Blowing up problem when using sediment

[zip]

hello everyone
I use ROMS to simulate the sandwaves in a ideal flume by change the parameters in ana_grid.h and ana_m2obc.h file,but the work blow up immediately when i use a large timestep(dt):10s. Then i use a small dt :1s but it just delay the blow up, it computes for 600000 steps then blowing up, after that, i use 0.5s dt ,but it waste too much time to compute one step, so i want to ask how to deal with this problem.

Thank you for your help!

Best
Zip

The log file is listed as follows:

Model Input Parameters: ROMS/TOMS version 3.7
Tuesday - March 26, 2019 - 5:39:34 PM
-----------------------------------------------------------------------------

Suspended Sediment Test in an Estuary

Operating system : Linux
CPU/hardware : x86_64
Compiler system : gfortran
Compiler command : /vol6/home/zhipeng/software/openmpi/bin/mpif90
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

Input Script :

SVN Root URL : https://www.myroms.org/svn/src/trunk
SVN Revision : 853M

Local Root : /vol6/home/zhipeng/ROMS/chenkai/trunk_853
Header Dir : /vol6/home/zhipeng/ROMS/chenkai/test2
Header file : estuary_test.h
Analytical Dir: /vol6/home/zhipeng/ROMS/chenkai/test2

Resolution, Grid 01: 0600x0005x030, Parallel Nodes: 6, Tiling: 006x001


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

525960 ntimes Number of timesteps for 3-D equations.
10.000 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.
10000 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).
100 nHIS Number of timesteps between the writing fields
into history file.
0 nQCK Number of timesteps between the writing fields
into quicksave file.
1 ntsAVG Starting timestep for the accumulation of output
time-averaged data.
100000 nAVG Number of timesteps between the writing of
time-averaged data into averages 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: salt
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
5.0000E-06 Akt_bak(01) Background vertical mixing coefficient (m2/s)
for tracer 01: temp
5.0000E-06 Akt_bak(02) Background vertical mixing coefficient (m2/s)
for tracer 02: salt
5.0000E-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).
2.0000E-03 rdrg2 Quadratic bottom drag coefficient.
1.5000E-02 Zob Bottom roughness (m).
5.0000E-03 Zos Surface roughness (m).
2 Vtransform S-coordinate transformation equation.
3 Vstretching S-coordinate stretching function.
1.0000E+00 theta_s S-coordinate surface control parameter.
3.0000E+00 theta_b S-coordinate bottom control parameter.
1.000 Tcline S-coordinate surface/bottom layer width (m) used
in vertical coordinate stretching.
1028.000 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)
1.2500E-01 Tnudg(01) Nudging/relaxation time scale (days)
for tracer 01: temp
1.2500E-01 Tnudg(02) Nudging/relaxation time scale (days)
for tracer 02: salt
1.0000E-03 Znudg Nudging/relaxation time scale (days)
for free-surface.
1.0000E-03 M2nudg Nudging/relaxation time scale (days)
for 2D momentum.
1.0000E-03 M3nudg Nudging/relaxation time scale (days)
for 3D momentum.
1.0000E+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(idBath) Write out time-dependent bathymetry.
T Hout(idUbar) Write out 2D U-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(idUbms) Write out bottom U-momentum stress.

T Aout(idUbar) Write out averaged 2D U-momentum component.
T Aout(idUvel) Write out averaged 3D U-momentum component.
T Aout(idUbms) Write out averaged bottom U-momentum stress.

Output/Input Files:

Output Restart File: ocean_rst.nc
Output History File: ocean_his.nc
Output Averages File: ocean_avg.nc

Tile partition information for Grid 01: 0600x0005x0030 tiling: 006x001

tile Istr Iend Jstr Jend Npts

0 1 100 1 5 15000
1 101 200 1 5 15000
2 201 300 1 5 15000
3 301 400 1 5 15000
4 401 500 1 5 15000
5 501 600 1 5 15000

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

tile Xmin Xmax Ymin Ymax grid

0 0.50 100.50 0.50 5.50 RHO-points
1 100.50 200.50 0.50 5.50 RHO-points
2 200.50 300.50 0.50 5.50 RHO-points
3 300.50 400.50 0.50 5.50 RHO-points
4 400.50 500.50 0.50 5.50 RHO-points
5 500.50 600.50 0.50 5.50 RHO-points

