sediment bug in the latest verison 429

Bug reports, work arounds and fixes

Moderators: arango, robertson

Post Reply
Message
Author
leon
Posts: 78
Joined: Mon Mar 03, 2008 4:14 am

sediment bug in the latest verison 429

#1 Unread post by leon »

The error is in checkvar.F, when set the sediment on. The mud_01 and snad_01 are considered as mud_ and sand_



error information:

NLM:checkvar unable to find model variable : mud_

User avatar
arango
Site Admin
Posts: 1347
Joined: Wed Feb 26, 2003 4:41 pm
Location: DMCS, Rutgers University
Contact:

Re: sediment bug in the latest verison 429

#2 Unread post by arango »

Yes, I missed this one. Good catch, thank you. Please update. Check the following :arrow: ticket for details.

leon
Posts: 78
Joined: Mon Mar 03, 2008 4:14 am

Re: sediment bug in the latest verison 429

#3 Unread post by leon »

I'm afraid there are still some problems with the variables, maybe with the bry file varibles. Pls check out~

User avatar
arango
Site Admin
Posts: 1347
Joined: Wed Feb 26, 2003 4:41 pm
Location: DMCS, Rutgers University
Contact:

Re: sediment bug in the latest verison 429

#4 Unread post by arango »

I did check all the logic for the sediment variables in the debugger and all the boundary metadata is defined correctly. In this new version, all the sediment model metadata is now processed in new include file ROMS/Nonlinear/Sediment/sediment_var.h. See the following :arrow: ticket for details.

If there is still a problem, you need to be more specific and provide the error printed to the standard output file. Also you need to check the last line of that file that prints the NetCDF library error string explaining the problem. You always need to look the standard out file carefully :!: You need to redirect this to a log file, for example:

Code: Select all

 % mpirun -np 2 oceanM ocean.in > & log &
and not print directly to the screen because you can miss the error. We have recommeded this so many times in this forum and explained well in the Wiki.

leon
Posts: 78
Joined: Mon Mar 03, 2008 4:14 am

Re: sediment bug in the latest verison 429

#5 Unread post by leon »

Sorry for that. Actually, the error is about the river sediment. The files are all the same, But it is right in the ROMS version 399 and wrong in the verison 429 or the lastest one. The north south east and west boundary sediment condition all exist in the bry file. Log files are below:

Code: Select all

Time is date
cat ${PSB_NODEFILE}
This job has allocated 64 nodes
 Process Information: Node # 38 (pid=    3784) is active. Node # 22 (pid=   13451) is active. Node # 37 (pid=    3782) is active. Node # 39 (pid=    3785) is active.

 Node # 44 (pid=    3790) is active. Node # 36 (pid=    3781) is active.
 Node # 45 (pid=    3791) is active.

 Node # 33 (pid=    3778) is active. Node # 34 (pid=    3779) is active. Node # 43 (pid=    3789) is active.

 Node # 42 (pid=    3788) is active.
 Node # 35 (pid=    3780) is active. Node # 46 (pid=    3792) is active. Node # 47 (pid=    3793) is active. Node # 41 (pid=    3787) is active. Node # 40 (pid=    3786) is active.






 Node # 20 (pid=   13449) is active.
 Node # 23 (pid=   13452) is active.

 Node # 19 (pid=   13448) is active. Node # 18 (pid=   13447) is active.

 Node # 29 (pid=   13458) is active. Node # 28 (pid=   13457) is active.
 Node # 31 (pid=   13460) is active. Node # 25 (pid=   13454) is active. Node # 21 (pid=   13450) is active.
 Node # 30 (pid=   13459) is active.


 Node # 17 (pid=   13446) is active.

 Node # 16 (pid=   13445) is active.
 Node # 53 (pid=   21320) is active. Node # 54 (pid=   21321) is active. Node # 48 (pid=   21315) is active.

 Node # 50 (pid=   21317) is active. Node # 52 (pid=   21319) is active.


 Node # 55 (pid=   21322) is active.
 Node # 51 (pid=   21318) is active. Node # 49 (pid=   21316) is active. Node # 63 (pid=   21330) is active. Node # 62 (pid=   21329) is active. Node # 60 (pid=   21327) is active. Node # 61 (pid=   21328) is active.





 Node # 59 (pid=   21326) is active.
 Node # 56 (pid=   21323) is active.
 Node # 58 (pid=   21325) is active. Node # 57 (pid=   21324) is active.



 Node # 12 (pid=   25681) is active. Node # 13 (pid=   25682) is active. Node #  5 (pid=   25674) is active.
 Node #  6 (pid=   25675) is active.


 Node # 11 (pid=   25680) is active. Node #  8 (pid=   25677) is active. Node #  9 (pid=   25678) is active.

 Node #  7 (pid=   25676) is active.
 Node # 10 (pid=   25679) is active. Node #  2 (pid=   25671) is active.
 Node #  1 (pid=   25670) is active.
 Node #  4 (pid=   25673) is active. Node #  3 (pid=   25672) is active. Node # 15 (pid=   25684) is active.




 Node # 14 (pid=   25683) is active.
 Node #  0 (pid=   25669) is active.
 Node # 32 (pid=    3777) is active.
 Node # 24 (pid=   13453) is active.
 Node # 26 (pid=   13455) is active.
 Node # 27 (pid=   13456) is active.

 Model Input Parameters:  ROMS/TOMS version 3.4  
                          Sunday - January 10, 2010 -  9:02:15 PM
 -----------------------------------------------------------------------------

 East China Sea Sediment

 Operating system : Linux
 CPU/hardware     : x86_64
 Compiler system  : pgi
 Compiler command : /opt/mpi/mvapich/1.1/gcc.pgf90/bin/mpif90
 Compiler flags   :  -O3 -tp k8-64 -Mfree

 Input Script  : /dcfs2/users/leon/Documents/trunk/User/External/ecs22.in

 SVN Root URL  : https://www.myroms.org/svn/src/trunk
 SVN Revision  : 405:437M

 Local Root    : /dcfs2/users/leon/Documents/trunk
 Header Dir    : /dcfs2/users/leon/Documents/trunk/ROMS/Include
 Header file   : bedload.h
 Analytical Dir: /dcfs2/users/leon/Documents/trunk/ROMS/Functionals

 Resolution, Grid 01: 0368x0440x030,  Parallel Nodes:  64,  Tiling: 008x008


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

     466560  ntimes          Number of timesteps for 3-D equations.
    200.000  dt              Timestep size (s) for 3-D equations.
         50  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.
      12960  nRST            Number of timesteps between the writing of data
                               into restart fields.
         10  ninfo           Number of timesteps between print of information
                               to standard output.
          T  ldefout         Switch to create a new output NetCDF file(s).
      12960  nHIS            Number of timesteps between the writing fields
                               into history file.
      12960  ntsAVG          Starting timestep for the accumulation of output
                               time-averaged data.
      12960  nAVG            Number of timesteps between the writing of
                               time-averaged data into averages file.
      12960  ndefAVG         Number of timesteps between creation of new
                               time-averaged file.
 2.0000E+01  nl_tnu2(01)     NLM Horizontal, harmonic mixing coefficient
                               (m2/s) for tracer 01: temp
 2.0000E+01  nl_tnu2(02)     NLM Horizontal, harmonic mixing coefficient
                               (m2/s) for tracer 02: salt
 4.0000E+01  nl_visc2        NLM Horizontal, harmonic mixing coefficient
                               (m2/s) for momentum.
 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: 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).
      0.250  sz_alpha        Factor for Wave dissipation surface tke flux .
    100.000  crgban_cw       Factor for Craig/Banner surface tke flux.
 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).
 2.0000E-02  Zos             Surface roughness (m).
          2  Vtransform      S-coordinate transformation equation.
          2  Vstretching     S-coordinate stretching function.
 3.0000E+00  theta_s         S-coordinate surface control parameter.
 5.0000E+00  theta_b         S-coordinate bottom  control parameter.
      5.000  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).
      0.000  tide_start      Reference time origin for tidal forcing (days).
      -1.00  time_ref        Reference time for units attribute (yyyymmdd.dd)
 3.0000E+01  Tnudg(01)       Nudging/relaxation time scale (days)
                               for tracer 01: temp
 3.0000E+01  Tnudg(02)       Nudging/relaxation time scale (days)
                               for tracer 02: salt
 3.0000E+01  Znudg           Nudging/relaxation time scale (days)
                               for free-surface.
 3.0000E+01  M2nudg          Nudging/relaxation time scale (days)
                               for 2D momentum.
 3.0000E+01  M3nudg          Nudging/relaxation time scale (days)
                               for 3D momentum.
 1.0000E+01  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).
          F  LtracerSrc(01)  Processing point sources/Sink on tracer 01: temp
          F  LtracerSrc(02)  Processing point sources/Sink on tracer 02: salt
          T  Hout(idBath)    Write out time-dependent bathymetry.
          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(idBott)    Write out bottom property 01: grain_diameter
          T  Hout(idBott)    Write out bottom property 02: grain_density
          T  Hout(idBott)    Write out bottom property 03: settling_vel
          T  Hout(idBott)    Write out bottom property 04: erosion_stress
          T  Hout(idBott)    Write out bottom property 05: ripple_length
          T  Hout(idBott)    Write out bottom property 06: ripple_height
          T  Hout(idBott)    Write out bottom property 07: bed_wave_amp
          T  Hout(idBott)    Write out bottom property 08: Zo_def
          T  Hout(idBott)    Write out bottom property 09: Zo_app
          T  Hout(idTsur)    Write out surface net heat flux.
          T  Hout(idTsur)    Write out surface net salt flux.
          T  Hout(idVvis)    Write out vertical viscosity coefficient.
          T  Hout(idTdif)    Write out vertical T-diffusion coefficient.

