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ROMS/TOMS

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PostPosted: Wed Feb 22, 2017 11:22 am 
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Joined: Tue Jan 14, 2014 3:02 pm
Posts: 16
Location: University of Copenhagen
I am running a 5 year simulation of an idealized model domain, on a modified grid from the upwelling test case. I initialize my model with a uniform sediment bed thickness of 1 m throughout the grid. After around 1000 timesteps (500 model days), i start getting deposits of up to 6 meters, which should be alright, but at around 1700 timesteps (850 model days), the bed thickness starts getting into 40-50 meters. There shouldn't be that amount of sediment in the domain.

Image

I thought there might be an increase in bed porosity, so I tried getting a sum of the bed mud mass over the entire grid for each timestep (in Python:
Code:
for tt in range(timelength):
   mudsum=np.sum(mudmass[tt,:,:,:]
)

This gives an increase of 33 times the original mass of sediment in the domain grid over the model run:

Image

Suspended sediment also reaches extreme values over time:

Image

Is this a known issue? I have no sediment sources, and I set the boundary conditions to closed in sediment.in:

Quote:
! Keyword Lateral Boundary Condition Type
!
! Cla Clamped _____N_____ j=Mm
! Clo Closed | 4 |
! Gra Gradient | |
! Nes Nested 1 W E 3
! Nud Nudging | |
! Per Periodic |_____S_____|
! Rad Radiation 2 j=1
! i=1 i=Lm
! W S E N
! e o a o
! s u s r
! t t t t
! h h
!
! 1 2 3 4

LBC(isTvar) == Clo Clo Clo Clo ! idsed(:), compact

! Adjoint-based algorithms can have different lateral boundary
! conditions keywords.

ad_LBC(isTvar) == Clo Clo Clo Clo ! idsed(:), compact


My boundary conditions in ocean.in are set like this:

Quote:
! Keyword Lateral Boundary Condition Type
!
! Cha Chapman_implicit (free-surface)
! Che Chapman_explicit (free-surface)
! Cla Clamped
! Clo Closed
! Fla Flather (2D momentum) _____N_____ j=Mm
! Gra Gradient | 4 |
! Nes Nested (refinement) | |
! Nud Nudging 1 W E 3
! Per Periodic | |
! Rad Radiation |_____S_____|
! Red Reduced Physics (2D momentum) 2 j=1
! Shc Shchepetkin (2D momentum) i=1 i=Lm
!
! W S E N
! e o a o
! s u s r
! t t t t
! h h
!
! 1 2 3 4

LBC(isFsur) == Cha Per Clo Per ! free-surface
LBC(isUbar) == Fla Per Clo Per ! 2D U-momentum
LBC(isVbar) == Fla Per Clo Per ! 2D V-momentum
LBC(isUvel) == Gra Per Clo Per ! 3D U-momentum
LBC(isVvel) == Gra Per Clo Per ! 3D V-momentum
LBC(isMtke) == Gra Per Clo Per ! mixing TKE

LBC(isTvar) == Cla Per Clo Per \ ! temperature
Cla Per Clo Per \ ! salinity
Clo Per Clo Per ! passive

! Adjoint-based algorithms can have different lateral boundary
! conditions keywords.

ad_LBC(isFsur) == Che Per Clo Per ! free-surface
ad_LBC(isUbar) == Red Per Clo Per ! 2D U-momentum
ad_LBC(isVbar) == Red Per Clo Per ! 2D U-momentum
ad_LBC(isUvel) == Gra Per Clo Per ! 3D U-momentum
ad_LBC(isVvel) == Gra Per Clo Per ! 3D V-momentum
ad_LBC(isMtke) == Gra Per Clo Per ! mixing TKE

ad_LBC(isTvar) == Cla Per Clo Per \ ! temperature
Cla Per Clo Per \ ! salinity
Clo Per Clo Per ! passive


The initialization of the model looks like this:

Quote:
Model Input Parameters: ROMS/TOMS version 3.7
Friday - February 17, 2017 - 12:08:21 PM
-----------------------------------------------------------------------------

Wind-Driven Upwelling/Downwelling over a Periodic Channel

Operating system : Linux
CPU/hardware : x86_64
Compiler system : gfortran
Compiler command : /usr/local/bin/mpif90
Compiler flags : -frepack-arrays -O3 -ffast-math -ffree-form -ffree-line-length-none -ffree-form -ffree-line-length-none

Input Script :