0 1.00 100.50 0.50 5.50 U-points
1 100.50 200.50 0.50 5.50 U-points
2 200.50 300.50 0.50 5.50 U-points
3 300.50 400.50 0.50 5.50 U-points
4 400.50 500.50 0.50 5.50 U-points
5 500.50 600.00 0.50 5.50 U-points

0 0.50 100.50 1.00 5.00 V-points
1 100.50 200.50 1.00 5.00 V-points
2 200.50 300.50 1.00 5.00 V-points
3 300.50 400.50 1.00 5.00 V-points
4 400.50 500.50 1.00 5.00 V-points
5 500.50 600.50 1.00 5.00 V-points

Maximum halo size in XI and ETA directions:

HaloSizeI(1) = 224
HaloSizeJ(1) = 30
TileSide(1) = 106
TileSize(1) = 954



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


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

1 2.0000E-01 0.0000E+00 2.6500E+03 1.5000E+01 5.0000E-03 5.0000E-01

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

1 1.5000E-01 1.5000E-01 0.0000E+00 0.0000E+00 5.0000E-06 0.0000E+00

morph_fac
(nondim)

1 1.2000E+01

New bed layer formed when deposition exceeds 0.10000E+00 (m).
Two first layers are combined when 2nd layer smaller than 0.00000E+00 (m).
Rate coefficient for bed load transport = 0.15000E+01

F LtracerSponge(03Turning OFF sponge on tracer 03: sand_01
F LtracerSrc(03) Turning OFF point sources/Sink on tracer 03: sand_01
F LtracerCLM(03) Turning OFF processing of climatology tracer 03: sand_01
F LnudgeTCLM(03) Turning OFF nudging of climatology tracer 03: sand_01

T Hout(idTvar) Write out sediment01: sand_01
T Hout(idfrac) Write out mass, sediment 01: sandmass_01
T Hout(idSbed) Write out BED property 01: bed_thickness
T Hout(idSbed) Write out BED property 02: bed_age
T Hout(idBott) Write out BOTTOM property 01: grain_diameter
T Hout(idBott) Write out BOTTOM property 05: ripple_length
T Hout(idBott) Write out BOTTOM property 06: ripple_height

T Aout(idTvar) Write out averaged sediment01: sand_01
T Aout(idUbld) Write out U-bedload, sediment 01: bedload_Usand_01
T Aout(idVbld) Write out V-bedload, sediment 01: bedload_Vsand_01

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

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

zeta 1 Radiation Closed Radiation Closed

ubar 1 Clamped Closed Clamped Closed

vbar 1 Clamped Closed Clamped Closed

u 1 Radiation Closed Radiation Closed

v 1 Radiation Closed Radiation Closed

temp 1 Radiation Closed Radiation Closed

salt 1 Radiation Closed Radiation Closed

sand_01 1 Radiation Closed Radiation Closed

tke 1 Gradient Closed Gradient Closed

Activated C-preprocessing Options:

ESTUARY_TEST Suspended Sediment Test in an Estuary
ANA_BPFLUX Analytical bottom passive tracers fluxes.
ANA_BSFLUX Analytical kinematic bottom salinity flux.
ANA_BTFLUX Analytical kinematic bottom temperature flux.
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_SEDIMENT Analytical sediment initial conditions.
ANA_SMFLUX Analytical kinematic surface momentum flux.
ANA_SPFLUX Analytical surface passive tracer fluxes.
ANA_SSFLUX Analytical kinematic surface salinity flux.
ANA_STFLUX Analytical kinematic surface temperature flux.
ANA_WWAVE Analytical wind induced waves.
ASSUMED_SHAPE Using assumed-shape arrays.
AVERAGES Writing out time-averaged nonlinear model fields.
BEDLOAD_SOULSBY Activate bed load sediment transport Soulsby formula.
DJ_GRADPS Parabolic Splines density Jacobian (Shchepetkin, 2002).
DOUBLE_PRECISION Double precision arithmetic.
GLS_MIXING Generic Length-Scale turbulence closure.
KANTHA_CLAYSON Kantha and Clayson stability function formulation.
MIX_S_TS Mixing of tracers along constant S-surfaces.
MIX_S_UV Mixing of momentum along constant S-surfaces.
MPI MPI distributed-memory configuration.
NONLINEAR Nonlinear Model.
!NONLIN_EOS Linear Equation of State for seawater.
N2S2_HORAVG Horizontal smoothing of buoyancy and shear.
POWER_LAW Power-law shape time-averaging barotropic filter.
PROFILE Time profiling activated .
K_GSCHEME Third-order upstream advection of TKE fields.
RADIATION_2D Use tangential phase speed in radiation conditions.
RI_SPLINES Parabolic Spline Reconstruction for Richardson Number.
!RST_SINGLE Double precision fields in restart NetCDF file.
SEDIMENT Cohesive and noncohesive sediments.
SED_MORPH Allow bottom model elevation to evolve.
SUSPLOAD Activate suspended sediment transport.
SOLVE3D Solving 3D Primitive Equations.
SSW_BBL Styles and Glenn Bottom Boundary Layer - modified.
SSW_CALC_ZNOT Internal computation of bottom roughness.
TS_C4HADVECTION Fourth-order centered horizontal advection of tracers.
TS_C4VADVECTION Fourth-order centered 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_VIS2 Harmonic mixing of momentum.
VAR_RHO_2D Variable density barotropic mode.
Node # 5 (pid= 5807) is active.