 Output/Input Files:

             Output Restart File:  /dcfs2/users/leon/Documents/roms_examples/ecs22/ecs22_rst.nc
             Output History File:  /dcfs2/users/leon/Documents/roms_examples/ecs22/ecs22_his.nc
       Prefix for Averages Files:  /dcfs2/users/leon/Documents/roms_examples/ecs22/ecs22_avg
                 Input Grid File:  /dcfs2/users/leon/Documents/roms_examples/ecs22/ecs22-grid.nc
    Input Nonlinear Initial File:  /dcfs2/users/leon/Documents/roms_examples/ecs22/ecs22-init.nc
           Input Forcing File 01:  /dcfs2/users/leon/Documents/roms_examples/ecs22/ecs22-forc.nc
           Input Forcing File 02:  /dcfs2/users/leon/Documents/roms_examples/ecs22/ecs22-tide72.nc
             Input Boundary File:  /dcfs2/users/leon/Documents/roms_examples/ecs22/ecs22-bry.nc

 Tile partition information for Grid 01:  0368x0440x0030  tiling: 008x008

     tile     Istr     Iend     Jstr     Jend     Npts

        0        1       46        1       55    75900
        1       47       92        1       55    75900
        2       93      138        1       55    75900
        3      139      184        1       55    75900
        4      185      230        1       55    75900
        5      231      276        1       55    75900
        6      277      322        1       55    75900
        7      323      368        1       55    75900
        8        1       46       56      110    75900
        9       47       92       56      110    75900
       10       93      138       56      110    75900
       11      139      184       56      110    75900
       12      185      230       56      110    75900
       13      231      276       56      110    75900
       14      277      322       56      110    75900
       15      323      368       56      110    75900
       16        1       46      111      165    75900
       17       47       92      111      165    75900
       18       93      138      111      165    75900
       19      139      184      111      165    75900
       20      185      230      111      165    75900
       21      231      276      111      165    75900
       22      277      322      111      165    75900
       23      323      368      111      165    75900
       24        1       46      166      220    75900
       25       47       92      166      220    75900
       26       93      138      166      220    75900
       27      139      184      166      220    75900
       28      185      230      166      220    75900
       29      231      276      166      220    75900
       30      277      322      166      220    75900
       31      323      368      166      220    75900
       32        1       46      221      275    75900
       33       47       92      221      275    75900
       34       93      138      221      275    75900
       35      139      184      221      275    75900
       36      185      230      221      275    75900
       37      231      276      221      275    75900
       38      277      322      221      275    75900
       39      323      368      221      275    75900
       40        1       46      276      330    75900
       41       47       92      276      330    75900
       42       93      138      276      330    75900
       43      139      184      276      330    75900
       44      185      230      276      330    75900
       45      231      276      276      330    75900
       46      277      322      276      330    75900
       47      323      368      276      330    75900
       48        1       46      331      385    75900
       49       47       92      331      385    75900
       50       93      138      331      385    75900
       51      139      184      331      385    75900
       52      185      230      331      385    75900
       53      231      276      331      385    75900
       54      277      322      331      385    75900
       55      323      368      331      385    75900
       56        1       46      386      440    75900
       57       47       92      386      440    75900
       58       93      138      386      440    75900
       59      139      184      386      440    75900
       60      185      230      386      440    75900
       61      231      276      386      440    75900
       62      277      322      386      440    75900
       63      323      368      386      440    75900

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

     tile     Xmin     Xmax     Ymin     Ymax     grid

        0     0.50    46.50     0.50    55.50  RHO-points
        1    46.50    92.50     0.50    55.50  RHO-points
        2    92.50   138.50     0.50    55.50  RHO-points
        3   138.50   184.50     0.50    55.50  RHO-points
        4   184.50   230.50     0.50    55.50  RHO-points
        5   230.50   276.50     0.50    55.50  RHO-points
        6   276.50   322.50     0.50    55.50  RHO-points
        7   322.50   368.50     0.50    55.50  RHO-points
        8     0.50    46.50    55.50   110.50  RHO-points
        9    46.50    92.50    55.50   110.50  RHO-points
       10    92.50   138.50    55.50   110.50  RHO-points
       11   138.50   184.50    55.50   110.50  RHO-points
       12   184.50   230.50    55.50   110.50  RHO-points
       13   230.50   276.50    55.50   110.50  RHO-points
       14   276.50   322.50    55.50   110.50  RHO-points
       15   322.50   368.50    55.50   110.50  RHO-points
       16     0.50    46.50   110.50   165.50  RHO-points
       17    46.50    92.50   110.50   165.50  RHO-points
       18    92.50   138.50   110.50   165.50  RHO-points
       19   138.50   184.50   110.50   165.50  RHO-points
       20   184.50   230.50   110.50   165.50  RHO-points
       21   230.50   276.50   110.50   165.50  RHO-points
       22   276.50   322.50   110.50   165.50  RHO-points
       23   322.50   368.50   110.50   165.50  RHO-points
       24     0.50    46.50   165.50   220.50  RHO-points
       25    46.50    92.50   165.50   220.50  RHO-points
       26    92.50   138.50   165.50   220.50  RHO-points
       27   138.50   184.50   165.50   220.50  RHO-points
       28   184.50   230.50   165.50   220.50  RHO-points
       29   230.50   276.50   165.50   220.50  RHO-points
       30   276.50   322.50   165.50   220.50  RHO-points
       31   322.50   368.50   165.50   220.50  RHO-points
       32     0.50    46.50   220.50   275.50  RHO-points
       33    46.50    92.50   220.50   275.50  RHO-points
       34    92.50   138.50   220.50   275.50  RHO-points
       35   138.50   184.50   220.50   275.50  RHO-points
       36   184.50   230.50   220.50   275.50  RHO-points
       37   230.50   276.50   220.50   275.50  RHO-points
       38   276.50   322.50   220.50   275.50  RHO-points
       39   322.50   368.50   220.50   275.50  RHO-points
       40     0.50    46.50   275.50   330.50  RHO-points
       41    46.50    92.50   275.50   330.50  RHO-points
       42    92.50   138.50   275.50   330.50  RHO-points
       43   138.50   184.50   275.50   330.50  RHO-points
       44   184.50   230.50   275.50   330.50  RHO-points
       45   230.50   276.50   275.50   330.50  RHO-points
       46   276.50   322.50   275.50   330.50  RHO-points
       47   322.50   368.50   275.50   330.50  RHO-points
       48     0.50    46.50   330.50   385.50  RHO-points
       49    46.50    92.50   330.50   385.50  RHO-points
       50    92.50   138.50   330.50   385.50  RHO-points
       51   138.50   184.50   330.50   385.50  RHO-points
       52   184.50   230.50   330.50   385.50  RHO-points
       53   230.50   276.50   330.50   385.50  RHO-points
       54   276.50   322.50   330.50   385.50  RHO-points
       55   322.50   368.50   330.50   385.50  RHO-points
       56     0.50    46.50   385.50   440.50  RHO-points
       57    46.50    92.50   385.50   440.50  RHO-points
       58    92.50   138.50   385.50   440.50  RHO-points
       59   138.50   184.50   385.50   440.50  RHO-points
       60   184.50   230.50   385.50   440.50  RHO-points
       61   230.50   276.50   385.50   440.50  RHO-points
       62   276.50   322.50   385.50   440.50  RHO-points
       63   322.50   368.50   385.50   440.50  RHO-points

        0     1.00    46.50     0.50    55.50    U-points
        1    46.50    92.50     0.50    55.50    U-points
        2    92.50   138.50     0.50    55.50    U-points
        3   138.50   184.50     0.50    55.50    U-points
        4   184.50   230.50     0.50    55.50    U-points
        5   230.50   276.50     0.50    55.50    U-points
        6   276.50   322.50     0.50    55.50    U-points
        7   322.50   368.00     0.50    55.50    U-points
        8     1.00    46.50    55.50   110.50    U-points
        9    46.50    92.50    55.50   110.50    U-points
       10    92.50   138.50    55.50   110.50    U-points
       11   138.50   184.50    55.50   110.50    U-points
       12   184.50   230.50    55.50   110.50    U-points
       13   230.50   276.50    55.50   110.50    U-points
       14   276.50   322.50    55.50   110.50    U-points
       15   322.50   368.00    55.50   110.50    U-points
       16     1.00    46.50   110.50   165.50    U-points
       17    46.50    92.50   110.50   165.50    U-points
       18    92.50   138.50   110.50   165.50    U-points
       19   138.50   184.50   110.50   165.50    U-points
       20   184.50   230.50   110.50   165.50    U-points
       21   230.50   276.50   110.50   165.50    U-points
       22   276.50   322.50   110.50   165.50    U-points
       23   322.50   368.00   110.50   165.50    U-points
       24     1.00    46.50   165.50   220.50    U-points
       25    46.50    92.50   165.50   220.50    U-points
       26    92.50   138.50   165.50   220.50    U-points
       27   138.50   184.50   165.50   220.50    U-points
       28   184.50   230.50   165.50   220.50    U-points
       29   230.50   276.50   165.50   220.50    U-points
       30   276.50   322.50   165.50   220.50    U-points
       31   322.50   368.00   165.50   220.50    U-points
       32     1.00    46.50   220.50   275.50    U-points
       33    46.50    92.50   220.50   275.50    U-points
       34    92.50   138.50   220.50   275.50    U-points
       35   138.50   184.50   220.50   275.50    U-points
       36   184.50   230.50   220.50   275.50    U-points
       37   230.50   276.50   220.50   275.50    U-points
       38   276.50   322.50   220.50   275.50    U-points
       39   322.50   368.00   220.50   275.50    U-points
       40     1.00    46.50   275.50   330.50    U-points
       41    46.50    92.50   275.50   330.50    U-points
       42    92.50   138.50   275.50   330.50    U-points
       43   138.50   184.50   275.50   330.50    U-points
       44   184.50   230.50   275.50   330.50    U-points
       45   230.50   276.50   275.50   330.50    U-points
       46   276.50   322.50   275.50   330.50    U-points
       47   322.50   368.00   275.50   330.50    U-points
       48     1.00    46.50   330.50   385.50    U-points
       49    46.50    92.50   330.50   385.50    U-points
       50    92.50   138.50   330.50   385.50    U-points
       51   138.50   184.50   330.50   385.50    U-points
       52   184.50   230.50   330.50   385.50    U-points
       53   230.50   276.50   330.50   385.50    U-points
       54   276.50   322.50   330.50   385.50    U-points
       55   322.50   368.00   330.50   385.50    U-points
       56     1.00    46.50   385.50   440.50    U-points
       57    46.50    92.50   385.50   440.50    U-points
       58    92.50   138.50   385.50   440.50    U-points
       59   138.50   184.50   385.50   440.50    U-points
       60   184.50   230.50   385.50   440.50    U-points
       61   230.50   276.50   385.50   440.50    U-points
       62   276.50   322.50   385.50   440.50    U-points
       63   322.50   368.00   385.50   440.50    U-points

