I set my tracer concentrations in ana_passive, which I copied into an Inc directory in my project dir, and set the OBC for the passive tracer to periodic in ocean.in.
Now, when I run the model, I get this output:
Code: Select all
Model Input Parameters: ROMS/TOMS version 3.7
Monday - May 29, 2017 - 3:51:54 PM
-----------------------------------------------------------------------------
Tall Isolated Seamount Test
Operating system : Linux
CPU/hardware : x86_64
Compiler system : gfortran
Compiler command : /usr/local/bin/mpif90
Compiler flags : -frepack-arrays -O3 -ffast-math -ffree-form -ffree-line-length-none -ffree-form -ffree-line-length-none
Input Script :
SVN Root URL : https://www.myroms.org/svn/src/trunk
SVN Revision : 802M
Local Root : /home/nws747/trunk
Header Dir : /home/nws747/seamount/Inc
Header file : seamount.h
Analytical Dir: /home/nws747/seamount/Inc
Resolution, Grid 01: 0049x0048x013, Parallel Nodes: 1, Tiling: 001x001
Physical Parameters, Grid: 01
=============================
259200 ntimes Number of timesteps for 3-D equations.
60.000 dt Timestep size (s) for 3-D equations.
20 ndtfast Number of timesteps for 2-D equations between
each 3D timestep.
1 ERstr Starting ensemble/perturbation run number.
1 ERend Ending ensemble/perturbation run number.
0 nrrec Number of restart records to read from disk.
T LcycleRST Switch to recycle time-records in restart file.
14400 nRST Number of timesteps between the writing of data
into restart fields.
1 ninfo Number of timesteps between print of information
to standard output.
T ldefout Switch to create a new output NetCDF file(s).
1440 nHIS Number of timesteps between the writing fields
into history file.
0.0000E+00 nl_tnu2(01) NLM Horizontal, harmonic mixing coefficient
(m2/s) for tracer 01: temp
0.0000E+00 nl_tnu2(02) NLM Horizontal, harmonic mixing coefficient
(m2/s) for tracer 02: dye_01
0.0000E+00 nl_visc2 NLM Horizontal, harmonic mixing coefficient
(m2/s) for momentum.
F LuvSponge Turning OFF sponge on horizontal momentum.
F LtracerSponge(01) Turning OFF sponge on tracer 01: temp
F LtracerSponge(02) Turning OFF sponge on tracer 02: dye_01
1.0000E-06 Akt_bak(01) Background vertical mixing coefficient (m2/s)
for tracer 01: temp
1.0000E-06 Akt_bak(02) Background vertical mixing coefficient (m2/s)
for tracer 02: dye_01
1.0000E-05 Akv_bak Background vertical mixing coefficient (m2/s)
for momentum.
3.0000E-04 rdrg Linear bottom drag coefficient (m/s).
3.0000E-03 rdrg2 Quadratic bottom drag coefficient.
2.0000E-02 Zob Bottom roughness (m).
2 Vtransform S-coordinate transformation equation.
4 Vstretching S-coordinate stretching function.
6.5000E+00 theta_s S-coordinate surface control parameter.
2.0000E+00 theta_b S-coordinate bottom control parameter.
100.000 Tcline S-coordinate surface/bottom layer width (m) used
in vertical coordinate stretching.
1025.000 rho0 Mean density (kg/m3) for Boussinesq approximation.
0.000 dstart Time-stamp assigned to model initialization (days).
0.00 time_ref Reference time for units attribute (yyyymmdd.dd)
0.0000E+00 Tnudg(01) Nudging/relaxation time scale (days)
for tracer 01: temp
0.0000E+00 Tnudg(02) Nudging/relaxation time scale (days)
for tracer 02: dye_01
0.0000E+00 Znudg Nudging/relaxation time scale (days)
for free-surface.
0.0000E+00 M2nudg Nudging/relaxation time scale (days)
for 2D momentum.
0.0000E+00 M3nudg Nudging/relaxation time scale (days)
for 3D momentum.
0.0000E+00 obcfac Factor between passive and active
open boundary conditions.
F VolCons(1) NLM western edge boundary volume conservation.
F VolCons(2) NLM southern edge boundary volume conservation.