Process Information:

Node # 0 (pid= 5797) is active.
Node # 1 (pid= 5799) is active.
Node # 2 (pid= 5801) is active.
Node # 3 (pid= 5803) is active.
Node # 4 (pid= 5805) 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

30 0.0000000 0.0000000 0.000 0.000 0.000 0.000
29 -0.0333333 -0.0091908 -0.294 -0.021 -0.307 -0.320
28 -0.0666667 -0.0246480 -0.766 -0.046 -0.801 -0.835
27 -0.1000000 -0.0465229 -1.420 -0.073 -1.486 -1.552
26 -0.1333333 -0.0748645 -2.259 -0.104 -2.365 -2.470
25 -0.1666667 -0.1096016 -3.279 -0.138 -3.434 -3.589
24 -0.2000000 -0.1505193 -4.476 -0.175 -4.688 -4.901
23 -0.2333333 -0.1972327 -5.837 -0.215 -6.115 -6.394
22 -0.2666667 -0.2491614 -7.346 -0.258 -7.698 -8.050
21 -0.3000000 -0.3055125 -8.982 -0.303 -9.413 -9.845
20 -0.3333333 -0.3652803 -10.714 -0.349 -11.230 -11.746
19 -0.3666667 -0.4272698 -12.510 -0.397 -13.114 -13.717
18 -0.4000000 -0.4901463 -14.331 -0.445 -15.023 -15.716
17 -0.4333333 -0.5525108 -16.138 -0.493 -16.918 -17.698
16 -0.4666667 -0.6129904 -17.890 -0.540 -18.756 -19.622
15 -0.5000000 -0.6703344 -19.554 -0.585 -20.501 -21.447
14 -0.5333333 -0.7234995 -21.099 -0.628 -22.121 -23.142
13 -0.5666667 -0.7717134 -22.503 -0.669 -23.593 -24.682
12 -0.6000000 -0.8145063 -23.752 -0.707 -24.903 -26.053
11 -0.6333333 -0.8517082 -24.843 -0.743 -26.046 -27.248
10 -0.6666667 -0.8834166 -25.777 -0.775 -27.025 -28.272
9 -0.7000000 -0.9099419 -26.564 -0.805 -27.849 -29.134
8 -0.7333333 -0.9317437 -27.217 -0.833 -28.533 -29.848
7 -0.7666667 -0.9493675 -27.750 -0.858 -29.091 -30.432
6 -0.8000000 -0.9633892 -28.181 -0.882 -29.542 -30.903
5 -0.8333333 -0.9743731 -28.526 -0.904 -29.902 -31.278
4 -0.8666667 -0.9828430 -28.799 -0.925 -30.187 -31.576
3 -0.9000000 -0.9892666 -29.014 -0.945 -30.412 -31.809
2 -0.9333333 -0.9940485 -29.183 -0.964 -30.587 -31.991
1 -0.9666667 -0.9975313 -29.314 -0.982 -30.723 -32.132
0 -1.0000000 -1.0000000 -29.416 -1.000 -30.829 -32.241