        0     0.50    46.50     1.00    55.50    V-points
        1    46.50    92.50     1.00    55.50    V-points
        2    92.50   138.50     1.00    55.50    V-points
        3   138.50   184.50     1.00    55.50    V-points
        4   184.50   230.50     1.00    55.50    V-points
        5   230.50   276.50     1.00    55.50    V-points
        6   276.50   322.50     1.00    55.50    V-points
        7   322.50   368.50     1.00    55.50    V-points
        8     0.50    46.50    55.50   110.50    V-points
        9    46.50    92.50    55.50   110.50    V-points
       10    92.50   138.50    55.50   110.50    V-points
       11   138.50   184.50    55.50   110.50    V-points
       12   184.50   230.50    55.50   110.50    V-points
       13   230.50   276.50    55.50   110.50    V-points
       14   276.50   322.50    55.50   110.50    V-points
       15   322.50   368.50    55.50   110.50    V-points
       16     0.50    46.50   110.50   165.50    V-points
       17    46.50    92.50   110.50   165.50    V-points
       18    92.50   138.50   110.50   165.50    V-points
       19   138.50   184.50   110.50   165.50    V-points
       20   184.50   230.50   110.50   165.50    V-points
       21   230.50   276.50   110.50   165.50    V-points
       22   276.50   322.50   110.50   165.50    V-points
       23   322.50   368.50   110.50   165.50    V-points
       24     0.50    46.50   165.50   220.50    V-points
       25    46.50    92.50   165.50   220.50    V-points
       26    92.50   138.50   165.50   220.50    V-points
       27   138.50   184.50   165.50   220.50    V-points
       28   184.50   230.50   165.50   220.50    V-points
       29   230.50   276.50   165.50   220.50    V-points
       30   276.50   322.50   165.50   220.50    V-points
       31   322.50   368.50   165.50   220.50    V-points
       32     0.50    46.50   220.50   275.50    V-points
       33    46.50    92.50   220.50   275.50    V-points
       34    92.50   138.50   220.50   275.50    V-points
       35   138.50   184.50   220.50   275.50    V-points
       36   184.50   230.50   220.50   275.50    V-points
       37   230.50   276.50   220.50   275.50    V-points
       38   276.50   322.50   220.50   275.50    V-points
       39   322.50   368.50   220.50   275.50    V-points
       40     0.50    46.50   275.50   330.50    V-points
       41    46.50    92.50   275.50   330.50    V-points
       42    92.50   138.50   275.50   330.50    V-points
       43   138.50   184.50   275.50   330.50    V-points
       44   184.50   230.50   275.50   330.50    V-points
       45   230.50   276.50   275.50   330.50    V-points
       46   276.50   322.50   275.50   330.50    V-points
       47   322.50   368.50   275.50   330.50    V-points
       48     0.50    46.50   330.50   385.50    V-points
       49    46.50    92.50   330.50   385.50    V-points
       50    92.50   138.50   330.50   385.50    V-points
       51   138.50   184.50   330.50   385.50    V-points
       52   184.50   230.50   330.50   385.50    V-points
       53   230.50   276.50   330.50   385.50    V-points
       54   276.50   322.50   330.50   385.50    V-points
       55   322.50   368.50   330.50   385.50    V-points
       56     0.50    46.50   385.50   440.00    V-points
       57    46.50    92.50   385.50   440.00    V-points
       58    92.50   138.50   385.50   440.00    V-points
       59   138.50   184.50   385.50   440.00    V-points
       60   184.50   230.50   385.50   440.00    V-points
       61   230.50   276.50   385.50   440.00    V-points
       62   276.50   322.50   385.50   440.00    V-points
       63   322.50   368.50   385.50   440.00    V-points

 Maximum halo size in XI and ETA directions:

               HaloSizeI(1) =     180
               HaloSizeJ(1) =     207
                TileSide(1) =      63
                TileSize(1) =    3402



 Sediment Parameters, Grid: 01
 =============================


 Size     Sd50        Csed        Srho        Wsed        Erate       poros
 Class    (mm)       (kg/m3)     (kg/m3)     (mm/s)     (kg/m2/s)    (nondim)

   1    8.0000E-03  0.0000E+00  2.6500E+03  3.5700E-02  5.0000E-04  6.8240E-01
   2    8.0000E-02  0.0000E+00  2.6500E+03  4.1879E+00  1.0000E-04  4.8510E-01

         tau_ce      tau_cd      nl_tnu2     nl_tnu4     Akt_bak      Tnudg
         (N/m2)      (N/m2)      (m2/s)      (m4/s)       (m2/s)      (day)

   1    2.2431E-02  9.9690E-03  0.0000E+00  0.0000E+00  5.0000E-06  0.0000E+00
   2    1.0394E-01  4.6194E-02  0.0000E+00  0.0000E+00  5.0000E-06  0.0000E+00

         morph_fac
         (nondim)

   1    1.0000E+01
   2    1.0000E+01

 New bed layer formed when deposition exceeds 0.10000E-01 (m).
 Two first layers are combined when 2nd layer smaller than 0.10000E-01 (m).
 Rate coefficient for bed load transport = 0.50000E-01

          F  LtracerSrc(03)  Processing point sources/Sink on tracer 03: mud_01
          F  LtracerSrc(04)  Processing point sources/Sink on tracer 04: sand_01
          T  Hout(idTvar)   Write out sediment01: mud_01
          T  Hout(idTvar)   Write out sediment02: sand_01
          T  Hout(idfrac)   Write out bed fraction, sediment 01: mudfrac_01
          T  Hout(idfrac)   Write out bed fraction, sediment 02: sandfrac_01
          T  Hout(idfrac)   Write out mass, sediment 01: mudmass_01
          T  Hout(idfrac)   Write out mass, sediment 02: sandmass_01
          T  Hout(idUbld)   Write out bed load at U-points, sediment 01: bedload_Umud_01
          T  Hout(idVbld)   Write out bed load at V-points, sediment 01: bedload_Vmud_01
          T  Hout(idUbld)   Write out bed load at U-points, sediment 02: bedload_Usand_01
          T  Hout(idVbld)   Write out bed load at V-points, sediment 02: bedload_Vsand_01
          T  Hout(idSbed)   Write out BED property 01: bed_thickness
          T  Hout(idSbed)   Write out BED property 02: bed_age
          T  Hout(idSbed)   Write out BED property 03: bed_porosity

 Activated C-preprocessing Options:

 BEDLOAD             East China Sea Sediment
 ADD_FSOBC           Adding tidal elevation to proccesed OBC data.
 ADD_M2OBC           Adding tidal currents to proccesed OBC data.
 ANA_BPFLUX          Analytical bottom passive tracers fluxes.
 ANA_BSFLUX          Analytical kinematic bottom salinity flux.
 ANA_BTFLUX          Analytical kinematic bottom temperature flux.
 ANA_SPFLUX          Analytical surface passive tracer fluxes.
 ASSUMED_SHAPE       Using assumed-shape arrays.
 AVERAGES            Writing out time-averaged fields.
 BEDLOAD_MPM         Activate bed load sediment transport Meyer-Peter-Mueller.
 CURVGRID            Orthogonal curvilinear grid.
 DJ_GRADPS           Parabolic Splines density Jacobian (Shchepetkin, 2002).
 DOUBLE_PRECISION    Double precision arithmetic.
 EAST_FSCHAPMAN      Eastern edge, free-surface, Chapman condition.
 EAST_M2FLATHER      Eastern edge, 2D momentum, Flather condition.
 EAST_M3GRADIENT     Eastern edge, 3D momentum, gradient condition.
 EAST_TNUDGING       Eastern edge, tracers, passive/active outflow/inflow.
 EAST_TRADIATION     Eastern edge, tracers, radiation condition.
 GLS_MIXING          Generic Length-Scale turbulence closure.
 KANTHA_CLAYSON      Kantha and Clayson stability function formulation.
 MASKING             Land/Sea masking.
 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          Nonlinear Equation of State for seawater.
 NORTH_FSCHAPMAN     Northern edge, free-surface, Chapman condition.
 NORTH_M2FLATHER     Northern edge, 2D momentum, Flather condition.
 NORTH_M3GRADIENT    Northern edge, 3D momentum, gradient condition.
 NORTH_TNUDGING      Northern edge, tracers, passive/active outflow/inflow.
 NORTH_TRADIATION    Northern edge, tracers, radiation condition.
 N2S2_HORAVG         Horizontal smoothing of buoyancy and shear.
 OUT_DOUBLE          Double precision output fields in NetCDF files.
 POWER_LAW           Power-law shape time-averaging barotropic filter.
 PROFILE             Time profiling activated .
 QCORRECTION         Surface net heat flux correction.
 K_GSCHEME           Third-order upstream advection of TKE fields.
 !RST_SINGLE         Double precision fields in restart NetCDF file.
 SALINITY            Using salinity.
 SCORRECTION         Surface salinity flux correction.
 SEDIMENT            Cohesive and noncohesive sediments.
 SED_MORPH           Allow bottom model elevation to evolve.
 SUSPLOAD            Activate suspended sediment transport.
 SOLVE3D             Solving 3D Primitive Equations.
 SOUTH_FSCHAPMAN     Southern edge, free-surface, Chapman condition.
 SOUTH_M2FLATHER     Southern edge, 2D momentum, Flather condition.
 SOUTH_M3GRADIENT    Southern edge, 3D momentum, gradient condition.
 SOUTH_TNUDGING      Southern edge, tracers, passive/active outflow/inflow.
 SOUTH_TRADIATION    Southern edge, tracers, radiation condition.
 SPLINES             Conservative parabolic spline reconstruction.
 SPONGE              Enhanced horizontal mixing in the sponge areas.
 SSH_TIDES           Add tidal elevation to SSH climatology.
 THREE_GHOST         Using three Ghost Points in halo regions.
 TS_MPDATA           Recursive flux corrected MPDATA 3D 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_TIDES            Add tidal currents to 2D momentum climatologies.
 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          at_hmin  over_slope     at_hmax

    30   0.0000000   0.0000000           0.000       0.000       0.000
    29  -0.0333333  -0.0007218          -0.085      -2.475      -4.783
    28  -0.0666667  -0.0034632          -0.175     -11.406     -22.480
    27  -0.1000000  -0.0088852          -0.272     -28.910     -57.320
    26  -0.1333333  -0.0174334          -0.377     -56.409    -112.153
    25  -0.1666667  -0.0293918          -0.490     -94.813    -188.794
    24  -0.2000000  -0.0449244          -0.612    -144.645    -288.291
    23  -0.2333333  -0.0641059          -0.744    -206.144    -411.123
    22  -0.2666667  -0.0869446          -0.884    -279.337    -557.343
    21  -0.3000000  -0.1133988          -1.033    -364.091    -726.684
    20  -0.3333333  -0.1433880          -1.192    -460.148    -918.632
    19  -0.3666667  -0.1768003          -1.359    -567.151   -1132.470
    18  -0.4000000  -0.2134957          -1.534    -684.651   -1367.304
    17  -0.4333333  -0.2533078          -1.717    -812.117   -1622.069
    16  -0.4666667  -0.2960427          -1.907    -948.929   -1895.526
    15  -0.5000000  -0.3414759          -2.104   -1094.368   -2186.238
    14  -0.5333333  -0.3893475          -2.307   -1247.604   -2492.544
    13  -0.5666667  -0.4393561          -2.515   -1407.673   -2812.515
    12  -0.6000000  -0.4911506          -2.728   -1573.453   -3143.908
    11  -0.6333333  -0.5443212          -2.944   -1743.633   -3484.101
    10  -0.6666667  -0.5983879          -3.163   -1916.678   -3830.023
     9  -0.7000000  -0.6527875          -3.382   -2090.788   -4178.076
     8  -0.7333333  -0.7068593          -3.600   -2263.849   -4524.032
     7  -0.7666667  -0.7598274          -3.816   -2433.382   -4862.930
     6  -0.8000000  -0.8107817          -4.027   -2596.475   -5188.949
     5  -0.8333333  -0.8586552          -4.230   -2749.717   -5495.267
     4  -0.8666667  -0.9021993          -4.422   -2889.116   -5773.898
     3  -0.9000000  -0.9399541          -4.600   -3010.004   -6015.507
     2  -0.9333333  -0.9702163          -4.759   -3106.933   -6209.200
     1  -0.9666667  -0.9910011          -4.894   -3173.559   -6342.285
     0  -1.0000000  -1.0000000          -5.000   -3202.500   -6400.000