SVN Root URL : https://www.myroms.org/svn/src/trunk
SVN Revision : 802M

Local Root : /home/nws747/trunk
Header Dir : /home/nws747/cor_yearmodel/Inc
Header file : upwelling.h
Analytical Dir: /home/nws747/cor_yearmodel/Inc

Resolution, Grid 01: 0162x0032x032, Parallel Nodes: 16, Tiling: 004x004


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

10368000 ntimes Number of timesteps for 3-D equations.
15.000 dt Timestep size (s) for 3-D equations.
30 ndtfast Number of timesteps for 2-D equations between
each 3D timestep.
1 ERstr Starting ensemble/perturbation run number.
1 ERend Ending ensemble/perturbation run number.
0 nrrec Number of restart records to read from disk.
T LcycleRST Switch to recycle time-records in restart file.
2880 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).
2880 nHIS Number of timesteps between the writing fields
into history file.
518400 ndefHIS Number of timesteps between creation of new
history files.
1 ntsAVG Starting timestep for the accumulation of output
time-averaged data.
5760 nAVG Number of timesteps between the writing of
time-averaged data into averages file.
518400 ndefAVG Number of timesteps between creation of new
time-averaged file.
1 ntsDIA Starting timestep for the accumulation of output
time-averaged diagnostics data.
2880 nDIA Number of timesteps between the writing of
time-averaged data into diagnostics file.
518400 ndefDIA Number of timesteps between creation of new
diagnostic 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_tnu2(03) NLM Horizontal, harmonic mixing coefficient
(m2/s) for tracer 03: dye_01
5.0000E+00 nl_visc2 NLM Horizontal, harmonic mixing coefficient
(m2/s) for momentum.
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
F LtracerSponge(03) Turning OFF sponge on tracer 03: dye_01
1.0000E-06 Akt_bak(01) Background vertical mixing coefficient (m2/s)
for tracer 01: temp
1.0000E-06 Akt_bak(02) Background vertical mixing coefficient (m2/s)
for tracer 02: salt
1.0000E-06 Akt_bak(03) Background vertical mixing coefficient (m2/s)
for tracer 03: dye_01
1.0000E-05 Akv_bak Background vertical mixing coefficient (m2/s)
for momentum.
5.0000E-06 Akk_bak Background vertical mixing coefficient (m2/s)
for turbulent energy.
5.0000E-06 Akp_bak Background vertical mixing coefficient (m2/s)
for turbulent generic statistical field.
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).
3.0000E-03 rdrg2 Quadratic bottom drag coefficient.
2.0000E-02 Zob Bottom roughness (m).
2.0000E-02 Zos Surface roughness (m).
2 Vtransform S-coordinate transformation equation.
4 Vstretching S-coordinate stretching function.
3.0000E+00 theta_s S-coordinate surface control parameter.
5.0000E-01 theta_b S-coordinate bottom control parameter.
25.000 Tcline S-coordinate surface/bottom layer width (m) used
in vertical coordinate stretching.
1025.000 rho0 Mean density (kg/m3) for Boussinesq approximation.
180.000 dstart Time-stamp assigned to model initialization (days).
0.00 time_ref Reference time for units attribute (yyyymmdd.dd)
2.0000E+00 Tnudg(01) Nudging/relaxation time scale (days)
for tracer 01: temp
2.0000E+00 Tnudg(02) Nudging/relaxation time scale (days)
for tracer 02: salt
2.0000E+00 Tnudg(03) Nudging/relaxation time scale (days)
for tracer 03: dye_01
0.0000E+00 Znudg Nudging/relaxation time scale (days)
for free-surface.
0.0000E+00 M2nudg Nudging/relaxation time scale (days)
for 2D momentum.
0.0000E+00 M3nudg Nudging/relaxation time scale (days)
for 3D momentum.
0.0000E+00 obcfac Factor between passive and active
open boundary conditions.
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.
14.000 T0 Background potential temperature (C) constant.
35.000 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).
0.0000E+00 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 LtracerSrc(03) Turning OFF point Sources/Sinks on tracer 03: dye_01
F LsshCLM Turning OFF processing of SSH climatology.
F Lm2CLM Turning OFF processing of 2D momentum climatology.
F Lm3CLM Turning OFF processing of 3D momentum climatology.
F LtracerCLM(01) Turning OFF processing of climatology tracer 01: temp
F LtracerCLM(02) Turning OFF processing of climatology tracer 02: salt
F LtracerCLM(03) Turning OFF processing of climatology tracer 03: dye_01
F LnudgeM2CLM Turning OFF nudging of 2D momentum climatology.
F LnudgeM3CLM Turning OFF nudging of 3D momentum climatology.
F LnudgeTCLM(01) Turning OFF nudging of climatology tracer 01: temp
F LnudgeTCLM(02) Turning OFF nudging of climatology tracer 02: salt
F LnudgeTCLM(03) Turning OFF nudging of climatology tracer 03: dye_01
T Hout(idFsur) Write out free-surface.
T Hout(idUbar) Write out 2D U-momentum component.
T Hout(idVbar) Write out 2D V-momentum component.
T Hout(idUvel) Write out 3D U-momentum component.
T Hout(idVvel) Write out 3D V-momentum component.
T Hout(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(idUbms) Write out bottom U-momentum stress.
T Hout(idVbms) Write out bottom V-momentum stress.
T Hout(idUbrs) Write out bottom U-current stress.
T Hout(idVbrs) Write out bottom V-current stress.
T Hout(idUbws) Write out wind-induced, bottom U-wave stress.
T Hout(idVbws) Write out wind-induced, bottom V-wave stress.
T Hout(idUbcs) Write out max wind + current, bottom U-wave stress.
T Hout(idVbcs) Write out max wind + current, bottom V-wave stress.
T Hout(inert) Write out inert passive tracer 01: dye_01
T Hout(idBott) Write out bottom property 01: grain_diameter
T Hout(idBott) Write out bottom property 02: grain_density
T Hout(idBott) Write out bottom property 03: settling_vel
T Hout(idBott) Write out bottom property 04: erosion_stress
T Hout(idBott) Write out bottom property 05: ripple_length
T Hout(idBott) Write out bottom property 06: ripple_height
T Hout(idBott) Write out bottom property 07: bed_wave_amp
T Hout(idBott) Write out bottom property 08: Zo_def
T Hout(idBott) Write out bottom property 09: Zo_app
T Hout(idTsur) Write out surface net heat flux.
T Hout(idTsur) Write out surface net salt flux.
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
T Aout(inert) Write out averaged inert passive tracer 01: dye_01

