stdout

[redhat007]

i am using 13 files as roms forces (sms, shflux,swrad,Tair, Qair,Pair,wind,rain, cloud, sensible,latent,lwrad, river). But in stdout file there are some parts which show just five of them . Some thing like this:

Code: Select all

GET_NGFLD   - river runoff mass transport,               t =    31 00:00:00 
                   (Rec=0002, Index=1, File: rivers_force_08.nc) 
                   (Tmin=          0.0000 Tmax=        335.0000) 
                   (Min =  8.10000000E+00 Max =  1.80850150E+02) 
    GET_NGFLD   - river runoff potential temperature,        t =    31 00:00:00 
                   (Rec=0002, Index=1, File: rivers_force_08.nc) 
                   (Tmin=          0.0000 Tmax=        335.0000) 
                   (Min =  0.00000000E+00 Max =  5.70000000E+00) 
    GET_NGFLD   - river runoff salinity,                     t =    31 00:00:00 
                   (Rec=0002, Index=1, File: rivers_force_08.nc) 
                   (Tmin=          0.0000 Tmax=        335.0000) 
                   (Min =  0.00000000E+00 Max =  0.00000000E+00) 
    GET_2DFLD   - surface u-momentum stress,                 t =     0 04:30:00 
                   (Rec=0002, Index=2, File: CS_sms2_era_08.nc) 
                   (Tmin=          0.0625 Tmax=        365.9375) 
                   (Min = -8.81097026E-05 Max =  1.11008348E-04) 
    GET_2DFLD   - surface v-momentum stress,                 t =     0 04:30:00 
                   (Rec=0002, Index=2, File: CS_sms2_era_08.nc) 
                   (Tmin=          0.0625 Tmax=        365.9375) 
                   (Min = -9.29573630E-05 Max =  1.26521028E-04) 
    GET_2DFLD   - surface net heat flux,                     t =     0 04:30:00 
                   (Rec=0002, Index=2, File: CS_shflux2_era_08.nc) 
                   (Tmin=          0.0625 Tmax=        365.9375) 
                   (Min = -6.13341848E-05 Max =  6.77839475E-06) 
    GET_2DFLD   - surface net freswater flux, (E-P),         t =     0 04:30:00 
                   (Rec=0002, Index=2, File: CS_swflux2_era_08.nc) 
                   (Tmin=          0.0625 Tmax=        365.9375) 
                   (Min = -2.98790427E-07 Max =  5.04688906E-08) 

does it mean that other force files have not been applied by roms ?
my header file is:
#define ROMS_MODEL
#define SALINITY
#define SOLVE3D
#define MASKING
#define SPLINES /*activate parabolic splines reconstruction */
#undef WET_DRY
#define OUT_DOUBLE /*writing double precision output fields*/
/* advection, dissipation, pressure grad, etc. */
#define DJ_GRADPS /*splines density Jacobian (Shchepetkin, 2000) */
#define UV_ADV /*turn on advection terms*/
#define UV_COR /*turn on Coriolis term*/
#undef UV_SADVECTION
/*tracer advection*/
#define TS_U3HADVECTION /*3rd-order upstream horiz. advection*/
#define TS_C4VADVECTION
!#define TS_MPDATA
#define NONLIN_EOS
#define UV_QDRAG /*quardatic bottom friction*/
#define UV_VIS2 /*harmonic horizantal mixixng*/
#define MIX_S_UV /*4th-order centered vertical advection */
#define TS_DIF2 /*tracer harmonic horizontal mixing */
#define MIX_S_TS
/* Boundary Conditions */
#define EASTERN_WALL
#define WESTERN_WALL
#define NORTHERN_WALL
#define SOUTHERN_WALL
/* output stuff */
#define AVERAGES /*writing out time-averaged data */
#define DIAGNOSTICS_UV /*writing out momentum diagnostics */
#define DIAGNOSTICS_TS /*writing out tracer diagnostics */
/* roms quirks */
#undef ANA_GRID
#undef ANA_INITIAL
#undef ANA_SMFLUX
# undef ANA_STFLUX
# undef ANA_SSFLUX
# define ANA_BTFLUX
# define ANA_BSFLUX
/*river*/
#define UV_PSOURCE
#define TS_PSOURCE
#undef Q_PSOURCE
/* vertical mixing */
#define GLS_MIXING /*Generic Length-Scale mixing */
#if defined GLS_MIXING
# define KANTHA_CLAYSON
# undef CANUTO_A
# define N2S2_HORAVG
#else
# define ANA_VMIX
#endif
#ifdef PERFECT_RESTART
# undef AVERAGES
# undef DIAGNOSTICS_BIO
# undef DIAGNOSTICS_TS
# undef DIAGNOSTICS_UV
# define OUT_DOUBLE
#endif

Best
redhat

[kate]

Yes, that's right. You didn't #define BULK_FLUXES so it doesn't need Tair and friends and therefore doesn't read them. If you provide the wind stress and heat/salt flux, you don't need to compute them from atmospheric fields.

[redhat007]

Dear kate
thanks.
Are

Tair and friends

: Pair, Qair , rain and cloud and

atmospheric fields

: latent, sensible, solar and thermal radiation?
With regard that Bulk flux equations are empirical and each sea needs its own formulation, Which one it better: using #define Bulk flux or providing wind stress, fresh water flux and heat flux fields directly?
Cheers
redhat

[kate]

Yes, that's the list of atmospheric fields, though I'm reading albedo and not clouds. It depends. Because the heat fluxes are sensitive to SST, I believe one should compute them based on your local SST or at the very least include the dQdSST term when reading in fluxes.

That said, I have colleagues who don't like the default bulk_flux routine and prefer the algorithm used in CESM. We therefore have an alternate CCSM_FLUXES option which happens to include the surface ocean currents in its calculation.

[redhat007]

Many thanks.
you mean that dQdsst (surface net heat flux sensitivity to sst ) should be used instead of shflux or both of them should be used.