 Time Splitting Weights: ndtfast =  50    nfast =  69

    Primary            Secondary            Accumulated to Current Step

  1-0.0004563262418391 0.0200000000000000-0.0004563262418391 0.0200000000000000
  2-0.0008555246732536 0.0200091265248368-0.0013118509150927 0.0400091265248368
  3-0.0011975957891734 0.0200262370183019-0.0025094467042661 0.0600353635431387
  4-0.0014825415143255 0.0200501889340853-0.0039919882185915 0.0800855524772240
  5-0.0017103668530001 0.0200798397643718-0.0057023550715916 0.1001653922415958
  6-0.0018810821987231 0.0201140471014318-0.0075834372703147 0.1202794393430276
  7-0.0019947063038349 0.0201516687454063-0.0095781435741496 0.1404311080884340
  8-0.0020512699089757 0.0201915628714830-0.0116294134831253 0.1606226709599169
  9-0.0020508200324769 0.0202325882696625-0.0136802335156022 0.1808552592295795
 10-0.0019934249196594 0.0202736046703121-0.0156736584352616 0.2011288638998915
 11-0.0018791796520380 0.0203134731687052-0.0175528380872996 0.2214423370685968
 12-0.0017082124164322 0.0203510567617460-0.0192610505037318 0.2417933938303428
 13-0.0014806914339834 0.0203852210100746-0.0207417419377152 0.2621786148404174
 14-0.0011968325490789 0.0204148348387543-0.0219385744867941 0.2825934496791717
 15-0.0008569074781817 0.0204387714897359-0.0227954819649758 0.3030322211689075
 16-0.0004612527185669 0.0204559096392995-0.0232567346835427 0.3234881308082070
 17-0.0000102791169649 0.0204651346936709-0.0232670138005077 0.3439532655018779
 18 0.0004955179018893 0.0204653402760102-0.0227714958986183 0.3644186057778880
 19 0.0010555474468010 0.0204554299179724-0.0217159484518173 0.3848740356958604
 20 0.0016691116117526 0.0204343189690364-0.0200468368400647 0.4053083546648968
 21 0.0023353932676362 0.0204009367368013-0.0177114435724285 0.4257092914016981
 22 0.0030534431940779 0.0203542288714486-0.0146580003783505 0.4460635202731467
 23 0.0038221665513568 0.0202931600075670-0.0108358338269937 0.4663566802807137
 24 0.0046403086924171 0.0202167166765399-0.0061955251345765 0.4865733969572536
 25 0.0055064403149742 0.0201239105026915-0.0006890848196024 0.5066973074599451
 26 0.0064189419537136 0.0200137816963921 0.0057298571341112 0.5267110891563371
 27 0.0073759878125848 0.0198854028573178 0.0131058449466960 0.5465964920136549
 28 0.0083755289371871 0.0197378831010661 0.0214813738838831 0.5663343751147210
 29 0.0094152757272501 0.0195703725223223 0.0308966496111332 0.5859047476370433
 30 0.0104926797892080 0.0193820670077773 0.0413893294003412 0.6052868146448206
 31 0.0116049151288660 0.0191722134119932 0.0529942445292072 0.6244590280568137
 32 0.0127488586841624 0.0189401151094159 0.0657431032133696 0.6433991431662296
 33 0.0139210701980223 0.0186851379357326 0.0796641734113919 0.6620842811019622
 34 0.0151177714313064 0.0184067165317722 0.0947819448426983 0.6804909976337343
 35 0.0163348247158524 0.0181043611031460 0.1111167695585507 0.6985953587368804
 36 0.0175677108476106 0.0177776646088290 0.1286844804061612 0.7163730233457094
 37 0.0188115063198728 0.0174263103918768 0.1474959867260340 0.7337993337375862
 38 0.0200608598965948 0.0170500802654793 0.1675568466226288 0.7508494140030655
 39 0.0213099685258127 0.0166488630675474 0.1888668151484416 0.7674982770706129
 40 0.0225525525931525 0.0162226636970312 0.2114193677415941 0.7837209407676441
 41 0.0237818305154335 0.0157716126451681 0.2352011982570276 0.7994925534128122
 42 0.0249904926743652 0.0152959760348595 0.2601916909313928 0.8147885294476717
 43 0.0261706746903379 0.0147961661813722 0.2863623656217307 0.8295846956290438
 44 0.0273139300363068 0.0142727526875654 0.3136762956580375 0.8438574483166091
 45 0.0284112019917697 0.0137264740868393 0.3420874976498072 0.8575839224034484
 46 0.0294527949368383 0.0131582500470039 0.3715402925866456 0.8707421724504523
 47 0.0304283449864031 0.0125691941482671 0.4019686375730487 0.8833113665987193
 48 0.0313267899643920 0.0119606272485390 0.4332954275374407 0.8952719938472583
 49 0.0321363387181221 0.0113340914492512 0.4654317662555627 0.9066060852965095
 50 0.0328444397727456 0.0106913646748887 0.4982762060283084 0.9172974499713983
 51 0.0334377493257894 0.0100344758794338 0.5317139553540977 0.9273319258508321
 52 0.0339020985817871 0.0093657208929180 0.5656160539358848 0.9366976467437502
 53 0.0342224604270064 0.0086876789212823 0.5998385143628912 0.9453853256650325
 54 0.0343829154442684 0.0080032297127422 0.6342214298071596 0.9533885553777747
 55 0.0343666172678620 0.0073155714038568 0.6685880470750215 0.9607041267816315
 56 0.0341557572785502 0.0066282390584996 0.7027438043535718 0.9673323658401310
 57 0.0337315286386720 0.0059451239129286 0.7364753329922438 0.9732774897530596
 58 0.0330740896673358 0.0052704933401551 0.7695494226595796 0.9785479830932148
 59 0.0321625265557082 0.0046090115468084 0.8017119492152878 0.9831569946400232
 60 0.0309748154223953 0.0039657610156942 0.8326867646376830 0.9871227556557174
 61 0.0294877837089178 0.0033462647072463 0.8621745483466008 0.9904690203629637
 62 0.0276770709152801 0.0027565090330680 0.8898516192618808 0.9932255293960317
 63 0.0255170886756324 0.0022029676147624 0.9153687079375131 0.9954284970107941
 64 0.0229809801740268 0.0016926258412497 0.9383496881115398 0.9971211228520438
 65 0.0200405789002670 0.0012330062377692 0.9583902670118067 0.9983541290898130
 66 0.0166663667458513 0.0008321946597639 0.9750566337576579 0.9991863237495768
 67 0.0128274314400094 0.0004988673248468 0.9878840651976674 0.9996851910744237
 68 0.0084914233258330 0.0002423186960466 0.9963754885235003 0.9999275097704703
 69 0.0036245114764992 0.0000724902295300 0.9999999999999996 1.0000000000000000

 ndtfast, nfast =   50  69   nfast/ndtfast = 1.38000

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

    1.000000000000 1.033396903681 0.516698451840 1.000000000000 1.000000000000

 Power filter parameters, Fgamma, gamma =  0.28400   0.22720

 Minimum X-grid spacing, DXmin =  3.45982981E+00 km
 Maximum X-grid spacing, DXmax =  4.22577922E+00 km
 Minimum Y-grid spacing, DYmin =  4.11249518E+00 km
 Maximum Y-grid spacing, DYmax =  5.02293410E+00 km
 Minimum Z-grid spacing, DZmin =  8.51378686E-02 m
 Maximum Z-grid spacing, DZmax =  3.48052605E+02 m

 Minimum barotropic Courant Number =  8.68999059E-03
 Maximum barotropic Courant Number =  3.21482984E-01
 Maximum Coriolis   Courant Number =  1.91235784E-02


