nudge one kind of passive traces

[zhaoqian]

Hi all:
If I want to nudge one kind of passive traces during simulating, then first I should make the climatology file of this trace. Should I define the structure of this climatology variable in varinfo.dat file ?
Thank you!

[rsoutelino]

You can find an example for the structure of the tracers climatology netcdf file at the clm_ts.cdl file, that comes with your ROMS source package.

[zhaoqian]

Hi all:
In order to nudge the tracers（active and passive） , first I fill the climatology date into the file of clm_ts.nc which is created by clm_ts.cdl file, then I define the Climatotogy variable of dye in varinfo.dat as follows:
'dye_'
'dye climatology'
'kilogram meter-3'
'dye_, scalar, series'
'dye_time'
'idTclm(inert(i))'
'r3dvar'
1.0d0
After this I nudge temp、salt and dye together. The nudging of t and s works well but that of dye fails. Would you please give some instruction for me.Thank you!

[kate]

Looking in mod_clima.F and in step3d_t.F, it allocates for all tracers and nudges for all tracers. Did you set the Tnudgcof for the passive tracers? It looks like that happens in ana_nudgcoef.h. This is from a few minutes with grep - grep is your friend!

[zhaoqian]

Hi Kate and all, I have known the reason now,but I can't solve it yet.
In get_data.F, the code getting the climatology data is
# if !defined ANA_TCLIMA && defined TCLIMATOLOGY
DO i=1,NAT
CALL get_3dfld (ng, iNLM, idTclm(i), ncCLMid(ng), 1, &
& CLMname(ng), update(1), &
& LBi, UBi, LBj, UBj, 1, N(ng), 2, 1, &
it should be changed into
DO i=1,NAT+NPT
In set_data.F, the code setting the climatology data is
# if defined SOLVE3D && defined TCLIMATOLOGY
!
!-----------------------------------------------------------------------
! Set tracer climatology.
!-----------------------------------------------------------------------
!
# ifdef ANA_TCLIMA
CALL ana_tclima (ng, tile, iNLM)
# else
DO itrc=1,NAT
CALL set_3dfld_tile (ng, tile, iNLM, idTclm(itrc), &
& LBi, UBi, LBj, UBj, 1, N(ng), &
& CLIMA(ng)%tclmG(:,:,:,:,itrc), &
& CLIMA(ng)%tclm (:,:,:,itrc), &
& update)
END DO
# endif
# endif
The line following else should be changed into Do itrc=1,NAT+NPT.After I changed these code ,compiled and run it,there still existed some problem:
GET_3DFLD - unable to find requested variable:
in input NetCDF file: /data1/qzhao/ldw5mnew/0501my_shuizhi/clm_ts1.nc.
By the way, I have already created the clm_ts1.nc file and add the variable of dye in varinfo.dat file.
Would you please give me some advice, thank you!

[kate]

It seems even though you updated varinfo.dat, there's still something missing. I suggest print statements.

[zhaoqian]

Hi Kate and all :
the varinfo of dye in clm_ts.cdl is
float dye_01(dye_time, s_rho, eta_rho, xi_rho) ;
dye_01:long_name = "COD" ;
dye_01:time = "dye_time" ;
dye_01:coordinates = "lon_rho lat_rho s_rho dye_time" ;
float dye_02(dye_time, s_rho, eta_rho, xi_rho) ;
dye_02:long_name = "N" ;
dye_02:time = "dye_time" ;
dye_02:coordinates = "lon_rho lat_rho s_rho dye_time" ;
float dye_03(dye_time, s_rho, eta_rho, xi_rho) ;
dye_03:long_name = "P" ;
dye_03:time = "dye_time" ;
dye_03:coordinates = "lon_rho lat_rho s_rho dye_time" ;

the variable of dye in varinfo.dat is
'dye_' ! Input
'dye climatology'
'kilogram meter-3' ! [kg/m3]
'dye_, scalar, series'
'dye_time'
'idTclm(inert(i))'
'r3dvar'
1.0d0

The output message is as follows.
qzhao@altix450:~/ldw5mnew/0501my_shuizhi> /opt/mpich2-ifort/bin/mpirun -np 32 ./oceanM ocean_ldwsea.in
Process Information:

Node # 0 (pid= 59225) is active.
Node # 1 (pid= 59194) is active.
Node # 3 (pid= 59196) is active.
Node # 8 (pid= 59201) is active.
Node # 4 (pid= 59197) is active.
Node # 9 (pid= 59202) is active.
Node # 16 (pid= 59209) is active.
Node # 2 (pid= 59195) is active.
Node # 11 (pid= 59204) is active.
Node # 5 (pid= 59198) is active.
Node # 24 (pid= 59216) is active.
Node # 26 (pid= 59219) is active.
Node # 12 (pid= 59206) is active.

Model Input Parameters: ROMS/TOMS version 3.4
Tuesday - June 21, 2011 - 11:35:28 AM
-----------------------------------------------------------------------------
Node # 10 (pid= 59203) is active.
Node # 21 (pid= 59214) is active.
Node # 22 (pid= 59221) is active.
Node # 25 (pid= 59217) is active.
Node # 23 (pid= 59215) is active.