Also would you please if you know any good way to calculate dQdsst, tell it to me.
Thanks again
cheers
redhat

[kate]

The ROMS flag QCORRECTION enables this code:

Code: Select all

          stflx(i,j,itemp)=stflx(i,j,itemp)+                            &    
     &                     dqdt(i,j)*(t(i,j,N(ng),nrhs,itemp)-sst(i,j))

You need the three fields stflx(itemp), dqdt (dQdSST) and sst (the SST used when computing stflx(itemp)).

[wilkin]

See the paper:

B. Barnier, L. Siefridt, P. Marchesiello, Thermal forcing for a global ocean circulation model using a three-year climatology of ECMWF analyses, J. Marine Sys., 2005, 6, 363-380

for one approach toward setting appropriate values for dQdSST.

You could adapt that method to code the algorithm in Functionals/ana_dqdsst.h for typical values of SST, Tair, rho_atmosphere, wind speed and humidity in your region of interest, or write time and space evolving dqdsst to a forcing netcdf file from your other forcing data. It's up to you how to do it.

Among the IRD Matlab Roms_tools http://www.romsagrif.org/index.php/download there is a file get_dqdsst.m that does the calculation in Matlab.

[redhat007]

Dear
thanks for good information
i am really eager to know if surface net heat flux, surface fresh water flux and wind stress (as well as river , if there is) are enough forces in Roms model?
Cheers
redhat

[kate]

If you turn on SOLAR_SOURCE, ROMS will also want incoming shortwave radiation for solar heating below the surface.

[redhat007]

Dear
i make decision to use #define BULK_FLUXES .
Same setting with same initial file which used for model with out #define BULK_FLUXES ( run with out problem) have been used but with Pair, Tair,Qair,rain,cloud,sward and lwrad and river as a force files. But new model BLOW UP just after 9 min. also when i use #define LONGWAVE and #define SHORTWAVE instead of lwrad and swrad, respectively, this blow up happened again.
In restart file current speed is less that 2m/s and tracers are in correct limit. But just zeta is out of range (about 1.2 m in some region).
Would you please tell me what s problem?

Code: Select all

 Node #  0 (pid=   17197) is active.

 Model Input Parameters:  ROMS/TOMS version 3.4  
                          Monday - June 16, 2014 -  1:15:35 PM
 -----------------------------------------------------------------------------
 Node #  1 (pid=   17198) is active.


 Operating system : Linux
 CPU/hardware     : i686
 Compiler system  : gfortran
 Compiler command : /usr/lib/mpich2/bin/mpif90
 Compiler flags   : -frepack-arrays -O3 -ffast-math -ffree-form -ffree-line-length-none -ffree-form -ffree-line-length-none

 Input Script  : ocean_rip_current.in

 SVN Root URL  : 
 SVN Revision  : 791M

 Local Root    : /home/COAWST
 Header Dir    : /home/COAWST/project/p5_07022
 Header file   : rip_current.h
 Analytical Dir: /home/COAWST/project/Roms_only/p5_07022