 NLM: GET_STATE - Read state initial conditions,             t =    15 00:00:00
                   (File: ecs22-init.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 =  1.11511000E-01 Max =  2.46325836E+01)
                - salinity
                   (Min =  2.84233093E+01 Max =  3.49072609E+01)
                - suspended cohesive sediment, size class 01
                   (Min =  0.00000000E+00 Max =  0.00000000E+00)
                - suspended noncohesive sediment, size class 01
                   (Min =  0.00000000E+00 Max =  0.00000000E+00)
                - cohesive sediment fraction, size class 01
                   (Min =  5.00000000E-01 Max =  5.00000000E-01)
                - cohesive sediment mass, size class 01
                   (Min =  0.00000000E+00 Max =  0.00000000E+00)
                - noncohesive sediment fraction, size class 01
                   (Min =  5.00000000E-01 Max =  5.00000000E-01)
                - noncohesive sediment mass, size class 01
                   (Min =  0.00000000E+00 Max =  0.00000000E+00)
                - sediment bed layer thickness
                   (Min =  0.00000000E+00 Max =  0.00000000E+00)
                - sediment layer age
                   (Min =  0.00000000E+00 Max =  0.00000000E+00)
                - sediment layer porosity
                   (Min =  5.00000000E-01 Max =  5.00000000E-01)
                - biodiffusivity at bottom of each layer
                   (Min =  0.00000000E+00 Max =  0.00000000E+00)
                - sediment median grain diameter size
                   (Min =  2.52982213E-05 Max =  2.52982213E-05)
                - sediment median grain density
                   (Min =  2.65000000E+03 Max =  2.65000000E+03)
                - sediment median grain settling velocity
                   (Min =  3.86662682E-04 Max =  3.86662682E-04)
                - sediment median critical erosion stress
                   (Min =  4.82846854E-02 Max =  4.82846854E-02)
                - bottom ripple length
                   (Min =  1.00000000E-01 Max =  1.00000000E-01)
                - bottom ripple height
                   (Min =  1.00000000E-02 Max =  1.00000000E-02)
    GET_NGFLD   - tidal period
                   (Min =  4.32000000E+04 Max =  9.29494800E+04)
    GET_2DFLD   - tidal elevation amplitude
                   (Min =  0.00000000E+00 Max =  6.13701777E+00)
    GET_2DFLD   - tidal elevation phase angle
                   (Min =  1.37093384E-04 Max =  6.28299337E+00)
    GET_2DFLD   - tidal current inclination angle
                   (Min =  0.00000000E+00 Max =  3.14159265E+00)
    GET_2DFLD   - tidal current phase angle
                   (Min =  0.00000000E+00 Max =  6.28317670E+00)
    GET_2DFLD   - maximum tidal current, ellipse major axis
                   (Min =  0.00000000E+00 Max =  6.04248924E+00)
    GET_2DFLD   - minimum tidal current, ellipse minor axis
                   (Min = -7.02054542E-02 Max =  1.10750142E-01)
    GET_NGFLD   - river runoff  XI-positions at RHO-points
                   (Min =  1.11000000E+02 Max =  1.11000000E+02)
    GET_NGFLD   - river runoff ETA-positions at RHO-points
                   (Min =  2.12000000E+02 Max =  2.12000000E+02)
    GET_NGFLD   - river runoff direction
                   (Min =  0.00000000E+00 Max =  0.00000000E+00)
    GET_NGFLD   - river runoff mass transport vertical profile
                   (Min =  3.33333333E-02 Max =  3.33333333E-02)
    GET_NGFLD   - river runoff mass transport,               t =    15 00:00:00
                   (Rec=0001, Index=1, File: ecs22-forc.nc)
                   (Tmin=         15.0000 Tmax=        345.0000)
                   (Min =  1.07000000E+04 Max =  1.07000000E+04)
    GET_2DFLD   - surface u-momentum stress,                 t =    15 00:00:00
                   (Rec=0001, Index=1, File: ecs22-forc.nc)
                   (Tmin=         15.0000 Tmax=        345.0000)
                   (Min = -9.63994182E-05 Max =  8.67807185E-05)
    GET_2DFLD   - surface v-momentum stress,                 t =    15 00:00:00
                   (Rec=0001, Index=1, File: ecs22-forc.nc)
                   (Tmin=         15.0000 Tmax=        345.0000)
                   (Min = -1.70242822E-04 Max = -5.18803996E-05)
    GET_2DFLD   - surface net heat flux,                     t =    15 00:00:00
                   (Rec=0001, Index=1, File: ecs22-forc.nc)
                   (Tmin=         15.0000 Tmax=        345.0000)
                   (Min =  0.00000000E+00 Max =  0.00000000E+00)
    GET_2DFLD   - sea surface temperature climatology,       t =    15 00:00:00
                   (Rec=0001, Index=1, File: ecs22-forc.nc)
                   (Tmin=         15.0000 Tmax=        345.0000)
                   (Min =  2.56314001E+00 Max =  2.46325831E+01)
    GET_2DFLD   - surface net heat flux sensitivity to SST,  t =    15 00:00:00
                   (Rec=0001, Index=1, File: ecs22-forc.nc)
                   (Tmin=         15.0000 Tmax=        345.0000)
                   (Min = -1.88635921E-05 Max = -8.02302277E-06)
    GET_2DFLD   - surface net freswater flux, (E-P),         t =    15 00:00:00
                   (Rec=0001, Index=1, File: ecs22-forc.nc)
                   (Tmin=         15.0000 Tmax=        345.0000)
                   (Min =  0.00000000E+00 Max =  0.00000000E+00)
    GET_2DFLD   - sea surface salinity climatology,          t =    15 00:00:00
                   (Rec=0001, Index=1, File: ecs22-forc.nc)
                   (Tmin=         15.0000 Tmax=        345.0000)
                   (Min =  2.84413709E+01 Max =  3.48685579E+01)
    GET_NGFLD   - free-surface eastern boundary condition,   t =    15 00:00:00
                   (Rec=0001, Index=2, File: ecs22-bry.nc)
                   (Tmin=         15.0000 Tmax=        345.0000)
                   (Min = -1.23256712E-01 Max =  9.66403893E-01)
    GET_NGFLD   - free-surface southern boundary condition,  t =    15 00:00:00
                   (Rec=0001, Index=2, File: ecs22-bry.nc)
                   (Tmin=         15.0000 Tmax=        345.0000)
                   (Min = -2.49090120E-02 Max =  9.14263226E-01)
    GET_NGFLD   - free-surface northern boundary condition,  t =    15 00:00:00
                   (Rec=0001, Index=2, File: ecs22-bry.nc)
                   (Tmin=         15.0000 Tmax=        345.0000)
                   (Min = -2.12015561E-01 Max =  3.04446945E-02)
    GET_NGFLD   - 2D u-momentum eastern boundary condition,  t =    15 00:00:00
                   (Rec=0001, Index=2, File: ecs22-bry.nc)
                   (Tmin=         15.0000 Tmax=        345.0000)
                   (Min = -9.57948996E-02 Max =  3.86646355E-01)
    GET_NGFLD   - 2D v-momentum eastern boundary condition,  t =    15 00:00:00
                   (Rec=0001, Index=2, File: ecs22-bry.nc)
                   (Tmin=         15.0000 Tmax=        345.0000)
                   (Min = -1.87730295E-01 Max =  1.44428503E-01)
    GET_NGFLD   - 2D u-momentum southern boundary condition, t =    15 00:00:00
                   (Rec=0001, Index=2, File: ecs22-bry.nc)
                   (Tmin=         15.0000 Tmax=        345.0000)
                   (Min = -1.98771698E-01 Max =  2.37601863E-01)
    GET_NGFLD   - 2D v-momentum southern boundary condition, t =    15 00:00:00
                   (Rec=0001, Index=2, File: ecs22-bry.nc)
                   (Tmin=         15.0000 Tmax=        345.0000)
                   (Min = -7.00757756E-01 Max =  4.10468666E-01)
    GET_NGFLD   - 2D u-momentum northern boundary condition, t =    15 00:00:00
                   (Rec=0001, Index=2, File: ecs22-bry.nc)
                   (Tmin=         15.0000 Tmax=        345.0000)
                   (Min = -7.15604833E-01 Max =  2.44446378E-01)
    GET_NGFLD   - 2D v-momentum northern boundary condition, t =    15 00:00:00
                   (Rec=0001, Index=2, File: ecs22-bry.nc)
                   (Tmin=         15.0000 Tmax=        345.0000)
                   (Min = -2.91737026E-01 Max =  6.85510640E-02)
    GET_NGFLD   - temperature eastern boundary condition,    t =    15 00:00:00
                   (Rec=0001, Index=2, File: ecs22-bry.nc)
                   (Tmin=         15.0000 Tmax=        345.0000)
                   (Min =  1.21501069E-01 Max =  2.37951673E+01)
    GET_NGFLD   - salinity eastern boundary condition,       t =    15 00:00:00
                   (Rec=0001, Index=2, File: ecs22-bry.nc)
                   (Tmin=         15.0000 Tmax=        345.0000)
                   (Min =  3.39003970E+01 Max =  3.49070123E+01)
    GET_NGFLD   - suspended cohesive sediment eastern boundart =    15 00:00:00class 01,
                   (Rec=0001, Index=2, File: ecs22-bry.nc)
                   (Tmin=         15.0000 Tmax=        345.0000)
                   (Min =  0.00000000E+00 Max =  0.00000000E+00)
    GET_NGFLD   - suspended noncohesive sediment eastern bount =    15 00:00:00ze class 01,
                   (Rec=0001, Index=2, File: ecs22-bry.nc)
                   (Tmin=         15.0000 Tmax=        345.0000)
                   (Min =  0.00000000E+00 Max =  0.00000000E+00)
    GET_NGFLD   - temperature southern boundary condition,   t =    15 00:00:00
                   (Rec=0001, Index=2, File: ecs22-bry.nc)
                   (Tmin=         15.0000 Tmax=        345.0000)
                   (Min =  1.48498585E+00 Max =  2.46325831E+01)
    GET_NGFLD   - salinity southern boundary condition,      t =    15 00:00:00
                   (Rec=0001, Index=2, File: ecs22-bry.nc)
                   (Tmin=         15.0000 Tmax=        345.0000)
                   (Min =  3.41652605E+01 Max =  3.49048230E+01)
    GET_NGFLD   - suspended cohesive sediment southern boundat =    15 00:00:00 class 01,
                   (Rec=0001, Index=2, File: ecs22-bry.nc)
                   (Tmin=         15.0000 Tmax=        345.0000)
                   (Min =  0.00000000E+00 Max =  0.00000000E+00)
    GET_NGFLD   - suspended noncohesive sediment southern bout =    15 00:00:00ize class 01,
                   (Rec=0001, Index=2, File: ecs22-bry.nc)
                   (Tmin=         15.0000 Tmax=        345.0000)
                   (Min =  0.00000000E+00 Max =  0.00000000E+00)
    GET_NGFLD   - temperature northern boundary condition,   t =    15 00:00:00
                   (Rec=0001, Index=2, File: ecs22-bry.nc)
                   (Tmin=         15.0000 Tmax=        345.0000)
                   (Min =  1.11510998E-01 Max =  5.85751113E+00)
    GET_NGFLD   - salinity northern boundary condition,      t =    15 00:00:00
                   (Rec=0001, Index=2, File: ecs22-bry.nc)
                   (Tmin=         15.0000 Tmax=        345.0000)
                   (Min =  2.84233091E+01 Max =  3.41462627E+01)
    GET_NGFLD   - suspended noncohesive sediment northern bout =    15 00:00:00ize class 01,
                   (Rec=0001, Index=2, File: ecs22-bry.nc)
                   (Tmin=         15.0000 Tmax=        345.0000)
                   (Min =  0.00000000E+00 Max =  0.00000000E+00)










 GET_NGFLD   - unable to find requested variable: ^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@

              in file: /dcfs2/users/leon/Documents/roms_examples/ecs22/ecs22-bry.nc

 Elapsed CPU time (seconds):

 Node   #  0 CPU:      10.936
 Node   # 12 CPU:      10.961
 Node   # 13 CPU:      10.961
 Node   # 14 CPU:      10.961
 Node   # 15 CPU:      10.961
 Node   #  6 CPU:      10.961
 Node   #  4 CPU:      10.961
 Node   #  7 CPU:      10.961
 Node   #  9 CPU:      10.961
 Node   #  8 CPU:      10.961
 Node   # 11 CPU:      10.961
 Node   #  3 CPU:      10.961
 Node   # 10 CPU:      10.961 Node   #  1 CPU:      10.961

 Node   #  2 CPU:      10.961
 Node   #  5 CPU:      10.961
 Node   # 38 CPU:      10.961
 Node   # 21 CPU:      10.961
 Node   # 39 CPU:      10.961
 Node   # 37 CPU:      10.961 Node   # 36 CPU:      10.961

 Node   # 34 CPU:      10.961
 Node   # 47 CPU:      10.961
 Node   # 43 CPU:      10.961
 Node   # 33 CPU:      10.961
 Node   # 42 CPU:      10.961 Node   # 40 CPU:      10.961

 Node   # 44 CPU:      10.961 Node   # 41 CPU:      10.961 Node   # 35 CPU:      10.961


 Node   # 54 CPU:      10.961
 Node   # 55 CPU:      10.961 Node   # 52 CPU:      10.961

