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ROMS/TOMS

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PostPosted: Mon May 29, 2017 2:02 pm 
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Joined: Tue Jan 14, 2014 3:02 pm
Posts: 16
Location: University of Copenhagen
I am trying to add a passive tracer to a modified seamount set up. I have changed the boundary conditions to get a westward flowing current, and now I want to add a passive tracer to part of my domain, to see what happens to the water above the sea mount (or sea hill, in this case).

I set my tracer concentrations in ana_passive, which I copied into an Inc directory in my project dir, and set the OBC for the passive tracer to periodic in ocean.in.

Now, when I run the model, I get this output:

Code:
 Model Input Parameters:  ROMS/TOMS version 3.7 
                          Monday - May 29, 2017 -  3:51:54 PM
 -----------------------------------------------------------------------------

 Tall Isolated Seamount Test

 Operating system : Linux
 CPU/hardware     : x86_64
 Compiler system  : gfortran
 Compiler command : /usr/local/bin/mpif90
 Compiler flags   : -frepack-arrays -O3 -ffast-math -ffree-form -ffree-line-length-none -ffree-form -ffree-line-length-none

 Input Script  :

 SVN Root URL  : https://www.myroms.org/svn/src/trunk
 SVN Revision  : 802M

 Local Root    : /home/nws747/trunk
 Header Dir    : /home/nws747/seamount/Inc
 Header file   : seamount.h
 Analytical Dir: /home/nws747/seamount/Inc

 Resolution, Grid 01: 0049x0048x013,  Parallel Nodes:   1,  Tiling: 001x001


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

     259200  ntimes            Number of timesteps for 3-D equations.
     60.000  dt                Timestep size (s) for 3-D equations.
         20  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.
      14400  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).
       1440  nHIS              Number of timesteps between the writing fields
                                 into history file.
 0.0000E+00  nl_tnu2(01)       NLM Horizontal, harmonic mixing coefficient
                                 (m2/s) for tracer 01: temp
 0.0000E+00  nl_tnu2(02)       NLM Horizontal, harmonic mixing coefficient
                                 (m2/s) for tracer 02: dye_01
 0.0000E+00  nl_visc2          NLM Horizontal, harmonic mixing coefficient
                                 (m2/s) for momentum.
          F  LuvSponge         Turning OFF sponge on horizontal momentum.
          F  LtracerSponge(01) Turning OFF sponge on tracer 01: temp
          F  LtracerSponge(02) Turning OFF sponge on tracer 02: dye_01
 1.0000E-06  Akt_bak(01)       Background vertical mixing coefficient (m2/s)
                                 for tracer 01: temp
 1.0000E-06  Akt_bak(02)       Background vertical mixing coefficient (m2/s)
                                 for tracer 02: dye_01
 1.0000E-05  Akv_bak           Background vertical mixing coefficient (m2/s)
                                 for momentum.
 3.0000E-04  rdrg              Linear bottom drag coefficient (m/s).
 3.0000E-03  rdrg2             Quadratic bottom drag coefficient.
 2.0000E-02  Zob               Bottom roughness (m).
          2  Vtransform        S-coordinate transformation equation.
          4  Vstretching       S-coordinate stretching function.
 6.5000E+00  theta_s           S-coordinate surface control parameter.
 2.0000E+00  theta_b           S-coordinate bottom  control parameter.
    100.000  Tcline            S-coordinate surface/bottom layer width (m) used
                                 in vertical coordinate stretching.
   1025.000  rho0              Mean density (kg/m3) for Boussinesq approximation.
      0.000  dstart            Time-stamp assigned to model initialization (days).
       0.00  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: dye_01
 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.
          F  VolCons(1)        NLM western  edge boundary volume conservation.
          F  VolCons(2)        NLM southern edge boundary volume conservation.
          F  VolCons(3)        NLM eastern  edge boundary volume conservation.
          F  VolCons(4)        NLM northern edge boundary volume conservation.
     10.000  T0                Background potential temperature (C) constant.
     32.000  S0                Background salinity (PSU) constant.
   1027.000  R0                Background density (kg/m3) used in linear Equation
                                 of State.
 1.7000E-04  Tcoef             Thermal expansion coefficient (1/Celsius).
 7.6000E-04  Scoef             Saline contraction coefficient (1/PSU).
     -1.000  gamma2            Slipperiness variable: free-slip (1.0) or
                                                      no-slip (-1.0).
          F  LuvSrc            Turning OFF momentum point Sources/Sinks.
          F  LwSrc             Turning OFF volume influx point Sources/Sinks.
          F  LtracerSrc(01)    Turning OFF point Sources/Sinks on tracer 01: temp
          F  LtracerSrc(02)    Turning OFF  point Sources/Sinks on tracer 02: dye_01
          F  LsshCLM           Turning OFF processing of SSH climatology.
          F  Lm2CLM            Turning OFF processing of 2D momentum climatology.
          F  Lm3CLM            Turning OFF processing of 3D momentum climatology.
          F  LtracerCLM(01)    Turning OFF processing of climatology tracer 01: temp
          F  LtracerCLM(02)    Turning OFF processing of climatology tracer 02: dye_01
          F  LnudgeM2CLM       Turning OFF nudging of 2D momentum climatology.
          F  LnudgeM3CLM       Turning OFF nudging of 3D momentum climatology.
          F  LnudgeTCLM(01)    Turning OFF nudging of climatology tracer 01: temp
          F  LnudgeTCLM(02)    Turning OFF nudging of climatology tracer 02: dye_01
          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(inert)       Write out inert passive tracer 01: dye_01