 Resolution, Grid 01: 0194x0344x032,  Parallel Nodes:   2,  Tiling: 001x002


 Physical Parameters, Grid: 01
 =============================

      15360  ntimes          Number of timesteps for 3-D equations.
     90.000  dt              Timestep size (s) for 3-D equations.
         30  ndtfast         Number of timesteps for 2-D equations between
                               each 3D timestep.
          1  ERstr           Starting ensemble/perturbation run number.
          1  ERend           Ending ensemble/perturbation run number.
          0  nrrec           Number of restart records to read from disk.
          T  LcycleRST       Switch to recycle time-records in restart file.
        960  nRST            Number of timesteps between the writing of data
                               into restart fields.
          1  ninfo           Number of timesteps between print of information
                               to standard output.
          T  ldefout         Switch to create a new output NetCDF file(s).
        480  nHIS            Number of timesteps between the writing fields
                               into history file.
          1  ntsAVG          Starting timestep for the accumulation of output
                               time-averaged data.
       9600  nAVG            Number of timesteps between the writing of
                               time-averaged data into averages file.
          1  ntsDIA          Starting timestep for the accumulation of output
                               time-averaged diagnostics data.
      28800  nDIA            Number of timesteps between the writing of
                               time-averaged data into diagnostics file.
 1.0000E+02  nl_tnu2(01)     NLM Horizontal, harmonic mixing coefficient
                               (m2/s) for tracer 01: temp
 1.0000E+02  nl_tnu2(02)     NLM Horizontal, harmonic mixing coefficient
                               (m2/s) for tracer 02: salt
 1.0000E+01  nl_visc2        NLM Horizontal, harmonic mixing coefficient
                               (m2/s) for momentum.
 5.0000E-06  Akt_bak(01)     Background vertical mixing coefficient (m2/s)
                               for tracer 01: temp
 5.0000E-06  Akt_bak(02)     Background vertical mixing coefficient (m2/s)
                               for tracer 02: salt
 1.0000E-05  Akv_bak         Background vertical mixing coefficient (m2/s)
                               for momentum.
 5.0000E-06  Akk_bak         Background vertical mixing coefficient (m2/s)
                               for turbulent energy.
 5.0000E-06  Akp_bak         Background vertical mixing coefficient (m2/s)
                               for turbulent generic statistical field.
      3.000  gls_p           GLS stability exponent.
      1.500  gls_m           GLS turbulent kinetic energy exponent.
     -1.000  gls_n           GLS turbulent length scale exponent.
 7.6000E-06  gls_Kmin        GLS minimum value of turbulent kinetic energy.
 1.0000E-12  gls_Pmin        GLS minimum value of dissipation.
 5.4770E-01  gls_cmu0        GLS stability coefficient.
 1.4400E+00  gls_c1          GLS shear production coefficient.
 1.9200E+00  gls_c2          GLS dissipation coefficient.
-4.0000E-01  gls_c3m         GLS stable buoyancy production coefficient.
 1.0000E+00  gls_c3p         GLS unstable buoyancy production coefficient.
 1.0000E+00  gls_sigk        GLS constant Schmidt number for TKE.
 1.3000E+00  gls_sigp        GLS constant Schmidt number for PSI.
   1400.000  charnok_alpha   Charnok factor for Zos calculation.
      0.500  zos_hsig_alpha  Factor for Zos calculation using Hsig(Awave).
      0.020  sz_alpha        Factor for Wave dissipation surface tke flux .
    100.000  crgban_cw       Factor for Craig/Banner surface tke flux.
 2.0000E-04  rdrg            Linear bottom drag coefficient (m/s).
 3.3000E-03  rdrg2           Quadratic bottom drag coefficient.
 2.0000E-02  Zob             Bottom roughness (m).
 2.0000E-02  Zos             Surface roughness (m).
 2.0000E+00  blk_ZQ          Height (m) of surface air humidity measurement.
 2.0000E+00  blk_ZT          Height (m) of surface air temperature measurement.
 1.0000E+01  blk_ZW          Height (m) of surface winds measurement.
          1  lmd_Jwt         Jerlov water type.
          2  Vtransform      S-coordinate transformation equation.
          4  Vstretching     S-coordinate stretching function.
 8.0000E+00  theta_s         S-coordinate surface control parameter.
 4.0000E-01  theta_b         S-coordinate bottom  control parameter.
      6.000  Tcline          S-coordinate surface/bottom layer width (m) used
                               in vertical coordinate stretching.
   1025.000  rho0            Mean density (kg/m3) for Boussinesq approximation.
     53.000  dstart          Time-stamp assigned to model initialization (days).
20070101.00  time_ref        Reference time for units attribute (yyyymmdd.dd)
 0.0000E+00  Tnudg(01)       Nudging/relaxation time scale (days)
                               for tracer 01: temp
 0.0000E+00  Tnudg(02)       Nudging/relaxation time scale (days)
                               for tracer 02: salt
 0.0000E+00  Znudg           Nudging/relaxation time scale (days)
                               for free-surface.
 0.0000E+00  M2nudg          Nudging/relaxation time scale (days)
                               for 2D momentum.
 0.0000E+00  M3nudg          Nudging/relaxation time scale (days)
                               for 3D momentum.
 0.0000E+00  obcfac          Factor between passive and active
                               open boundary conditions.
     10.000  T0              Background potential temperature (C) constant.
     35.000  S0              Background salinity (PSU) constant.
      1.000  gamma2          Slipperiness variable: free-slip (1.0) or 
                                                    no-slip (-1.0).
          T  LtracerSrc(01)  Processing point sources/Sink on tracer 01: temp
          T  LtracerSrc(02)  Processing point sources/Sink on tracer 02: salt
          T  Hout(idFsur)    Write out free-surface.
          T  Hout(idUbar)    Write out 2D U-momentum component.
          T  Hout(idVbar)    Write out 2D V-momentum component.
          T  Hout(idUvel)    Write out 3D U-momentum component.
          T  Hout(idVvel)    Write out 3D V-momentum component.
          T  Hout(idWvel)    Write out W-momentum component.
          T  Hout(idOvel)    Write out omega vertical velocity.
          T  Hout(idTvar)    Write out tracer 01: temp
          T  Hout(idTvar)    Write out tracer 02: salt
          T  Hout(idUsms)    Write out surface U-momentum stress.
          T  Hout(idVsms)    Write out surface V-momentum stress.
          T  Hout(idUbms)    Write out bottom U-momentum stress.
          T  Hout(idVbms)    Write out bottom V-momentum stress.
          T  Hout(idVvis)    Write out vertical viscosity coefficient.
          T  Hout(idMtke)    Write out turbulent kinetic energy.
          T  Hout(idMtls)    Write out turbulent generic length-scale.

 Output/Input Files:

             Output Restart File:  ocean_rip_current_rst.nc
             Output History File:  ocean_rip_current_his.nc
            Output Averages File:  ocean_rip_current_avg.nc
         Output Diagnostics File:  ocean_rip_current_dia.nc
                 Input Grid File:  /home/grid/grid_3.nc
    Input Nonlinear Initial File:  /home/clim-init/initial_feb_23.nc
           Input Forcing File 01:  /home/cloud2_era_07.nc
           Input Forcing File 02:  /home/Pair2_era_07.nc
           Input Forcing File 03:  /home/Qair2_era_07.nc
           Input Forcing File 04:  /home/Tair2_era_07.nc
           Input Forcing File 05:  /home/uwnd2_era_07.nc
           Input Forcing File 06:  /home/vwnd2_era_07.nc
           Input Forcing File 07:  /home/rain2_era_07.nc
           Input Forcing File 08:  /home/lwrad2_era_07.nc
           Input Forcing File 09:  /home/swrad2_era_07.nc
           Input Forcing File 10:  /home/rivers_force_07.nc

 Tile partition information for Grid 01:  0194x0344x0032  tiling: 001x002

     tile     Istr     Iend     Jstr     Jend     Npts

        0        1      194        1      172  1067776
        1        1      194      173      344  1067776

 Tile minimum and maximum fractional grid coordinates:
   (interior points only)

     tile     Xmin     Xmax     Ymin     Ymax     grid

        0     0.50   194.50     0.50   172.50  RHO-points
        1     0.50   194.50   172.50   344.50  RHO-points

        0     1.00   194.00     0.50   172.50    U-points
        1     1.00   194.00   172.50   344.50    U-points

        0     0.50   194.50     1.00   172.50    V-points
        1     0.50   194.50   172.50   344.00    V-points

 Maximum halo size in XI and ETA directions:

               HaloSizeI(1) =     410
               HaloSizeJ(1) =     368
                TileSide(1) =     199
                TileSize(1) =   35422


 Activated C-preprocessing Options:

