NESTING GRID blow up first step NaN problem

[flcastej]

Dear all,

Finally I have been able to prepare all the needed files for my nesting aplication, a very simple case, a coarse grid and one refined grid. I have used coarse2fine to generate the refined grid and contact.m to get the contact file. I have been able to compile the model and I am able to run the model. But.... we get a blow up at the first time step. I have tried different things in order to detect the problem.

1.) Use different time steps.
2.) Prepare new refined grids with different refined factor.
3.) Put the bathymetry homogeneus in all the domain.
4.) Place the refined grid far from the land mask.
5.) Check my initials files and forcing to be sure that I dont have NaN values on it.
6.) Check the *.rst files, but I couldn´t see nothing strange.
7.) In all the test done with different grid, the blow up always happen on the top-right corner of the refined grid.

But I always get the same error and I don´t know what to do more. Attached you will find my configuration files. I will be really grateful if someone could help me or give any clue.

Model output

Model Input Parameters: ROMS/TOMS version 3.7
Monday - August 10, 2015 - 8:35:45 PM
-----------------------------------------------------------------------------

Mar Menor, Julio 2015

Operating system : Linux
CPU/hardware : x86_64
Compiler system : gfortran-4.7
Compiler command : /usr/bin/gfortran-4.7
Compiler flags : -frepack-arrays -O3 -ffast-math -ffree-form -ffree-line-length-none -ffree-form -ffree-line-length-none -ffree-form -ffree-line-length-none

SVN Root URL : https://www.myroms.org/svn/src/trunk
SVN Revision : 772M

Local Root : /home/trabajo/modelos/ROMS
Header Dir : /home/trabajo/modelos/ROMS/real_cases/marmenor/anidamiento/marmenor_marmenor
Header file : marmenor.h
Analytical Dir: /home/trabajo/modelos/ROMS/real_cases/marmenor/anidamiento/marmenor_marmenor

Resolution, Grid 01: 0332x0332x010, Parallel Threads: 1, Tiling: 001x001


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

300 ntimes Number of timesteps for 3-D equations.
30.000 dt Timestep size (s) for 3-D equations.
15 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.
1 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).
1 nHIS Number of timesteps between the writing fields
into history file.
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: salt
1.0000E-05 Akt_bak(01) Background vertical mixing coefficient (m2/s)
for tracer 01: temp
1.0000E-05 Akt_bak(02) Background vertical mixing coefficient (m2/s)
for tracer 02: salt
1.0000E-02 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.
0.0000E+00 Zob Bottom roughness (m).
1 Vtransform S-coordinate transformation equation.
1 Vstretching S-coordinate stretching function.
1.0000E-01 theta_s S-coordinate surface control parameter.
1.0000E-01 theta_b S-coordinate bottom control parameter.
0.100 Tcline S-coordinate surface/bottom layer width (m) used
in vertical coordinate stretching.
1026.000 rho0 Mean density (kg/m3) for Boussinesq approximation.
15749.000 dstart Time-stamp assigned to model initialization (days).
19680523.00 time_ref Reference time for units attribute (yyyymmdd.dd)
0.0000E+00 Tnudg(01) Nudging/relaxation time scale (days)
for tracer 01: temp
0.0000E+00 Tnudg(02) Nudging/relaxation time scale (days)
for tracer 02: salt
0.0000E+00 Znudg Nudging/relaxation time scale (days)
for free-surface.
0.0000E+00 M2nudg Nudging/relaxation time scale (days)
for 2D momentum.
0.0000E+00 M3nudg Nudging/relaxation time scale (days)
for 3D momentum.
0.0000E+00 obcfac Factor between passive and active
open boundary conditions.
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.
30.000 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: salt
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: salt
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: salt
T Hout(idFsur) Write out free-surface.
T Hout(idUbar) Write out 2D U-momentum component.
T Hout(idVbar) Write out 2D V-momentum component.
T Hout(idUvel) Write out 3D U-momentum component.
T Hout(idVvel) Write out 3D V-momentum component.
T Hout(idWvel) Write out W-momentum component.
T Hout(idOvel) Write out omega vertical velocity.
T Hout(idTvar) Write out tracer 01: temp
T Hout(idTvar) Write out tracer 02: salt
T Hout(idUsms) Write out surface U-momentum stress.
T Hout(idVsms) Write out surface V-momentum stress.
T Hout(idDano) Write out density anomaly.
T Hout(idVvis) Write out vertical viscosity: AKv.
T Hout(idTdif) Write out vertical diffusion: AKt(itemp).
T Hout(idSdif) Write out vertical diffusion: AKt(isalt).

Output/Input Files:

Output Restart File: OUTPUT/marmenor_rst.nc
Output History File: OUTPUT/marmenor_his.nc
Input Grid File: INPUT/marmenor_grd.nc
Nesting grid connectivity File: INPUT/contact_mm_enc.nc
Input Nonlinear Initial File: INPUT/marmenor_ini.nc
Input Forcing File 01: INPUT/marmenor_frz.nc

Resolution, Grid 02: 0105x0180x010, Parallel Threads: 1, Tiling: 001x001


Physical Parameters, Grid: 02
=============================

100 ntimes Number of timesteps for 3-D equations.
10.000 dt Timestep size (s) for 3-D equations.
15 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.
1 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).
1 nHIS Number of timesteps between the writing fields
into history file.
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: salt
1.0000E-05 Akt_bak(01) Background vertical mixing coefficient (m2/s)
for tracer 01: temp
1.0000E-05 Akt_bak(02) Background vertical mixing coefficient (m2/s)
for tracer 02: salt
1.0000E-02 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.
0.0000E+00 Zob Bottom roughness (m).
1 Vtransform S-coordinate transformation equation.
1 Vstretching S-coordinate stretching function.
1.0000E-01 theta_s S-coordinate surface control parameter.
1.0000E-01 theta_b S-coordinate bottom control parameter.
0.100 Tcline S-coordinate surface/bottom layer width (m) used
in vertical coordinate stretching.
1026.000 rho0 Mean density (kg/m3) for Boussinesq approximation.
15749.000 dstart Time-stamp assigned to model initialization (days).
19680523.00 time_ref Reference time for units attribute (yyyymmdd.dd)
0.0000E+00 Tnudg(01) Nudging/relaxation time scale (days)
for tracer 01: temp
0.0000E+00 Tnudg(02) Nudging/relaxation time scale (days)
for tracer 02: salt
0.0000E+00 Znudg Nudging/relaxation time scale (days)
for free-surface.
0.0000E+00 M2nudg Nudging/relaxation time scale (days)
for 2D momentum.
0.0000E+00 M3nudg Nudging/relaxation time scale (days)
for 3D momentum.
0.0000E+00 obcfac Factor between passive and active
open boundary conditions.
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.
30.000 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: salt
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: salt
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: salt
T Hout(idFsur) Write out free-surface.
T Hout(idUbar) Write out 2D U-momentum component.
T Hout(idVbar) Write out 2D V-momentum component.
T Hout(idUvel) Write out 3D U-momentum component.
T Hout(idVvel) Write out 3D V-momentum component.
T Hout(idWvel) Write out W-momentum component.
T Hout(idOvel) Write out omega vertical velocity.
T Hout(idTvar) Write out tracer 01: temp
T Hout(idTvar) Write out tracer 02: salt
T Hout(idUsms) Write out surface U-momentum stress.
T Hout(idVsms) Write out surface V-momentum stress.
T Hout(idDano) Write out density anomaly.
T Hout(idVvis) Write out vertical viscosity: AKv.
T Hout(idTdif) Write out vertical diffusion: AKt(itemp).
T Hout(idSdif) Write out vertical diffusion: AKt(isalt).

