Ocean Modeling Discussion

nganju

Apologies for cross-postings, the USGS is seeking a motivated postdoctoral researcher for a two-year Mendenhall position. The goal of this research opportunity is to investigate the influence of vegetation and geomorphic type on marsh edge dynamics and marsh resilience with numerical modeling. The ...

nganju

The USGS Woods Hole Coastal and Marine Science Center is looking for creative scientists to explore connections between hydrodynamics, vegetation, and ecosystem services using numerical models. The complete announcement is here:
http://geology.usgs.gov/postdoc/opps/20 ... 0Ganju.htm

nganju

ignore that...just reread Wilkin's post more carefully.

nganju

I tried AVERAGES_DETIDE, and the averages file contained "zeta_detided" etc but none of the mentioned harmonic fit coefficients. Did I mess something up with the file writing specs (relevant ones below)? I can provide more info but assumed this is a straightforward error on my part. DT = 5.0 NTIMES ...

nganju

Dear colleagues- The Sediment Transport Group of the U.S. Geological Survey Woods Hole Coastal and Marine Science Center is pleased to announce a new postdoctoral opportunity through the Mendenhall Research Fellowship Program. RO 14-44: Understanding estuarine geomorphic change under hurricane ...

nganju

Linking hydrodynamic and ecological models in estuaries: a workshop to discuss recent advances and approaches September 10-11, 2013 U.S. Geological Survey Woods Hole Science Center Woods Hole, MA We are convening a workshop to discuss advances in understanding estuarine ecology through coupled ...

nganju

I think it's important for modelers to be able to defend their approaches, terminology, and philosophy to non-modelers. There are many disparaging comments made about models/modelers with little consideration for the value of model-derived information. There is substantial literature on the ...

nganju

I ran into this problem a few years ago and added in zeta...but to be consistent you should really be updating the wave field (height, period, dir) as water level (zeta+h) changes. Which is why a better option would be ROMS-SWAN coupling. If you don't have the computational power to do that, you ...

nganju

you probably want to define SUSPLOAD (suspended-sediment transport) in your header file.
As John pointed out, be careful about the indices also, that can cause problems if you are off by one...

nganju

are you missing a boundary cell in the analytical forcing? plot the output for ubar/vbar/zeta along the boundary and see if one cell is being held at zero instead of varying with your function.

nganju

could you post an image of your grid, and perhaps a zoom-in of where the blow-up is happening?

nganju

you have a dx between 13 and 58 m, and a dy between 13 and 84 m, a timestep of 100 s, and a Courant number of 4.
I would try reducing the timestep. Also make sure you have no depth values less than zero, even if they are masked.

nganju

what does your vertical stretching look like?

nganju

Is it stalling on the first time step, at some random spot, or just before writing to a history file? I recall having a similar problem...

nganju

Yes, even with masking the minimum depth must be greater than zero, even in masked cells. With wetting and drying, you activate "WET_DRY", and specify your mask as cells which should never become wet. You then have the option of making any wet cell a negative depth. When zeta exceeds that depth ...

nganju

and your courant number is 0.8.
I would also reduce the timestep by half.

nganju

If you look at the output for vertical stretching, it looks like your shallowest depth is zero in your grid file.
All cells must be greater than zero unless using wetting/drying.

nganju

I think you have a bad continutation of the line in your input file. It is probably repeating the last value on the first line and not seeing the remaining entries. Did you edit the file in Windows? If so try dos2unix on your sediment input file. In any case, 42 sediment classes is a lot. It ...

nganju

I've found the best way to diagnose a blow-up like the one you describe is to save restart output very frequently and look at the fields of zeta, u, v; and also the change in those fields between the last time step and the second-to-last time step. This usually shows you where problems may be.

nganju

I think it's "GLS_Kmin", and in gls_corstep.h the tke is set to MAX(Tke,gls_kmin)...
You can try dropping this value to 1e-9 and see if changing AKt_bak now gives different results...

nganju

Malcolm Scully at ODU has nicely illustrated that the "Galperin correction" in the turbulence scheme effectively sets a minimum TKE value that overrides the change in Akt_bak. Hopefully he will see this and give the detailed explanation, but I think the solution is to change TKE_min in the input ...

nganju

Hi-
Is respiration by phytoplankton represented in the Fasham/Fennel code somewhere? I have a hard time finding it, but I've been assured it's in there. Thanks...

nganju

sorry, ignore this....it makes complete sense as is.