 RIPCURRENT          Rip Current from Haas and Warner
 ANA_BSFLUX          Analytical kinematic bottom salinity flux.
 ANA_BTFLUX          Analytical kinematic bottom temperature flux.
 ASSUMED_SHAPE       Using assumed-shape arrays.
 AVERAGES            Writing out time-averaged fields.
 BULK_FLUXES         Surface bulk fluxes parametererization.
 COOL_SKIN           Surface cool skin correction.
 DIAGNOSTICS_TS      Computing and writing tracer diagnostic terms.
 DIAGNOSTICS_UV      Computing and writing momentum diagnostic terms.
 DJ_GRADPS           Parabolic Splines density Jacobian (Shchepetkin, 2002).
 DOUBLE_PRECISION    Double precision arithmetic.
 EASTERN_WALL        Wall boundary at Eastern edge.
 EMINUSP             Compute Salt Flux using E-P.
 GLS_MIXING          Generic Length-Scale turbulence closure.
 KANTHA_CLAYSON      Kantha and Clayson stability function formulation.
 MASKING             Land/Sea masking.
 MIX_S_TS            Mixing of tracers along constant S-surfaces.
 MIX_S_UV            Mixing of momentum along constant S-surfaces.
 MPI                 MPI distributed-memory configuration.
 NONLINEAR           Nonlinear Model.
 NONLIN_EOS          Nonlinear Equation of State for seawater.
 NORTHERN_WALL       Wall boundary at Northern edge.
 N2S2_HORAVG         Horizontal smoothing of buoyancy and shear.
 OUT_DOUBLE          Double precision output fields in NetCDF files.
 PERFECT_RESTART     Processing perfect restart variables.
 POWER_LAW           Power-law shape time-averaging barotropic filter.
 PROFILE             Time profiling activated .
 K_GSCHEME           Third-order upstream advection of TKE fields.
 !RST_SINGLE         Double precision fields in restart NetCDF file.
 SALINITY            Using salinity.
 SOLAR_SOURCE        Solar Radiation Source Term.
 SOLVE3D             Solving 3D Primitive Equations.
 SOUTHERN_WALL       Wall boundary at Southern edge.
 SPLINES             Conservative parabolic spline reconstruction.
 TS_U3HADVECTION     Third-order upstream horizontal advection of tracers.
 TS_C4VADVECTION     Fourth-order centered vertical advection of tracers.
 TS_DIF2             Harmonic mixing of tracers.
 TS_PSOURCE          Tracers point sources and sinks.
 UV_ADV              Advection of momentum.
 UV_COR              Coriolis term.
 UV_U3HADVECTION     Third-order upstream horizontal advection of 3D momentum.
 UV_C4VADVECTION     Fourth-order centered vertical advection of momentum.
 UV_QDRAG            Quadratic bottom stress.
 UV_PSOURCE          Mass point sources and sinks.
 UV_VIS2             Harmonic mixing of momentum.
 VAR_RHO_2D          Variable density barotropic mode.
 WESTERN_WALL        Wall boundary at Western edge.

 INITIAL: Configuring and initializing forward nonlinear model ...


 Vertical S-coordinate System: 

 level   S-coord     Cs-curve   Z   at hmin       at hc    half way     at hmax

    32   0.0000000   0.0000000        0.000       0.000       0.000       0.000
    31  -0.0312500  -0.0000256       -0.101      -0.094      -0.198      -0.211
    30  -0.0625000  -0.0001040       -0.202      -0.188      -0.421      -0.474
    29  -0.0937500  -0.0002400       -0.304      -0.282      -0.672      -0.792
    28  -0.1250000  -0.0004423       -0.406      -0.376      -0.956      -1.175
    27  -0.1562500  -0.0007236       -0.508      -0.471      -1.278      -1.635
    26  -0.1875000  -0.0011014       -0.610      -0.566      -1.647      -2.188
    25  -0.2187500  -0.0015996       -0.713      -0.661      -2.074      -2.858
    24  -0.2500000  -0.0022492       -0.816      -0.757      -2.575      -3.675
    23  -0.2812500  -0.0030910       -0.920      -0.853      -3.170      -4.679
    22  -0.3125000  -0.0041778       -1.025      -0.950      -3.884      -5.921
    21  -0.3437500  -0.0055774       -1.132      -1.048      -4.749      -7.467
    20  -0.3750000  -0.0073773       -1.239      -1.147      -5.810      -9.402
    19  -0.4062500  -0.0096898       -1.349      -1.248      -7.119     -11.834
    18  -0.4375000  -0.0126588       -1.461      -1.350      -8.748     -14.904
    17  -0.4687500  -0.0164685       -1.576      -1.456     -10.786     -18.791
    16  -0.5000000  -0.0213546       -1.696      -1.564     -13.346     -23.723
    15  -0.5312500  -0.0276179       -1.820      -1.677     -16.577     -29.993
    14  -0.5625000  -0.0356419       -1.952      -1.794     -20.663     -37.973
    13  -0.5937500  -0.0459141       -2.091      -1.919     -25.843     -48.136
    12  -0.6250000  -0.0590529       -2.242      -2.052     -32.416     -61.084
    11  -0.6562500  -0.0758390       -2.406      -2.196     -40.763     -77.575
    10  -0.6875000  -0.0972542       -2.588      -2.354     -51.360     -98.561
     9  -0.7187500  -0.1245249       -2.791      -2.530     -64.804    -125.235
     8  -0.7500000  -0.1591703       -3.023      -2.728     -81.834    -159.072
     7  -0.7812500  -0.2030516       -3.289      -2.953    -103.354    -201.879
     6  -0.8125000  -0.2584153       -3.599      -3.213    -130.457    -255.839
     5  -0.8437500  -0.3279186       -3.962      -3.515    -164.434    -323.533
     4  -0.8750000  -0.4146160       -4.390      -3.869    -206.771    -407.927
     3  -0.9062500  -0.5218760       -4.895      -4.284    -259.106    -512.293
     2  -0.9375000  -0.6531834       -5.491      -4.772    -323.132    -640.016
     1  -0.9687500  -0.8117684       -6.190      -5.342    -400.420    -794.233
     0  -1.0000000  -1.0000000       -7.000      -6.000    -492.123    -977.246