T Dout(M2rate) Write out 2D momentum acceleration.
T Dout(M2pgrd) Write out 2D momentum pressure gradient.
T Dout(M2fcor) Write out 2D momentum Coriolis force.
T Dout(M2hadv) Write out 2D momentum horizontal advection.
T Dout(M2xadv) Write out 2D momentum horizontal X-advection.
T Dout(M2yadv) Write out 2D momentum horizontal Y-advection.
T Dout(M2hvis) Write out 2D momentum horizontal viscosity.
T Dout(M2xvis) Write out 2D momentum horizontal X-viscosity.
T Dout(M2yvis) Write out 2D momentum horizontal Y-viscosity.
T Dout(M2sstr) Write out 2D momentum surface stress.
T Dout(M2bstr) Write out 2D momentum bottom stress.

T Dout(M3rate) Write out 3D momentum acceleration.
T Dout(M3pgrd) Write out 3D momentum pressure gradient.
T Dout(M3fcor) Write out 3D momentum Coriolis force.
T Dout(M3hadv) Write out 3D momentum horizontal advection.
T Dout(M3xadv) Write out 3D momentum horizontal X-advection.
T Dout(M3yadv) Write out 3D momentum horizontal Y-advection.
T Dout(M3vadv) Write out 3D momentum vertical advection.
T Dout(M3hvis) Write out 3D momentum horizontal viscosity.
T Dout(M3xvis) Write out 3D momentum horizontal X-viscosity.
T Dout(M3yvis) Write out 3D momentum horizontal Y-viscosity.
T Dout(M3vvis) Write out 3D momentum vertical viscosity.