 Output/Input Files:

             Output Restart File:  output/50passive_rst.nc
             Output History File:  output/50passive_his.nc

 Tile partition information for Grid 01:  0049x0048x0013  tiling: 001x001

     tile     Istr     Iend     Jstr     Jend     Npts

        0        1       49        1       48    30576

 Tile minimum and maximum fractional coordinates for Grid 01:
   (interior points only)

     tile     Xmin     Xmax     Ymin     Ymax     grid

        0     0.50    49.50     0.50    48.50  RHO-points

        0     1.00    49.00     0.50    48.50    U-points

        0     0.50    49.50     1.00    48.00    V-points

 Maximum halo size in XI and ETA directions:

               HaloSizeI(1) =     186
               HaloSizeJ(1) =     177
                TileSide(1) =      56
                TileSize(1) =    2968


 Lateral Boundary Conditions: NLM
 ============================

 Variable               Grid  West Edge    South Edge   East Edge    North Edge
 ---------              ----  ----------   ----------   ----------   ----------

 zeta                     1   Chapman Imp  Closed       Chapman Imp  Closed

 ubar                     1   Flather      Closed       Clamped      Closed

 vbar                     1   Flather      Closed       Clamped      Closed

 u                        1   Rad + Nud    Closed       Clamped      Closed

 v                        1   Rad + Nud    Closed       Clamped      Closed

 temp                     1   Periodic     Closed       Periodic     Closed

 dye_01                   1   Periodic     Closed       Periodic     Closed

 Activated C-preprocessing Options:

 SEAMOUNT            Tall Isolated Seamount Test
 ANA_BTFLUX          Analytical kinematic bottom temperature flux.
 ANA_DIAG            Customized diagnostics.
 ANA_FSOBC           Analytical free-surface boundary conditions.
 ANA_GRID            Analytical grid set-up.
 ANA_INITIAL         Analytical initial conditions.
 ANA_M2OBC           Analytical 2D momentum boundary conditions.
 ANA_M3OBC           Analytical 3D momentum boundary conditions.
 ANA_PASSIVE         Analytical initial conditions for inert tracers.
 ANA_SMFLUX          Analytical kinematic surface momentum flux.
 ANA_STFLUX          Analytical kinematic surface temperature flux.
 ASSUMED_SHAPE       Using assumed-shape arrays.
 DEBUGGING           Internal debugging switch activated.
 DJ_GRADPS           Parabolic Splines density Jacobian (Shchepetkin, 2002).
 DOUBLE_PRECISION    Double precision arithmetic.
 MIX_GEO_TS          Mixing of tracers along geopotential surfaces.
 MIX_S_UV            Mixing of momentum along constant S-surfaces.
 MPI                 MPI distributed-memory configuration.
 NONLINEAR           Nonlinear Model.
 !NONLIN_EOS         Linear Equation of State for seawater.
 POWER_LAW           Power-law shape time-averaging barotropic filter.
 PROFILE             Time profiling activated .
 !RST_SINGLE         Double precision fields in restart NetCDF file.
 SOLVE3D             Solving 3D Primitive Equations.
 SPLINES_VDIFF       Parabolic Spline Reconstruction for Vertical Diffusion.
 SPLINES_VVISC       Parabolic Spline Reconstruction for Vertical Viscosity.
 T_PASSIVE           Advecting and diffusing inert passive tracer.
 TS_A4HADVECTION     Fourth-order Akima horizontal advection of tracers.
 TS_A4VADVECTION     Fourth-order Akima vertical advection of tracers.
 TS_DIF2             Harmonic mixing of tracers.
 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_VIS2             Harmonic mixing of momentum.
 VAR_RHO_2D          Variable density barotropic mode.