 Time Splitting Weights: ndtfast =  30    nfast =  42

    Primary            Secondary            Accumulated to Current Step

  1-0.0008094437383769 0.0333333333333333-0.0008094437383769 0.0333333333333333
  2-0.0014053566728197 0.0333603147912792-0.0022148004111966 0.0666936481246126
  3-0.0017877524645903 0.0334071600137066-0.0040025528757869 0.1001008081383191
  4-0.0019566842408176 0.0334667517625262-0.0059592371166046 0.1335675599008453
  5-0.0019122901320372 0.0335319745705535-0.0078715272486418 0.1670995344713988
  6-0.0016548570247459 0.0335957175749547-0.0095263842733877 0.2006952520463536
  7-0.0011849025289723 0.0336508794757796-0.0107112868023601 0.2343461315221331
  8-0.0005032751608632 0.0336903762267453-0.0112145619632232 0.2680365077488784
  9 0.0003887272597151 0.0337071520654408-0.0108258347035082 0.3017436598143192
 10 0.0014892209965583 0.0336941944901169-0.0093366137069499 0.3354378543044362
 11 0.0027955815694920 0.0336445537902317-0.0065410321374578 0.3690824080946679
 12 0.0043042707117221 0.0335513677379153-0.0022367614257357 0.4026337758325831
 13 0.0060106451121704 0.0334078920475245 0.0037738836864347 0.4360416678801077
 14 0.0079087469427945 0.0332075372104522 0.0116826306292292 0.4692492050905598
 15 0.0099910761708919 0.0329439123123590 0.0216737068001212 0.5021931174029188
 16 0.0122483446563884 0.0326108764399960 0.0339220514565096 0.5348039938429148
 17 0.0146692120341107 0.0322025982847830 0.0485912634906203 0.5670065921276978
 18 0.0172400033810439 0.0317136245503127 0.0658312668716642 0.5987202166780105
 19 0.0199444086685725 0.0311389577709445 0.0857756755402366 0.6298591744489550
 20 0.0227631639997064 0.0304741441486588 0.1085388395399430 0.6603333185976138
 21 0.0256737146312910 0.0297153720153352 0.1342125541712340 0.6900486906129490
 22 0.0286498597812016 0.0288595815276255 0.1628624139524357 0.7189082721405746
 23 0.0316613792205219 0.0279045862015855 0.1945237931729576 0.7468128583421600
 24 0.0346736416507075 0.0268492068942347 0.2291974348236651 0.7736620652363948
 25 0.0376471948657328 0.0256934188392112 0.2668446296893979 0.7993554840756060
 26 0.0405373376992232 0.0244385123436867 0.3073819673886211 0.8237939964192927
 27 0.0432936737565710 0.0230872677537126 0.3506756411451921 0.8468812641730054
 28 0.0458596469320356 0.0216441452951603 0.3965352880772277 0.8685254094681656
 29 0.0481720587108284 0.0201154903974257 0.4447073467880561 0.8886408998655914
 30 0.0501605672561820 0.0185097551070648 0.4948679140442381 0.9071506549726561
 31 0.0517471682814030 0.0168377361985254 0.5466150823256412 0.9239883911711815
 32 0.0528456577069106 0.0151128305891453 0.5994607400325518 0.9391012217603267
 33 0.0533610761022577 0.0133513086655816 0.6528218161348095 0.9524525304259084
 34 0.0531891349131379 0.0115726061288397 0.7060109510479474 0.9640251365547481
 35 0.0522156244733761 0.0097996349650684 0.7582265755213234 0.9738247715198165
 36 0.0503158038019030 0.0080591141492892 0.8085423793232265 0.9818838856691057
 37 0.0473537721847154 0.0063819206892258 0.8558961515079418 0.9882658063583315
 38 0.0431818225418188 0.0048034616164019 0.8990779740497606 0.9930692679747335
 39 0.0376397765791564 0.0033640675316746 0.9367177506289170 0.9964333355064081
 40 0.0305543017255207 0.0021094083123694 0.9672720523544377 0.9985427438187775
 41 0.0217382098544505 0.0010909315881854 0.9890102622088881 0.9996336754069629
 42 0.0109897377911118 0.0003663245930371 0.9999999999999999 1.0000000000000000

 ndtfast, nfast =   30  42   nfast/ndtfast = 1.40000

 Centers of gravity and integrals (values must be 1, 1, approx 1/2, 1, 1):

    1.000000000000 1.047601458608 0.523800729304 1.000000000000 1.000000000000

 Power filter parameters, Fgamma, gamma =  0.28400   0.18933

 Minimum X-grid spacing, DXmin =  3.33514538E+00 km
 Maximum X-grid spacing, DXmax =  3.98831267E+00 km
 Minimum Y-grid spacing, DYmin =  3.33800882E+00 km
 Maximum Y-grid spacing, DYmax =  3.98739982E+00 km
 Minimum Z-grid spacing, DZmin =  1.01057987E-01 m
 Maximum Z-grid spacing, DZmax =  1.83012378E+02 m

 Minimum barotropic Courant Number =  8.90418085E-03
 Maximum barotropic Courant Number =  1.08159505E-01
 Maximum Coriolis   Courant Number =  9.58513554E-03