nganju

In fennel.h, line 707 has: ! Phytoplankton grazing by zooplankton. ! cff1=fac1*Bio(i,k,iZoop)*Bio(i,k,iPhyt)/ & & (K_Phy(ng)+Bio(i,k,iPhyt)*Bio(i,k,iPhyt)) cff3=1.0_r8/(1.0_r8+cff1) Bio(i,k,iPhyt)=cff3*Bio(i,k,iPhyt) as the grazing rate; but Fennel (2006), Eq. 7 has Phytoplankton^2 in the numerator ...

nganju

I am still debating how to deal with it...I suppose macroalgae should have a vertical component, as it will grow vertically in response to light and nutrients. But I am not sure I want it advecting around, as in the areas I am working in, it is usually attached to the bottom substrate. Is there a ...

nganju

I am adding macroalgae dynamics to fennel.h. I plan on treating it not as a tracer but as a variable whose density changes as a function of nutrients, light, etc. If I add it as 2D (r2dvar) biological tracer will it automatically be advected around by step3d_t or is there an easy hack? Is there a ...

nganju

Has anyone attempted to pass ROMS-calculated mass fluxes and tracers to the EPA's water quality model, WASP? The WASP model is linked offline with other codes (e.g. EFDC), so I think this should be easy to do. Any information or advice is appreciated, thanks...

nganju

the command "dos2unix" will convert the file, as in "dos2unix build.bash"

nganju

One option is to use the SSW_BBL option in ROMS, and directly specify wave height and period throughout the domain, thereby avoiding SWAN. You can use simple wave formulas, for a given wind speed, fetch, and water depth to calculate the wave characteristics, and put those in a netcdf forcing file ...

nganju

Should the wet/dry masks (e.g. rmask_wet, umask_wet) be used in step3d_t, step2d_lf_am3, etc? They are defined and read into those routines, but never actually used. I am having problems with anomalously high salinities and temperatures on the edges of wet/dry masks, and I wonder if fill values are ...

nganju

Hi- If you are using the the logarithmic formulation, then ROMS will only use the defined ZoB to calculate ustar and bottom stress. If you use SSW_BBL for the bottom boundary calculations, you can then use SSW_CALC_ZNOT, which will sum the roughness contributions from grain roughness (ZoN), sediment ...

nganju

Hi Rebecca- (1) If you break the surface (i.e. negative h), mask_rho needs to have a value of 0 instead of 1. If you are using ana_grid, you can specify the masked areas easily enough using ana_mask.h. For this domain, you should probably have the seamount break the surface. (2) I don't know if you ...

nganju

Hello- I am boldly straying into new territory with a very crude sense of biology, so any help is appreciated. We plan to simulate nutrient dynamics in a shallow estuary, where the following processes are most important: 1. nitrification/denitrification in the sediments; 2. uptake of nitrate and ...

nganju

Can anyone recommend seminal or recent papers on the effect of horizontal resolution on simulated flows in the nearshore? I have found several papers dealing with oceanic circulation and resolution, but nothing for inner shelf or nearshore regions. Thanks...

nganju

the values of hc and Tcline in your *.in file need to match the values in the initialization file.
negative depths are allowed with WET_DRY.

nganju

I'm fairly certain my problem is not related to tabs, since I've added variables before with no problems. But I am now trying to split the ubar_hadv diagnostic into the u*du/dx and v*du/dy terms, add them as idDu2d variables, and having the same problem reported above. I'm sure it's a silly error ...

nganju

Did you try changing the max file number to something larger than 200?

nganju

The ROMS run is instructed to run for 86400 time steps at 360 s per time step = 360 days The SWAN run is instructed to run from 1/1/04 to 12/10/04 = 344 days This will cause SWAN to stop coupling and ROMS to sit and wait. These times need to match, for both coupling and the length of your SWAN input ...

nganju

I also think the first error may be fixed by changing the "highest file ref. number" in the SWAN configuration file (swaninit)

nganju

I think the problem is the time step and duration of the ROMS and SWAN runs not matching. Can you show us the number and size of the ROMS time steps?

nganju

if SED_MORPH is turned on, the new variable that is reported in the history files is "bath", which is the new updated water depth. The change in depth is the difference in "bath" from each successive time step. The change in bed thickness is the difference in "bed_thickness". Bed thickness is ...

nganju

The variable "bath" tracks changes in depth, assuming you are using the "SED_MORPH" option to actively update the bathymetry. If you are not using SED_MORPH, but just want to track erosion and deposition, the variable "bed_thickness" tracks the net erosion or deposition.

nganju

I used Mathieu's toolbox for interpolation, but found a few bugs where the main function (e.g. NEST_CreateNestingTotalArray) calls other routines (e.g. InterpolGetSpMat...) with a different set of arguments than the routine is expecting. I think there were about 5 of these I had to correct. Once ...

nganju

sorry, we see Zt_avg1 is calculated in set_zeta...