Output/Input Files:

Output Restart File: OUTPUT/marmenorHR_rst.nc
Output History File: OUTPUT/marmenorHR_his.nc
Input Grid File: INPUT/marmenorHR_grd.nc
Nesting grid connectivity File: INPUT/contact_mm_enc.nc
Input Nonlinear Initial File: INPUT/marmenorHR_ini.nc
Input Forcing File 01: INPUT/marmenorHR_frz.nc

Tile partition information for Grid 01: 0332x0332x0010 tiling: 001x001

tile Istr Iend Jstr Jend Npts

0 1 332 1 332 1102240

Tile partition information for Grid 02: 0105x0180x0010 tiling: 001x001

tile Istr Iend Jstr Jend Npts

0 1 105 1 180 189000

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

tile Xmin Xmax Ymin Ymax grid

0 0.50 333.50 0.50 333.50 RHO-points

0 0.00 333.00 0.50 333.50 U-points

0 0.50 333.50 0.00 333.00 V-points

Tile minimum and maximum fractional coordinates for Grid 02:
(interior points only)

tile Xmin Xmax Ymin Ymax grid

0 -2.50 107.50 -2.50 182.50 RHO-points

0 -3.00 107.00 -2.50 182.50 U-points

0 -2.50 107.50 -3.00 182.00 V-points

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

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

zeta 1 Closed Closed Closed Closed
2 Nested Nested Nested Nested

ubar 1 Closed Closed Closed Closed
2 Nested Nested Nested Nested

vbar 1 Closed Closed Closed Closed
2 Nested Nested Nested Nested

u 1 Closed Closed Closed Closed
2 Nested Nested Nested Nested

v 1 Closed Closed Closed Closed
2 Nested Nested Nested Nested

temp 1 Closed Closed Closed Closed
2 Nested Nested Nested Nested

salt 1 Closed Closed Closed Closed
2 Nested Nested Nested Nested

Activated C-preprocessing Options:

Marmenor Mar Menor, Julio 2015
ANA_BSFLUX Analytical kinematic bottom salinity flux.
ANA_BTFLUX Analytical kinematic bottom temperature flux.
ASSUMED_SHAPE Using assumed-shape arrays.
CURVGRID Orthogonal curvilinear grid.
DJ_GRADPS Parabolic Splines density Jacobian (Shchepetkin, 2002).
DOUBLE_PRECISION Double precision arithmetic.
MASKING Land/Sea masking.
MIX_S_UV Mixing of momentum along constant S-surfaces.
NESTING Nesting grids: Composite and Refinement.
NONLINEAR Nonlinear Model.
!NONLIN_EOS Linear Equation of State for seawater.
!ONE_WAY Two-way nesting in refinement grids.
POWER_LAW Power-law shape time-averaging barotropic filter.
PROFILE Time profiling activated .
!RST_SINGLE Double precision fields in restart NetCDF file.
SALINITY Using salinity.
SOLVE3D Solving 3D Primitive Equations.
TS_U3HADVECTION Third-order upstream horizontal advection of tracers.
TS_C4VADVECTION Fourth-order centered vertical advection 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:

Thread # 0 (pid= 18001) is active.
Thread # 0 (pid= 18001) 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

10 0.0000000 0.0000000 0.000 0.000 0.000 0.000
9 -0.1000000 -0.0998397 -0.050 -0.010 -2.203 -4.356
8 -0.2000000 -0.1996963 -0.100 -0.020 -4.407 -8.713
7 -0.3000000 -0.2995770 -0.150 -0.030 -6.611 -13.072
6 -0.4000000 -0.3994885 -0.200 -0.040 -8.815 -17.431
5 -0.5000000 -0.4994381 -0.250 -0.050 -11.021 -21.792
4 -0.6000000 -0.5994326 -0.300 -0.060 -13.227 -26.155
3 -0.7000000 -0.6994790 -0.350 -0.070 -15.435 -30.520
2 -0.8000000 -0.7995844 -0.400 -0.080 -17.644 -34.888
1 -0.9000000 -0.8997557 -0.450 -0.090 -19.855 -39.259
0 -1.0000000 -1.0000000 -0.500 -0.100 -22.067 -43.633

Vertical S-coordinate System, Grid 02:

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

10 0.0000000 0.0000000 0.000 0.000 0.000 0.000
9 -0.1000000 -0.0998397 -0.566 -0.010 -0.603 -0.639
8 -0.2000000 -0.1996963 -1.133 -0.020 -1.205 -1.278
7 -0.3000000 -0.2995770 -1.700 -0.030 -1.808 -1.917
6 -0.4000000 -0.3994885 -2.266 -0.040 -2.412 -2.557
5 -0.5000000 -0.4994381 -2.833 -0.050 -3.015 -3.196
4 -0.6000000 -0.5994326 -3.401 -0.060 -3.619 -3.836
3 -0.7000000 -0.6994790 -3.968 -0.070 -4.222 -4.477
2 -0.8000000 -0.7995844 -4.536 -0.080 -4.827 -5.117
1 -0.9000000 -0.8997557 -5.105 -0.090 -5.431 -5.758
0 -1.0000000 -1.0000000 -5.673 -0.100 -6.036 -6.400

Time Splitting Weights for Grid 01: ndtfast = 15 nfast = 22
==================================

Primary Secondary Accumulated to Current Step

1-0.0006740978872509 0.0666666666666667-0.0006740978872509 0.0666666666666667
2-0.0001913161153518 0.0667116065258167-0.0008654140026027 0.1333782731924834
3 0.0014472038369421 0.0667243609335069 0.0005817898343395 0.2001026341259903
4 0.0042370228855824 0.0666278806777107 0.0048188127199218 0.2667305148037010
5 0.0081665994120431 0.0663454124853385 0.0129854121319649 0.3330759272890396
6 0.0132119623624627 0.0658009725245357 0.0261973744944276 0.3988768998135752
7 0.0193298623751124 0.0649201750337048 0.0455272368695400 0.4637970748472801
8 0.0264494009361902 0.0636315175420307 0.0719766378057303 0.5274285923893107
9 0.0344621375639418 0.0618682241462847 0.1064387753696720 0.5892968165355954
10 0.0432106750211074 0.0595707483086885 0.1496494503907794 0.6488675648442840
11 0.0524757225556949 0.0566900366406147 0.2021251729464743 0.7055576014848987
12 0.0619616371700794 0.0531916551369017 0.2640868101165537 0.7587492566218004
13 0.0712804429184289 0.0490608793255631 0.3353672530349826 0.8078101359473635
14 0.0799343282324558 0.0443088497976678 0.4153015812674384 0.8521189857450313
15 0.0872966212754959 0.0389798945821708 0.5025982025429343 0.8910988803272021
16 0.0925912433249121 0.0331601198304711 0.5951894458678464 0.9242590001576731
17 0.0948706401828253 0.0269873702754769 0.6900600860506717 0.9512463704331501
18 0.0929921916151718 0.0206626609299552 0.7830522776658435 0.9719090313631054
19 0.0855930988190858 0.0144631814889438 0.8686453764849293 0.9863722128520491
20 0.0710637499186094 0.0087569749010047 0.9397091264035388 0.9951291877530538
21 0.0475195634887281 0.0040193915730974 0.9872286898922669 0.9991485793261512
22 0.0127713101077333 0.0008514206738489 1.0000000000000002 1.0000000000000000

ndtfast, nfast = 15 22 nfast/ndtfast = 1.46667

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

1.000000000000 1.070450639131 0.535225319565 1.000000000000 1.000000000000

Power filter parameters, Fgamma, gamma = 0.28400 0.09467

Time Splitting Weights for Grid 02: ndtfast = 15 nfast = 22
==================================