 NLM: GET_STATE - Read state initial conditions,             t =    52 24:00:00
                   (File: initial_feb_23.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 = -4.20086944E+00 Max =  1.28952207E+01)
                - salinity
                   (Min = -4.95809949E-01 Max =  1.88765502E+01)
    GET_NGFLD   - river runoff  XI-positions at RHO-points
                   (Min =  1.80000000E+01 Max =  1.11000000E+02)
    GET_NGFLD   - river runoff ETA-positions at RHO-points
                   (Min =  8.50000000E+01 Max =  3.31000000E+02)
    GET_NGFLD   - river runoff direction
                   (Min =  0.00000000E+00 Max =  1.00000000E+00)
    GET_NGFLD   - river runoff mass transport vertical profile
                   (Min =  0.00000000E+00 Max =  7.63425333E-02)
    GET_NGFLD   - river runoff mass transport,               t =    45 15:45:00
                   (Rec=0002, Index=2, File: rivers_force_07.nc)
                   (Tmin=         15.2188 Tmax=        350.0313)
                   (Min =  8.10000000E+00 Max =  1.80850150E+02)
    GET_NGFLD   - river runoff potential temperature,        t =    45 15:45:00
                   (Rec=0002, Index=2, File: rivers_force_07.nc)
                   (Tmin=         15.2188 Tmax=        350.0313)
                   (Min =  0.00000000E+00 Max =  5.70000000E+00)
    GET_NGFLD   - river runoff salinity,                     t =    45 15:45:00
                   (Rec=0002, Index=2, File: rivers_force_07.nc)
                   (Tmin=         15.2188 Tmax=        350.0313)
                   (Min =  0.00000000E+00 Max =  0.00000000E+00)
    GET_2DFLD   - surface u-wind component,                  t =    52 24:00:00
                   (Rec=0424, Index=1, File:uwnd2_era_07.nc)
                   (Tmin=          0.1250 Tmax=        365.0000)
                   (Min = -7.74161853E+00 Max =  1.07270185E+01)
    GET_2DFLD   - surface v-wind component,                  t =    52 24:00:00
                   (Rec=0424, Index=1, File: vwnd2_era_07.nc)
                   (Tmin=          0.1250 Tmax=        365.0000)
                   (Min = -7.15289563E+00 Max =  2.31153406E+00)
    GET_2DFLD   - cloud fraction,                            t =    52 24:00:00
                   (Rec=0424, Index=1, File: cloud2_era_07.nc)
                   (Tmin=          0.1250 Tmax=        365.0000)
                   (Min =  2.01395231E-06 Max =  9.99995078E-01)
    GET_2DFLD   - solar shortwave radiation flux,            t =    52 22:30:00
                   (Rec=0424, Index=1, File: swrad2_era_07.nc)
                   (Tmin=          0.0625 Tmax=        364.9375)
                   (Min =  0.00000000E+00 Max =  0.00000000E+00)
    GET_2DFLD   - net longwave radiation flux,               t =    52 22:30:00
                   (Rec=0424, Index=1, File: lwrad2_era_07.nc)
                   (Tmin=          0.0625 Tmax=        364.9375)
                   (Min = -3.36537199E-05 Max = -2.44188518E-06)
    GET_2DFLD   - surface air pressure,                      t =    52 24:00:00
                   (Rec=0424, Index=1, File:Pair2_era_07.nc)
                   (Tmin=          0.1250 Tmax=        365.0000)
                   (Min =  1.00973711E+01 Max =  1.02177491E+01)
    GET_2DFLD   - surface air temperature,                   t =    52 24:00:00
                   (Rec=0424, Index=1, File: Tair2_era_07.nc)
                   (Tmin=          0.1250 Tmax=        365.0000)
                   (Min = -1.32895356E+01 Max =  1.05571051E+01)
    GET_2DFLD   - surface air relative humidity,             t =    52 24:00:00
                   (Rec=0424, Index=1, File: Qair2_era_07.nc)
                   (Tmin=          0.1250 Tmax=        365.0000)
                   (Min =  3.92107980E+01 Max =  9.98422398E+01)
    GET_2DFLD   - rain fall rate,                            t =    52 22:30:00
                   (Rec=0424, Index=1, File: rain2_era_07.nc)
                   (Tmin=          0.0625 Tmax=        364.9375)
                   (Min =  0.00000000E+00 Max =  9.99754352E-05)

 Maximum grid stiffness ratios:  rx0 =   2.334384E-01 (Beckmann and Haidvogel)
                                 rx1 =   2.465125E+00 (Haney)


 Initial basin volumes: TotVolume =  7.6973949537E+13 m3
                        MinVolume =  1.1438083862E+06 m3
                        MaxVolume =  2.6995814696E+09 m3
                          Max/Min =  2.3601693274E+03

NL ROMS/TOMS: started time-stepping: (Grid: 01 TimeSteps: 00000001 - 00015360)
    GET_NGFLD   - river runoff mass transport,               t =    76 02:15:00
                   (Rec=0003, Index=1, File: rivers_force_07.nc)
                   (Tmin=         15.2188 Tmax=        350.0313)
                   (Min =  1.03500000E+01 Max =  1.80990150E+02)
    GET_NGFLD   - river runoff potential temperature,        t =    76 02:15:00
                   (Rec=0003, Index=1, File: rivers_force_07.nc)
                   (Tmin=         15.2188 Tmax=        350.0313)
                   (Min =  1.00000000E+00 Max =  8.50000000E+00)
    GET_NGFLD   - river runoff salinity,                     t =    76 02:15:00
                   (Rec=0003, Index=1, File: rivers_force_07.nc)
                   (Tmin=         15.2188 Tmax=        350.0313)
                   (Min =  0.00000000E+00 Max =  0.00000000E+00)
    GET_2DFLD   - surface u-wind component,                  t =    53 03:00:00
                   (Rec=0425, Index=2, File: uwnd2_era_07.nc)
                   (Tmin=          0.1250 Tmax=        365.0000)
                   (Min = -6.57603001E+00 Max =  1.11504230E+01)
    GET_2DFLD   - surface v-wind component,                  t =    53 03:00:00
                   (Rec=0425, Index=2, File: vwnd2_era_07.nc)
                   (Tmin=          0.1250 Tmax=        365.0000)
                   (Min = -6.86435918E+00 Max =  2.28099857E+00)
    GET_2DFLD   - cloud fraction,                            t =    53 03:00:00
                   (Rec=0425, Index=2, File: cloud2_era_07.nc)
                   (Tmin=          0.1250 Tmax=        365.0000)
                   (Min =  3.32647248E-04 Max =  1.00000763E+00)
    GET_2DFLD   - solar shortwave radiation flux,            t =    53 01:30:00
                   (Rec=0425, Index=2, File: swrad2_era_07.nc)
                   (Tmin=          0.0625 Tmax=        364.9375)
                   (Min =  0.00000000E+00 Max =  0.00000000E+00)
    GET_2DFLD   - net longwave radiation flux,               t =    53 01:30:00
                   (Rec=0425, Index=2, File: lwrad2_era_07.nc)
                   (Tmin=          0.0625 Tmax=        364.9375)
                   (Min = -2.93528307E-05 Max = -3.13833471E-06)
    GET_2DFLD   - surface air pressure,                      t =    53 03:00:00
                   (Rec=0425, Index=2, File: Pair2_era_07.nc)
                   (Tmin=          0.1250 Tmax=        365.0000)
                   (Min =  1.01237279E+01 Max =  1.02222626E+01)
    GET_2DFLD   - surface air temperature,                   t =    53 03:00:00
                   (Rec=0425, Index=2, File: Tair2_era_07.nc)
                   (Tmin=          0.1250 Tmax=        365.0000)
                   (Min = -1.45091888E+01 Max =  8.87779870E+00)
    GET_2DFLD   - surface air relative humidity,             t =    53 03:00:00
                   (Rec=0425, Index=2, File:Qair2_era_07.nc)
                   (Tmin=          0.1250 Tmax=        365.0000)
                   (Min =  3.84657750E+01 Max =  9.98664843E+01)
    GET_2DFLD   - rain fall rate,                            t =    53 01:30:00
                   (Rec=0425, Index=2, File: rain2_era_07.nc)
                   (Tmin=          0.0625 Tmax=        364.9375)
                   (Min = -3.21245078E-19 Max =  7.43657791E-05)