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
3-0.0011514592651645 0.0501156998674241-0.0034654566136460 0.1501639558342179
4-0.0003735756740661 0.0501732728306823-0.0038390322877122 0.2003372286649002
5 0.0009829200513762 0.0501919516143856-0.0028561122363360 0.2505291802792858
6 0.0029141799764308 0.0501428056118168 0.0000580677400948 0.3006719858911026
7 0.0054132615310267 0.0499970966129952 0.0054713292711215 0.3506690825040978
8 0.0084687837865132 0.0497264335364439 0.0139401130576347 0.4003955160405417
9 0.0120633394191050 0.0493029943471183 0.0260034524767397 0.4496985103876600
10 0.0161716623600090 0.0486998273761630 0.0421751148367486 0.4983983377638230
11 0.0207585511322367 0.0478912442581626 0.0629336659689853 0.5462895820219856
12 0.0257765478740990 0.0468533167015507 0.0887102138430843 0.5931428987235363
13 0.0311633730493853 0.0455644893078458 0.1198735868924696 0.6387073880313821
14 0.0368391158442262 0.0440063206553765 0.1567127027366958 0.6827137086867585
15 0.0427031802506397 0.0421643648631652 0.1994158829873354 0.7248780735499237
16 0.0486309868367616 0.0400292058506332 0.2480468698240970 0.7649072794005569
17 0.0544704302037591 0.0375976565087951 0.3025173000278562 0.8025049359093520
18 0.0600380921294285 0.0348741349986072 0.3625553921572847 0.8373790709079592
19 0.0651152103984763 0.0318722303921358 0.4276706025557610 0.8692513013000949
20 0.0694434033194839 0.0286164698722119 0.4971140058752449 0.8978677711723068
21 0.0727201499285569 0.0251442997062377 0.5698341558038018 0.9230120708785445
22 0.0745940258796570 0.0215082922098099 0.6444281816834588 0.9445203630883544
23 0.0746596950216180 0.0177785909158270 0.7190878767050768 0.9622989540041814
24 0.0724526566618460 0.0140456061647461 0.7915405333669228 0.9763445601689276
25 0.0674437485167025 0.0104229733316538 0.8589842818836253 0.9867675335005814
26 0.0590334053485720 0.0070507859058187 0.9180176872321973 0.9938183194064002
27 0.0465456732896125 0.0040991156383901 0.9645633605218099 0.9979174350447904
28 0.0292219798521905 0.0017718319739095 0.9937853403740005 0.9996892670186999
29 0.0062146596259994 0.0003107329813000 0.9999999999999999 0.9999999999999999

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 = 2.00000000E-03 km
Maximum X-grid spacing, DXmax = 2.00000000E-03 km
Minimum Y-grid spacing, DYmin = 2.00000000E-03 km
Maximum Y-grid spacing, DYmax = 2.00000000E-03 km
Minimum Z-grid spacing, DZmin = 1.02470447E-01 m
Maximum Z-grid spacing, DZmax = 1.99857522E+00 m

Minimum barotropic Courant Number = 6.00599151E+00
Maximum barotropic Courant Number = 6.28777113E+00
Maximum Coriolis Courant Number = 0.00000000E+00


Basin information for Grid 01:

Maximum grid stiffness ratios: rx0 = 6.523764E-03 (Beckmann and Haidvogel)
rx1 = 3.771659E+00 (Haney)

Initial basin volumes: TotVolume = 3.7398438720E+05 m3
MinVolume = 4.0988178890E-01 m3
MaxVolume = 7.9943008726E+00 m3
Max/Min = 1.9503918176E+01

NL ROMS/TOMS: started time-stepping: (Grid: 01 TimeSteps: 00000001 - 00525960)


TIME-STEP YYYY-MM-DD hh:mm:ss.ss KINETIC_ENRG POTEN_ENRG TOTAL_ENRG NET_VOLUME
C => (i,j,k) Cu Cv Cw Max Speed

0 0001-01-01 00:00:00.00 0.000000E+00 1.527725E+02 1.527725E+02 3.739844E+05
(000,0,00) 0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00
DEF_HIS - creating history file, Grid 01: ocean_his.nc
WRT_HIS - wrote history fields (Index=1,1) in record = 0000001
DEF_AVG - creating average file, Grid 01: ocean_avg.nc
1 0001-01-01 00:00:10.00 NaN NaN NaN NaN
(600,5,01) NaN NaN NaN NaN

Blowing-up: Saving latest model state into RESTART file

WRT_RST - wrote re-start fields (Index=2,2) in record = 0000001

Elapsed CPU time (seconds):