F VolCons(3) NLM eastern edge boundary volume conservation.
F VolCons(4) NLM northern edge boundary volume conservation.
10.000 T0 Background potential temperature (C) constant.
32.000 S0 Background salinity (PSU) constant.
1027.000 R0 Background density (kg/m3) used in linear Equation
of State.
1.7000E-04 Tcoef Thermal expansion coefficient (1/Celsius).
7.6000E-04 Scoef Saline contraction coefficient (1/PSU).
-1.000 gamma2 Slipperiness variable: free-slip (1.0) or
no-slip (-1.0).
F LuvSrc Turning OFF momentum point Sources/Sinks.
F LwSrc Turning OFF volume influx point Sources/Sinks.
F LtracerSrc(01) Turning OFF point Sources/Sinks on tracer 01: temp
F LtracerSrc(02) Turning OFF point Sources/Sinks on tracer 02: dye_01
F LsshCLM Turning OFF processing of SSH climatology.
F Lm2CLM Turning OFF processing of 2D momentum climatology.
F Lm3CLM Turning OFF processing of 3D momentum climatology.
F LtracerCLM(01) Turning OFF processing of climatology tracer 01: temp
F LtracerCLM(02) Turning OFF processing of climatology tracer 02: dye_01
F LnudgeM2CLM Turning OFF nudging of 2D momentum climatology.
F LnudgeM3CLM Turning OFF nudging of 3D momentum climatology.
F LnudgeTCLM(01) Turning OFF nudging of climatology tracer 01: temp
F LnudgeTCLM(02) Turning OFF nudging of climatology tracer 02: dye_01
T Hout(idFsur) Write out free-surface.
T Hout(idUbar) Write out 2D U-momentum component.
T Hout(idVbar) Write out 2D V-momentum component.
T Hout(idUvel) Write out 3D U-momentum component.
T Hout(idVvel) Write out 3D V-momentum component.
T Hout(idWvel) Write out W-momentum component.
T Hout(idOvel) Write out omega vertical velocity.
T Hout(idTvar) Write out tracer 01: temp
T Hout(inert) Write out inert passive tracer 01: dye_01
Output/Input Files:
Output Restart File: output/50passive_rst.nc
Output History File: output/50passive_his.nc
Tile partition information for Grid 01: 0049x0048x0013 tiling: 001x001
tile Istr Iend Jstr Jend Npts
0 1 49 1 48 30576
Tile minimum and maximum fractional coordinates for Grid 01:
(interior points only)
tile Xmin Xmax Ymin Ymax grid
0 0.50 49.50 0.50 48.50 RHO-points
0 1.00 49.00 0.50 48.50 U-points
0 0.50 49.50 1.00 48.00 V-points
Maximum halo size in XI and ETA directions:
HaloSizeI(1) = 186
HaloSizeJ(1) = 177
TileSide(1) = 56
TileSize(1) = 2968
Lateral Boundary Conditions: NLM
============================
Variable Grid West Edge South Edge East Edge North Edge
--------- ---- ---------- ---------- ---------- ----------
zeta 1 Chapman Imp Closed Chapman Imp Closed
ubar 1 Flather Closed Clamped Closed
vbar 1 Flather Closed Clamped Closed
u 1 Rad + Nud Closed Clamped Closed
v 1 Rad + Nud Closed Clamped Closed
temp 1 Periodic Closed Periodic Closed
dye_01 1 Periodic Closed Periodic Closed
Activated C-preprocessing Options:
SEAMOUNT Tall Isolated Seamount Test
ANA_BTFLUX Analytical kinematic bottom temperature flux.
ANA_DIAG Customized diagnostics.
ANA_FSOBC Analytical free-surface boundary conditions.
ANA_GRID Analytical grid set-up.
ANA_INITIAL Analytical initial conditions.
ANA_M2OBC Analytical 2D momentum boundary conditions.
ANA_M3OBC Analytical 3D momentum boundary conditions.
ANA_PASSIVE Analytical initial conditions for inert tracers.
ANA_SMFLUX Analytical kinematic surface momentum flux.
ANA_STFLUX Analytical kinematic surface temperature flux.