 Node   # 53 CPU:      10.961
 Node   # 49 CPU:      10.961
 Node   # 61 CPU:      10.961
 Node   # 62 CPU:      10.961 Node   # 56 CPU:      10.961

 Node   # 57 CPU:      10.961
 Node   # 50 CPU:      10.961
 Node   # 63 CPU:      10.961
 Node   # 60 CPU:      10.961 Node   # 58 CPU:      10.961

 Node   # 51 CPU:      10.961 Node   # 59 CPU:      10.961

 Node   # 48 CPU:      10.961
 Node   # 22 CPU:      10.961
 Node   # 23 CPU:      10.961
 Node   # 17 CPU:      10.961
 Node   # 29 CPU:      10.961
 Node   # 26 CPU:      10.961 Node   # 18 CPU:      10.961 Node   # 28 CPU:      10.961
 Node   # 25 CPU:      10.961
 Node   # 20 CPU:      10.961


 Node   # 27 CPU:      10.961
 Node   # 30 CPU:      10.961 Node   # 19 CPU:      10.961 Node   # 24 CPU:      10.961


 Node   # 31 CPU:      10.961
 Node   # 16 CPU:      10.961
 Node   # 46 CPU:      10.961
 Node   # 45 CPU:      10.961
 Node   # 32 CPU:      10.961
 Total:               701.464

 Nonlinear model elapsed time profile:

  Reading of input data ............................       282.823  (40.3190 %)
  2D/3D coupling, vertical metrics .................         0.391  ( 0.0558 %)
  Omega vertical velocity ..........................         0.266  ( 0.0379 %)
  Equation of state for seawater ...................         1.048  ( 0.1494 %)
                                              Total:       284.529   40.5621

 Nonlinear model message Passage profile:

  Message Passage: 2D halo exchanges ...............         4.276  ( 0.6095 %)
  Message Passage: 3D halo exchanges ...............         1.492  ( 0.2127 %)
  Message Passage: data broadcast ..................       382.823  (54.5748 %)
  Message Passage: data reduction ..................         0.064  ( 0.0091 %)
  Message Passage: data scattering..................       219.459  (31.2858 %)
                                              Total:       608.113   86.6920

 All percentages are with respect to total time =          701.464

 ROMS/TOMS - Output NetCDF summary for Grid 01:

 Analytical header files used:

     ROMS/Functionals/ana_hmixcoef.h
     ROMS/Functionals/ana_nudgcoef.h

 ROMS/TOMS - Input error ............. exit_flag:   2


 ERROR: Abnormal termination: NetCDF INPUT.
 REASON: No error                                                                        
Thank you~

User avatar
arango
Site Admin
Posts: 1347
Joined: Wed Feb 26, 2003 4:41 pm
Location: DMCS, Rutgers University
Contact:

Re: sediment bug in the latest verison 429

#6 Unread post by arango »

Yes, the problem was in varinfo.dat. This has been there since revision 383. There was a typo when defining the variable sand_north_. Please update and check the following :arrow: trac ticket for details. Thank you for reporting this problem.

I also noticed that the logical flag LtracerSrc is false for your sediment tracers. I don't know if this is what you intended. If you want to have point sources for a particular sediment tracer at the river locations, you need to activate its associated switch.

leon
Posts: 78
Joined: Mon Mar 03, 2008 4:14 am

Re: sediment bug in the latest verison 429

#7 Unread post by leon »

First, thank you very much~ I update the code and there are still some errors.
In the previous verison, there is no Ltracer option for mud or sand in the sediment.in file. The model is running ok. After updating to the latest version, the model runs well when the Ltracer option is F in sediment.in file. However, if I set the Ltracer on for the mud and sand in sediment.in file, errors come. The log file is as follow:

Code: Select all

Time is date
cat ${PSB_NODEFILE}
This job has allocated 1 nodes
 Process Information:

 Node #  0 (pid=   27008) is active.

 Model Input Parameters:  ROMS/TOMS version 3.4  
                          Monday - January 11, 2010 -  2:10:23 PM
 -----------------------------------------------------------------------------

 East China Sea Sediment

 Operating system : Linux
 CPU/hardware     : x86_64
 Compiler system  : pgi
 Compiler command : /opt/mpi/mvapich/1.1/gcc.pgf90/bin/mpif90
 Compiler flags   :  -O3 -tp k8-64 -Mfree

 Input Script  : /dcfs2/users/leon/Documents/trunk/User/External/ecs22.in

 SVN Root URL  : https://www.myroms.org/svn/src/trunk
 SVN Revision  : 405:438M

 Local Root    : /dcfs2/users/leon/Documents/trunk
 Header Dir    : /dcfs2/users/leon/Documents/trunk/ROMS/Include
 Header file   : bedload.h
 Analytical Dir: /dcfs2/users/leon/Documents/trunk/ROMS/Functionals

 Resolution, Grid 01: 0368x0440x030,  Parallel Nodes:   1,  Tiling: 001x001


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

     466560  ntimes          Number of timesteps for 3-D equations.
    200.000  dt              Timestep size (s) for 3-D equations.
         50  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.
      12960  nRST            Number of timesteps between the writing of data
                               into restart fields.
         10  ninfo           Number of timesteps between print of information
                               to standard output.
          T  ldefout         Switch to create a new output NetCDF file(s).
      12960  nHIS            Number of timesteps between the writing fields
                               into history file.
      12960  ntsAVG          Starting timestep for the accumulation of output
                               time-averaged data.
      12960  nAVG            Number of timesteps between the writing of
                               time-averaged data into averages file.
      12960  ndefAVG         Number of timesteps between creation of new
                               time-averaged file.
 2.0000E+01  nl_tnu2(01)     NLM Horizontal, harmonic mixing coefficient
                               (m2/s) for tracer 01: temp
 2.0000E+01  nl_tnu2(02)     NLM Horizontal, harmonic mixing coefficient
                               (m2/s) for tracer 02: salt
 4.0000E+01  nl_visc2        NLM Horizontal, harmonic mixing coefficient
                               (m2/s) for momentum.
 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: 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).
      0.250  sz_alpha        Factor for Wave dissipation surface tke flux .
    100.000  crgban_cw       Factor for Craig/Banner surface tke flux.
 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).
 2.0000E-02  Zos             Surface roughness (m).
          2  Vtransform      S-coordinate transformation equation.
          2  Vstretching     S-coordinate stretching function.
 3.0000E+00  theta_s         S-coordinate surface control parameter.
 5.0000E+00  theta_b         S-coordinate bottom  control parameter.
      5.000  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).
      0.000  tide_start      Reference time origin for tidal forcing (days).
      -1.00  time_ref        Reference time for units attribute (yyyymmdd.dd)
 3.0000E+01  Tnudg(01)       Nudging/relaxation time scale (days)
                               for tracer 01: temp
 3.0000E+01  Tnudg(02)       Nudging/relaxation time scale (days)
                               for tracer 02: salt
 3.0000E+01  Znudg           Nudging/relaxation time scale (days)
                               for free-surface.
 3.0000E+01  M2nudg          Nudging/relaxation time scale (days)
                               for 2D momentum.
 3.0000E+01  M3nudg          Nudging/relaxation time scale (days)
                               for 3D momentum.
 1.0000E+01  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(idBath)    Write out time-dependent bathymetry.
          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(idBott)    Write out bottom property 01: grain_diameter
          T  Hout(idBott)    Write out bottom property 02: grain_density
          T  Hout(idBott)    Write out bottom property 03: settling_vel
          T  Hout(idBott)    Write out bottom property 04: erosion_stress
          T  Hout(idBott)    Write out bottom property 05: ripple_length
          T  Hout(idBott)    Write out bottom property 06: ripple_height
          T  Hout(idBott)    Write out bottom property 07: bed_wave_amp
          T  Hout(idBott)    Write out bottom property 08: Zo_def
          T  Hout(idBott)    Write out bottom property 09: Zo_app
          T  Hout(idTsur)    Write out surface net heat flux.
          T  Hout(idTsur)    Write out surface net salt flux.
          T  Hout(idVvis)    Write out vertical viscosity coefficient.
          T  Hout(idTdif)    Write out vertical T-diffusion coefficient.

 Output/Input Files:

             Output Restart File:  /dcfs2/users/leon/Documents/roms_examples/ecs22/ecs22_rst.nc
             Output History File:  /dcfs2/users/leon/Documents/roms_examples/ecs22/ecs22_his.nc
       Prefix for Averages Files:  /dcfs2/users/leon/Documents/roms_examples/ecs22/ecs22_avg
                 Input Grid File:  /dcfs2/users/leon/Documents/roms_examples/ecs22/ecs22-grid.nc
    Input Nonlinear Initial File:  /dcfs2/users/leon/Documents/roms_examples/ecs22/ecs22-init.nc
           Input Forcing File 01:  /dcfs2/users/leon/Documents/roms_examples/ecs22/ecs22-forc.nc
           Input Forcing File 02:  /dcfs2/users/leon/Documents/roms_examples/ecs22/ecs22-tide72.nc
             Input Boundary File:  /dcfs2/users/leon/Documents/roms_examples/ecs22/ecs22-bry.nc

 Tile partition information for Grid 01:  0368x0440x0030  tiling: 001x001

     tile     Istr     Iend     Jstr     Jend     Npts

        0        1      368        1      440  4857600

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

     tile     Xmin     Xmax     Ymin     Ymax     grid

        0     0.50   368.50     0.50   440.50  RHO-points

        0     1.00   368.00     0.50   440.50    U-points

        0     0.50   368.50     1.00   440.00    V-points

 Maximum halo size in XI and ETA directions:

               HaloSizeI(1) =    1137
               HaloSizeJ(1) =    1353
                TileSide(1) =     445
                TileSize(1) =  165985



 Sediment Parameters, Grid: 01
 =============================


 Size     Sd50        Csed        Srho        Wsed        Erate       poros
 Class    (mm)       (kg/m3)     (kg/m3)     (mm/s)     (kg/m2/s)    (nondim)

   1    8.0000E-03  0.0000E+00  2.6500E+03  3.5700E-02  5.0000E-04  6.8240E-01
   2    8.0000E-02  0.0000E+00  2.6500E+03  4.1879E+00  1.0000E-04  4.8510E-01

         tau_ce      tau_cd      nl_tnu2     nl_tnu4     Akt_bak      Tnudg
         (N/m2)      (N/m2)      (m2/s)      (m4/s)       (m2/s)      (day)

   1    2.2431E-02  9.9690E-03  0.0000E+00  0.0000E+00  5.0000E-06  0.0000E+00
   2    1.0394E-01  4.6194E-02  0.0000E+00  0.0000E+00  5.0000E-06  0.0000E+00

         morph_fac
         (nondim)

   1    1.0000E+01
   2    1.0000E+01

 New bed layer formed when deposition exceeds 0.10000E-01 (m).
 Two first layers are combined when 2nd layer smaller than 0.10000E-01 (m).
 Rate coefficient for bed load transport = 0.50000E-01

