Vertical mixing scheme in ROMS

Discussion of how to use ROMS on different regional and basin scale applications.

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susonic
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Vertical mixing scheme in ROMS

#1 Post by susonic » Mon Sep 21, 2009 9:35 pm

Hi, I'm trying to use GLS vertical mixing with k-epsilon.
First of all, I ran under Kantha clayson with k-epsilon. It ran until 9th model day
and blew up. Then I changed stability function to CANUTO_A. The model ran until 20th model day.
I also changed the viscosity value. But it didn't help me out to fix this problem.
I don't really know what the problem is. I'm trying to attach my log file. But I don't know
how to attach my file.

Regards,

-Peter
Resolution, Grid 01: 0147x0161x020, Parallel Nodes: 8, Tiling: 004x002


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

105120 ntimes Number of timesteps for 3-D equations.
300.000 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.
28800 nRST Number of timesteps between the writing of data
into restart fields.
1 ninfo Number of timesteps between print of information
to standard output.
12 nSTA Number of timesteps between the writing of data
the stations file.
T ldefout Switch to create a new output NetCDF file(s).
144 nHIS Number of timesteps between the writing fields
into history file.
8640 ndefHIS Number of timesteps between creation of new
history files.
1 ntsAVG Starting timestep for the accumulation of output
time-averaged data.
288 nAVG Number of timesteps between the writing of
time-averaged data into averages file.
17280 ndefAVG Number of timesteps between creation of new
time-averaged file.
1.0000E-06 Akt_bak(01) Background vertical mixing coefficient (m2/s)
for tracer 01: temp
1.0000E-06 Akt_bak(02) Background vertical mixing coefficient (m2/s)
for tracer 02: salt
1.0000E-05 Akv_bak Background vertical mixing coefficient (m2/s)
for momentum.
5.0000E-06 Akk_bak Background vertical mixing coefficient (m2/s)
for turbulent energy.
5.0000E-06 Akp_bak Background vertical mixing coefficient (m2/s)
for turbulent generic statistical field.
3.000 gls_p GLS stability exponent.
1.500 gls_m GLS turbulent kinetic energy exponent.
-1.000 gls_n GLS turbulent length scale exponent.
7.6000E-06 gls_Kmin GLS minimum value of turbulent kinetic energy.
1.0000E-12 gls_Pmin GLS minimum value of dissipation.
5.4770E-01 gls_cmu0 GLS stability coefficient.
1.4400E+00 gls_c1 GLS shear production coefficient.
1.9200E+00 gls_c2 GLS dissipation coefficient.
-4.0000E-01 gls_c3m GLS stable buoyancy production coefficient.
1.0000E+00 gls_c3p GLS unstable buoyancy production coefficient.
1.0000E+00 gls_sigk GLS constant Schmidt number for TKE.
1.3000E+00 gls_sigp GLS constant Schmidt number for PSI.
1400.000 charnok_alpha Charnok factor for Zos calculation.
0.500 zos_hsig_alpha Factor for Zos calculation using Hsig(Awave).
0.250 sz_alpha Factor for Wave dissipation surface tke flux .
100.000 crgban_cw Factor for Craig/Banner surface tke flux.
3.0000E-04 rdrg Linear bottom drag coefficient (m/s).
2.5000E-03 rdrg2 Quadratic bottom drag coefficient.
1.0000E-03 Zob Bottom roughness (m).
2.0000E-02 Zos Surface roughness (m).
1.0000E+01 blk_ZQ Height (m) of surface air humidity measurement.
1.0000E+01 blk_ZT Height (m) of surface air temperature measurement.
1.0000E+01 blk_ZW Height (m) of surface winds measurement.
1 lmd_Jwt Jerlov water type.
1 Vtransform S-coordinate transformation equation.
1 Vstretching S-coordinate stretching function.
5.0000E+00 theta_s S-coordinate surface control parameter.
4.0000E-01 theta_b S-coordinate bottom control parameter.
50.000 Tcline S-coordinate surface/bottom layer width (m) used
in vertical coordinate stretching.
1025.000 rho0 Mean density (kg/m3) for Boussinesq approximation.
1.000 dstart Time-stamp assigned to model initialization (days).
1.000 tide_start Reference time origin for tidal forcing (days).
19960101.00 time_ref Reference time for units attribute (yyyymmdd.dd)
3.6000E+02 Tnudg(01) Nudging/relaxation time scale (days)
for tracer 01: temp
1.2000E+02 Tnudg(02) Nudging/relaxation time scale (days)
for tracer 02: salt
3.6500E+02 Znudg Nudging/relaxation time scale (days)
for free-surface.
3.6500E+02 M2nudg Nudging/relaxation time scale (days)
for 2D momentum.
3.6500E+02 M3nudg Nudging/relaxation time scale (days)
for 3D momentum.
1.2000E+02 obcfac Factor between passive and active
open boundary conditions.
14.000 T0 Background potential temperature (C) constant.
35.000 S0 Background salinity (PSU) constant.
1.000 gamma2 Slipperiness variable: free-slip (1.0) or
no-slip (-1.0).
my cpp header is like this
Activated C-preprocessing Options:

ECSY10 ROMS 3.2 - East China Sea & Yellow sea
ADD_FSOBC Adding tidal elevation to proccesed OBC data.
ADD_M2OBC Adding tidal currents to proccesed OBC data.
ANA_BSFLUX Analytical kinematic bottom salinity flux.
ANA_BTFLUX Analytical kinematic bottom temperature flux.
ANA_CLOUD Analytical cloud fraction.
ANA_RAIN Analytical rain fall rate.
ASSUMED_SHAPE Using assumed-shape arrays.
AVERAGES Writing out time-averaged fields.
AVERAGES_AKS Writing out time-averaged vertical S-diffusion.
AVERAGES_AKT Writing out time-averaged vertical T-diffusion.
AVERAGES_FLUXES Writing out time-averaged surface fluxes.
BULK_FLUXES Surface bulk fluxes parametererization.
CANUTO_B Canuto B-stability function formulation.
CURVGRID Orthogonal curvilinear grid.
DIFF_3DCOEF Horizontal, time-dependent 3D diffusion coefficient.
DJ_GRADPS Parabolic Splines density Jacobian (Shchepetkin, 2002).
DOUBLE_PRECISION Double precision arithmetic.
EAST_FSCHAPMAN Eastern edge, free-surface, Chapman condition.
EAST_M2FLATHER Eastern edge, 2D momentum, Flather condition.
EAST_M3CLAMPED Eastern edge, 3D momentum, Clamped condition.
EAST_TCLAMPED Eastern edge, tracers, Clamped condition.
GLS_MIXING Generic Length-Scale turbulence closure.
LONGWAVE Compute net longwave radiation internally.
MASKING Land/Sea masking.
MPI MPI distributed-memory configuration.
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.
PERFECT_RESTART Processing perfect restart variables.
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.
SOLAR_SOURCE Solar Radiation Source Term.
SOLVE3D Solving 3D Primitive Equations.
SOUTH_FSCHAPMAN Southern edge, free-surface, Chapman condition.
SOUTH_M2FLATHER Southern edge, 2D momentum, Flather condition.
SOUTH_M3CLAMPED Southern edge, 3D momentum, Clamped condition.
SOUTH_TCLAMPED Southern edge, tracers, Clamped condition.
SPLINES Conservative parabolic spline reconstruction.
SSH_TIDES Add tidal elevation to SSH climatology.
STATIONS Writing out station data.
TS_U3HADVECTION Third-order upstream horizontal advection of tracers.
TS_C4VADVECTION Fourth-order centered vertical advection of tracers.
TS_PSOURCE Tracers point sources and sinks.
UV_ADV Advection of momentum.
UV_COR Coriolis term.
UV_U3HADVECTION Third-order upstream horizontal advection of 3D momentum.
UV_C4VADVECTION Fourth-order centered vertical advection of momentum.
UV_QDRAG Quadratic bottom stress.
UV_PSOURCE Mass point sources and sinks.
UV_TIDES Add tidal currents to 2D momentum climatologies.
VAR_RHO_2D Variable density barotropic mode.
VISC_3DCOEF Horizontal, time-dependent 3D viscosity coefficient.
WEST_FSCHAPMAN Western edge, free-surface, Chapman condition.
WEST_M2FLATHER Western edge, 2D momentum, Flather condition.
WEST_M3CLAMPED Western edge, 3D momentum, Clamped condition.
WEST_TCLAMPED Western edge, tracers, Clamped condition.
Sorry for the long post.

jcwarner
Posts: 798
Joined: Wed Dec 31, 2003 6:16 pm
Location: USGS, USA

Re: Vertical mixing scheme in ROMS

#2 Post by jcwarner » Tue Sep 22, 2009 12:51 am

it is difficult to determine why your application is having troubles. It may/may not be related to the vertical mixing scheme that was selected. You need to investigate why it blew up. Is the problem at a lateral boundary? At an internal land/sea boundary? At a river source ????

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susonic
Posts: 159
Joined: Tue Aug 21, 2007 5:44 pm
Location: Jeju National University
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Re: Vertical mixing scheme in ROMS

#3 Post by susonic » Tue Sep 22, 2009 6:10 am

Hi Dr.Warner,

I already tested my application with using LMD and MY 2.5 vertical scheme. It ran well without any
problem. And I have just tested k-omega and gen vertical mixing and it also ran well without any problem. For the k-epsilon, my final history file gives me that there is an increasing speed at the lateral boundary. But it didn't happen with other stability functions as well as vertical schemes.
It blew up only with k-epsilon scheme.

Anyway, if the lateral boundary current speed increasing is the problem, what do I need to do?
Would you give me a suggestion?


Best,

-Peter

ggerbi
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Location: Skidmore College
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Re: Vertical mixing scheme in ROMS

#4 Post by ggerbi » Tue Sep 22, 2009 1:13 pm

Peter,

I have had trouble with k-epsilon being a bit less stable than the other closure schemes. Reducing the time step has helped fix this. Not an entirely satisfactory solution, I know.

Greg

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susonic
Posts: 159
Joined: Tue Aug 21, 2007 5:44 pm
Location: Jeju National University
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Re: Vertical mixing scheme in ROMS

#5 Post by susonic » Wed Sep 23, 2009 4:51 am

Hi ggerbi,

Thank you for your suggestion.
I'm running the model with time reduced(one third of the original time step). And now
it's woring without any problem.
It has still a little bit unstable speed near the boundary, though.

Again, thank you so much for your advice.

Best,

-Peter

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