ASSUMED_SHAPE Using assumed-shape arrays.
DEBUGGING Internal debugging switch activated.
DJ_GRADPS Parabolic Splines density Jacobian (Shchepetkin, 2002).
DOUBLE_PRECISION Double precision arithmetic.
MIX_GEO_TS Mixing of tracers along geopotential surfaces.
MIX_S_UV Mixing of momentum along constant S-surfaces.
MPI MPI distributed-memory configuration.
NONLINEAR Nonlinear Model.
!NONLIN_EOS Linear Equation of State for seawater.
POWER_LAW Power-law shape time-averaging barotropic filter.
PROFILE Time profiling activated .
!RST_SINGLE Double precision fields in restart NetCDF file.
SOLVE3D Solving 3D Primitive Equations.
SPLINES_VDIFF Parabolic Spline Reconstruction for Vertical Diffusion.
SPLINES_VVISC Parabolic Spline Reconstruction for Vertical Viscosity.
T_PASSIVE Advecting and diffusing inert passive tracer.
TS_A4HADVECTION Fourth-order Akima horizontal advection of tracers.
TS_A4VADVECTION Fourth-order Akima vertical advection of tracers.
TS_DIF2 Harmonic mixing of tracers.
UV_ADV Advection of momentum.
UV_COR Coriolis term.
UV_U3HADVECTION Third-order upstream horizontal advection of 3D momentum.
UV_C4VADVECTION Fourth-order centered vertical advection of momentum.
UV_QDRAG Quadratic bottom stress.
UV_VIS2 Harmonic mixing of momentum.
VAR_RHO_2D Variable density barotropic mode.
Process Information:
Node # 0 (pid= 538) is active.
INITIAL: Configuring and initializing forward nonlinear model ...
*******
Vertical S-coordinate System, Grid 01:
level S-coord Cs-curve Z at hmin at hc half way at hmax
13 0.0000000 0.0000000 0.000 0.000 0.000 0.000
12 -0.0769231 -0.0008900 -5.656 -3.891 -5.822 -5.969
11 -0.1538462 -0.0037823 -11.670 -7.881 -12.047 -12.389
10 -0.2307692 -0.0093960 -18.171 -12.008 -18.822 -19.422
9 -0.3076923 -0.0191094 -25.405 -16.340 -26.425 -27.377
8 -0.3846154 -0.0352542 -33.790 -20.993 -35.325 -36.778
7 -0.4615385 -0.0615570 -43.992 -26.155 -46.276 -48.466
6 -0.5384615 -0.1036895 -57.026 -32.108 -60.421 -63.715
5 -0.6153846 -0.1697046 -74.332 -39.254 -79.387 -84.337
4 -0.6923077 -0.2696632 -97.710 -48.099 -105.203 -112.597
3 -0.7692308 -0.4128642 -128.824 -59.105 -139.747 -150.587
2 -0.8461538 -0.6002708 -167.845 -72.321 -183.213 -198.522
1 -0.9230769 -0.8118860 -211.198 -86.748 -231.564 -251.905
0 -1.0000000 -1.0000000 -250.346 -100.000 -275.173 -300.000
Time Splitting Weights for Grid 01: ndtfast = 20 nfast = 29
==================================
Primary Secondary Accumulated to Current Step
1-0.0009651193358779 0.0500000000000000-0.0009651193358779 0.0500000000000000
2-0.0013488780126037 0.0500482559667939-0.0023139973484816 0.1000482559667939
3-0.0011514592651644 0.0501156998674241-0.0034654566136460 0.1501639558342180
4-0.0003735756740661 0.0501732728306823-0.0038390322877122 0.2003372286649003
5 0.0009829200513762 0.0501919516143856-0.0028561122363360 0.2505291802792859
6 0.0029141799764308 0.0501428056118168 0.0000580677400949 0.3006719858911027
7 0.0054132615310267 0.0499970966129953 0.0054713292711215 0.3506690825040980
8 0.0084687837865133 0.0497264335364439 0.0139401130576348 0.4003955160405419
9 0.0120633394191050 0.0493029943471183 0.0260034524767398 0.4496985103876601
10 0.0161716623600090 0.0486998273761630 0.0421751148367488 0.4983983377638231
11 0.0207585511322367 0.0478912442581626 0.0629336659689855 0.5462895820219857