T Dout(iTrate) Write out rate of change of tracer 01: temp
T Dout(iTrate) Write out rate of change of tracer 02: salt
T Dout(iTrate) Write out rate of change of tracer 03: dye_01
T Dout(iThadv) Write out horizontal advection, tracer 01: temp
T Dout(iThadv) Write out horizontal advection, tracer 02: salt
T Dout(iThadv) Write out horizontal advection, tracer 03: dye_01
T Dout(iTxadv) Write out horizontal X-advection, tracer 01: temp
T Dout(iTxadv) Write out horizontal X-advection, tracer 02: salt
T Dout(iTxadv) Write out horizontal X-advection, tracer 03: dye_01
T Dout(iTyadv) Write out horizontal Y-advection, tracer 01: temp
T Dout(iTyadv) Write out horizontal Y-advection, tracer 02: salt
T Dout(iTyadv) Write out horizontal Y-advection, tracer 03: dye_01
T Dout(iTvadv) Write out vertical advection, tracer 01: temp
T Dout(iTvadv) Write out vertical advection, tracer 02: salt
T Dout(iTvadv) Write out vertical advection, tracer 03: dye_01
T Dout(iThdif) Write out horizontal diffusion, tracer 01: temp
T Dout(iThdif) Write out horizontal diffusion, tracer 02: salt
T Dout(iThdif) Write out horizontal diffusion, tracer 03: dye_01
T Dout(iTxdif) Write out horizontal X-diffusion, tracer 01: temp
T Dout(iTxdif) Write out horizontal X-diffusion, tracer 02: salt
T Dout(iTxdif) Write out horizontal X-diffusion, tracer 03: dye_01
T Dout(iTydif) Write out horizontal Y-diffusion , tracer 01: temp
T Dout(iTydif) Write out horizontal Y-diffusion , tracer 02: salt
T Dout(iTydif) Write out horizontal Y-diffusion, tracer 03: dye_01
T Dout(iTvdif) Write out vertical diffusion, tracer 01: temp
T Dout(iTvdif) Write out vertical diffusion, tracer 02: salt
T Dout(iTvdif) Write out vertical diffusion, tracer 03: dye_01

Output/Input Files:

Output Restart File: /home/nws747/hdrive/Documents/clusteroutput/dwc/5yearcorcalmobcdeep_rst.nc
Prefix for History Files: /home/nws747/hdrive/Documents/clusteroutput/dwc/5yearcorcalmobcdeep_his
Prefix for Averages Files: /home/nws747/hdrive/Documents/clusteroutput/dwc/5yearcorcalmobcdeep_avg
Prefix for Diagnostics Files: /home/nws747/hdrive/Documents/clusteroutput/dwc/5yearcorcalmobcdeep_dia

Tile partition information for Grid 01: 0162x0032x0032 tiling: 004x004

tile Istr Iend Jstr Jend Npts

0 1 40 1 8 10240
1 41 81 1 8 10496
2 82 122 1 8 10496
3 123 162 1 8 10240
4 1 40 9 16 10240
5 41 81 9 16 10496
6 82 122 9 16 10496
7 123 162 9 16 10240
8 1 40 17 24 10240
9 41 81 17 24 10496
10 82 122 17 24 10496
11 123 162 17 24 10240
12 1 40 25 32 10240
13 41 81 25 32 10496
14 82 122 25 32 10496
15 123 162 25 32 10240

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

tile Xmin Xmax Ymin Ymax grid

0 0.50 40.50 0.50 8.50 RHO-points
1 40.50 81.50 0.50 8.50 RHO-points
2 81.50 122.50 0.50 8.50 RHO-points
3 122.50 162.50 0.50 8.50 RHO-points
4 0.50 40.50 8.50 16.50 RHO-points
5 40.50 81.50 8.50 16.50 RHO-points
6 81.50 122.50 8.50 16.50 RHO-points
7 122.50 162.50 8.50 16.50 RHO-points
8 0.50 40.50 16.50 24.50 RHO-points
9 40.50 81.50 16.50 24.50 RHO-points
10 81.50 122.50 16.50 24.50 RHO-points
11 122.50 162.50 16.50 24.50 RHO-points
12 0.50 40.50 24.50 32.50 RHO-points
13 40.50 81.50 24.50 32.50 RHO-points
14 81.50 122.50 24.50 32.50 RHO-points
15 122.50 162.50 24.50 32.50 RHO-points

0 1.00 40.50 0.50 8.50 U-points
1 40.50 81.50 0.50 8.50 U-points
2 81.50 122.50 0.50 8.50 U-points
3 122.50 162.00 0.50 8.50 U-points
4 1.00 40.50 8.50 16.50 U-points
5 40.50 81.50 8.50 16.50 U-points
6 81.50 122.50 8.50 16.50 U-points
7 122.50 162.00 8.50 16.50 U-points
8 1.00 40.50 16.50 24.50 U-points
9 40.50 81.50 16.50 24.50 U-points
10 81.50 122.50 16.50 24.50 U-points
11 122.50 162.00 16.50 24.50 U-points
12 1.00 40.50 24.50 32.50 U-points
13 40.50 81.50 24.50 32.50 U-points
14 81.50 122.50 24.50 32.50 U-points
15 122.50 162.00 24.50 32.50 U-points