nganju

Hopefully this is a stupid question...which routine is responsible for adding zeta to bathymetry (h) in the computation of time-evolving vertical stretching/layer thicknesses? We don't see any reference to zeta in either set_depth or set_scoord, only references to the initial bathymetry. Thanks in ...

nganju

To hopefully save someone else a little time... In the supplied examples of Externals/coupling_*.in files, SWAN does not provide bottom orbital velocites or wave dissipation to ROMS. If you want this field passed, you need to add the Wubot (or Wdiss) field to Export(waves) and Import(ocean). If you ...

nganju

SWAN spec2d files are about 1MB, ROMS output looks fine, I can try with one processor and report back. I will also update if necessary...

nganju

The offending output command in the SWAN input file is SPECOUT (output 2D spectra); the TABLE command (output parameters in ascii format) has also caused the same problem. The ROMS output file stops after writing a typical line (time, kinetic energy, etc). The most recently written-to SWAN PRINT ...

nganju

On separate occassions, at different times during the same simulation, ROMS/SWAN coupled runs halt in the middle of the run. There is no error in the ROMS output file, the SWAN PRINT file is usually in the middle of processing an output request, and the cluster issues an error file with the phrase ...

nganju

Another resolved problem to report for this one...in set_scoord.F # if defined WET_DRY hc(ng)=MIN(MAX(hmin(ng),0.0_r8),Tcline(ng)) # else hc(ng)=MIN(hmin(ng),Tcline(ng)) # endif If you are using SED_MORPH, hmin should technically be variable, but it looks like it is pulled once, at the beginning of ...

nganju

Just to update, my problem (for both versions of the code) was that I had commented out the matlab file output commands (BLOCK) in the SWAN input file. Apparently those output commands must be specified for SWAN to pass information to ROMS. One additional note: SWAN's begin time is not considered ...

nganju

Hello Hernan- Thanks for the information; I try my best to troubleshoot before posting to the board. I don't expect to have my problems solved by others, I only want to share the information in case others duplicate the problem. In the original post, what is odd is that TEST_HEAD and INLET_TEST run ...

nganju

I updated to release 177, and now compilation fails... cd Build; ifort -c -O2 /align /G7 /MD /Ox -I/cygdrive/c/ROMS/MPICH2/include init ial.f90 /object:initial.o Intel(R) Fortran Compiler for 32-bit applications, Version 9.0 Build 20050430 Z Package ID: W_FC_P_9.0.018 Copyright (C) 1985-2005 Intel ...

nganju

I successfully compiled and ran TEST_HEAD and INLET_TEST with waves-ocean coupling. I also successfully compiled and ran the CBLAST application, without coupling. I also ran CBLAST with SWAN alone, no problems. I compiled CBLAST successfully with SWAN_COUPLING activated, but when I try to run the ...

nganju

found it... mpiexec -localonly....
it's running now...

nganju

After using the untouched-CSTM branch I created a few weeks back, and reinstalling MCT outside of the branch, I compiled with no problems. When I try to execute mpiexec -np 2 ./oceanM.exe ROMS/External/coupling_inlet_test.in I get a uniquely USGS-type error... Credentials for nganju-pr rejected ...

nganju

The MCT libraries were built with fmpich2.lib, and my makefile flag also uses fmpich2.lib. I have a feeling it may be a path issue: when I added the /usr/local/lib and /usr/local/include paths (where libmpeu.a and libmct.a are located), all unresolved externals went away except for the MPI-related ...

nganju

I installed MPICH2, and built the MCT libraries successfully (CYGWIN-ifort dual-core Windows computer). I used the same flags in my ROMS makefile as the MCT makefile. Compilation for TEST_HEAD goes smoothly until very near the end, where I get a plethora of "IPO errors". Previous postings on this ...

nganju

sorry, i was late to the dance

nganju

From the output file: your barotropic courant number (>5) seems high, i think <1 is more appropriate...perhaps your grid resolution is too fine (dx = 3.8 e -5 km = 0.038 m ???????). something is wrong with your grid spacing, i assume?

nganju

In my case, those errors arose when the netcdf libraries are built with a different compiler than the one you are using to compile ROMS. Perhaps you can check the netcdf website for successful build output for your system, and make sure the libraries were built correctly. other than that, i have no ...

nganju

Did this work in the end? I am trying to install ROMS 3.0 and netcdf 3.6.2 on my cygwin machine/ifort and having the same problem.

nganju

Many people use Matlab to create and modify the *.nc (netcdf) files that are used for grid, forcing, and output files. To do this, you need to install the mexcdf interface for Matlab. I think there are other postings on the board that explain how to do this. good luck...