Primary Secondary Accumulated to Current Step

1-0.0006740978872509 0.0666666666666667-0.0006740978872509 0.0666666666666667
2-0.0001913161153518 0.0667116065258167-0.0008654140026027 0.1333782731924834
3 0.0014472038369421 0.0667243609335069 0.0005817898343395 0.2001026341259903
4 0.0042370228855824 0.0666278806777107 0.0048188127199218 0.2667305148037010
5 0.0081665994120431 0.0663454124853385 0.0129854121319649 0.3330759272890396
6 0.0132119623624627 0.0658009725245357 0.0261973744944276 0.3988768998135752
7 0.0193298623751124 0.0649201750337048 0.0455272368695400 0.4637970748472801
8 0.0264494009361902 0.0636315175420307 0.0719766378057303 0.5274285923893107
9 0.0344621375639418 0.0618682241462847 0.1064387753696720 0.5892968165355954
10 0.0432106750211074 0.0595707483086885 0.1496494503907794 0.6488675648442840
11 0.0524757225556949 0.0566900366406147 0.2021251729464743 0.7055576014848987
12 0.0619616371700794 0.0531916551369017 0.2640868101165537 0.7587492566218004
13 0.0712804429184289 0.0490608793255631 0.3353672530349826 0.8078101359473635
14 0.0799343282324558 0.0443088497976678 0.4153015812674384 0.8521189857450313
15 0.0872966212754959 0.0389798945821708 0.5025982025429343 0.8910988803272021
16 0.0925912433249121 0.0331601198304711 0.5951894458678464 0.9242590001576731
17 0.0948706401828253 0.0269873702754769 0.6900600860506717 0.9512463704331501
18 0.0929921916151718 0.0206626609299552 0.7830522776658435 0.9719090313631054
19 0.0855930988190858 0.0144631814889438 0.8686453764849293 0.9863722128520491
20 0.0710637499186094 0.0087569749010047 0.9397091264035388 0.9951291877530538
21 0.0475195634887281 0.0040193915730974 0.9872286898922669 0.9991485793261512
22 0.0127713101077333 0.0008514206738489 1.0000000000000002 1.0000000000000000

ndtfast, nfast = 15 22 nfast/ndtfast = 1.46667

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

1.000000000000 1.070450639131 0.535225319565 1.000000000000 1.000000000000

Power filter parameters, Fgamma, gamma = 0.28400 0.09467

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

Minimum X-grid spacing, DXmin = 5.13006381E-02 km
Maximum X-grid spacing, DXmax = 5.90138925E-02 km
Minimum Y-grid spacing, DYmin = 6.31138901E-02 km
Maximum Y-grid spacing, DYmax = 6.76060742E-02 km
Minimum Z-grid spacing, DZmin = 4.99358728E-02 m
Maximum Z-grid spacing, DZmax = 4.37394549E+00 m

Minimum barotropic Courant Number = 1.07019289E-01
Maximum barotropic Courant Number = 9.96831808E-01
Maximum Coriolis Courant Number = 2.68255786E-03


Metrics information for Grid 02:
===============================

Minimum X-grid spacing, DXmin = 1.73342850E-02 km
Maximum X-grid spacing, DXmax = 1.74328026E-02 km
Minimum Y-grid spacing, DYmin = 2.23989981E-02 km
Maximum Y-grid spacing, DYmax = 2.24492431E-02 km
Minimum Z-grid spacing, DZmin = 5.61013281E-01 m
Maximum Z-grid spacing, DZmax = 6.41510173E-01 m

Minimum barotropic Courant Number = 3.60408169E-01
Maximum barotropic Courant Number = 3.84596320E-01
Maximum Coriolis Courant Number = 8.92822667E-04


Refined Nested Grid(s) Information:
==================================

Refined Donor Refined Timestep Refined
Grid Grid Scale Ratio Timesteps

02 01 03 3.00000 03

WARNING: Usually the number of Refined Timesteps must be the same
as the Refined Scale for numerical stability.


NLM: GET_STATE - Read state initial conditions, t = 15749 00:00:00
(Grid 01, File: marmenor_ini.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 = 1.50000000E+01 Max = 1.50000000E+01)
- salinity
(Min = 3.70000000E+01 Max = 3.70000000E+01)

NLM: GET_STATE - Read state initial conditions, t = 15749 00:00:00
(Grid 02, File: marmenorHR_ini.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 = 1.50000000E+01 Max = 1.50000000E+01)
- salinity
(Min = 3.70000000E+01 Max = 3.70000000E+01)
GET_2DFLD - surface u-momentum stress, t = 15748 00:00:00
(Rec=0000001, Index=1, File: marmenor_frz.nc)
(Tmin= 15748.0000 Tmax= 15766.0000)
(Min = 0.00000000E+00 Max = 0.00000000E+00)
GET_2DFLD - surface v-momentum stress, t = 15748 00:00:00
(Rec=0000001, Index=1, File: marmenor_frz.nc)
(Tmin= 15748.0000 Tmax= 15766.0000)
(Min = 0.00000000E+00 Max = 0.00000000E+00)
GET_2DFLD - surface net heat flux, t = 15748 00:00:00
(Rec=0000001, Index=1, File: marmenor_frz.nc)
(Tmin= 15748.0000 Tmax= 15766.0000)
(Min = 0.00000000E+00 Max = 0.00000000E+00)
GET_2DFLD - surface net freswater flux, (E-P), t = 15748 00:00:00
(Rec=0000001, Index=1, File: marmenor_frz.nc)
(Tmin= 15748.0000 Tmax= 15766.0000)
(Min = 0.00000000E+00 Max = 0.00000000E+00)
GET_2DFLD - surface u-momentum stress, t = 15748 00:00:00
(Rec=0000001, Index=1, File: marmenorHR_frz.nc)
(Tmin= 15748.0000 Tmax= 15766.0000)
(Min = 0.00000000E+00 Max = 0.00000000E+00)
GET_2DFLD - surface v-momentum stress, t = 15748 00:00:00
(Rec=0000001, Index=1, File: marmenorHR_frz.nc)
(Tmin= 15748.0000 Tmax= 15766.0000)
(Min = 0.00000000E+00 Max = 0.00000000E+00)
GET_2DFLD - surface net heat flux, t = 15748 00:00:00
(Rec=0000001, Index=1, File: marmenorHR_frz.nc)
(Tmin= 15748.0000 Tmax= 15766.0000)
(Min = 0.00000000E+00 Max = 0.00000000E+00)
GET_2DFLD - surface net freswater flux, (E-P), t = 15748 00:00:00
(Rec=0000001, Index=1, File: marmenorHR_frz.nc)
(Tmin= 15748.0000 Tmax= 15766.0000)
(Min = 0.00000000E+00 Max = 0.00000000E+00)

Basin information for Grid 01:

Maximum grid stiffness ratios: rx0 = 9.458743E-01 (Beckmann and Haidvogel)
rx1 = 1.792598E+01 (Haney)

Initial basin volumes: TotVolume = 2.8554180914E+09 m3
MinVolume = 1.7297458432E+02 m3
MaxVolume = 1.5143647000E+04 m3
Max/Min = 8.7548393654E+01

Basin information for Grid 02:

Maximum grid stiffness ratios: rx0 = 1.883611E-03 (Beckmann and Haidvogel)
rx1 = 3.569831E-02 (Haney)

Initial basin volumes: TotVolume = 4.5499995884E+07 m3
MinVolume = 2.2132154882E+02 m3
MaxVolume = 2.5004607741E+02 m3
Max/Min = 1.1297864069E+00

NL ROMS/TOMS: started time-stepping: (Grid: 01 TimeSteps: 00000001 - 00000300)
NL ROMS/TOMS: started time-stepping: (Grid: 02 TimeSteps: 00000001 - 00000100)

GET_2DFLD - surface u-momentum stress, t = 15766 00:00:00
(Rec=0000002, Index=2, File: marmenor_frz.nc)
(Tmin= 15748.0000 Tmax= 15766.0000)
(Min = 0.00000000E+00 Max = 0.00000000E+00)
GET_2DFLD - surface v-momentum stress, t = 15766 00:00:00
(Rec=0000002, Index=2, File: marmenor_frz.nc)
(Tmin= 15748.0000 Tmax= 15766.0000)
(Min = 0.00000000E+00 Max = 0.00000000E+00)
GET_2DFLD - surface net heat flux, t = 15766 00:00:00
(Rec=0000002, Index=2, File: marmenor_frz.nc)
(Tmin= 15748.0000 Tmax= 15766.0000)
(Min = 0.00000000E+00 Max = 0.00000000E+00)
GET_2DFLD - surface net freswater flux, (E-P), t = 15766 00:00:00
(Rec=0000002, Index=2, File: marmenor_frz.nc)
(Tmin= 15748.0000 Tmax= 15766.0000)
(Min = 0.00000000E+00 Max = 0.00000000E+00)

STEP Day HH:MM:SS KINETIC_ENRG POTEN_ENRG TOTAL_ENRG NET_VOLUME Grid
C => (i,j,k) Cu Cv Cw Max Speed