0 0.50 40.50 1.00 8.50 V-points
1 40.50 81.50 1.00 8.50 V-points
2 81.50 122.50 1.00 8.50 V-points
3 122.50 162.50 1.00 8.50 V-points
4 0.50 40.50 8.50 16.50 V-points
5 40.50 81.50 8.50 16.50 V-points
6 81.50 122.50 8.50 16.50 V-points
7 122.50 162.50 8.50 16.50 V-points
8 0.50 40.50 16.50 24.50 V-points
9 40.50 81.50 16.50 24.50 V-points
10 81.50 122.50 16.50 24.50 V-points
11 122.50 162.50 16.50 24.50 V-points
12 0.50 40.50 24.50 32.00 V-points
13 40.50 81.50 24.50 32.00 V-points
14 81.50 122.50 24.50 32.00 V-points
15 122.50 162.50 24.50 32.00 V-points

Maximum halo size in XI and ETA directions:

HaloSizeI(1) = 220
HaloSizeJ(1) = 92
TileSide(1) = 49
TileSize(1) = 833



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


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

1 1.0000E-03 0.0000E+00 2.6500E+03 5.0000E-02 1.0000E-03 8.0000E-01

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

1 4.5000E-02 4.0000E-02 0.0000E+00 0.0000E+00 5.0000E-06 0.0000E+00

morph_fac
(nondim)

1 1.0000E+00

New bed layer formed when deposition exceeds 0.1000E-01 (m).
Two first layers are combined when 2nd layer smaller than 0.0000E+00 (m).
Rate coefficient for bed load transport = 0.5000E-01

F LtracerSponge(04Turning OFF sponge on tracer 04: mud_01
F LtracerSrc(04) Turning OFF point sources/Sink on tracer 04: mud_01
F LtracerCLM(04) Turning OFF processing of climatology tracer 04: mud_01
F LnudgeTCLM(04) Turning OFF nudging of climatology tracer 04: mud_01
T Hout(idTvar) Write out sediment01: mud_01
T Hout(idfrac) Write out bed fraction, sediment 01: mudfrac_01
T Hout(idfrac) Write out mass, sediment 01: mudmass_01
T Hout(idSbed) Write out BED property 01: bed_thickness
T Hout(idSbed) Write out BED property 02: bed_age
T Hout(idSbed) Write out BED property 03: bed_porosity

T Aout(idTvar) Write out averaged sediment01: mud_01

T Dout(iTrate) Write out rate of change of tracer 04: mud_01
T Dout(iThadv) Write out horizontal advection, tracer 04: mud_01
T Dout(iTxadv) Write out horizontal X-advection, tracer 04: mud_01
T Dout(iTyadv) Write out horizontal Y-advection, tracer 04: mud_01
T Dout(iTvadv) Write out vertical advection, tracer 04: mud_01
T Dout(iThdif) Write out horizontal diffusion, tracer 04: mud_01
T Dout(iTxdif) Write out horizontal X-diffusion, tracer 04: mud_01
T Dout(iTydif) Write out horizontal Y-diffusion, tracer 04: mud_01
T Dout(iTvdif) Write out vertical diffusion, tracer 04: mud_01

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

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

zeta 1 Chapman Imp Periodic Closed Periodic

ubar 1 Flather Periodic Closed Periodic

vbar 1 Flather Periodic Closed Periodic

u 1 Gradient Periodic Closed Periodic

v 1 Gradient Periodic Closed Periodic

temp 1 Clamped Periodic Closed Periodic

salt 1 Clamped Periodic Closed Periodic

dye_01 1 Closed Periodic Closed Periodic

mud_01 1 Closed Closed Closed Closed

tke 1 Gradient Periodic Closed Periodic

Activated C-preprocessing Options:

UPWELLING Wind-Driven Upwelling/Downwelling over a Periodic Channel
ANA_BPFLUX Analytical bottom passive tracers fluxes.
ANA_BSFLUX Analytical kinematic bottom salinity flux.
ANA_BTFLUX Analytical kinematic bottom temperature flux.
ANA_DQDSST Analytical surface heat flux sensitivity to SST.
ANA_FSOBC Analytical free-surface boundary conditions.
ANA_GRID Analytical grid set-up.
ANA_INITIAL Analytical initial conditions.
ANA_M2OBC Analytical 2D momentum boundary conditions.
ANA_M3OBC Analytical 3D momentum boundary conditions.
ANA_PASSIVE Analytical initial conditions for inert tracers.
ANA_SEDIMENT Analytical sediment initial conditions.
ANA_SMFLUX Analytical kinematic surface momentum flux.
ANA_SPFLUX Analytical surface passive tracer fluxes.
ANA_SST Analytical sea surface temperature, SST.
ANA_SSFLUX Analytical kinematic surface salinity flux.
ANA_STFLUX Analytical kinematic surface temperature flux.
ANA_TOBC Analytical tracers boundary conditions.
ANA_WWAVE Analytical wind induced waves.
ASSUMED_SHAPE Using assumed-shape arrays.
AVERAGES Writing out time-averaged nonlinear model fields.
DIAGNOSTICS_TS Computing and writing tracer diagnostic terms.
DIAGNOSTICS_UV Computing and writing momentum diagnostic terms.
DJ_GRADPS Parabolic Splines density Jacobian (Shchepetkin, 2002).
DOUBLE_PRECISION Double precision arithmetic.
FSOBC_REDUCED Using free-surface data in reduced physics conditions
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 .
QCORRECTION Surface net heat flux correction.
K_GSCHEME Third-order upstream advection of TKE fields.
RI_SPLINES Parabolic Spline Reconstruction for Richardson Number.
!RST_SINGLE Double precision fields in restart NetCDF file.
SALINITY Using salinity.
SEDIMENT Cohesive and noncohesive sediments.
SED_DENS Include density of suspended sediment in equation of state.
SUSPLOAD Activate suspended sediment transport.
SOLVE3D Solving 3D Primitive Equations.
SPLINES_VDIFF Parabolic Spline Reconstruction for Vertical Diffusion.
SPLINES_VVISC Parabolic Spline Reconstruction for Vertical Viscosity.
SSW_BBL Styles and Glenn Bottom Boundary Layer - modified.
SSW_CALC_UB Internal computation of bottom orbital velocity.
SSW_CALC_ZNOT Internal computation of bottom roughness.
T_PASSIVE Advecting and diffusing inert passive tracer.
TS_MPDATA Recursive flux corrected MPDATA 3D 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_SADVECTION Parabolic splines vertical advection of momentum.
UV_VIS2 Harmonic mixing of momentum.
VAR_RHO_2D Variable density barotropic mode.

Process Information:

Node # 0 (pid= 23267) is active.
Node # 1 (pid= 23268) is active.
Node # 2 (pid= 23269) is active.
Node # 3 (pid= 23270) is active.
Node # 4 (pid= 23271) is active.
Node # 5 (pid= 23272) is active.
Node # 6 (pid= 23273) is active.
Node # 7 (pid= 23274) is active.
Node # 8 (pid= 23275) is active.
Node # 9 (pid= 23276) is active.
Node # 10 (pid= 23277) is active.
Node # 11 (pid= 23278) is active.
Node # 12 (pid= 23279) is active.
Node # 13 (pid= 23281) is active.
Node # 14 (pid= 23282) is active.
Node # 15 (pid= 23283) 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