Wind-Driven Upwelling/Downwelling over a Periodic Channel

Operating system : Linux
CPU/hardware : ia64
Compiler system : ifort
Compiler command : /opt/mpich2-ifort/bin/mpif90
Compiler flags : -ip -O3 -free

Input Script : ocean_ldwsea.in

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

Local Root : /data1/qzhao/trunk34
Header Dir : /data1/qzhao/ldw5mnew/0501my_shuizhi
Header file : ldwsea.h
Analytical Dir: /data1/qzhao/ldw5mnew/0501my_shuizhi/Functionals

Resolution, Grid 01: 0338x0268x005, Parallel Nodes: 32, Tiling: 008x004


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

7000 ntimes Number of timesteps for 3-D equations.
120.000 dt Timestep size (s) for 3-D equations.
30 ndtfast Number of timesteps for 2-D equations between
each 3D timestep.
1 ERstr Starting ensemble/perturbation run number.
1 ERend Ending ensemble/perturbation run number.
0 nrrec Number of restart records to read from disk.
T LcycleRST Switch to recycle time-records in restart file.
720 nRST Number of timesteps between the writing of data
into restart fields.
1 ninfo Number of timesteps between print of information
to standard output.
1 nSTA Number of timesteps between the writing of data
the stations file.
T ldefout Switch to create a new output NetCDF file(s).
30 nHIS Number of timesteps between the writing fields
into history file.
30 ndefHIS Number of timesteps between creation of new
history files.
0.0000E+00 nl_tnu2(01) NLM Horizontal, harmonic mixing coefficient
(m2/s) for tracer 01: temp
0.0000E+00 nl_tnu2(02) NLM Horizontal, harmonic mixing coefficient
(m2/s) for tracer 02: salt
0.0000E+00 nl_tnu2(03) NLM Horizontal, harmonic mixing coefficient
(m2/s) for tracer 03: dye_01
5.0000E+00 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-06 Akt_bak(03) Background vertical mixing coefficient (m2/s)
for tracer 03: dye_01
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.
1.0000E-04 rdrg Linear bottom drag coefficient (m/s).
1.0000E-03 rdrg2 Quadratic bottom drag coefficient.
1.0000E-03 Zob Bottom roughness (m).
3.0000E-01 Dcrit Minimum depth for wetting and drying (m).
1 Vtransform S-coordinate transformation equation.
1 Vstretching S-coordinate stretching function.
2.0000E+00 theta_s S-coordinate surface control parameter.
1.0000E-01 theta_b S-coordinate bottom control parameter.
2.000 Tcline S-coordinate surface/bottom layer width (m) used
in vertical coordinate stretching.
1025.000 rho0 Mean density (kg/m3) for Boussinesq approximation.
120.000 dstart Time-stamp assigned to model initialization (days).
0.000 tide_start Node # 15 (pid= 59208) is active.
Node # 7 (pid= 59200) is active.
Node # 31 (pid= 59224) is active.
Node # 18 (pid= 59210) is active.
Node # 17 (pid= 59211) is active.
Reference time origin for tidal forcing (days).
20100501.00 time_ref Reference time for units attribute (yyyymmdd.dd)
9.0000E+01 Tnudg(01) Nudging/relaxation time scale (days)
for tracer 01: temp
9.0000E+01 Tnudg(02) Nudging/relaxation time scale (days)
for tracer 02: salt
9.0000E+01 Tnudg(03) Nudging/relaxation time scale (days)
for tracer 03: dye_01
0.0000E+00 Znudg Nudging/relaxation time scale (days)
for free-surface.
0.0000E+00 M2nudg Nudging/relaxation time scale (days)
for 2D momentum.
0.0000E+00 M3nudg Nudging/relaxation time scale (days)
for 3D momentum.
0.0000E+00 obcfac Factor between passive and active
open boundary conditions.
14.000 T0 Background potential temperature (C) constant.
Node # 20 (pid= 59213) is active.
31.000 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 LtracerSrc(03) Processing point sources/Sink on tracer 03: dye_01
T Hout(idFsur) Write out free-surface.
T Hout(idUbar) Write out 2D U-momentum component.
T Hout(idVbar) Write out 2D V-momentum component.
T Hout(idUvel) Write out 3D U-momentum component.
T Hout(idVvel) Write out 3D V-momentum component.
T Hout(idTvar) Write out tracer 01: temp
T Hout(idTvar) Write out tracer 02: salt
T Hout(inert) Write out inert passive tracer 01: dye_01

Output/Input Files:

Output Restart File: ocean_rst.nc
Prefix for Histo Node # 6 (pid= 59199) is active.
ry Files: /is2202/ldw5mnew/0501my_shuizhi/ldw_his_nudging
Output Stations File: ocean_sta.nc
Input Grid File: /data1/qzhao/ldw5mnew/ocean_grd.nc
Input Climatology File: /data1/qzhao/ldw5mnew/0501my_shuizhi/clm_ts1.nc
Station positions File: stations.in