  GRID  STEP   Day HH:MM:SS  KINETIC_ENRG   POTEN_ENRG    TOTAL_ENRG    NET_VOLUME

   1       0    52 24:00:00  0.000000E+00  2.676897E+03  2.676897E+03  8.067723E+13
      DEF_HIS   - creating history file: ocean_rip_current_his.nc
      WRT_HIS   - wrote history  fields (Index=1,1) into time record = 0000001
      DEF_AVG   - creating average file: ocean_rip_current_avg.nc
   1       1    53 00:01:30  1.391354E-04  2.676849E+03  2.676850E+03  8.067724E+13
   1       2    53 00:03:00  4.958762E-04  2.676660E+03  2.676661E+03  8.067725E+13
   1       3    53 00:04:30  9.625364E-04  2.676449E+03  2.676450E+03  8.067726E+13
   1       4    53 00:06:00  1.442661E-03  2.676260E+03  2.676262E+03  8.067728E+13
   1       5    53 00:07:30  1.916653E-03  2.676073E+03  2.676075E+03  8.067729E+13
   1       6    53 00:09:00  2.346807E-03  2.675890E+03  2.675893E+03  8.067730E+13

 ROMS/TOMS - Blows up ................ exit_flag:   1


 Blowing-up: Saving latest model state into  RESTART file

      WRT_RST   - wrote re-start fields (Index=1,1) into time record = 0000001

 Elapsed CPU time (seconds):

 Node   #  0 CPU:      37.938
 Node   #  1 CPU:     119.167
 Total:               157.105

 Nonlinear model elapsed time profile:

  Initialization ...................................        39.047  (24.8541 %)
  OI data assimilation .............................         0.001  ( 0.0006 %)
  Reading of input data ............................        34.456  (21.9317 %)
  Processing of input data .........................         0.020  ( 0.0127 %)
  Processing of output time averaged data ..........         2.631  ( 1.6744 %)
  Computation of vertical boundary conditions ......         0.005  ( 0.0032 %)
  Computation of global information integrals ......         0.180  ( 0.1146 %)
  Writing of output data ...........................        18.403  (11.7139 %)
  Model 2D kernel ..................................        19.281  (12.2727 %)
  2D/3D coupling, vertical metrics .................         0.145  ( 0.0923 %)
  Omega vertical velocity ..........................         0.197  ( 0.1254 %)
  Equation of state for seawater ...................         1.461  ( 0.9298 %)
  Atmosphere-Ocean bulk flux parameterization ......         0.838  ( 0.5333 %)
  GLS vertical mixing parameterization .............         8.301  ( 5.2836 %)
  3D equations right-side terms ....................         1.446  ( 0.9203 %)
  3D equations predictor step ......................         3.944  ( 2.5107 %)
  Pressure gradient ................................         0.991  ( 0.6307 %)
  Harmonic mixing of tracers, S-surfaces ...........         0.462  ( 0.2940 %)
  Harmonic stress tensor, S-surfaces ...............         0.875  ( 0.5569 %)
  Corrector time-step for 3D momentum ..............         4.547  ( 2.8944 %)
  Corrector time-step for tracers ..................         2.432  ( 1.5478 %)
                                              Total:       139.662   88.8970

 Nonlinear model message Passage profile:

  Message Passage: 2D halo exchanges ...............         1.127  ( 0.7172 %)
  Message Passage: 3D halo exchanges ...............         1.183  ( 0.7529 %)
  Message Passage: 4D halo exchanges ...............         0.422  ( 0.2686 %)
  Message Passage: data broadcast ..................        79.158  (50.3854 %)
  Message Passage: data reduction ..................         2.710  ( 1.7247 %)
  Message Passage: data gathering ..................        17.503  (11.1412 %)
  Message Passage: data scattering..................         1.211  ( 0.7707 %)
                                              Total:       103.313   65.7606

 All percentages are with respect to total time =          157.105

 ROMS/TOMS - Output NetCDF summary for Grid 01:
             number of time records written in HISTORY file = 00000001
             number of time records written in RESTART file = 00000001

 Analytical header files used:

     ROMS/Functionals/ana_btflux.h

 ROMS/TOMS - Blows up ................ exit_flag:   1


 MAIN: Abnormal termination: BLOWUP.

[wilkin]

Your initial conditions for temp and salt ...

- potential temperature
(Min = -4.20086944E+00 Max = 1.28952207E+01)
- salinity
(Min = -4.95809949E-01 Max = 1.88765502E+01)

are a bit odd. Salinity < 0. This of itself won't immediately cause a blow-up. But it might mean you initial conditions are not what you intended them to be.

You have quite large horizontal mixing coefficients (100 m2/s) for a 3000 m grid, and your mixing is along s-coordinate surfaces (you do not have MIX_GEO_TS) which could drive appreciable diapyncal mixing and convection at the start of your run.

Remember, on blow-up the model state is written to record 3 of the restart file. So look at that to see where the problem is occurring and that may guide you toward a source of the problem.

[redhat007]

Dear Wilkin
Thanks for your reply. I set initial values to zero and TNU2== 50 50. changing some options, for example #define MIX_GEO_TS instead of #define MIX_S_TS, and #define ana_STFLUX,or #Undef TS_DIF2 can not solve problem and blow up happened after 13 min. In last step of restart file there are some values for temperature in the surface layer that seems this is problem (about 40 c). I have checked Tair data, there was not strange values (all data about 10c). running model for different time (second run) face with blow up, too.