32 0.0000000 0.0000000 0.000 0.000 0.000 0.000
31 -0.0312500 -0.0006162 -0.943 -0.398 -1.273 -1.584
30 -0.0625000 -0.0024694 -2.312 -0.812 -3.578 -4.807
29 -0.0937500 -0.0055732 -4.110 -1.242 -6.927 -9.688
28 -0.1250000 -0.0099501 -6.346 -1.687 -11.338 -16.257
27 -0.1562500 -0.0156320 -9.030 -2.149 -16.837 -24.555
26 -0.1875000 -0.0226598 -12.177 -2.627 -23.459 -34.637
25 -0.2187500 -0.0310838 -15.804 -3.123 -31.246 -46.569
24 -0.2500000 -0.0409634 -19.931 -3.637 -40.247 -60.431
23 -0.2812500 -0.0523675 -24.582 -4.170 -50.520 -76.314
22 -0.3125000 -0.0653746 -29.784 -4.723 -62.131 -94.321
21 -0.3437500 -0.0800722 -35.567 -5.298 -75.152 -114.569
20 -0.3750000 -0.0965575 -41.965 -5.894 -89.664 -137.187
19 -0.4062500 -0.1149368 -49.013 -6.515 -105.756 -162.315
18 -0.4375000 -0.1353252 -56.752 -7.160 -123.525 -190.105
17 -0.4687500 -0.1578467 -65.224 -7.832 -143.072 -220.724
16 -0.5000000 -0.1826330 -74.475 -8.533 -164.510 -254.344
15 -0.5312500 -0.2098233 -84.552 -9.263 -187.953 -291.150
14 -0.5625000 -0.2395630 -95.505 -10.026 -213.523 -331.336
13 -0.5937500 -0.2720024 -107.386 -10.822 -241.345 -375.099
12 -0.6250000 -0.3072950 -120.248 -11.654 -271.547 -422.645
11 -0.6562500 -0.3455957 -134.143 -12.523 -304.259 -474.178
10 -0.6875000 -0.3870577 -149.125 -13.432 -339.608 -529.901
9 -0.7187500 -0.4318298 -165.245 -14.382 -377.719 -590.011
8 -0.7500000 -0.4800524 -182.551 -15.376 -418.708 -654.695
7 -0.7812500 -0.5318532 -201.087 -16.414 -462.683 -724.121
6 -0.8125000 -0.5873421 -220.890 -17.498 -509.734 -798.436
5 -0.8437500 -0.6466051 -241.990 -18.629 -559.934 -877.753
4 -0.8750000 -0.7096981 -264.407 -19.809 -613.329 -962.147
3 -0.9062500 -0.7766394 -288.147 -21.036 -669.935 -1051.641
2 -0.9375000 -0.8474014 -313.199 -22.311 -729.728 -1146.200
1 -0.9687500 -0.9219029 -339.537 -23.633 -792.641 -1245.715
0 -1.0000000 -1.0000000 -367.111 -25.000 -858.553 -1349.996

Time Splitting Weights for Grid 01: ndtfast = 30 nfast = 42
==================================

Primary Secondary Accumulated to Current Step

1-0.0008094437383769 0.0333333333333333-0.0008094437383769 0.0333333333333333
2-0.0014053566728197 0.0333603147912792-0.0022148004111966 0.0666936481246126
3-0.0017877524645903 0.0334071600137066-0.0040025528757869 0.1001008081383191
4-0.0019566842408176 0.0334667517625262-0.0059592371166046 0.1335675599008453
5-0.0019122901320372 0.0335319745705535-0.0078715272486418 0.1670995344713988
6-0.0016548570247459 0.0335957175749547-0.0095263842733877 0.2006952520463536
7-0.0011849025289723 0.0336508794757796-0.0107112868023600 0.2343461315221331
8-0.0005032751608631 0.0336903762267453-0.0112145619632232 0.2680365077488784
9 0.0003887272597151 0.0337071520654408-0.0108258347035081 0.3017436598143192
10 0.0014892209965583 0.0336941944901169-0.0093366137069498 0.3354378543044362
11 0.0027955815694920 0.0336445537902317-0.0065410321374578 0.3690824080946679
12 0.0043042707117221 0.0335513677379153-0.0022367614257357 0.4026337758325831
13 0.0060106451121704 0.0334078920475245 0.0037738836864347 0.4360416678801076
14 0.0079087469427945 0.0332075372104522 0.0116826306292293 0.4692492050905598
15 0.0099910761708920 0.0329439123123590 0.0216737068001212 0.5021931174029188
16 0.0122483446563884 0.0326108764399960 0.0339220514565096 0.5348039938429148
17 0.0146692120341107 0.0322025982847830 0.0485912634906203 0.5670065921276978
18 0.0172400033810439 0.0317136245503127 0.0658312668716642 0.5987202166780105
19 0.0199444086685725 0.0311389577709445 0.0857756755402367 0.6298591744489550
20 0.0227631639997064 0.0304741441486588 0.1085388395399431 0.6603333185976138
21 0.0256737146312910 0.0297153720153352 0.1342125541712341 0.6900486906129490
22 0.0286498597812016 0.0288595815276255 0.1628624139524357 0.7189082721405746
23 0.0316613792205220 0.0279045862015855 0.1945237931729577 0.7468128583421600
24 0.0346736416507075 0.0268492068942347 0.2291974348236651 0.7736620652363948
25 0.0376471948657328 0.0256934188392112 0.2668446296893979 0.7993554840756060
26 0.0405373376992232 0.0244385123436867 0.3073819673886211 0.8237939964192927
27 0.0432936737565711 0.0230872677537126 0.3506756411451922 0.8468812641730054
28 0.0458596469320356 0.0216441452951603 0.3965352880772278 0.8685254094681656
29 0.0481720587108284 0.0201154903974257 0.4447073467880562 0.8886408998655914
30 0.0501605672561820 0.0185097551070648 0.4948679140442381 0.9071506549726561
31 0.0517471682814030 0.0168377361985254 0.5466150823256412 0.9239883911711815
32 0.0528456577069106 0.0151128305891453 0.5994607400325517 0.9391012217603267
33 0.0533610761022577 0.0133513086655816 0.6528218161348094 0.9524525304259084
34 0.0531891349131379 0.0115726061288397 0.7060109510479473 0.9640251365547481
35 0.0522156244733761 0.0097996349650684 0.7582265755213234 0.9738247715198165
36 0.0503158038019031 0.0080591141492892 0.8085423793232265 0.9818838856691057
37 0.0473537721847153 0.0063819206892258 0.8558961515079418 0.9882658063583315
38 0.0431818225418188 0.0048034616164019 0.8990779740497606 0.9930692679747335
39 0.0376397765791564 0.0033640675316746 0.9367177506289170 0.9964333355064081
40 0.0305543017255206 0.0021094083123694 0.9672720523544377 0.9985427438187775
41 0.0217382098544505 0.0010909315881854 0.9890102622088881 0.9996336754069629
42 0.0109897377911119 0.0003663245930371 1.0000000000000000 1.0000000000000000