0 15749 00:00:00 0.000000E+00 1.032857E+02 1.032857E+02 2.921251E+09 01
(000,000,00) 0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00
DEF_HIS - creating history file, Grid 01: OUTPUT/marmenor_his.nc
WRT_HIS - wrote history fields (Index=1,1) into time record = 0000001 01
GET_2DFLD - surface u-momentum stress, t = 15766 00:00:00
(Rec=0000002, Index=2, File: marmenorHR_frz.nc)
(Tmin= 15748.0000 Tmax= 15766.0000)
(Min = 0.00000000E+00 Max = 0.00000000E+00)
GET_2DFLD - surface v-momentum stress, t = 15766 00:00:00
(Rec=0000002, Index=2, File: marmenorHR_frz.nc)
(Tmin= 15748.0000 Tmax= 15766.0000)
(Min = 0.00000000E+00 Max = 0.00000000E+00)
GET_2DFLD - surface net heat flux, t = 15766 00:00:00
(Rec=0000002, Index=2, File: marmenorHR_frz.nc)
(Tmin= 15748.0000 Tmax= 15766.0000)
(Min = 0.00000000E+00 Max = 0.00000000E+00)
GET_2DFLD - surface net freswater flux, (E-P), t = 15766 00:00:00
(Rec=0000002, Index=2, File: marmenorHR_frz.nc)
(Tmin= 15748.0000 Tmax= 15766.0000)
(Min = 0.00000000E+00 Max = 0.00000000E+00)
0 15749 00:00:00 0.000000E+00 3.046833E+01 3.046833E+01 4.550000E+07 02
(000,000,00) 0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00
DEF_HIS - creating history file, Grid 02: OUTPUT/marmenorHR_his.nc
WRT_HIS - wrote history fields (Index=1,1) into time record = 0000001 02
1 15749 00:00:10 NaN NaN NaN NaN 02
(105,180,01) NaN NaN NaN 0.000000E+00

Blowing-up: Saving latest model state into RESTART file

WRT_RST - wrote re-start fields (Index=1,1) into time record = 0000001 01

Blowing-up: Saving latest model state into RESTART file

WRT_RST - wrote re-start fields (Index=1,2) into time record = 0000001 02

Elapsed CPU time (seconds):

Thread # 0 CPU: 2.772
Total: 2.772

Nonlinear model elapsed time profile:

Allocation and array initialization .............. 0.232 ( 8.3694 %)
Ocean state initialization ....................... 0.048 ( 1.7316 %)
Reading of input data ............................ 0.016 ( 0.5772 %)
Computation of global information integrals ...... 0.024 ( 0.8658 %)
Writing of output data ........................... 0.340 (12.2655 %)
Model 2D kernel .................................. 0.788 (28.4271 %)
2D/3D coupling, vertical metrics ................. 0.040 ( 1.4430 %)
Omega vertical velocity .......................... 0.020 ( 0.7215 %)
Equation of state for seawater ................... 0.020 ( 0.7215 %)
3D equations right-side terms .................... 0.076 ( 2.7417 %)
3D equations predictor step ...................... 0.092 ( 3.3189 %)
Pressure gradient ................................ 0.056 ( 2.0202 %)
Harmonic stress tensor, S-surfaces ............... 0.044 ( 1.5873 %)
Corrector time-step for 3D momentum .............. 0.076 ( 2.7417 %)
Corrector time-step for tracers .................. 0.080 ( 2.8860 %)
Total: 1.952 70.4185

All percentages are with respect to total time = 2.772
Thread # 0 CPU: 2.772
Total: 2.772

Nonlinear model elapsed time profile:

Allocation and array initialization .............. 0.232 ( 8.3694 %)
Ocean state initialization ....................... 0.036 ( 1.2987 %)
Reading of input data ............................ 0.004 ( 0.1443 %)
Computation of global information integrals ...... 0.036 ( 1.2987 %)
Writing of output data ........................... 0.060 ( 2.1645 %)
Model 2D kernel .................................. 0.132 ( 4.7619 %)
2D/3D coupling, vertical metrics ................. 0.008 ( 0.2886 %)
Omega vertical velocity .......................... 0.004 ( 0.1443 %)
Equation of state for seawater ................... 0.012 ( 0.4329 %)
3D equations right-side terms .................... 0.016 ( 0.5772 %)
3D equations predictor step ...................... 0.020 ( 0.7215 %)
Pressure gradient ................................ 0.008 ( 0.2886 %)
Harmonic stress tensor, S-surfaces ............... 0.004 ( 0.1443 %)
Corrector time-step for 3D momentum .............. 0.012 ( 0.4329 %)
Corrector time-step for tracers .................. 0.016 ( 0.5772 %)
Total: 0.600 21.6450

All percentages are with respect to total time = 2.772

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

ROMS/TOMS - Output NetCDF summary for Grid 02:
number of time records written in HISTORY file = 00000001
number of time records written in RESTART file = 00000001

Analytical header files used:

ROMS/Functionals/ana_btflux.h

ROMS/TOMS: DONE... Monday - August 10, 2015 - 8:35:47 PM

Thanks a lot in advance.

-Francisco

[kate]

Getting a NaN that early in the run is probably something like a configuration problem, not a timestepping instability. Before everything was IEEE floating point standards, a job would die at the first divide by zero. That's what you want it to do now - check your compiler options for such a thing and recompile with that flag. Something about a floating point trap. You probably want to compile with USE_DEBUG on and ask for bounds checking and so forth. Then if you can get it to die, it might give you useful info about which file, which line caused the problem.

[flcastej]

Dear Kate,

THANKS !!! a lot for your answer. I am going to start to follow your instruction and I will inform about the results obtained.

-Francisco

[flcastej]

Dear Kate,

You were right, after some test, set the debugging mode, activate the floating point for gfortran and set the initial conditions analytical, finally has been able to detect the problem, although I haven´t been able to resolve it. The results obtained in my test point out to the NDTFAST as the responsable of the problem, changes in his value give different results but always with an error.

I will keep on trying to resolve it but if anybody have any idea, it will be really welcome.

The error:


Program received signal SIGFPE: Floating-point exception - erroneous arithmetic operation.

Backtrace for this error:
#0 0x2ACD2BB0F667
#1 0x2ACD2BB0FC34
#2 0x2ACD2C50A1DF
#3 0x659C46 in __step2d_mod_MOD_step2d_tile at step2d.f90:457
#4 0x68C160 in __step2d_mod_MOD_step2d at step2d.f90:101
#5 0x4D4B81 in main3d_ at main3d.f90:335
#6 0x403B21 in __ocean_control_mod_MOD_roms_run at ocean_control.f90:160
#7 0x403134 in ocean at master.f90:86
Excepción de coma flotant

[wilkin]

Have you run the parent grid stand-alone without nesting to check that the basic set-up is stable? That's a basic sanity check on configuration.

Beyond that, a few things I notice in your list of CPP options and the logfile...

You have #defined UV_VIS2 but have the parameter nl_visc2=0 in both grids. So there is no explicit horizontal viscosity applied to help smooth things out. But this should only be a problem later once the run starts.

I don't see an option defined to activate vertical mixing / turbulence closure. I'm not sure what ROMS defaults to in that case, but it may be that the vertical divergence of the horizontal momentum flux (surface stress) goes entirely into the first s-coordinate level.

In that regard, your choice of theta_s, theta_b values in the s-coord stretching leads to a very thin surface layer (0.5 cm) at your minimum depth. See the info in the logfile under ...

Vertical S-coordinate System, Grid 01:
level S-coord Cs-curve Z at hmin at hc half way at hmax

(Also, read the notes in ocean.in about Vtransform and Vstretching. We encourage different choices there).

[flcastej]

Dear John,

First of all, thanks a lot for your help. I really appreciate it a lot.

I tested the parent and the grid alone, and they run without problems.