 Process Information:

 Node #  0 (pid=     538) is active.

 INITIAL: Configuring and initializing forward nonlinear model ...
 *******

 Vertical S-coordinate System, Grid 01:

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

    13   0.0000000   0.0000000        0.000       0.000       0.000       0.000
    12  -0.0769231  -0.0008900       -5.656      -3.891      -5.822      -5.969
    11  -0.1538462  -0.0037823      -11.670      -7.881     -12.047     -12.389
    10  -0.2307692  -0.0093960      -18.171     -12.008     -18.822     -19.422
     9  -0.3076923  -0.0191094      -25.405     -16.340     -26.425     -27.377
     8  -0.3846154  -0.0352542      -33.790     -20.993     -35.325     -36.778
     7  -0.4615385  -0.0615570      -43.992     -26.155     -46.276     -48.466
     6  -0.5384615  -0.1036895      -57.026     -32.108     -60.421     -63.715
     5  -0.6153846  -0.1697046      -74.332     -39.254     -79.387     -84.337
     4  -0.6923077  -0.2696632      -97.710     -48.099    -105.203    -112.597
     3  -0.7692308  -0.4128642     -128.824     -59.105    -139.747    -150.587
     2  -0.8461538  -0.6002708     -167.845     -72.321    -183.213    -198.522
     1  -0.9230769  -0.8118860     -211.198     -86.748    -231.564    -251.905
     0  -1.0000000  -1.0000000     -250.346    -100.000    -275.173    -300.000

 Time Splitting Weights for Grid 01:    ndtfast =  20    nfast =  29
 ==================================

    Primary            Secondary            Accumulated to Current Step

  1-0.0009651193358779 0.0500000000000000-0.0009651193358779 0.0500000000000000
  2-0.0013488780126037 0.0500482559667939-0.0023139973484816 0.1000482559667939
  3-0.0011514592651644 0.0501156998674241-0.0034654566136460 0.1501639558342180
  4-0.0003735756740661 0.0501732728306823-0.0038390322877122 0.2003372286649003
  5 0.0009829200513762 0.0501919516143856-0.0028561122363360 0.2505291802792859
  6 0.0029141799764308 0.0501428056118168 0.0000580677400949 0.3006719858911027
  7 0.0054132615310267 0.0499970966129953 0.0054713292711215 0.3506690825040980
  8 0.0084687837865133 0.0497264335364439 0.0139401130576348 0.4003955160405419
  9 0.0120633394191050 0.0493029943471183 0.0260034524767398 0.4496985103876601
 10 0.0161716623600090 0.0486998273761630 0.0421751148367488 0.4983983377638231
 11 0.0207585511322367 0.0478912442581626 0.0629336659689855 0.5462895820219857
 12 0.0257765478740990 0.0468533167015507 0.0887102138430846 0.5931428987235364
 13 0.0311633730493853 0.0455644893078458 0.1198735868924699 0.6387073880313822
 14 0.0368391158442262 0.0440063206553765 0.1567127027366961 0.6827137086867586
 15 0.0427031802506397 0.0421643648631652 0.1994158829873358 0.7248780735499238
 16 0.0486309868367616 0.0400292058506332 0.2480468698240974 0.7649072794005570
 17 0.0544704302037592 0.0375976565087951 0.3025173000278565 0.8025049359093521
 18 0.0600380921294286 0.0348741349986072 0.3625553921572851 0.8373790709079593
 19 0.0651152103984763 0.0318722303921357 0.4276706025557614 0.8692513013000950
 20 0.0694434033194839 0.0286164698722119 0.4971140058752453 0.8978677711723069
 21 0.0727201499285570 0.0251442997062377 0.5698341558038023 0.9230120708785446
 22 0.0745940258796570 0.0215082922098099 0.6444281816834592 0.9445203630883545
 23 0.0746596950216179 0.0177785909158270 0.7190878767050771 0.9622989540041815
 24 0.0724526566618460 0.0140456061647461 0.7915405333669231 0.9763445601689277
 25 0.0674437485167025 0.0104229733316538 0.8589842818836255 0.9867675335005816
 26 0.0590334053485720 0.0070507859058187 0.9180176872321975 0.9938183194064003
 27 0.0465456732896125 0.0040991156383901 0.9645633605218099 0.9979174350447905
 28 0.0292219798521905 0.0017718319739095 0.9937853403740003 0.9996892670187000
 29 0.0062146596259993 0.0003107329813000 0.9999999999999997 1.0000000000000000