nganju

it looks like you need to edit snc_roms_get_grid to set hmin=0 instead of hmin=min(min(h)), since h does not exist when SED_MORPH is on

nganju

Are there any known attempts to couple ROMS with groundwater models, e.g. for studies of coastal saltwater intrusion, submarine groundwater discharge, etc.? Is this something that could be handled by the Model Coupling Toolkit? Just curious...

nganju

Hello Shih-Nan-
I haven't figured it out yet, and I am first trying to get a complete run with sed_morph before i try switching wet_dry on again. When I do get to that point, I will probably just run it in serial, and do two runs at once on my machine...

nganju

Wetting and drying is off right now... I put in a catch and the restarted model went for another few days before a different problem emerged (rapid bed deposition in the same spot, with large negative sediment concentrations?). Back to the first crash: bustrc and buvstrc were Nan's in the time step ...

nganju

I have been having problems with shallow cells, especially when using SED_MORPH to accelerate bed change. The domain is a relatively shallow subembayment of SF Bay, with tides and freshwater input. Larger SED_MORPH causes an earlier crash, in the same cell. After some troubleshooting, I determined ...

nganju

Hello- I have two computers: a dual-processor Linux with Intel 9, and a dual-core windowsXP/Cygwin with Intel 8. The configuration that I have been running on the Linux machine for some time has been with WET_DRY off. When I turn WET_DRY on, I get a segmentation fault after the first time step ...

nganju

thanks for the advice, that is exactly what i needed...

nganju

Hello-
I am running on a dual-processor Linux desktop, and I want to have a simple shell script command that recognizes when the oceanO process ends, and invokes a command to start another run. I am not very familiar with linux-type commands, so any help is appreciated, thanks in advance...

nganju

i ran a similar configuration, instead of clamping the inflow at the north and gradient for the outflow in the south, I clamped the outflow in the south, and gradient for the inflow at the north. This worked well for me, and gave me the correct inflow at the north once it reached steady-state...

nganju

Hello- My windows/cygwin computer was recently replaced, and after reinstalling cygwin, I find that access and permissions to compiled files are modified. For example, when I execute "make clean", cygwin reports that some of the files are protected (mostly SWAN-related files like waves_coupler.o ...

nganju

When using the SEDMORPH option, what is an appropriate "mud_morph_fac"? Does a value of 10, for example, mean the bed changes are scaled up by 10 at every time-step? Thanks in advance...

nganju

Hello-
Other than modifying "dcrit" in the *.in file, is there any modification needed in the grid file to use wetting and drying? If a certain cell should be available for wetting/drying, is it identified as a "1" in the masks? Thanks in advance...

nganju

Hello everyone- I have a river point source that runs into the domain in a diagonal fashion (does not run parallel to eta or xi directions). I am looking at effects close to this point source so I need the direction to be realistic near the source. Do I need to split up the total discharge (Qbar in ...

nganju

Thanks for the offer Rich- I was getting the files ready for you, and I tried something different: I created the grid, opened it in Matlab, and recomputed the depths using: zi=griddata(xbathy,ybathy,zbathy,lon_rho,lat_rho); I got the same strange result as seagrid gave. Then I remembered a problem I ...

nganju

I was going to stay quiet, since seagrid has always worked ok for me, but i have always had the same quirks mentioned by sandro (except for the presto path issue). I get more orthogonal results with mex off, and the cell density is always changed when i convert to a roms file using seagrid2roms. i ...

nganju

thanks for everyone's suggestions, all is running now. on a side note, I am getting a slight speed-up (~1-2%) when hyperthreading is turned off. I tried various tilings and in all cases it was faster with HT off. any reason to leave HT on?

nganju

It looks like at least one person has had success building netcdf with ifort 9.0. what flags might you have used and what adjustments did you have to make for env. variables? I am still getting an error "skipping incompatible /lib*.* when searching for -lm", and I have tried adding all sorts of ...

nganju

ifort 32 and 64 installed ok on the system (i had to install it to my user and not the root--i lack access still). I am not trying to install netcdf with the 64 bit until i can get 32 bit running.

nganju

I am still working on installing the netcdf libraries. there is a file needed by the ./configure called "crt1.o" that is supposed to be in usr/bin/lib, on my machine it is in the folder usr/bin/lib64. So I simply need to copy the file, but alas the systems administrator did not give me full rights ...

nganju

Hello, I just purchased a dual-processor 3.6Ghz Xeon machine (Dell Precision 670n) with "Red Hat Enterprise Linux WS v4Intel EM64T 64 bit" operating system. I plan on installing the recent Intel compiler (9.0) which claims to "support" 64bit Intel processors. Dell's website says "All XEON Processors ...

Search found 83 matches