12 0.0257765478740990 0.0468533167015507 0.0887102138430846 0.5931428987235364
13 0.0311633730493853 0.0455644893078458 0.1198735868924699 0.6387073880313822
14 0.0368391158442262 0.0440063206553765 0.1567127027366961 0.6827137086867586
15 0.0427031802506397 0.0421643648631652 0.1994158829873358 0.7248780735499238
16 0.0486309868367616 0.0400292058506332 0.2480468698240974 0.7649072794005570
17 0.0544704302037592 0.0375976565087951 0.3025173000278565 0.8025049359093521
18 0.0600380921294286 0.0348741349986072 0.3625553921572851 0.8373790709079593
19 0.0651152103984763 0.0318722303921357 0.4276706025557614 0.8692513013000950
20 0.0694434033194839 0.0286164698722119 0.4971140058752453 0.8978677711723069
21 0.0727201499285570 0.0251442997062377 0.5698341558038023 0.9230120708785446
22 0.0745940258796570 0.0215082922098099 0.6444281816834592 0.9445203630883545
23 0.0746596950216179 0.0177785909158270 0.7190878767050771 0.9622989540041815
24 0.0724526566618460 0.0140456061647461 0.7915405333669231 0.9763445601689277
25 0.0674437485167025 0.0104229733316538 0.8589842818836255 0.9867675335005816
26 0.0590334053485720 0.0070507859058187 0.9180176872321975 0.9938183194064003
27 0.0465456732896125 0.0040991156383901 0.9645633605218099 0.9979174350447905
28 0.0292219798521905 0.0017718319739095 0.9937853403740003 0.9996892670187000
29 0.0062146596259993 0.0003107329813000 0.9999999999999997 1.0000000000000000
ndtfast, nfast = 20 29 nfast/ndtfast = 1.45000
Centers of gravity and integrals (values must be 1, 1, approx 1/2, 1, 1):
1.000000000000 1.060707743385 0.530353871693 1.000000000000 1.000000000000
Power filter parameters, Fgamma, gamma = 0.28400 0.14200
Metrics information for Grid 01:
===============================
Minimum X-grid spacing, DXmin = 6.53061224E+00 km
Maximum X-grid spacing, DXmax = 6.53061224E+00 km
Minimum Y-grid spacing, DYmin = 6.66666667E+00 km
Maximum Y-grid spacing, DYmax = 6.66666667E+00 km
Minimum Z-grid spacing, DZmin = 5.65588275E+00 m
Maximum Z-grid spacing, DZmax = 5.33826473E+01 m
Minimum barotropic Courant Number = 3.18680830E-02
Maximum barotropic Courant Number = 3.48856020E-02
Maximum Coriolis Courant Number = 6.00000000E-03
NETCDF_OPEN - unable to open existing NetCDF file:
ocean_frc.nc
call from: inquire.F
Elapsed CPU time (seconds):
Node # 0 CPU: 0.010
Total: 0.010
Nonlinear model elapsed time profile, Grid: 01
Allocation and array initialization .............. 0.006 (61.5515 %)
2D/3D coupling, vertical metrics ................. 0.001 ( 7.3591 %)
Equation of state for seawater ................... 0.000 ( 3.6845 %)
Total: 0.007 72.5951
Nonlinear model message Passage profile, Grid: 01
Message Passage: 2D halo exchanges ............... 0.000 ( 0.8962 %)
Message Passage: data reduction .................. 0.000 ( 0.0896 %)
Total: 0.000 0.9859
All percentages are with respect to total time = 0.010
ROMS/TOMS - Output NetCDF summary for Grid 01:
Analytical header files used:
/home/nws747/seamount/Inc/ana_grid.h
/home/nws747/seamount/Inc/ana_initial.h
/home/nws747/seamount/Inc/ana_passive.h
ROMS/TOMS - Output error ............ exit_flag: 3
ERROR: Abnormal termination: NetCDF OUTPUT.
REASON: No such file or directory
I can't find any reason for this - is it a known issue? Or does anyone have a suggestion for what might be wrong?