 ndtfast, nfast =   20  29   nfast/ndtfast =  1.45000

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

    1.000000000000 1.060707743385 0.530353871693 1.000000000000 1.000000000000

 Power filter parameters, Fgamma, gamma =  0.28400   0.14200

 Metrics information for Grid 01:
 ===============================

 Minimum X-grid spacing, DXmin =  6.53061224E+00 km
 Maximum X-grid spacing, DXmax =  6.53061224E+00 km
 Minimum Y-grid spacing, DYmin =  6.66666667E+00 km
 Maximum Y-grid spacing, DYmax =  6.66666667E+00 km
 Minimum Z-grid spacing, DZmin =  5.65588275E+00 m
 Maximum Z-grid spacing, DZmax =  5.33826473E+01 m

 Minimum barotropic Courant Number =  3.18680830E-02
 Maximum barotropic Courant Number =  3.48856020E-02
 Maximum Coriolis   Courant Number =  6.00000000E-03


 NETCDF_OPEN - unable to open existing NetCDF file:
               ocean_frc.nc
               call from:  inquire.F

 Elapsed CPU time (seconds):

 Node   #  0 CPU:       0.010
 Total:                 0.010

 Nonlinear model elapsed time profile, Grid: 01

  Allocation and array initialization ..............         0.006  (61.5515 %)
  2D/3D coupling, vertical metrics .................         0.001  ( 7.3591 %)
  Equation of state for seawater ...................         0.000  ( 3.6845 %)
                                              Total:         0.007   72.5951

 Nonlinear model message Passage profile, Grid: 01

  Message Passage: 2D halo exchanges ...............         0.000  ( 0.8962 %)
  Message Passage: data reduction ..................         0.000  ( 0.0896 %)
                                              Total:         0.000    0.9859

 All percentages are with respect to total time =            0.010


 ROMS/TOMS - Output NetCDF summary for Grid 01:

 Analytical header files used:

     /home/nws747/seamount/Inc/ana_grid.h
     /home/nws747/seamount/Inc/ana_initial.h
     /home/nws747/seamount/Inc/ana_passive.h

 ROMS/TOMS - Output error ............ exit_flag:   3


 ERROR: Abnormal termination: NetCDF OUTPUT.
 REASON: No such file or directory                                                       



where I'm basically asked for a forcing file, even though I have set all forcing analytically. The same setup works when ana_passive is disables, and all ana_* files specified in preprocessing are used. Here, however, it doesn't seem to use any other files than ana_grid, ana_initial and ana_passive, which I suppose is the reason it asks for a forcing file, but why doesn't it read those files?
I can't find any reason for this - is it a known issue? Or does anyone have a suggestion for what might be wrong?


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PostPosted: Mon May 29, 2017 3:17 pm 
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Joined: Wed Jul 02, 2003 5:29 pm
Posts: 3251
Location: IMS/UAF, USA
Quote:
ANA_SMFLUX Analytical kinematic surface momentum flux.
ANA_STFLUX Analytical kinematic surface temperature flux.

You need these as well:
Quote:
# define ANA_BPFLUX /* analytical bottom passive tracers fluxes */
# define ANA_SPFLUX


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PostPosted: Mon May 29, 2017 6:49 pm 
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Joined: Tue Jan 14, 2014 3:02 pm
Posts: 16
Location: University of Copenhagen
kate wrote:
Quote:
ANA_SMFLUX Analytical kinematic surface momentum flux.
ANA_STFLUX Analytical kinematic surface temperature flux.

You need these as well:
Quote:
# define ANA_BPFLUX /* analytical bottom passive tracers fluxes */
# define ANA_SPFLUX


Of course, that makes sense. Thank you!


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