Although I tried different values of theta_s, theta_b.. without any advance, today I have tried it again. Reviewing the value in the logfile and I realized of something strange. The model read properly theta_b,theta_s, but I always get the same value for S-coord, Cs-curve,... For example

Configuration 1 (an extreme one)

THETA_S == 2*0.0d0 ! surface stretching parameter
THETA_B == 2*0.0d0 ! bottom stretching parameter
TCLINE == 2*0.0d0 ! critical depth (m)

Getting:

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

10 0.0000000 0.0000000 0.000 0.000 0.000 0.000
9 -0.1000000 -0.1000000 -0.050 -0.000 -2.207 -4.363
8 -0.2000000 -0.2000000 -0.100 -0.000 -4.413 -8.727
7 -0.3000000 -0.3000000 -0.150 -0.000 -6.620 -13.090
6 -0.4000000 -0.4000000 -0.200 -0.000 -8.827 -17.453
5 -0.5000000 -0.5000000 -0.250 -0.000 -11.033 -21.817
4 -0.6000000 -0.6000000 -0.300 -0.000 -13.240 -26.180
3 -0.7000000 -0.7000000 -0.350 -0.000 -15.447 -30.543
2 -0.8000000 -0.8000000 -0.400 -0.000 -17.653 -34.906
1 -0.9000000 -0.9000000 -0.450 -0.000 -19.860 -39.270
0 -1.0000000 -1.0000000 -0.500 -0.000 -22.067 -43.633

Vertical S-coordinate System, Grid 02:

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

10 0.0000000 0.0000000 0.000 0.000 0.000 0.000
9 -0.1000000 -0.1000000 -0.567 -0.000 -0.604 -0.640
8 -0.2000000 -0.2000000 -1.135 -0.000 -1.207 -1.280
7 -0.3000000 -0.3000000 -1.702 -0.000 -1.811 -1.920
6 -0.4000000 -0.4000000 -2.269 -0.000 -2.415 -2.560
5 -0.5000000 -0.5000000 -2.837 -0.000 -3.018 -3.200
4 -0.6000000 -0.6000000 -3.404 -0.000 -3.622 -3.840
3 -0.7000000 -0.7000000 -3.971 -0.000 -4.226 -4.480
2 -0.8000000 -0.8000000 -4.539 -0.000 -4.829 -5.120
1 -0.9000000 -0.9000000 -5.106 -0.000 -5.433 -5.760
0 -1.0000000 -1.0000000 -5.673 -0.000 -6.036 -6.400


Configuration 2 (a more realistic one)

Vtransform == 2*1 ! transformation equation
Vstretching == 2*1 ! stretching function

! Vertical S-coordinates parameters (see below for details), [1:Ngrids].

THETA_S == 2*7.0d0 ! surface stretching parameter
THETA_B == 2*0.4d0 ! bottom stretching parameter
TCLINE == 2*2.0d0

The model read it properly:

1 Vtransform S-coordinate transformation equation.
1 Vstretching S-coordinate stretching function.
7.0000E+00 theta_s S-coordinate surface control parameter.
4.0000E-01 theta_b S-coordinate bottom control parameter.
2.000 Tcline S-coordinate surface/bottom layer width (m) used

But again, I get:

Vertical S-coordinate System, Grid 01:

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

10 0.0000000 -0.0000000 0.000 0.000 -0.000 -0.000
9 -0.1000000 -0.0019414 -0.050 -0.050 -0.092 -0.134
8 -0.2000000 -0.0076391 -0.100 -0.100 -0.265 -0.429
7 -0.3000000 -0.0270074 -0.150 -0.150 -0.732 -1.315
6 -0.4000000 -0.0878699 -0.200 -0.200 -2.095 -3.990
5 -0.5000000 -0.2181019 -0.250 -0.250 -4.954 -9.657
4 -0.6000000 -0.3575721 -0.300 -0.300 -8.012 -15.723
3 -0.7000000 -0.4508634 -0.350 -0.350 -10.074 -19.797
2 -0.8000000 -0.5424010 -0.400 -0.400 -12.098 -23.795
1 -0.9000000 -0.6968391 -0.450 -0.450 -15.478 -30.507
0 -1.0000000 -1.0000000 -0.500 -0.500 -22.067 -43.633

Vertical S-coordinate System, Grid 02:

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

10 0.0000000 -0.0000000 -0.000 0.000 -0.000 -0.000
9 -0.1000000 -0.0019414 -0.207 -0.200 -0.208 -0.209
8 -0.2000000 -0.0076391 -0.428 -0.400 -0.431 -0.434
7 -0.3000000 -0.0270074 -0.699 -0.600 -0.709 -0.719
6 -0.4000000 -0.0878699 -1.123 -0.800 -1.155 -1.187
5 -0.5000000 -0.2181019 -1.801 -1.000 -1.880 -1.960
4 -0.6000000 -0.3575721 -2.513 -1.200 -2.643 -2.773
3 -0.7000000 -0.4508634 -3.056 -1.400 -3.220 -3.384
2 -0.8000000 -0.5424010 -3.592 -1.600 -3.789 -3.986
1 -0.9000000 -0.6968391 -4.360 -1.800 -4.613 -4.866
0 -1.0000000 -1.0000000 -5.673 -2.000 -6.036 -6.400


Do you have any idea about what is it happening?.

Thanks a lot John.

[wilkin]

After reading initial conditions for grid 2 ...

NLM: GET_STATE - Read state initial conditions, t = 15749 00:00:00
(Grid 02, File: marmenorHR_ini.nc, Rec=0001, Index=1)

ROMS goes on to read forcing data for both grids for t = 15749.

But if you look immediately prior to the report in your logfile of:

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

you'll see ROMS reads forcing data from marmenor_frz.nc for t = 15766 00:00:00 but not from marmenorHR_frz.nc.

You didn't declare the number of forcing files for grid 2, which you should. But the problem is probably embedding comment !Forcing Mar Menor in the FRCNAME list after the continuation character \ and before the next file name.

Change your ocean.in from:

NFFILES == 1 ! number of forcing files

FRCNAME == INPUT/marmenor_frz.nc \ !Forcing Mar Menor
INPUT/marmenorHR_frz.nc

to

NFFILES == 1 1 ! number of forcing files

FRCNAME == INPUT/marmenor_frz.nc \
INPUT/marmenorHR_frz.nc

[flcastej]

Dear John,

Thanks a lot for your help, every answer give me hopes to resolve this problem.

I did the changes proposed but I am still getting the error. In order to be sure that I don´t have any problem with my initial files or forcing files, I have defined them analytically, but without any improvement. Below you will find the error output and my *.h options.

I am really confused, cause as I explained in my last post, I always get the same value for S-coord using different values for theta_s,theta_b,... checking the log output I can see that the model read them properly but it has not affected to the s-coord calculation. In a extreme test I have removed the lines regarding THETA_S,THETA_B,.... from the *.in file and the model still use the same s-coord.

LOG OUTPUT


Model Input Parameters: ROMS/TOMS version 3.7
Thursday - August 13, 2015 - 5:42:45 PM
-----------------------------------------------------------------------------

Mar Menor, Julio 2015

Operating system : Linux
CPU/hardware : x86_64
Compiler system : gfortran-4.7
Compiler command : /usr/bin/gfortran-4.7
Compiler flags : -frepack-arrays -O3 -ffast-math -ffree-form -ffree-line-length-none -ffree-form -ffree-line-length-none -ffree-form -ffree-line-length-none

SVN Root URL : https://www.myroms.org/svn/src/trunk
SVN Revision : 772M

Local Root : /home/trabajo/modelos/ROMS
Header Dir : /home/trabajo/modelos/ROMS/real_cases/marmenor/anidamiento/marmenor_marmenor
Header file : marmenor.h
Analytical Dir: /home/trabajo/modelos/ROMS/real_cases/marmenor/anidamiento/marmenor_marmenor