Tile partition information for Grid 01: 0338x0268x0005 tiling: 008x004

tile Istr Iend Jstr Jend Npts

0 1 40 1 67 13400
1 41 83 1 67 14405
2 84 126 1 67 14405
3 127 169 1 67 14405
4 170 212 1 67 14405
5 213 255 1 67 14405
6 256 298 1 67 14405
7 299 338 1 67 13400
8 1 40 68 134 13400
9 41 83 68 134 14405
10 84 126 6 Node # 13 (pid= 59205) is active.
Node # 27 (pid= 59218) is active.
Node # 28 (pid= 59220) is active.
Node # 14 (pid= 59207) is active.
Node # 29 (pid= 59222) is active.
Node # 30 (pid= 59223) is active.
8 134 14405
11 127 169 68 134 14405
12 170 212 68 134 14405
13 213 255 68 134 14405
14 256 298 68 134 14405
15 299 338 68 134 13400
16 1 40 135 201 13400
17 41 83 135 201 14405
18 84 126 135 201 14405
19 127 169 135 201 14405
20 170 212 135 201 14405
21 213 255 135 201 14405
22 256 298 135 201 14405
23 299 338 135 201 13400
24 1 40 202 268 13400
25 41 83 202 268 14405
26 84 126 202 268 14405
27 127 169 202 268 14405
28 170 212 202 268 14405
29 213 255 202 268 14405
30 256 298 202 268 14405
31 299 338 202 268 13400

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

tile Xmin Xmax Ymin Ymax grid

0 0.50 40.50 0.50 67.50 RHO-points
1 40.50 83.50 0.50 67.50 RHO-points
2 83.50 126.50 0.50 67.50 RHO-points
3 126.50 169.50 0.50 67.50 RHO-points
4 169.50 212.50 0.50 67.50 RHO-points
5 212.50 255.50 0.50 67.50 RHO-points
6 255.50 298.50 0.50 67.50 RHO-points
7 298.50 338.50 0.50 67.50 RHO-points
8 0.50 40.50 67.50 134.50 RHO-points
9 40.50 83.50 67.50 134.50 RHO-points
10 83.50 126.50 67.50 134.50 RHO-points
11 126.50 169.50 67.50 134.50 RHO-points
12 169.50 212.50 67.50 134.50 RHO-points
13 212.50 255.50 67.50 134.50 RHO-points
14 255.50 298.50 67.50 134.50 RHO-points
15 298.50 338.50 67.50 134.50 RHO-points
16 0.50 40.50 134.50 201.50 RHO-points
17 40.50 83.50 134.50 201.50 RHO-points
18 83.50 126.50 134.50 201.50 RHO-points
19 126.50 169.50 134.50 201.50 RHO-points
20 169.50 212.50 134.50 201.50 RHO-points
21 212.50 255.50 134.50 201.50 RHO-points
22 255.50 298.50 134.50 201.50 RHO-points
23 298.50 338.50 134.50 201.50 RHO-points
24 0.50 40.50 201.50 268.50 RHO-points
25 40.50 83.50 201.50 268.50 RHO-points
26 83.50 126.50 201.50 268.50 RHO-points
27 126.50 169.50 201.50 268.50 RHO-points
28 169.50 212.50 201.50 268.50 RHO-points
29 212.50 255.50 201.50 268.50 RHO-points
30 255.50 298.50 201.50 268.50 RHO-points
31 298.50 338.50 201.50 268.50 RHO-points

0 1.00 40.50 0.50 67.50 U-points
1 40.50 83.50 0.50 67.50 U-points
2 83.50 126.50 0.50 67.50 U-points
3 126.50 169.50 0.50 67.50 U-points
4 169.50 212.50 0.50 67.50 U-points
5 212.50 255.50 0.50 67.50 U-points
6 255.50 298.50 0.50 67.50 U-points
7 298.50 338.00 0.50 67.50 U-points
8 1.00 40.50 67.50 134.50 U-points
9 40.50 83.50 67.50 134.50 U-points
10 83.50 126.50 67.50 134.50 U-points
11 126.50 169.50 67.50 134.50 U-points
12 169.50 212.50 67.50 134.50 U-points
13 212.50 255.50 67.50 134.50 U-points
14 255.50 298.50 67.50 134.50 U-points
15 298.50 338.00 67.50 134.50 U-points
16 1.00 40.50 134.50 201.50 U-points
17 40.50 83.50 134.50 201.50 U-points
18 83.50 126.50 134.50 201.50 U-points
19 126.50 169.50 134.50 201.50 U-points
20 169.50 212.50 134.50 201.50 U-points
21 212.50 255.50 134.50 201.50 U-points
22 255.50 298.50 134.50 201.50 U-points
23 298.50 338.00 134.50 201.50 U-points
24 1.00 40.50 201.50 268.50 U-points
25 40.50 83.50 201.50 268.50 U-points
26 83.50 126.50 201.50 268.50 U-points
27 126.50 169.50 201.50 268.50 U-points
28 169.50 212.50 201.50 268.50 U-points
29 212.50 255.50 201.50 268.50 U-points
30 255.50 298.50 201.50 268.50 U-points
31 298.50 338.00 201.50 268.50 U-points