ndtfast, nfast = 30 42 nfast/ndtfast = 1.40000

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

1.000000000000 1.047601458608 0.523800729304 1.000000000000 1.000000000000

Power filter parameters, Fgamma, gamma = 0.28400 0.18933

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

Minimum X-grid spacing, DXmin = 1.00000000E+00 km
Maximum X-grid spacing, DXmax = 1.00000000E+00 km
Minimum Y-grid spacing, DYmin = 1.00000000E+00 km
Maximum Y-grid spacing, DYmax = 1.00000000E+00 km
Minimum Z-grid spacing, DZmin = 9.43240458E-01 m
Maximum Z-grid spacing, DZmax = 1.04280828E+02 m

Minimum barotropic Courant Number = 4.24344299E-02
Maximum barotropic Courant Number = 8.13740028E-02
Maximum Coriolis Courant Number = 1.54650000E-03


Basin information for Grid 01:

Maximum grid stiffness ratios: rx0 = 3.725851E-02 (Beckmann and Haidvogel)
rx1 = 9.521232E-01 (Haney)

Initial basin volumes: TotVolume = 5.7839568336E+12 m3
MinVolume = 9.4324045808E+05 m3
MaxVolume = 1.0428079379E+08 m3
Max/Min = 1.1055589579E+02


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PostPosted: Wed Mar 01, 2017 4:20 am 
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Joined: Wed Dec 31, 2003 6:16 pm
Posts: 673
Location: USGS, USA
looking at this quickly, i dont see a reason why the sediment should increase. there is no 'known issue' so it should conserve mass. where in the domain is the cross section?


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PostPosted: Wed Mar 01, 2017 1:43 pm 
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Joined: Tue Jan 14, 2014 3:02 pm
Posts: 16
Location: University of Copenhagen
The cross-sections are in the central part of the domain, going from the open boundary in the west to the closed, "coastal" boundary in the east.
Over time, the open boundary creates eddies, and current velocities increase, especially in the north-south direction. I suspect that this is where the problem arises.

Image

Image

Temperature and salinity are changing cyclically over time, as expected, but don't increase from year to year.

Image

Image


For comparison, there is a slight increase in sediment mass (on the scale of a few percent) in a similar model run with all OBC set to clamped. In this run, suspended sediment ends up being accumulated and deposited at the western boundary, where current velocities are 0:

Image


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PostPosted: Thu Mar 02, 2017 1:46 am 
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Joined: Wed Dec 31, 2003 6:16 pm
Posts: 673
Location: USGS, USA
if the domain is N-S periodic, are the results alongshore uniform? how long does this take to run? is it something i can grab and look at locally.
-j


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PostPosted: Fri Mar 03, 2017 9:42 am 
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Joined: Tue Jan 14, 2014 3:02 pm
Posts: 16
Location: University of Copenhagen
jcwarner wrote:
if the domain is N-S periodic, are the results alongshore uniform? how long does this take to run? is it something i can grab and look at locally.
-j


There are small variations in the along shore direction, but the results are essentially uniform. The sediment bed has a very clear along shore drift.

I would have to send you the whole project directory for you to compile and run locally. It takes around a week to run 5 model years on our system, running in parallel with 16 nodes. Or I could send you the output files from our run, if a week is too long.


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