          T  LtracerSrc(03)  Processing point sources/Sink on tracer 03: mud_01
          T  LtracerSrc(04)  Processing point sources/Sink on tracer 04: sand_01
          T  Hout(idTvar)   Write out sediment01: mud_01
          T  Hout(idTvar)   Write out sediment02: sand_01
          T  Hout(idfrac)   Write out bed fraction, sediment 01: mudfrac_01
          T  Hout(idfrac)   Write out bed fraction, sediment 02: sandfrac_01
          T  Hout(idfrac)   Write out mass, sediment 01: mudmass_01
          T  Hout(idfrac)   Write out mass, sediment 02: sandmass_01
          T  Hout(idUbld)   Write out bed load at U-points, sediment 01: bedload_Umud_01
          T  Hout(idVbld)   Write out bed load at V-points, sediment 01: bedload_Vmud_01
          T  Hout(idUbld)   Write out bed load at U-points, sediment 02: bedload_Usand_01
          T  Hout(idVbld)   Write out bed load at V-points, sediment 02: bedload_Vsand_01
          T  Hout(idSbed)   Write out BED property 01: bed_thickness
          T  Hout(idSbed)   Write out BED property 02: bed_age
          T  Hout(idSbed)   Write out BED property 03: bed_porosity

 Activated C-preprocessing Options:

 BEDLOAD             East China Sea Sediment
 ADD_FSOBC           Adding tidal elevation to proccesed OBC data.
 ADD_M2OBC           Adding tidal currents to proccesed OBC data.
 ANA_BPFLUX          Analytical bottom passive tracers fluxes.
 ANA_BSFLUX          Analytical kinematic bottom salinity flux.
 ANA_BTFLUX          Analytical kinematic bottom temperature flux.
 ANA_SPFLUX          Analytical surface passive tracer fluxes.
 ASSUMED_SHAPE       Using assumed-shape arrays.
 AVERAGES            Writing out time-averaged fields.
 BEDLOAD_MPM         Activate bed load sediment transport Meyer-Peter-Mueller.
 CURVGRID            Orthogonal curvilinear grid.
 DJ_GRADPS           Parabolic Splines density Jacobian (Shchepetkin, 2002).
 DOUBLE_PRECISION    Double precision arithmetic.
 EAST_FSCHAPMAN      Eastern edge, free-surface, Chapman condition.
 EAST_M2FLATHER      Eastern edge, 2D momentum, Flather condition.
 EAST_M3GRADIENT     Eastern edge, 3D momentum, gradient condition.
 EAST_TNUDGING       Eastern edge, tracers, passive/active outflow/inflow.
 EAST_TRADIATION     Eastern edge, tracers, radiation condition.
 GLS_MIXING          Generic Length-Scale turbulence closure.
 KANTHA_CLAYSON      Kantha and Clayson stability function formulation.
 MASKING             Land/Sea masking.
 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          Nonlinear Equation of State for seawater.
 NORTH_FSCHAPMAN     Northern edge, free-surface, Chapman condition.
 NORTH_M2FLATHER     Northern edge, 2D momentum, Flather condition.
 NORTH_M3GRADIENT    Northern edge, 3D momentum, gradient condition.
 NORTH_TNUDGING      Northern edge, tracers, passive/active outflow/inflow.
 NORTH_TRADIATION    Northern edge, tracers, radiation condition.
 N2S2_HORAVG         Horizontal smoothing of buoyancy and shear.
 OUT_DOUBLE          Double precision output fields in NetCDF files.
 POWER_LAW           Power-law shape time-averaging barotropic filter.
 PROFILE             Time profiling activated .
 QCORRECTION         Surface net heat flux correction.
 K_GSCHEME           Third-order upstream advection of TKE fields.
 !RST_SINGLE         Double precision fields in restart NetCDF file.
 SALINITY            Using salinity.
 SCORRECTION         Surface salinity flux correction.
 SEDIMENT            Cohesive and noncohesive sediments.
 SED_MORPH           Allow bottom model elevation to evolve.
 SUSPLOAD            Activate suspended sediment transport.
 SOLVE3D             Solving 3D Primitive Equations.
 SOUTH_FSCHAPMAN     Southern edge, free-surface, Chapman condition.
 SOUTH_M2FLATHER     Southern edge, 2D momentum, Flather condition.
 SOUTH_M3GRADIENT    Southern edge, 3D momentum, gradient condition.
 SOUTH_TNUDGING      Southern edge, tracers, passive/active outflow/inflow.
 SOUTH_TRADIATION    Southern edge, tracers, radiation condition.
 SPLINES             Conservative parabolic spline reconstruction.
 SPONGE              Enhanced horizontal mixing in the sponge areas.
 SSH_TIDES           Add tidal elevation to SSH climatology.
 THREE_GHOST         Using three Ghost Points in halo regions.
 TS_MPDATA           Recursive flux corrected MPDATA 3D 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_TIDES            Add tidal currents to 2D momentum climatologies.
 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          at_hmin  over_slope     at_hmax

    30   0.0000000   0.0000000           0.000       0.000       0.000
    29  -0.0333333  -0.0007218          -0.085      -2.475      -4.783
    28  -0.0666667  -0.0034632          -0.175     -11.406     -22.480
    27  -0.1000000  -0.0088852          -0.272     -28.910     -57.320
    26  -0.1333333  -0.0174334          -0.377     -56.409    -112.153
    25  -0.1666667  -0.0293918          -0.490     -94.813    -188.794
    24  -0.2000000  -0.0449244          -0.612    -144.645    -288.291
    23  -0.2333333  -0.0641059          -0.744    -206.144    -411.123
    22  -0.2666667  -0.0869446          -0.884    -279.337    -557.343
    21  -0.3000000  -0.1133988          -1.033    -364.091    -726.684
    20  -0.3333333  -0.1433880          -1.192    -460.148    -918.632
    19  -0.3666667  -0.1768003          -1.359    -567.151   -1132.470
    18  -0.4000000  -0.2134957          -1.534    -684.651   -1367.304
    17  -0.4333333  -0.2533078          -1.717    -812.117   -1622.069
    16  -0.4666667  -0.2960427          -1.907    -948.929   -1895.526
    15  -0.5000000  -0.3414759          -2.104   -1094.368   -2186.238
    14  -0.5333333  -0.3893475          -2.307   -1247.604   -2492.544
    13  -0.5666667  -0.4393561          -2.515   -1407.673   -2812.515
    12  -0.6000000  -0.4911506          -2.728   -1573.453   -3143.908
    11  -0.6333333  -0.5443212          -2.944   -1743.633   -3484.101
    10  -0.6666667  -0.5983879          -3.163   -1916.678   -3830.023
     9  -0.7000000  -0.6527875          -3.382   -2090.788   -4178.076
     8  -0.7333333  -0.7068593          -3.600   -2263.849   -4524.032
     7  -0.7666667  -0.7598274          -3.816   -2433.382   -4862.930
     6  -0.8000000  -0.8107817          -4.027   -2596.475   -5188.949
     5  -0.8333333  -0.8586552          -4.230   -2749.717   -5495.267
     4  -0.8666667  -0.9021993          -4.422   -2889.116   -5773.898
     3  -0.9000000  -0.9399541          -4.600   -3010.004   -6015.507
     2  -0.9333333  -0.9702163          -4.759   -3106.933   -6209.200
     1  -0.9666667  -0.9910011          -4.894   -3173.559   -6342.285
     0  -1.0000000  -1.0000000          -5.000   -3202.500   -6400.000