0 0.50 40.50 1.00 67.50 V-points
1 40.50 83.50 1.00 67.50 V-points
2 83.50 126.50 1.00 67.50 V-points
3 126.50 169.50 1.00 67.50 V-points
4 169.50 212.50 1.00 67.50 V-points
5 212.50 255.50 1.00 67.50 V-points
6 255.50 298.50 1.00 67.50 V-points
7 298.50 338.50 1.00 67.50 V-points
8 0.50 40.50 67.50 134.50 V-points
9 40.50 83.50 67.50 134.50 V-points
10 83.50 126.50 67.50 134.50 V-points
11 126.50 169.50 67.50 134.50 V-points
12 169.50 212.50 67.50 134.50 V-points
13 212.50 255.50 67.50 134.50 V-points
14 255.50 298.50 67.50 134.50 V-points
15 298.50 338.50 67.50 134.50 V-points
16 0.50 40.50 134.50 201.50 V-points
17 40.50 83.50 134.50 201.50 V-points
18 83.50 126.50 134.50 201.50 V-points
19 126.50 169.50 134.50 201.50 V-points
20 169.50 212.50 134.50 201.50 V-points
21 212.50 255.50 134.50 201.50 V-points
22 255.50 298.50 134.50 201.50 V-points
23 298.50 338.50 134.50 201.50 V-points
24 0.50 40.50 201.50 268.00 V-points
25 40.50 83.50 201.50 268.00 V-points
26 83.50 126.50 201.50 268.00 V-points
27 126.50 169.50 201.50 268.00 V-points
28 169.50 212.50 201.50 268.00 V-points
29 212.50 255.50 201.50 268.00 V-points
30 255.50 298.50 201.50 268.00 V-points
31 298.50 338.50 201.50 268.00 V-points

Maximum halo size in XI and ETA directions:

HaloSizeI(1) = 171
HaloSizeJ(1) = 243
TileSide(1) = 75
TileSize(1) = 3825

Node # 19 (pid= 59212) is active.


Stations Parameters, Grid: 01
=============================

12 Nstation Number of stations to write out into stations file.
T Sout(idFsur) Write out free-surface.
T Sout(idUbar) Write out 2D U-momentum component.
T Sout(idVbar) Write out 2D V-momentum component.
T Sout(idUvel) Write out 3D U-momentum component.
T Sout(idVvel) Write out 3D V-momentum component.
T Sout(idWvel) Write out W-momentum component.
T Sout(idOvel) Write out omega vertical velocity.
T Sout(idTvar) Write out tracer 01: temp
T Sout(idTvar) Write out tracer 02: salt
T Sout(idTvar) Write out tracer 03: dye_01
T Sout(idUsms) Write out surface U-momentum stress.
T Sout(idVsms) Write out surface V-momentum stress.
T Sout(idUbms) Write out bottom U-momentum stress.
T Sout(idVbms) Write out bottom V-momentum stress.
T Sout(idVvis) Write out vertical viscosity coefficient.
T Sout(idMtke) Write out turbulent kinetic energy.
T Sout(idMtls) Write out turbulent generic length-scale.

Flag and positions for station 0001: 1 121.2660 40.8469
Flag and positions for station 0002: 1 121.2400 40.8058
Flag and positions for station 0003: 1 121.2150 40.7538
Flag and positions for station 0004: 1 121.5240 40.7928
Flag and positions for station 0005: 1 121.4980 40.7492
Flag and positions for station 0006: 1 121.4650 40.6869
Flag and positions for station 0007: 1 121.7990 40.7612
Flag and positions for station 0008: 1 121.7890 40.6952
Flag and positions for station 0009: 1 121.7770 40.6386
Flag and positions for station 0010: 1 122.0650 40.6283
Flag and positions for station 0011: 1 122.0620 40.5776
Flag and positions for station 0012: 1 122.0650 40.5172

Activated C-preprocessing Options:

LDWSEA Wind-Driven Upwelling/Downwelling over a Periodic Channel
ANA_BSFLUX Analytical kinematic bottom salinity flux.
ANA_BTFLUX Analytical kinematic bottom temperature flux.
ANA_FSOBC Analytical free-surface boundary conditions.
ANA_INITIAL Analytical initial conditions.
ANA_M2OBC Analytical 2D momentum boundary conditions.
ANA_PASSIVE Analytical initial conditions for inert tracers.
ANA_SMFLUX Analytical kinematic surface momentum flux.
ANA_SSFLUX Analytical kinematic surface salinity flux.
ANA_STFLUX Analytical kinematic surface temperature flux.
ANA_TOBC Analytical tracers boundary conditions.
ASSUMED_SHAPE Using assumed-shape arrays.
DJ_GRADPS Parabolic Splines density Jacobian (Shchepetkin, 2002).
DOUBLE_PRECISION Double precision arithmetic.
EASTERN_WALL Wall boundary at Eastern edge.
FSOBC_REDUCED Using free-surface data in reduced physics condtions
INLINE_2DIO Processing 3D IO level by level to reduce memory needs.
KANTHA_CLAYSON Kantha and Clayson stability function formulation.
MASKING Land/Sea masking.
MIX_S_TS Mixing of tracers along constant S-surfaces.
MIX_S_UV Mixing of momentum along constant S-surfaces.
MPI MPI distributed-memory configuration.
MY25_MIXING Mellor/Yamada Level-2.5 mixing closure.
NONLINEAR Nonlinear Model.
NONLIN_EOS Nonlinear Equation of State for seawater.
NORTHERN_WALL Wall boundary at Northern edge.
N2S2_HORAVG Horizontal smoothing of buoyancy and shear.
POWER_LAW Power-law shape time-averaging barotropic filter.
PROFILE Time profiling activated .
K_GSCHEME Third-order upstream advection of TKE fields.
RAMP_TIDES Ramping tidal forcing for one day.
!RST_SINGLE Double precision fields in restart NetCDF file.
SALINITY Using salinity.
SOLVE3D Solving 3D Primitive Equations.
SOUTH_FSCHAPMAN Southern edge, free-surface, Chapman condition.
SOUTH_M2FLATHER Southern edge, 2D momentum, Flather condition.
SOUTH_M3RADIATION Southern edge, 3D momentum, radiation condition.
SOUTH_TRADIATION Southern edge, tracers, radiation condition.
SPLINES Conservative parabolic spline reconstruction.
SSH_TIDES Add tidal elevation to SSH climatology.
STATIONS Writing out station data.
TCLIMATOLOGY Processing tracer climatology data.
TCLM_NUDGING Nudging toward tracer climatology.
THREE_GHOST Using three Ghost Points in halo regions.
T_PASSIVE Advecting and diffusing inert passive tracer.
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_VIS2 Harmonic mixing of momentum.
VAR_RHO_2D Variable density barotropic mode.
WEST_FSCHAPMAN Western edge, free-surface, Chapman condition.
WEST_M2FLATHER Western edge, 2D momentum, Flather condition.
WEST_M3RADIATION Western edge, 3D momentum, radiation condition.
WEST_TRADIATION Western edge, tracers, radiation condition.
WET_DRY Wetting and drying activated.
tdays 120.000000000000
tdays 120.000000000000
time_code 120 00:00:00
tdays 120.000000000000
time_code 120 00:00:00
time_code 120 00:00:00
tdays 120.000000000000
tdays 120.000000000000
time_code 120 00:00:00
tdays 120.000000000000
tdays 120.000000000000
time_code 120 00:00:00
time_code 120 00:00:00
time_code 120 00:00:00
tdays 120.000000000000
time_code 120 00:00:00
tdays 120.000000000000
time_code 120 00:00:00
tdays 120.000000000000
time_code 120 00:00:00

INITIAL: Configuring and initializing forward nonlinear model ...

tdays 120.000000000000
time_code 120 00:00:00
tdays 120.000000000000
time_code 120 00:00:00
tdays 120.000000000000
time_code 120 00:00:00
tdays 120.000000000000
time_code 120 00:00:00
tdays 120.000000000000
tdays 120.000000000000
time_code 120 00:00:00
tdays 120.000000000000
time_code 120 00:00:00
tdays 120.000000000000
time_code 120 00:00:00
tdays 120.000000000000
time_code 120 00:00:00
tdays 120.000000000000
time_code 120 00:00:00
tdays 120.000000000000
time_code 120 00:00:00
tdays 120.000000000000
time_code 120 00:00:00
tdays 120.000000000000
time_code 120 00:00:00
tdays 120.000000000000
time_code 120 00:00:00
tdays 120.000000000000
time_code 120 00:00:00
tdays 120.000000000000
time_code 120 00:00:00
tdays 120.000000000000
time_code 120 00:00:00
tdays 120.000000000000
time_code 120 00:00:00
time_code 120 00:00:00
tdays 120.000000000000
time_code 120 00:00:00
tdays 120.000000000000
time_code 120 00:00:00
tdays 120.000000000000
time_code 120 00:00:00
tdays 120.000000000000
time_code 120 00:00:00

Vertical S-coordinate System:

level S-coord Cs-curve at_hmin over_slope at_hmax

5 0.0000000 0.0000000 0.000 0.000 0.000
4 -0.2000000 -0.1166693 -0.100 -3.954 -7.807
3 -0.4000000 -0.2574241 -0.200 -8.703 -17.205
2 -0.6000000 -0.4375286 -0.300 -14.752 -29.203
1 -0.8000000 -0.6747519 -0.400 -22.687 -44.974
0 -1.0000000 -1.0000000 -0.500 -33.530 -66.560