Code: Select all

Physical Parameters, Grid: 01 
 ============================= 

5.0000E+01  nl_tnu2(01)     NLM Horizontal, harmonic mixing coefficient 
                               (m2/s) for tracer 01: temp 
 5.0000E+01  nl_tnu2(02)     NLM Horizontal, harmonic mixing coefficient 
                               (m2/s) for tracer 02: salt 

Final header file contains:

Code: Select all

RIPCURRENT        
 ANA_BSFLUX         
 ANA_BTFLUX         
 ASSUMED_SHAPE        
 AVERAGES            
 BULK_FLUXES         
 COOL_SKIN          
 DIAGNOSTICS_TS      
 DIAGNOSTICS_UV      
 DJ_GRADPS           
 DOUBLE_PRECISION    
 EASTERN_WALL        
 EMINUSP            
 GLS_MIXING           
 KANTHA_CLAYSON      
 MASKING            
 MIX_S_TS            
 MIX_S_UV            
 MPI                
 NONLINEAR           
 NONLIN_EOS          
 NORTHERN_WALL       
 N2S2_HORAVG        
 OUT_DOUBLE          
 PERFECT_RESTART     
 POWER_LAW           
 PROFILE             
 K_GSCHEME            
 !RST_SINGLE         
 SALINITY            
 SOLAR_SOURCE       
 SOLVE3D             
 SOUTHERN_WALL       
 SPLINES             
 TS_U3HADVECTION     
 TS_C4VADVECTION      
 TS_DIF2              
 TS_PSOURCE          
 UV_ADV             
 UV_COR              
 UV_U3HADVECTION     
 UV_C4VADVECTION     
 UV_QDRAG            
 UV_PSOURCE          
 UV_VIS2            
 VAR_RHO_2D          
 WESTERN_WALL       .

I become really appreciate to receive your command.
Many thanks
redhat

[kate]

I would write out the computed heat fluxes and all the terms that go into it, such as latent and sensible heat. Also, check your Pair units. ROMS wants millibars, numbers close to 1000. You can scale it in varinfo.dat, or maybe you are inadvertantly already.

[redhat007]

Dear kate
Thanks .as you can see there are some odd values in sensible and latent flux which are written out.
I will be so grateful for receiving any command to solve it
Many thanks
redhat

[kate]

Urgent need is how you learn to develop some debugging skills. You can go to the bulk_flux code to see which fields enter into the computation of these fields. You can look at your forcing files to make sure they are sensible, but if ROMS is interpolating them, there shouldn't be these lone points of weirdness. You can start adding print statements to print out the relevant variables at those points. If running in parallel, the safest print statements in do loops are like:

Code: Select all

      if (i==54 .and. j==54) then
        print *, 'DEBUG t ', t(i,j,N(ng),:,:)
      end if

Instead, I do most of my debugging in totalview where I can query one field after another. ddt is similar. In the open source world there is gdb and ddd, but they can be tricky to use with fortran data structures.

[redhat007]

Dear Kate
1-would you please tell me when Qair (one input force file) is surface RELATIVE humidity (millibar), using #define SPECIFIC_HUMIDITY is wrong?
That is because when i use #undef SPECIFIC_HUMIDITY , model does not face with blow up.
2-also if it is possible please tell me where i should add following code:

Code: Select all

if (i==54 .and. j==54) then
        print *, 'DEBUG t ', t(i,j,N(ng),:,:)
      end if

Many thanks
redhat

[kate]

If you have relative humidity, you don't want to set SPECIFIC_HUMIDITY.

The print statement should go after:

Code: Select all

      DO j=Jstr-1,JendR
        DO i=Istr-1,IendR

and before the END DO.

[redhat007]

Dear Wilkin
i have read Barnier's article and set_dqdsst.m, too. Author spoke about ECMWF data but some of needed input parameters (rho_atm, qsea, sat) are not in that database. it just has sst and wind speed components. also COADS05 dataset has not requested data in my research region (caspian sea)
Therefore i become appreciate if you (or some one else) know how i can provide them to compute dqdsst, help me to compute dqdsst.

many thanks
redhat

[wilkin]

Reread my post of 13 May 2014 08:30 on this thread for pointers to ROMS Agrif Matlab code that shows one approach to computing dqdsst.

The atmosphere and ocean quantities required are most definitely available amongst the ECMWF ERA Interim data at http://apps.ecmwf.int/datasets/data/interim_full_daily/ ... but you will have to do a bit of reading to understand which variables to use and appropriate units conversions to make.

[redhat007]

Dear Wilkin
first of all thanks for your attention. I have used 3 hourly data from ECMWF_Interim and set them as:

Code: Select all

sst=ncread('CS_sst_era.nc','sst'); % sea surface temperature (Kelvin)
sst = sst - 273.15;                   % Kelvin to Celsius
sat=ncread('CS_Tair_era.nc','Tair');   %sea surface atmospheric temperature (Celsius) at 2m 
rho_atm =1.29;  %atmospheric density (kilogram meter-3)  
u=ncread('CS_wind_era.nc','Uwind');
v=ncread('CS_wind_era.nc','Vwind');
U        =(u.^2+v.^2).^.5;
qsea=qsat(sat);computes specific humidity at saturation(kg/kg) at air temperature which will be in 2 meter level
dqdsst =get_dqdsst(sst,sat,rho_atm,U,qsea);

i become so appreciate if there is any problem tell it to me (is there problem to use 2 m temperature data as a sat? because i can find just this parameter as a air temperature there aslo i cant find data for atmospheric density therefore set it as a fix value)
many many thanks for your patient
cheers
redhat

by following approach mean value of dqdsst computed equal to -21.0172

[redhat007]

Dear
i have checked all posts about dqdsst, no one explained how compute it. Also in Barnier mentioned to surface air temperature. And as you know surface air temperature is ECMWF-Interim (Tair) is actually in 2 m level. Now i would you please tell me that:
1-is 2 m air temperature (Tair) same sea surface air temperature? And therefore sea level specific humidity (which compute base on sea surface air temperature ) same 2 m specific humidity? or not, there is different between surface air temp and 2m air temp?
2- Is function P/R.T (p: surface air pressure, R=287.05 and T=Tair) appropriate way to compute atmospheric density?
Cheers
redhat