 Max = 2.07987626E+00)
GET_NGFLD - small fraction carbon detritus southern boundary 0001-01-16 00:00:00.00
(Grid= 01, Rec=0000001, Index=1, File: roms_bry.nc)
(Tmin= 15.0000 Tmax= 345.0000) t = 15.0000
(Min = -2.36041468E-03 Max = 2.07987626E+00)
GET_NGFLD - TIC southern boundary condition, 0001-01-16 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, 0001-01-16 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)

TIME-STEP YYYY-MM-DD hh:mm:ss.ss KINETIC_ENRG POTEN_ENRG TOTAL_ENRG NET_VOLUME
C => (i,j,k) Cu Cv Cw Max Speed

0 0001-01-01 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 0001-01-01 00:09:00.00 NaN NaN NaN NaN
(190,001,30) 1.953902E-02 7.791596E-03 0.000000E+00 Infinity

chaoyu1985
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

#5 Post by chaoyu1985 » Mon Sep 04, 2017 8:28 am

I found the min and max value of free surface,u-momentum component is zero. would that cold be a problem? the study area is 105-118E;17-24N.
should I use the woa or coads data to compute the free surface in the initial file.
NLM: GET_STATE - Read state initial conditions, 0001-01-01 00:00:00.00
(Grid 01, t = 0.0000, File: roms_ini.nc, Rec=0001, Index=1)
- free-surface
(Min = 0.00000000E+00 Max = 0.00000000E+00)
- vertically integrated u-momentum component
(Min = 0.00000000E+00 Max = 0.00000000E+00)
- vertically integrated v-momentum component
(Min = 0.00000000E+00 Max = 0.00000000E+00)
- u-momentum component
(Min = 0.00000000E+00 Max = 0.00000000E+00)
- v-momentum 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 = -1.84808126E-02 Max = 5.21889124E-01)
- 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 = -3.69616252E-03 Max = 1.04377825E-01)
- small fraction nitrogen detritus concentration
(Min = -7.39232503E-03 Max = 2.08755649E-01)
- large fraction carbon detritus concentration
(Min = -7.39232503E-02 Max = 2.08755649E+00)
- small fraction carbon detritus concentration
(Min = -7.39232503E-02 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 = 5.60665872E-06 Max = 1.40909152E+01)
GET_2DFLD - tidal elevation phase angle
(Grid = 01, Min = 4.78313257E-07 Max = 6.28318512E+00)

User avatar
kate
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Joined: Wed Jul 02, 2003 5:29 pm
Location: IMS/UAF, USA

Re: the parameter in the avg nc file is empty

#6 Post by kate » Mon Sep 04, 2017 3:46 pm

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:

Code: Select all

GET_2DFLD - surface u-wind component, 0001-01-16 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 v-wind component, 0001-01-16 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
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.

chaoyu1985
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

#7 Post by chaoyu1985 » Wed Sep 06, 2017 2:29 am

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.
thx,I really appreciated the suggestions you gave. it is important clue for me who only have biological background.
I changed the timestep.

Code: Select all

100  ntimes            Number of timesteps for 3-D equations.
90.000  dt                Timestep size (s) for 3-D equations.
5  ndtfast           Number of timesteps for 2-D equations between
write out the wind stress.

Code: Select all

T  Hout(idUsms)      Write out surface U-momentum stress.
T  Hout(idVsms)      Write out surface V-momentum stress.
ROMS can run and calculate:

Code: Select all

DEF_DIAGS   - creating  diagnostics  file, Grid 01: data2/ocean_dia.nc
         1 0001-01-01 00:01:30.00  2.119091E-03  1.022561E+02  1.022582E+02  4.712932E+11
                     (001,202,30)  1.451571E-01  2.060904E-03  0.000000E+00  1.980366E+00
         2 0001-01-01 00:03:00.00  3.008514E-03  1.022790E+02  1.022820E+02  4.711565E+11
                     (001,198,30)  1.850742E-01  1.725912E-04  3.389906E+01  2.188908E+00
         3 0001-01-01 00:04:30.00  4.848609E-03  1.023024E+02  1.023072E+02  4.710154E+11
                     (002,204,30)  
(100 steps were finished and I did not copy them all)
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 83 times
chlorophyll_sig_1_T=1_ .png
shflux_sig_1_T=1_ .png
swrad_sig_1_T=1_ .png

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kate
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Location: IMS/UAF, USA

Re: the parameter in the avg nc file is empty

#8 Post by kate » Wed Sep 06, 2017 4:16 am

Your surface heat flux looks bizarre to the south there.

chaoyu1985
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

#9 Post by chaoyu1985 » Thu Sep 14, 2017 3:17 am

kate wrote:Your surface heat flux looks bizarre to the south there.
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).
I go back to check the forcing file (roms_frc.nc) which I used "coads" and "NCEP/NCAR Reanalysis Monthly Means" data (attached below).
Attachments
temperature in history file
temperature in history file
shflux in history file
shflux in history file
sensible in history file
sensible in history file
lwrad in history file
lwrad in history file
latent in history file
latent in history file

chaoyu1985
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

#10 Post by chaoyu1985 » Thu Sep 14, 2017 4:06 am

kate wrote:Your surface heat flux looks bizarre to the south there.
here is dQdSST,"latent",lward,pair,sensible,shflux,sst in forcing file, roms_frc.nc
Attachments
SST_T=_ .png
shflux_T=_ .png
sensible_T=_ .png
lwrad_T=_ .png
latent_T=_ .png
dQdSST_T=_ .png

chaoyu1985
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

#11 Post by chaoyu1985 » Thu Sep 14, 2017 4:21 am

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.
Attachments
NH4_T=1_ .png

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