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