Time Splitting Weights: ndtfast = 30 nfast = 42

Primary Secondary Accumulated to Current Step

1-0.0008094437383769 0.0333333333333333-0.0008094437383769 0.0333333333333333
2-0.0014053566728197 0.0333603147912792-0.0022148004111966 0.0666936481246126
3-0.0017877524645903 0.0334071600137066-0.0040025528757869 0.1001008081383191
4-0.0019566842408176 0.0334667517625262-0.0059592371166046 0.1335675599008453
5-0.0019122901320372 0.0335319745705535-0.0078715272486418 0.1670995344713988
6-0.0016548570247459 0.0335957175749547-0.0095263842733877 0.2006952520463536
7-0.0011849025289723 0.0336508794757796-0.0107112868023600 0.2343461315221331
8-0.0005032751608631 0.0336903762267453-0.0112145619632232 0.2680365077488784
9 0.0003887272597151 0.0337071520654408-0.0108258347035081 0.3017436598143192
10 0.0014892209965583 0.0336941944901169-0.0093366137069498 0.3354378543044362
11 0.0027955815694920 0.0336445537902317-0.0065410321374578 0.3690824080946679
12 0.0043042707117221 0.0335513677379153-0.0022367614257357 0.4026337758325831
13 0.0060106451121704 0.0334078920475245 0.0037738836864348 0.4360416678801076
14 0.0079087469427945 0.0332075372104522 0.0116826306292293 0.4692492050905598
15 0.0099910761708919 0.0329439123123590 0.0216737068001212 0.5021931174029188
16 0.0122483446563884 0.0326108764399960 0.0339220514565096 0.5348039938429148
17 0.0146692120341107 0.0322025982847830 0.0485912634906204 0.5670065921276978
18 0.0172400033810439 0.0317136245503127 0.0658312668716642 0.5987202166780105
19 0.0199444086685725 0.0311389577709445 0.0857756755402367 0.6298591744489550
20 0.0227631639997064 0.0304741441486588 0.1085388395399431 0.6603333185976138
21 0.0256737146312910 0.0297153720153352 0.1342125541712341 0.6900486906129490
22 0.0286498597812016 0.0288595815276255 0.1628624139524358 0.7189082721405746
23 0.0316613792205219 0.0279045862015855 0.1945237931729577 0.7468128583421600
24 0.0346736416507075 0.0268492068942347 0.2291974348236652 0.7736620652363948
25 0.0376471948657328 0.0256934188392112 0.2668446296893979 0.7993554840756060
26 0.0405373376992232 0.0244385123436867 0.3073819673886212 0.8237939964192927
27 0.0432936737565710 0.0230872677537126 0.3506756411451922 0.8468812641730054
28 0.0458596469320356 0.0216441452951603 0.3965352880772278 0.8685254094681656
29 0.0481720587108284 0.0201154903974257 0.4447073467880562 0.8886408998655914
30 0.0501605672561820 0.0185097551070648 0.4948679140442381 0.9071506549726561
31 0.0517471682814030 0.0168377361985254 0.5466150823256412 0.9239883911711815
32 0.0528456577069106 0.0151128305891453 0.5994607400325517 0.9391012217603267
33 0.0533610761022577 0.0133513086655816 0.6528218161348094 0.9524525304259084
34 0.0531891349131379 0.0115726061288397 0.7060109510479473 0.9640251365547481
35 0.0522156244733761 0.0097996349650684 0.7582265755213234 0.9738247715198165
36 0.0503158038019030 0.0080591141492892 0.8085423793232265 0.9818838856691057
37 0.0473537721847154 0.0063819206892258 0.8558961515079418 0.9882658063583315
38 0.0431818225418188 0.0048034616164019 0.8990779740497606 0.9930692679747335
39 0.0376397765791564 0.0033640675316746 0.9367177506289170 0.9964333355064081
40 0.0305543017255207 0.0021094083123694 0.9672720523544377 0.9985427438187775
41 0.0217382098544504 0.0010909315881854 0.9890102622088881 0.9996336754069629
42 0.0109897377911119 0.0003663245930371 1.0000000000000000 1.0000000000000000

ndtfast, nfast = 30 42 nfast/ndtfast = 1.40000

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

1.000000000000 1.047601458608 0.523800729304 1.000000000000 1.000000000000

Power filter parameters, Fgamma, gamma = 0.28400 0.18933

Minimum X-grid spacing, DXmin = 8.14567084E-01 km
Maximum X-grid spacing, DXmax = 8.41636404E-01 km
Minimum Y-grid spacing, DYmin = 9.11444473E-01 km
Maximum Y-grid spacing, DYmax = 9.41733181E-01 km
Minimum Z-grid spacing, DZmin = 1.00000000E-01 m
Maximum Z-grid spacing, DZmax = 2.15858881E+01 m

Minimum barotropic Courant Number = 1.42627387E-02
Maximum barotropic Courant Number = 1.62876385E-01
Maximum Coriolis Courant Number = 1.14699039E-02