Resolution, Grid 01: 0332x0332x010, Parallel Threads: 1, Tiling: 001x001


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

180 ntimes Number of timesteps for 3-D equations.
3.000 dt Timestep size (s) for 3-D equations.
10 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.
1 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).
1 nHIS Number of timesteps between the writing fields
into history file.
1 ntsAVG Starting timestep for the accumulation of output
time-averaged data.
864000 nAVG Number of timesteps between the writing of
time-averaged data into averages file.
1.0000E-03 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: salt
1.0000E-05 Akt_bak(01) Background vertical mixing coefficient (m2/s)
for tracer 01: temp
1.0000E-05 Akt_bak(02) Background vertical mixing coefficient (m2/s)
for tracer 02: salt
1.0000E-02 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.
0.000 charnok_alpha Charnok factor for Zos calculation.
0.000 zos_hsig_alpha Factor for Zos calculation using Hsig(Awave).
0.000 sz_alpha Factor for Wave dissipation surface tke flux .
0.000 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.
0.0000E+00 Zob Bottom roughness (m).
0.0000E+00 Zos Surface roughness (m).
1 Vtransform S-coordinate transformation equation.
1 Vstretching S-coordinate stretching function.
0.0000E+00 theta_s S-coordinate surface control parameter.
0.0000E+00 theta_b S-coordinate bottom control parameter.
0.000 Tcline S-coordinate surface/bottom layer width (m) used
in vertical coordinate stretching.
1026.000 rho0 Mean density (kg/m3) for Boussinesq approximation.
15749.000 dstart Time-stamp assigned to model initialization (days).
19680523.00 time_ref Reference time for units attribute (yyyymmdd.dd)
0.0000E+00 Tnudg(01) Nudging/relaxation time scale (days)
for tracer 01: temp
0.0000E+00 Tnudg(02) Nudging/relaxation time scale (days)
for tracer 02: salt
0.0000E+00 Znudg Nudging/relaxation time scale (days)
for free-surface.
0.0000E+00 M2nudg Nudging/relaxation time scale (days)
for 2D momentum.
0.0000E+00 M3nudg Nudging/relaxation time scale (days)
for 3D momentum.
0.0000E+00 obcfac Factor between passive and active
open boundary conditions.
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.
17.000 T0 Background potential temperature (C) constant.
37.000 S0 Background salinity (PSU) constant.
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: salt
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: salt
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: salt
T Hout(idFsur) Write out free-surface.
T Hout(idUbar) Write out 2D U-momentum component.
T Hout(idVbar) Write out 2D V-momentum component.
T Hout(idUvel) Write out 3D U-momentum component.
T Hout(idVvel) Write out 3D V-momentum component.
T Hout(idWvel) Write out W-momentum component.
T Hout(idOvel) Write out omega vertical velocity.
T Hout(idTvar) Write out tracer 01: temp
T Hout(idTvar) Write out tracer 02: salt
T Hout(idUsms) Write out surface U-momentum stress.
T Hout(idVsms) Write out surface V-momentum stress.
T Hout(idDano) Write out density anomaly.
T Hout(idVvis) Write out vertical viscosity: AKv.
T Hout(idTdif) Write out vertical diffusion: AKt(itemp).
T Hout(idSdif) Write out vertical diffusion: AKt(isalt).
T Hout(idMtke) Write out turbulent kinetic energy.
T Hout(idMtls) Write out turbulent generic length-scale.

T Aout(idFsur) Write out averaged free-surface.
T Aout(idUbar) Write out averaged 2D U-momentum component.
T Aout(idVbar) Write out averaged 2D V-momentum component.
T Aout(idUvel) Write out averaged 3D U-momentum component.
T Aout(idVvel) Write out averaged 3D V-momentum component.
T Aout(idWvel) Write out averaged W-momentum component.
T Aout(idOvel) Write out averaged omega vertical velocity.
T Aout(idTvar) Write out averaged tracer 01: temp
T Aout(idTvar) Write out averaged tracer 02: salt

Output/Input Files:

Output Restart File: OUTPUT/marmenor_rst.nc
Output History File: OUTPUT/marmenor_his.nc
Output Averages File: OUTPUT/marmenor_avg.nc
Input Grid File: INPUT/marmenor_grd.nc
Nesting grid connectivity File: INPUT/contact_mm_enc.nc

Resolution, Grid 02: 0105x0180x010, Parallel Threads: 1, Tiling: 001x001


Physical Parameters, Grid: 02
=============================

540 ntimes Number of timesteps for 3-D equations.
1.000 dt Timestep size (s) for 3-D equations.
10 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.
1 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).
1 nHIS Number of timesteps between the writing fields
into history file.
1 ntsAVG Starting timestep for the accumulation of output
time-averaged data.
864000 nAVG Number of timesteps between the writing of
time-averaged data into averages file.
1.0000E-03 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: salt
1.0000E-05 Akt_bak(01) Background vertical mixing coefficient (m2/s)
for tracer 01: temp
1.0000E-05 Akt_bak(02) Background vertical mixing coefficient (m2/s)
for tracer 02: salt
1.0000E-02 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.
0.000 charnok_alpha Charnok factor for Zos calculation.
0.000 zos_hsig_alpha Factor for Zos calculation using Hsig(Awave).
0.000 sz_alpha Factor for Wave dissipation surface tke flux .
0.000 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.
0.0000E+00 Zob Bottom roughness (m).
1.0000E-02 Zos Surface roughness (m).
1 Vtransform S-coordinate transformation equation.
1 Vstretching S-coordinate stretching function.
0.0000E+00 theta_s S-coordinate surface control parameter.
0.0000E+00 theta_b S-coordinate bottom control parameter.
0.000 Tcline S-coordinate surface/bottom layer width (m) used
in vertical coordinate stretching.
1026.000 rho0 Mean density (kg/m3) for Boussinesq approximation.
15749.000 dstart Time-stamp assigned to model initialization (days).
19680523.00 time_ref Reference time for units attribute (yyyymmdd.dd)
0.0000E+00 Tnudg(01) Nudging/relaxation time scale (days)
for tracer 01: temp
0.0000E+00 Tnudg(02) Nudging/relaxation time scale (days)
for tracer 02: salt
0.0000E+00 Znudg Nudging/relaxation time scale (days)
for free-surface.
0.0000E+00 M2nudg Nudging/relaxation time scale (days)
for 2D momentum.
0.0000E+00 M3nudg Nudging/relaxation time scale (days)
for 3D momentum.
0.0000E+00 obcfac Factor between passive and active
open boundary conditions.
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.
17.000 T0 Background potential temperature (C) constant.
37.000 S0 Background salinity (PSU) constant.
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: salt
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: salt
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: salt
T Hout(idFsur) Write out free-surface.
T Hout(idUbar) Write out 2D U-momentum component.
T Hout(idVbar) Write out 2D V-momentum component.
T Hout(idUvel) Write out 3D U-momentum component.
T Hout(idVvel) Write out 3D V-momentum component.
T Hout(idWvel) Write out W-momentum component.
T Hout(idOvel) Write out omega vertical velocity.
T Hout(idTvar) Write out tracer 01: temp
T Hout(idTvar) Write out tracer 02: salt
T Hout(idUsms) Write out surface U-momentum stress.
T Hout(idVsms) Write out surface V-momentum stress.
T Hout(idDano) Write out density anomaly.
T Hout(idVvis) Write out vertical viscosity: AKv.
T Hout(idTdif) Write out vertical diffusion: AKt(itemp).
T Hout(idSdif) Write out vertical diffusion: AKt(isalt).
T Hout(idMtke) Write out turbulent kinetic energy.
T Hout(idMtls) Write out turbulent generic length-scale.

T Aout(idFsur) Write out averaged free-surface.
T Aout(idUbar) Write out averaged 2D U-momentum component.
T Aout(idVbar) Write out averaged 2D V-momentum component.
T Aout(idUvel) Write out averaged 3D U-momentum component.
T Aout(idVvel) Write out averaged 3D V-momentum component.
T Aout(idWvel) Write out averaged W-momentum component.
T Aout(idOvel) Write out averaged omega vertical velocity.
T Aout(idTvar) Write out averaged tracer 01: temp
T Aout(idTvar) Write out averaged tracer 02: salt

Output/Input Files:

Output Restart File: OUTPUT/marmenorHR_rst.nc
Output History File: OUTPUT/marmenorHR_his.nc
Output Averages File: OUTPUT/marmenorHR_avg.nc
Input Grid File: INPUT/marmenorHR_grd.nc
Nesting grid connectivity File: INPUT/contact_mm_enc.nc