Node # 0 CPU: 0.172
Total: 1.255

Nonlinear model elapsed time profile, Grid: 01

Allocation and array initialization .............. 0.055 ( 4.3824 %)
Ocean state initialization ....................... 0.123 ( 9.8008 %)
Reading of input data ............................ 0.001 ( 0.0797 %)
Processing of input data ......................... 0.051 ( 4.0636 %)
Computation of global information integrals ...... 0.011 ( 0.8766 %)
Writing of output data ........................... 0.412 (32.8287 %)
Model 2D kernel .................................. 0.029 ( 2.3107 %)
2D/3D coupling, vertical metrics ................. 0.018 ( 1.4342 %)
Omega vertical velocity .......................... 0.002 ( 0.1594 %)
Equation of state for seawater ................... 0.013 ( 1.0359 %)
Sediment tranport module, source/sink terms ...... 0.102 ( 8.1275 %)
GLS vertical mixing parameterization ............. 0.098 ( 7.8089 %)
3D equations right-side terms .................... 0.005 ( 0.3983 %)
3D equations predictor step ...................... 0.009 ( 0.7172 %)
Harmonic mixing of tracers, S-surfaces ........... 0.006 ( 0.4780 %)
Corrector time-step for 3D momentum .............. 0.007 ( 0.5578 %)
Corrector time-step for tracers .................. 0.012 ( 0.9562 %)
Bottom boundary layer module ..................... 0.010 ( 0.7969 %)
Total: 0.964 76.8128

Nonlinear model message Passage profile, Grid: 01

Message Passage: 2D halo exchanges ............... 0.024 ( 1.9126 %)
Message Passage: 3D halo exchanges ............... 0.017 ( 1.3545 %)
Message Passage: 4D halo exchanges ............... 0.001 ( 0.0797 %)
Message Passage: data broadcast .................. 0.500 (39.8408 %)
Message Passage: data reduction .................. 0.001 ( 0.0797 %)
Message Passage: data gathering .................. 0.030 ( 2.3903 %)
Total: 0.573 45.6575

All percentages are with respect to total time = 1.255

Node # 4 CPU: 0.216
Node # 1 CPU: 0.215
Node # 2 CPU: 0.217
Node # 3 CPU: 0.216
Node # 5 CPU: 0.219

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

Analytical header files used:

ROMS/Functionals/ana_btflux.h
ROMS/Functionals/ana_fsobc.h
ROMS/Functionals/ana_grid.h
ROMS/Functionals/ana_initial.h
ROMS/Functionals/ana_m2obc.h
ROMS/Functionals/ana_sediment.h
ROMS/Functionals/ana_smflux.h
ROMS/Functionals/ana_stflux.h
ROMS/Functionals/ana_wwave.h

ROMS/TOMS: DONE... Tuesday - March 26, 2019 - 5:39:35 PM

[jcwarner]

How about you look at the history file for these 600000 steps and see what is happening. is the model blowing up at the boundary (upstream or downstream), somewhere in the domain, what does the flow look like, etc. you may have to dig in and see how the solution looks to help figure out what is going on.

[c.drinkorn]

Maybe look at the rho, temp and sal values right before blow up.

[bjhaupt]

Check out your barotropic time step.

Do you have any channels in your model where you erode sediment and then create dense fast turbidity flows?

Go back to a run that has more output and check where it happens.

[luhputria]

Hi everyone,

My question is not related to blowing problem, but for modelling sandwave in ROMS.
I used estuary test case as a domain with flat seabed and tidal forcing condition.
I try to check whether I can activate ripple geometry or not. I hope if ripple can generate in this test case, I can model sand wave that has bigger dimension compare to ripple.

My question is:
1. Why ROMS generates only 1 ripple along the length of channel?
2. Why the results of ripple geometry have similar value with initial ripple geometry that we define in ana_sediment? And the shape is symmetry?
My expectation is ROMS generates several ripples in different locations.
Attached I sent picture of ripple height and length that I got.

3. Can we model starting from flat seabed condition (without any bottom perturbation) and expect for ROMS to automatically generate ripples?
4. Is it correct that ripple can be formed only in ssw_bbl bottom stress formulation? Because in ROMS, ripple formulation valid for wave-dominated conditions only as stated in https://www.myroms.org/wiki/SSW_BBL. And I also tried to model using 4 different bottom stress formulation such as ldrag, logdrag, qdrag and ssw_bbl. And only ssw_bbl can able to generate ripple.

[jcwarner]

I am not really clear what you are trying to do but here are some thoughts.