GET_NGFLD - tidal period
(Min = 4.30819210E+04 Max = 2.38071599E+06)
GET_2DFLD - tidal elevation amplitude
(Min = 2.69923067E-05 Max = 9.95791731E-01)
GET_2DFLD - tidal elevation phase angle
(Min = 1.03231464E-05 Max = 6.28318115E+00)
GET_NGFLD - river runoff XI-positions at RHO-points
(Min = 2.34000000E+02 Max = 3.25000000E+02)
GET_NGFLD - river runoff ETA-positions at RHO-points
(Min = 2.35000000E+02 Max = 2.66000000E+02)
GET_NGFLD - river runoff direction
(Min = 1.00000000E+00 Max = 1.00000000E+00)
GET_NGFLD - river runoff mass transport vertical profile
(Min = 2.00000000E-01 Max = 2.00000000E-01)
GET_NGFLD - river runoff mass transport, t = 120 00:00:00
(Rec=0001, Index=2, File: frc_rivers4.nc)
(Tmin= 120.0000 Tmax= 270.0000)
(Min = -1.24200000E+03 Max = -3.70000000E+00)
GET_NGFLD - river runoff potential temperature, t = 120 00:00:00
(Rec=0001, Index=2, File: frc_rivers4.nc)
(Tmin= 120.0000 Tmax= 270.0000)
(Min = 1.40000000E+01 Max = 1.40000000E+01)
GET_NGFLD - river runoff salinity, t = 120 00:00:00
(Rec=0001, Index=2, File: frc_rivers4.nc)
(Tmin= 120.0000 Tmax= 270.0000)
(Min = 3.10000000E+01 Max = 3.10000000E+01)
GET_NGFLD - river runoff dye concentration, type 01, t = 120 00:00:00
(Rec=0001, Index=2, File: frc_rivers4.nc)
(Tmin= 120.0000 Tmax= 270.0000)
(Min = 8.66000000E+00 Max = 3.46300000E+01)
GET_3DFLD - potential temperature climatology, t = 120 00:00:00
(Rec=0001, Index=1, File: clm_ts1.nc)
(Tmin= 120.0000 Tmax= 270.0000)
(Min = 1.60000000E+01 Max = 1.60000000E+01)
GET_3DFLD - salinity climatology, t = 120 00:00:00
(Rec=0001, Index=1, File: clm_ts1.nc)
(Tmin= 120.0000 Tmax= 270.0000)
(Min = 2.80000000E+01 Max = 2.80000000E+01)

GET_3DFLD - unable to find requested variable:
in input NetCDF file: /data1/qzhao/ldw5mnew/0501my_shuizhi/clm_ts1.nc



GET_3DFLD - unable to find requested variable:
in input NetCDF file: /data1/qzhao/ldw5mnew/0501my_shuizhi/clm_ts1.nc

GET_3DFLD - unable to find requested variable:
in input NetCDF file: /data1/qzhao/ldw5mnew/0501my_shuizhi/clm_ts1.nc
GET_3DFLD - unable to find requested variable:
in input NetCDF file: /data1/qzhao/ldw5mnew/0501my_shuizhi/clm_ts1.nc

GET_3DFLD - unable to find requested variable:
in input NetCDF file: /data1/qzhao/ldw5mnew/0501my_shuizhi/clm_ts1.nc



GET_3DFLD - unable to find requested variable:
in input NetCDF file: /data1/qzhao/ldw5mnew/0501my_shuizhi/clm_ts1.nc


GET_3DFLD - unable to find requested variable:
in input NetCDF file: /data1/qzhao/ldw5mnew/0501my_shuizhi/clm_ts1.nc

GET_3DFLD - unable to find requested variable:
in input NetCDF file: /data1/qzhao/ldw5mnew/0501my_shuizhi/clm_ts1.nc

GET_3DFLD - unable to find requested variable:
Elapsed CPU time (seconds):

GET_3DFLD - unable to find requested variable:
in input NetCDF file: /data1/qzhao/ldw5mnew/0501my_shuizhi/clm_ts1.nc

GET_3DFLD - unable to find requested variable:
in input NetCDF file: /data1/qzhao/ldw5mnew/0501my_shuizhi/clm_ts1.nc

GET_3DFLD - unable to find requested variable:
in input NetCDF file: /data1/qzhao/ldw5mnew/0501my_shuizhi/clm_ts1.nc

GET_3DFLD - unable to find requested variable:
in input NetCDF file: /data1/qzhao/ldw5mnew/0501my_shuizhi/clm_ts1.nc

GET_3DFLD - unable to find requested variable:
in input NetCDF file: /data1/qzhao/ldw5mnew/0501my_shuizhi/clm_ts1.nc

GET_3DFLD - unable to find requested variable:
in input NetCDF file: /data1/qzhao/ldw5mnew/0501my_shuizhi/clm_ts1.nc

in input NetCDF file: /data1/qzhao/ldw5mnew/0501my_shuizhi/clm_ts1.nc


GET_3DFLD - unable to find requested variable:
in input NetCDF file: /data1/qzhao/ldw5mnew/0501my_shuizhi/clm_ts1.nc

GET_3DFLD - unable to find requested variable:
in input NetCDF file: /data1/qzhao/ldw5mnew/0501my_shuizhi/clm_ts1.nc

GET_3DFLD - unable to find requested variable:
GET_3DFLD - unable to find requested variable:
in input NetCDF file: /data1/qzhao/ldw5mnew/0501my_shuizhi/clm_ts1.nc