Tile partition information for Grid 01: 0332x0332x0010 tiling: 001x001

tile Istr Iend Jstr Jend Npts

0 1 332 1 332 1102240

Tile partition information for Grid 02: 0105x0180x0010 tiling: 001x001

tile Istr Iend Jstr Jend Npts

0 1 105 1 180 189000

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

tile Xmin Xmax Ymin Ymax grid

0 0.50 333.50 0.50 333.50 RHO-points

0 0.00 333.00 0.50 333.50 U-points

0 0.50 333.50 0.00 333.00 V-points

Tile minimum and maximum fractional coordinates for Grid 02:
(interior points only)

tile Xmin Xmax Ymin Ymax grid

0 -2.50 107.50 -2.50 182.50 RHO-points

0 -3.00 107.00 -2.50 182.50 U-points

0 -2.50 107.50 -3.00 182.00 V-points

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

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

zeta 1 Closed Closed Closed Closed
2 Nested Nested Nested Nested

ubar 1 Closed Closed Closed Closed
2 Nested Nested Nested Nested

vbar 1 Closed Closed Closed Closed
2 Nested Nested Nested Nested

u 1 Closed Closed Closed Closed
2 Nested Nested Nested Nested

v 1 Closed Closed Closed Closed
2 Nested Nested Nested Nested

temp 1 Closed Closed Closed Closed
2 Nested Nested Nested Nested

salt 1 Closed Closed Closed Closed
2 Nested Nested Nested Nested

tke 1 Closed Closed Closed Closed
2 Nested Nested Nested Nested

Activated C-preprocessing Options:

Marmenor Mar Menor, Julio 2015
ANA_BSFLUX Analytical kinematic bottom salinity flux.
ANA_BTFLUX Analytical kinematic bottom temperature flux.
ANA_INITIAL Analytical initial conditions.
ANA_SMFLUX Analytical kinematic surface momentum flux.
ANA_SSFLUX Analytical kinematic surface salinity flux.
ANA_STFLUX Analytical kinematic surface temperature flux.
ASSUMED_SHAPE Using assumed-shape arrays.
AVERAGES Writing out time-averaged nonlinear model fields.
CURVGRID Orthogonal curvilinear grid.
DJ_GRADPS Parabolic Splines density Jacobian (Shchepetkin, 2002).
DOUBLE_PRECISION Double precision arithmetic.
GLS_MIXING Generic Length-Scale turbulence closure.
MASKING Land/Sea masking.
MIX_S_UV Mixing of momentum along constant S-surfaces.
NESTING Nesting grids: Composite and Refinement.
NONLINEAR Nonlinear Model.
NONLIN_EOS Nonlinear Equation of State for seawater.
N2S2_HORAVG Horizontal smoothing of buoyancy and shear.
!ONE_WAY Two-way nesting in refinement grids.
POWER_LAW Power-law shape time-averaging barotropic filter.
PROFILE Time profiling activated .
K_GSCHEME Third-order upstream advection of TKE fields.
!RST_SINGLE Double precision fields in restart NetCDF file.
SALINITY Using salinity.
SOLVE3D Solving 3D Primitive Equations.
TS_U3HADVECTION Third-order upstream horizontal advection of tracers.
TS_C4VADVECTION Fourth-order centered vertical advection 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_LOGDRAG Logarithmic bottom stress.
UV_VIS2 Harmonic mixing of momentum.
VAR_RHO_2D Variable density barotropic mode.

Process Information:

Thread # 0 (pid= 30723) is active.
Thread # 0 (pid= 30723) 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

10 0.0000000 0.0000000 0.000 0.000 0.000 0.000
9 -0.1000000 -0.1000000 -0.050 -0.000 -2.207 -4.363
8 -0.2000000 -0.2000000 -0.100 -0.000 -4.413 -8.727
7 -0.3000000 -0.3000000 -0.150 -0.000 -6.620 -13.090
6 -0.4000000 -0.4000000 -0.200 -0.000 -8.827 -17.453
5 -0.5000000 -0.5000000 -0.250 -0.000 -11.033 -21.817
4 -0.6000000 -0.6000000 -0.300 -0.000 -13.240 -26.180
3 -0.7000000 -0.7000000 -0.350 -0.000 -15.447 -30.543
2 -0.8000000 -0.8000000 -0.400 -0.000 -17.653 -34.906
1 -0.9000000 -0.9000000 -0.450 -0.000 -19.860 -39.270
0 -1.0000000 -1.0000000 -0.500 -0.000 -22.067 -43.633

Vertical S-coordinate System, Grid 02:

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

10 0.0000000 0.0000000 0.000 0.000 0.000 0.000
9 -0.1000000 -0.1000000 -0.567 -0.000 -0.604 -0.640
8 -0.2000000 -0.2000000 -1.135 -0.000 -1.207 -1.280
7 -0.3000000 -0.3000000 -1.702 -0.000 -1.811 -1.920
6 -0.4000000 -0.4000000 -2.269 -0.000 -2.415 -2.560
5 -0.5000000 -0.5000000 -2.837 -0.000 -3.018 -3.200
4 -0.6000000 -0.6000000 -3.404 -0.000 -3.622 -3.840
3 -0.7000000 -0.7000000 -3.971 -0.000 -4.226 -4.480
2 -0.8000000 -0.8000000 -4.539 -0.000 -4.829 -5.120
1 -0.9000000 -0.9000000 -5.106 -0.000 -5.433 -5.760
0 -1.0000000 -1.0000000 -5.673 -0.000 -6.036 -6.400

Time Splitting Weights for Grid 01: ndtfast = 10 nfast = 15
==================================

Primary Secondary Accumulated to Current Step

1 0.0014850648765542 0.1000000000000000 0.0014850648765542 0.1000000000000000
2 0.0059386031399402 0.0998514935123446 0.0074236680164944 0.1998514935123445
3 0.0133457074936657 0.0992576331983506 0.0207693755101601 0.2991091267106951
4 0.0236484051180389 0.0979230624489840 0.0444177806281990 0.3970321891596791
5 0.0366959666818608 0.0955582219371801 0.0811137473100598 0.4925904110968592
6 0.0521753389587947 0.0918886252689940 0.1332890862688545 0.5844790363658532
7 0.0695217010484137 0.0866710913731145 0.2028107873172682 0.6711501277389678
8 0.0878091442019233 0.0797189212682732 0.2906199315191915 0.7508690490072409
9 0.1056214752525633 0.0709380068480808 0.3962414067717548 0.8218070558553218
10 0.1209031436506851 0.0603758593228245 0.5171445504224399 0.8821829151781463
11 0.1307902921035067 0.0482855449577560 0.6479348425259466 0.9304684601359023
12 0.1314219308195445 0.0352065157474053 0.7793567733454911 0.9656749758833076
13 0.1177312353577226 0.0220643226654509 0.8970880087032138 0.9877392985487585
14 0.0832169680811588 0.0102911991296786 0.9803049767843727 0.9980304976784371
15 0.0196950232156274 0.0019695023215627 1.0000000000000000 0.9999999999999999

ndtfast, nfast = 10 15 nfast/ndtfast = 1.50000

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

1.000000000000 1.083803072626 0.541901536313 1.000000000000 1.000000000000

Power filter parameters, Fgamma, gamma = 0.28400 0.00000

Time Splitting Weights for Grid 02: ndtfast = 10 nfast = 15
==================================

Primary Secondary Accumulated to Current Step

1 0.0014850648765542 0.1000000000000000 0.0014850648765542 0.1000000000000000
2 0.0059386031399402 0.0998514935123446 0.0074236680164944 0.1998514935123445
3 0.0133457074936657 0.0992576331983506 0.0207693755101601 0.2991091267106951
4 0.0236484051180389 0.0979230624489840 0.0444177806281990 0.3970321891596791
5 0.0366959666818608 0.0955582219371801 0.0811137473100598 0.4925904110968592
6 0.0521753389587947 0.0918886252689940 0.1332890862688545 0.5844790363658532
7 0.0695217010484137 0.0866710913731145 0.2028107873172682 0.6711501277389678
8 0.0878091442019233 0.0797189212682732 0.2906199315191915 0.7508690490072409
9 0.1056214752525633 0.0709380068480808 0.3962414067717548 0.8218070558553218
10 0.1209031436506851 0.0603758593228245 0.5171445504224399 0.8821829151781463
11 0.1307902921035067 0.0482855449577560 0.6479348425259466 0.9304684601359023
12 0.1314219308195445 0.0352065157474053 0.7793567733454911 0.9656749758833076
13 0.1177312353577226 0.0220643226654509 0.8970880087032138 0.9877392985487585
14 0.0832169680811588 0.0102911991296786 0.9803049767843727 0.9980304976784371
15 0.0196950232156274 0.0019695023215627 1.0000000000000000 0.9999999999999999

ndtfast, nfast = 10 15 nfast/ndtfast = 1.50000

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

1.000000000000 1.083803072626 0.541901536313 1.000000000000 1.000000000000

Power filter parameters, Fgamma, gamma = 0.28400 0.00000

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

Minimum X-grid spacing, DXmin = 5.13006381E-02 km
Maximum X-grid spacing, DXmax = 5.90138925E-02 km
Minimum Y-grid spacing, DYmin = 6.31138901E-02 km
Maximum Y-grid spacing, DYmax = 6.76060742E-02 km
Minimum Z-grid spacing, DZmin = 5.00000000E-02 m
Maximum Z-grid spacing, DZmax = 4.36330972E+00 m