The estuary test case has grid cells on the order of 100m (or so, i dont remember exactly). So therefore it can not generate ripples that are on the order of 10's of cm. Instead, we have coded different methods to 'predict' what the ripple geometry would be based on grain size, currents, waves, etc. Those estimated values are computed, used to enhance bottom roughness, and written to output (if you look in ssw_bbl.h you can see the different methods in there). There are many in the literature, and they are not that hard to code. Here is a paper that has several methods in it

https://agupubs.onlinelibrary.wiley.com ... jgrc.20241
Nelson, T. R., G. Voulgaris, and P. Traykovski (2013), Predicting wave-induced ripple equilibrium geometry, J. Geophys.Res. Oceans, 118, 3202–3220, doi:10.1002/jgrc.20241

If you want to resolve ripples, then ROMS may not be the correct model, as non-hydrostatic effects may be important with flow separation off the ripple crests, etc. there are other efforts that have done that for example
https://agupubs.onlinelibrary.wiley.com ... jgrc.20120
Penko, Calantoni, Foster, Slinn, etc

If you start out roms with perfect flat and periodic, roms will stay that way - i mean that is is very accurate and small scale variations will not develop on their own. you would need to put them in. that is another set of studies but people like Nnafie, de Swart, Calvete etc. have shown how small scale perturbations can grow to produce large scale bedforms.

if you want to study flow over sand waves (order meters to 10's of meters to 100's of meters) then ROMS is ok. We have done this
Ocean Dynamics 64(12):1767
DOI: 10.1007/s10236-014-0781-y

hope that helps.
-j

[luhputria]

Thank you very much John.
Your feedback is very helpful.
I will check article that you recommend.

Regards,
Luh

[luhputria]

Hi John,

Thanks before for your previous email regarding paper of shoreface-connected ridges in Fire Island.
Actually, I want to investigate sandwave migration in detail. I made a rectangular domain with size 1200x300x30 m and sandwave seabed with 2m height and 300m wave length in ana_grid. My dx=dy= 5m and ds=0.5m. For boundary condition, I defined closed boundary on North and South and open boundary condition in west and east. I defined tidal force with ubar 1m/s in ana_m2obc and tidal amplitude 1 m in ana_fsobc. After 6hours of simulation, there is changing in my seabed and i also tried to change morphological factor, I got the changing as shown in attachment.
But I always failed and got a blow up after 6.6hours simulation with the reason maximum density. I read FAQ in wikiroms, and stated that if a blow up after longer simulation, I need to dig more deeply. Do you have a suggestion for this issue?

Thanks before.

Regards,
Luh

[jcwarner]

with any blowup, you need to look at the rst file, his file, and stdout to see what information it is telling you.
if you look at the rst file, where is the problem? at the boundary? at the wet/dry masking (for example).
try to restart it before the solution occurred. you can typically restart from rst files or from his files.
hard to tell you what to do with limited info on what went wrong.
-j

[luhputria]

Hi John,

Thank you for your reply.
I check roms_rst.nc file using ncview, what I got is a suspicious contour in the bottom right of bathymetry (bath.png picture).
And when I checked in this location and plot the graph with xi_rho as the horizontal direction, bathymetry is suddenly dropped as shown in the figure below (xi.jpg).
I defined bathymetry using ana_grid, so I didn't expect any problem in the bathymetry input file.

Regards,
Luh

[jcwarner]

time to put on your investigator hat. keep digging.
what else is weird there? what is forcing this? winds? tides? what did bottom stress look like? ubar? zeta?
the answer is in there.

[luhputria]

Hi John,

Thanks for your suggestion, my model is able to run without blow up again.

I also want to ask you regarding the surface erosion rate. I read your paper "Development of a three-dimensional, regional, coupled wave,current, and sediment-transport model" and from equation 23 in your paper, I know Es,m is a function of E0,m (bed erodibility constant), porosity and also bed shear stress. My question is "how you define this bed erodibility constant?" From your references, I see that may be you cite the paper by Ariathurai, C.R., Arulanandan, K., 1978. Erosion rates of cohesive soils. However, I can't access this paper, so I don't get the idea to calculate the surface erosion rate that we need to define in the sediment input file.

Thanks before.
Regards,
Luh

[jcwarner]

this gets into a world of research. Suggest you spend a good bit of time looking thru literature, and doing some model sensitivity tests. this all depends on fractions of non-cohesive, cohesive, is it mixed, etc. There are other sediment bed options in the code now for mixed beds. Here is an example of a paper on erosion rates:

https://setac.onlinelibrary.wiley.com/d ... 5630020106

https://scholarworks.wm.edu/cgi/viewcon ... msarticles

https://www.researchgate.net/publicatio ... ensitivity