GET_3DFLD - unable to find requested variable:
in input NetCDF file: /data1/qzhao/ldw5mnew/0501my_shuizhi/clm_ts1.nc

in input NetCDF file: /data1/qzhao/ldw5mnew/0501my_shuizhi/clm_ts1.nc
Node # 0 CPU: 0.708
Total: 22.492

Nonlinear model elapsed time profile:

Reading of input data ............................ 11.800 (52.4631 %)
2D/3D coupling, vertical metrics ................. 0.020 ( 0.0889 %)
Omega vertical velocity .......................... 0.028 ( 0.1245 %)
Equation of state for seawater ................... 0.032 ( 0.1423 %)
Total: 11.880 52.8188

Nonlinear model message Passage profile:

Message Passage: 2D halo exchanges ............... 0.220 ( 0.9781 %)
Message Passage: 3D halo exchanges ............... 0.064 ( 0.2845 %)
Message Passage: data broadcast .................. 7.740 (34.4122 %)
Message Passage: data reduction .................. 0.008 ( 0.0356 %)
Message Passage: data scattering.................. 12.244 (54.4371 %)
Total: 20.276 90.1476

All percentages are with respect to total time = 22.492

ROMS/TOMS - Output NetCDF summary for Grid 01:

Analytical header files used:

/data1/qzhao/ldw5mnew/0501my_shuizhi/Functionals/ana_initial.h
/data1/qzhao/ldw5mnew/0501my_shuizhi/Functionals/ana_nudgcoef.h
/data1/qzhao/ldw5mnew/0501my_shuizhi/Functionals/ana_passive.h

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


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

GET_3DFLD - unable to find requested variable:
in input NetCDF file: /data1/qzhao/ldw5mnew/0501my_shuizhi/clm_ts1.nc

GET_3DFLD - unable to find requested variable:
in input NetCDF file: /data1/qzhao/ldw5mnew/0501my_shuizhi/clm_ts1.nc
GET_3DFLD - unable to find requested variable:
in input NetCDF file: /data1/qzhao/ldw5mnew/0501my_shuizhi/clm_ts1.nc
Node # 1 CPU: 0.704
Node # 3 CPU: 0.700
Node # 18 CPU: 0.708
Node # 8 CPU: 0.704
Node # 17 CPU: 0.708
Node # 4 CPU: 0.704
Node # 7 CPU: 0.704
Node # 20 CPU: 0.700
Node # 9 CPU: 0.704
Node # 19 CPU: 0.684
Node # 16 CPU: 0.704
Node # 10 CPU: 0.708
Node # 21 CPU: 0.708
Node # 31 CPU: 0.704
Node # 15 CPU: 0.704
Node # 22 CPU: 0.700

GET_3DFLD - unable to find requested variable:
in input NetCDF file: /data1/qzhao/ldw5mnew/0501my_shuizhi/clm_ts1.nc

GET_3DFLD - unable to find requested variable:
in input NetCDF file: /data1/qzhao/ldw5mnew/0501my_shuizhi/clm_ts1.nc

GET_3DFLD - unable to find requested variable:
in input NetCDF file: /data1/qzhao/ldw5mnew/0501my_shuizhi/clm_ts1.nc

GET_3DFLD - unable to find requested variable:
in input NetCDF file: /data1/qzhao/ldw5mnew/0501my_shuizhi/clm_ts1.nc
GET_3DFLD - unable to find requested variable:
in input NetCDF file: /data1/qzhao/ldw5mnew/0501my_shuizhi/clm_ts1.nc
GET_3DFLD - unable to find requested variable:
in input NetCDF file: /data1/qzhao/ldw5mnew/0501my_shuizhi/clm_ts1.nc

GET_3DFLD - unable to find requested variable:
in input NetCDF file: /data1/qzhao/ldw5mnew/0501my_shuizhi/clm_ts1.nc

GET_3DFLD - unable to find requested variable:
in input NetCDF file: /data1/qzhao/ldw5mnew/0501my_shuizhi/clm_ts1.nc
GET_3DFLD - unable to find requested variable:
in input NetCDF file: /data1/qzhao/ldw5mnew/0501my_shuizhi/clm_ts1.nc
Node # 6 CPU: 0.704
Node # 13 CPU: 0.700
Node # 28 CPU: 0.700
Node # 5 CPU: 0.676
Node # 12 CPU: 0.704
Node # 26 CPU: 0.700
Node # 25 CPU: 0.704
Node # 2 CPU: 0.708
Node # 27 CPU: 0.708
Node # 24 CPU: 0.704
Node # 11 CPU: 0.704
Node # 14 CPU: 0.708
Node # 30 CPU: 0.704
Node # 23 CPU: 0.704
Node # 29 CPU: 0.708
qzhao@altix450:~/ldw5mnew/0501my_shuizhi>
Thank you for your instruction.

[kate]

I didn't mean that you should show us everything ROMS currently writes out. I meant that you can add print statements of your own for debugging purposes. None of us reading the forum immediately know the answer to your question, so you will have to do some digging to find out exactly what is the proper way to define the dye climatology. It's not something I've done before.