Minimum barotropic Courant Number = 1.60528934E-02
Maximum barotropic Courant Number = 1.49524771E-01
Maximum Coriolis Courant Number = 2.68255786E-04


Metrics information for Grid 02:
===============================

Minimum X-grid spacing, DXmin = 1.73342850E-02 km
Maximum X-grid spacing, DXmax = 1.74328026E-02 km
Minimum Y-grid spacing, DYmin = 2.23989981E-02 km
Maximum Y-grid spacing, DYmax = 2.24492431E-02 km
Minimum Z-grid spacing, DZmin = 5.61898073E-01 m
Maximum Z-grid spacing, DZmax = 6.39971063E-01 m

Minimum barotropic Courant Number = 5.40612253E-02
Maximum barotropic Courant Number = 5.76894480E-02
Maximum Coriolis Courant Number = 8.92822667E-05


Refined Nested Grid(s) Information:
==================================

Refined Donor Refined Timestep Refined
Grid Grid Scale Ratio Timesteps

02 01 03 3.00000 03

WARNING: Usually the number of Refined Timesteps must be the same
as the Refined Scale for numerical stability.


Basin information for Grid 01:

Maximum grid stiffness ratios: rx0 = 9.458743E-01 (Beckmann and Haidvogel)
rx1 = 1.797161E+01 (Haney)

Initial basin volumes: TotVolume = 2.8554180914E+09 m3
MinVolume = 1.7319671673E+02 m3
MaxVolume = 1.5106824075E+04 m3
Max/Min = 8.7223501465E+01

Basin information for Grid 02:

Maximum grid stiffness ratios: rx0 = 1.883611E-03 (Beckmann and Haidvogel)
rx1 = 3.578860E-02 (Haney)

Initial basin volumes: TotVolume = 4.5499995884E+07 m3
MinVolume = 2.2167067957E+02 m3
MaxVolume = 2.4944616710E+02 m3
Max/Min = 1.1253006829E+00

NL ROMS/TOMS: started time-stepping: (Grid: 01 TimeSteps: 00000001 - 00000180)
NL ROMS/TOMS: started time-stepping: (Grid: 02 TimeSteps: 00000001 - 00000540)


STEP Day HH:MM:SS KINETIC_ENRG POTEN_ENRG TOTAL_ENRG NET_VOLUME Grid
C => (i,j,k) Cu Cv Cw Max Speed

0 15749 00:00:00 0.000000E+00 1.028344E+02 1.028344E+02 2.921251E+09 01
(000,000,00) 0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00
DEF_HIS - creating history file, Grid 01: OUTPUT/marmenor_his.nc
WRT_HIS - wrote history fields (Index=1,1) into time record = 0000001 01
0 15749 00:00:00 0.000000E+00 3.033419E+01 3.033419E+01 4.550000E+07 02
(000,000,00) 0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00
DEF_HIS - creating history file, Grid 02: OUTPUT/marmenorHR_his.nc
WRT_HIS - wrote history fields (Index=1,1) into time record = 0000001 02
1 15749 00:00:01 NaN NaN NaN NaN 02
(105,180,01) NaN NaN NaN 0.000000E+00

Blowing-up: Saving latest model state into RESTART file

WRT_RST - wrote re-start fields (Index=2,1) into time record = 0000001 01

Blowing-up: Saving latest model state into RESTART file

WRT_RST - wrote re-start fields (Index=2,2) into time record = 0000001 02

Elapsed CPU time (seconds):

Thread # 0 CPU: 3.772
Total: 3.772

Nonlinear model elapsed time profile:

Allocation and array initialization .............. 0.328 ( 8.6957 %)
Ocean state initialization ....................... 0.052 ( 1.3786 %)
Computation of vertical boundary conditions ...... 0.004 ( 0.1060 %)
Computation of global information integrals ...... 0.024 ( 0.6363 %)
Writing of output data ........................... 0.400 (10.6045 %)
Model 2D kernel .................................. 0.548 (14.5281 %)
2D/3D coupling, vertical metrics ................. 0.052 ( 1.3786 %)
Omega vertical velocity .......................... 0.012 ( 0.3181 %)
Equation of state for seawater ................... 0.080 ( 2.1209 %)
GLS vertical mixing parameterization ............. 0.840 (22.2693 %)
3D equations right-side terms .................... 0.076 ( 2.0148 %)
3D equations predictor step ...................... 0.088 ( 2.3330 %)
Pressure gradient ................................ 0.064 ( 1.6967 %)
Harmonic stress tensor, S-surfaces ............... 0.040 ( 1.0605 %)
Corrector time-step for 3D momentum .............. 0.080 ( 2.1209 %)
Corrector time-step for tracers .................. 0.084 ( 2.2270 %)
Total: 2.772 73.4889

All percentages are with respect to total time = 3.772
Thread # 0 CPU: 3.772
Total: 3.772

Nonlinear model elapsed time profile:

Allocation and array initialization .............. 0.328 ( 8.6957 %)
Ocean state initialization ....................... 0.040 ( 1.0605 %)
Computation of global information integrals ...... 0.032 ( 0.8484 %)
Writing of output data ........................... 0.068 ( 1.8028 %)
Model 2D kernel .................................. 0.084 ( 2.2269 %)
2D/3D coupling, vertical metrics ................. 0.012 ( 0.3181 %)
Omega vertical velocity .......................... 0.004 ( 0.1060 %)
Equation of state for seawater ................... 0.028 ( 0.7423 %)
GLS vertical mixing parameterization ............. 0.176 ( 4.6660 %)
3D equations right-side terms .................... 0.012 ( 0.3181 %)
3D equations predictor step ...................... 0.020 ( 0.5302 %)
Pressure gradient ................................ 0.012 ( 0.3181 %)
Harmonic stress tensor, S-surfaces ............... 0.004 ( 0.1060 %)
Corrector time-step for 3D momentum .............. 0.016 ( 0.4242 %)
Corrector time-step for tracers .................. 0.016 ( 0.4242 %)
Total: 0.852 22.5875

All percentages are with respect to total time = 3.772

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

ROMS/TOMS - Output NetCDF summary for Grid 02:
number of time records written in HISTORY file = 00000001
number of time records written in RESTART file = 00000001

Analytical header files used:

ROMS/Functionals/ana_btflux.h
ROMS/Functionals/ana_initial.h
ROMS/Functionals/ana_smflux.h
ROMS/Functionals/ana_stflux.h

ROMS/TOMS: DONE... Thursday - August 13, 2015 - 5:42:49 PM

[wilkin]

Looking over the logfile output you've showed you haven't tried theta_s more than 0.1, so it will have very little effect. Strictly speaking theta_s = 0 is invalid, but the limit theta_s -> 0 is OK. You get regular sigma coordinates. You need theta_s of 3 or more to really see any appreciable stretching in the deepest water. Read more at https://www.myroms.org/wiki/index.php/V ... coordinate

But vertical coordinate does not appear to be your problem unless you are incorrectly evaluating the z coordinate in creating your initial conditions and introducing a lot of initial potential energy in the stratification. My intuition is to suspect your grid or initial conditions. I assume you plotted up the initial conditions file you were using before to make sure it is dynamically sensible.

Your time steps are extremely small (1 s for the baroclinic mode and 0.1 s for the barotropic) yet the run is blowing up on the very first time step of the nested grid, so I think the initial conditions are not dynamically sensible or include NaNs.

As a rule, I would say NDTFAST = 10 is too small. Recommended values are 20 or greater. I don't know if that cold be a problem or not.

[flcastej]

Dear John,

I have tried different values for THETA_S, including values higher than 3.

In my last runs, I have defined my initial condition by ANA_INITIAL, so I am not using any initial condition files.

Trying different things I have used several values for DT and NDTFAST but I haven´t get any advance.

Thanks John!!!