 Time Splitting Weights: ndtfast =  50    nfast =  69

    Primary            Secondary            Accumulated to Current Step

  1-0.0004563262418391 0.0200000000000000-0.0004563262418391 0.0200000000000000
  2-0.0008555246732536 0.0200091265248368-0.0013118509150927 0.0400091265248368
  3-0.0011975957891734 0.0200262370183019-0.0025094467042661 0.0600353635431387
  4-0.0014825415143255 0.0200501889340853-0.0039919882185915 0.0800855524772240
  5-0.0017103668530001 0.0200798397643718-0.0057023550715916 0.1001653922415958
  6-0.0018810821987231 0.0201140471014318-0.0075834372703147 0.1202794393430276
  7-0.0019947063038349 0.0201516687454063-0.0095781435741496 0.1404311080884340
  8-0.0020512699089757 0.0201915628714830-0.0116294134831253 0.1606226709599169
  9-0.0020508200324769 0.0202325882696625-0.0136802335156022 0.1808552592295795
 10-0.0019934249196594 0.0202736046703121-0.0156736584352616 0.2011288638998915
 11-0.0018791796520380 0.0203134731687052-0.0175528380872996 0.2214423370685968
 12-0.0017082124164322 0.0203510567617460-0.0192610505037318 0.2417933938303428
 13-0.0014806914339834 0.0203852210100746-0.0207417419377152 0.2621786148404174
 14-0.0011968325490789 0.0204148348387543-0.0219385744867941 0.2825934496791717
 15-0.0008569074781817 0.0204387714897359-0.0227954819649758 0.3030322211689075
 16-0.0004612527185669 0.0204559096392995-0.0232567346835427 0.3234881308082070
 17-0.0000102791169649 0.0204651346936709-0.0232670138005077 0.3439532655018779
 18 0.0004955179018893 0.0204653402760102-0.0227714958986183 0.3644186057778880
 19 0.0010555474468010 0.0204554299179724-0.0217159484518173 0.3848740356958604
 20 0.0016691116117526 0.0204343189690364-0.0200468368400647 0.4053083546648968
 21 0.0023353932676362 0.0204009367368013-0.0177114435724285 0.4257092914016981
 22 0.0030534431940779 0.0203542288714486-0.0146580003783505 0.4460635202731467
 23 0.0038221665513568 0.0202931600075670-0.0108358338269937 0.4663566802807137
 24 0.0046403086924171 0.0202167166765399-0.0061955251345765 0.4865733969572536
 25 0.0055064403149742 0.0201239105026915-0.0006890848196024 0.5066973074599451
 26 0.0064189419537136 0.0200137816963921 0.0057298571341112 0.5267110891563371
 27 0.0073759878125848 0.0198854028573178 0.0131058449466960 0.5465964920136549
 28 0.0083755289371871 0.0197378831010661 0.0214813738838831 0.5663343751147210
 29 0.0094152757272501 0.0195703725223223 0.0308966496111332 0.5859047476370433
 30 0.0104926797892080 0.0193820670077773 0.0413893294003412 0.6052868146448206
 31 0.0116049151288660 0.0191722134119932 0.0529942445292072 0.6244590280568137
 32 0.0127488586841624 0.0189401151094159 0.0657431032133696 0.6433991431662296
 33 0.0139210701980223 0.0186851379357326 0.0796641734113919 0.6620842811019622
 34 0.0151177714313064 0.0184067165317722 0.0947819448426983 0.6804909976337343
 35 0.0163348247158524 0.0181043611031460 0.1111167695585507 0.6985953587368804
 36 0.0175677108476106 0.0177776646088290 0.1286844804061612 0.7163730233457094
 37 0.0188115063198728 0.0174263103918768 0.1474959867260340 0.7337993337375862
 38 0.0200608598965948 0.0170500802654793 0.1675568466226288 0.7508494140030655
 39 0.0213099685258127 0.0166488630675474 0.1888668151484416 0.7674982770706129
 40 0.0225525525931525 0.0162226636970312 0.2114193677415941 0.7837209407676441
 41 0.0237818305154335 0.0157716126451681 0.2352011982570276 0.7994925534128122
 42 0.0249904926743652 0.0152959760348595 0.2601916909313928 0.8147885294476717
 43 0.0261706746903379 0.0147961661813722 0.2863623656217307 0.8295846956290438
 44 0.0273139300363068 0.0142727526875654 0.3136762956580375 0.8438574483166091
 45 0.0284112019917697 0.0137264740868393 0.3420874976498072 0.8575839224034484
 46 0.0294527949368383 0.0131582500470039 0.3715402925866456 0.8707421724504523
 47 0.0304283449864031 0.0125691941482671 0.4019686375730487 0.8833113665987193
 48 0.0313267899643920 0.0119606272485390 0.4332954275374407 0.8952719938472583
 49 0.0321363387181221 0.0113340914492512 0.4654317662555627 0.9066060852965095
 50 0.0328444397727456 0.0106913646748887 0.4982762060283084 0.9172974499713983
 51 0.0334377493257894 0.0100344758794338 0.5317139553540977 0.9273319258508321
 52 0.0339020985817871 0.0093657208929180 0.5656160539358848 0.9366976467437502
 53 0.0342224604270064 0.0086876789212823 0.5998385143628912 0.9453853256650325
 54 0.0343829154442684 0.0080032297127422 0.6342214298071596 0.9533885553777747
 55 0.0343666172678620 0.0073155714038568 0.6685880470750215 0.9607041267816315
 56 0.0341557572785502 0.0066282390584996 0.7027438043535718 0.9673323658401310
 57 0.0337315286386720 0.0059451239129286 0.7364753329922438 0.9732774897530596
 58 0.0330740896673358 0.0052704933401551 0.7695494226595796 0.9785479830932148
 59 0.0321625265557082 0.0046090115468084 0.8017119492152878 0.9831569946400232
 60 0.0309748154223953 0.0039657610156942 0.8326867646376830 0.9871227556557174
 61 0.0294877837089178 0.0033462647072463 0.8621745483466008 0.9904690203629637
 62 0.0276770709152801 0.0027565090330680 0.8898516192618808 0.9932255293960317
 63 0.0255170886756324 0.0022029676147624 0.9153687079375131 0.9954284970107941
 64 0.0229809801740268 0.0016926258412497 0.9383496881115398 0.9971211228520438
 65 0.0200405789002670 0.0012330062377692 0.9583902670118067 0.9983541290898130
 66 0.0166663667458513 0.0008321946597639 0.9750566337576579 0.9991863237495768
 67 0.0128274314400094 0.0004988673248468 0.9878840651976674 0.9996851910744237
 68 0.0084914233258330 0.0002423186960466 0.9963754885235003 0.9999275097704703
 69 0.0036245114764992 0.0000724902295300 0.9999999999999996 1.0000000000000000

 ndtfast, nfast =   50  69   nfast/ndtfast = 1.38000

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

    1.000000000000 1.033396903681 0.516698451840 1.000000000000 1.000000000000

 Power filter parameters, Fgamma, gamma =  0.28400   0.22720

 Minimum X-grid spacing, DXmin =  3.45982981E+00 km
 Maximum X-grid spacing, DXmax =  4.22577922E+00 km
 Minimum Y-grid spacing, DYmin =  4.11249518E+00 km
 Maximum Y-grid spacing, DYmax =  5.02293410E+00 km
 Minimum Z-grid spacing, DZmin =  8.51378686E-02 m
 Maximum Z-grid spacing, DZmax =  3.48052605E+02 m

 Minimum barotropic Courant Number =  8.68999059E-03
 Maximum barotropic Courant Number =  3.21482984E-01
 Maximum Coriolis   Courant Number =  1.91235784E-02


 NLM: GET_STATE - Read state initial conditions,             t =    15 00:00:00
                   (File: ecs22-init.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 =  1.11511000E-01 Max =  2.46325836E+01)
                - salinity
                   (Min =  2.84233093E+01 Max =  3.49072609E+01)
                - suspended cohesive sediment, size class 01
                   (Min =  0.00000000E+00 Max =  0.00000000E+00)
                - suspended noncohesive sediment, size class 01
                   (Min =  0.00000000E+00 Max =  0.00000000E+00)
                - cohesive sediment fraction, size class 01
                   (Min =  5.00000000E-01 Max =  5.00000000E-01)
                - cohesive sediment mass, size class 01
                   (Min =  0.00000000E+00 Max =  0.00000000E+00)
                - noncohesive sediment fraction, size class 01
                   (Min =  5.00000000E-01 Max =  5.00000000E-01)
                - noncohesive sediment mass, size class 01
                   (Min =  0.00000000E+00 Max =  0.00000000E+00)
                - sediment bed layer thickness
                   (Min =  0.00000000E+00 Max =  0.00000000E+00)
                - sediment layer age
                   (Min =  0.00000000E+00 Max =  0.00000000E+00)
                - sediment layer porosity
                   (Min =  5.00000000E-01 Max =  5.00000000E-01)
                - biodiffusivity at bottom of each layer
                   (Min =  0.00000000E+00 Max =  0.00000000E+00)
                - sediment median grain diameter size
                   (Min =  2.52982213E-05 Max =  2.52982213E-05)
                - sediment median grain density
                   (Min =  2.65000000E+03 Max =  2.65000000E+03)
                - sediment median grain settling velocity
                   (Min =  3.86662682E-04 Max =  3.86662682E-04)
                - sediment median critical erosion stress
                   (Min =  4.82846854E-02 Max =  4.82846854E-02)
                - bottom ripple length
                   (Min =  1.00000000E-01 Max =  1.00000000E-01)
                - bottom ripple height
                   (Min =  1.00000000E-02 Max =  1.00000000E-02)
    GET_NGFLD   - tidal period
                   (Min =  4.32000000E+04 Max =  9.29494800E+04)
    GET_2DFLD   - tidal elevation amplitude
                   (Min =  0.00000000E+00 Max =  6.13701777E+00)
    GET_2DFLD   - tidal elevation phase angle
                   (Min =  1.37093384E-04 Max =  6.28299337E+00)
    GET_2DFLD   - tidal current inclination angle
                   (Min =  0.00000000E+00 Max =  3.14159265E+00)
    GET_2DFLD   - tidal current phase angle
                   (Min =  0.00000000E+00 Max =  6.28317670E+00)
    GET_2DFLD   - maximum tidal current, ellipse major axis
                   (Min =  0.00000000E+00 Max =  6.04248924E+00)
    GET_2DFLD   - minimum tidal current, ellipse minor axis
                   (Min = -7.02054542E-02 Max =  1.10750142E-01)
    GET_NGFLD   - river runoff  XI-positions at RHO-points
                   (Min =  1.11000000E+02 Max =  1.11000000E+02)
    GET_NGFLD   - river runoff ETA-positions at RHO-points
                   (Min =  2.12000000E+02 Max =  2.12000000E+02)
    GET_NGFLD   - river runoff direction
                   (Min =  0.00000000E+00 Max =  0.00000000E+00)
    GET_NGFLD   - river runoff mass transport vertical profile
                   (Min =  3.33333333E-02 Max =  3.33333333E-02)
    GET_NGFLD   - river runoff mass transport,               t =    15 00:00:00
                   (Rec=0001, Index=1, File: ecs22-forc.nc)
                   (Tmin=         15.0000 Tmax=        345.0000)
                   (Min =  1.07000000E+04 Max =  1.07000000E+04)
    GET_NGFLD   - river runoff potential temperature,        t =    15 00:00:00
                   (Rec=0001, Index=1, File: ecs22-forc.nc)
                   (Tmin=         15.0000 Tmax=        345.0000)
                   (Min =  5.00000000E+00 Max =  5.00000000E+00)
    GET_NGFLD   - river runoff salinity,                     t =    15 00:00:00
                   (Rec=0001, Index=1, File: ecs22-forc.nc)
                   (Tmin=         15.0000 Tmax=        345.0000)
                   (Min =  0.00000000E+00 Max =  0.00000000E+00)

 GET_NGFLD   - unable to find requested variable: ^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@

               in file: /dcfs2/users/leon/Documents/roms_examples/ecs22/ecs22-forc.nc

 Elapsed CPU time (seconds):

 Node   #  0 CPU:       9.132
 Total:                 9.132

 Nonlinear model elapsed time profile:

  Reading of input data ............................         0.676  ( 7.4065 %)
  2D/3D coupling, vertical metrics .................         0.121  ( 1.3228 %)
  Omega vertical velocity ..........................         0.087  ( 0.9535 %)
  Equation of state for seawater ...................         0.766  ( 8.3927 %)
                                              Total:         1.651   18.0756

 Nonlinear model message Passage profile:

  Message Passage: 2D halo exchanges ...............         0.000  ( 0.0025 %)
  Message Passage: 3D halo exchanges ...............         0.017  ( 0.1829 %)
  Message Passage: data broadcast ..................         0.014  ( 0.1503 %)
  Message Passage: data reduction ..................         0.000  ( 0.0003 %)
  Message Passage: data scattering..................         0.818  ( 8.9619 %)
                                              Total:         0.849    9.2979

 All percentages are with respect to total time =            9.132

 ROMS/TOMS - Output NetCDF summary for Grid 01:

 Analytical header files used:

     ROMS/Functionals/ana_hmixcoef.h
     ROMS/Functionals/ana_nudgcoef.h

 ROMS/TOMS - Input error ............. exit_flag:   2


 ERROR: Abnormal termination: NetCDF INPUT.
 REASON: No error                                                                        

I have checked the focr file, and river_mud_01 and river_sand_01 are all existing.

Actually, I checked the adria example of ROMS, the Lstracer options of mud and sand in sediment_adria.in are all off. However, river sediments also exists in this example. So I am cofused about what you said above. What I want to do is to set sediment concerntration of the domain to be zeros and only to see how the river sediments are transported on the shelves.

User avatar
arango
Site Admin
Posts: 1347
Joined: Wed Feb 26, 2003 4:41 pm
Location: DMCS, Rutgers University
Contact:

Re: sediment bug in the latest verison 429

#8 Unread post by arango »

Yes, the same problem as before but now in the river metadata. I fixed the problem in sediment_var.h. I hope that this is the last one :oops: Please check the following :arrow: ticket for details. Thank you for reporting this problem.

Post Reply