Ocean Modeling Discussion

nacholibre

Lawrence, I would change the -100 m value on the masked cells to make sure they don't contribute to the a problem. This may not be the source of your blow-up issue, but it is also not the best practice in my opinion. Values in dry cells shouldn't be a concern, but... Because of the way that ROMS ...

nacholibre

CF recommends UDUNITS, which recommends "using a true calendar package rather than the UDUNITS-2 package". :roll: :D https://www.unidata.ucar.edu/software/udunits/udunits-current/doc/udunits/udunits2lib.html#Time 10 The Handling of Time You should use a true calendar package rather than the UDUNITS ...

nacholibre

Adding underscores may complicate matters in the decoding of time units of the form: double ocean_time(ocean_time) ; ocean_time:long_name = "time since initialization" ; ocean_time:units = "seconds since 1900-01-01 00:00:00" ; ocean_time:calendar = "proleptic_gregorian" ; What you will do in this ...

nacholibre

Thank you Hernan. This is helpful and those are very good points. My example was just for demonstration purposes. Surely there is no easy fix because the challenge of defining standard names spans across different disciplines, communities, applications etc... I appreciate your effort and future ...

nacholibre

I have recently started working on creating ISO metadata files for our model outputs and started to realize the challenges. One of them is linking to a units vocabulary for units definition. For example white spaces the units attribute with are problematic for automatically populating the units link ...

nacholibre

Did you make sure that your point source location is correct? See the following posts:
ROMS vs MATLAB indices explained (for rivers and others)
ROMS with river discharge
Zafer

nacholibre

For a second test, I've created a file with information also in the North and South boundary, but in this case the model blows immediately during the first time step. I would check the masking and bathymetry near the coastline at the southern and northern boundaries. You might have bad values in ...

nacholibre

Hao,
Probably a bit too late to be of any help to you, but I have provided some explanation on ROMS and MATLAB indices here. Hope this helps as a future reference to anybody who has issues with the river / point source locations.
Zafer

nacholibre

I have been thinking about posting on this topic for a while. ROMS horizontal discretization is very well defined in Numerical Solution Technique and placement of rivers in Description of River Input . However, I don't think the notation in MATLAB has been documented. I think this had also been a ...

nacholibre

The model needs boundary conditions to work, let it be defined analytically or read through files. If the ana_### switch is not turned on it will try to read it from a forcing file. mud_01 is a part of lateral boundary conditions, mud_01_bflux is a part of bottom boundary condition. mud_01 is a ...

nacholibre

The forcing field should have the dimensions of the boundary that you are applying it plus the time dimension. For example, to apply sediment concentration at an eastern boundary it looks something like this: nc_forc{'sand_east_01'} = ncdouble('sand_time','layers','eta_rho'); nc_forc{'sand_east_01 ...

nacholibre

It sounds to me like you are not providing mud_01_sflux & sand_01_sflux at all layers (maybe that's why you see a 2D forcing in your forcing files?).
Zafer

nacholibre

Do you think trying different vertical advection schemes for tracers or changing the stretching near surface might help you get a feel for how much of it could be a computational artifact? Just a thought...
Zafer

nacholibre

It seems like this issue was solved in revision 741 (ticket#648). Masks for the sediment output were switched from rmask_io back to rmask. Thanks.

nacholibre

I am not sure if there is any advantage to it, but in the recent version of the code sediment parameters (i.e sandmass, idBmas) are written to the his files after the wetdry mask is applied whereas in older versions it was out put as is. This change is somewhat problematic, because it makes it ...

nacholibre

I have a grid where most of the land is unmasked. After switching to COAWST version 3.1 I started getting spurious wet cells right after a few steps in to the simulation. They are spurious because the cells that get wet have elevations much higher than the tidal amplitude (e.g. -3 m of elevation ...

nacholibre

I assume the "drift" that you mention is actually because the model needs to read the forcing files ahead of time in order to interpolate them on the computational time step (the time steps of forcing files are usually much larger than the computational time steps). I also see the 1-sec difference ...

nacholibre

Have you tried M2REDUCED option?
Zafer

nacholibre

Did you make sure that your atmospheric forcing file domain has a larger footprint than your ROMS grid? Interpolation onto your domain may have a problem otherwise...
Zafer

nacholibre

My experience is that some sort of smoothing is usually required. You can tell it by looking at Beckmann & Haidvogel and Haney stiffness ratios (rx0 and rx1). The shallower the water, the more likely for the ratios to be exceeded more often. There are many options when it comes to smoothing, bin ...

nacholibre

Thanks to everybody who contributes to the discussion. I have a simulation which blows up frequently and/or I see unreasonably high tracer concentrations in shallow water and that is why this topic interested me. Even though we updated the code earlier to apply masking to dry cells with BULK_FLUXES ...

nacholibre

I am having a problem where my wetting-drying simulation in Cook Inlet blows-up at isolated cells from time to time and the blow-up is only associated with T and S values (not water elevations or currents) and occurs during the summertime heating and not during the winter/spring/fall times! Did you ...

nacholibre

Hi Kate, Did this change in step3d_uv.F work to prevent the tracers from updating in your case? I was wondering whether this worked or did not work and this change was rolled back, because I did not see it in the your repository. Thank you Zafer +# ifdef WET_DRY + Hvom(i,j,k)=Hvom(i,j,k)*vmask_wet(i ...

nacholibre

Hi Kate, I think I sometimes encounter a similar problem while working on my model. I would be happy to hear more about your problem and how you solve it. 1. Are you using constant tracers, if not does the salinity look just before the blow up? 2. How does the h+zeta change in time over the problem ...

nacholibre

Looks like I have barely missed the first anniversary of this question to reply it :shock: !!! Hopefully you moved on and this answer will be helpful for a future reference if not for you. When WET_DRY is defined in ROMS the following condition is applied over the entire grid: zeta=zeta+(Dcrit-h)*(1 ...

nacholibre

Fellow ROMS users, I would like to inform you about a proposal for a discussion board for technical questions from modelers who use ocean and atmospheric modeling systems. The proposed discussion board will be a page where users can ask questions, vote for useful questions and/or answers, and mark ...

nacholibre

viviocean, In order to do the stretching properly in Seagrid you will need to build the correct mex files for your system and add the folder that contains them to your Matlab path. Alternatively you can also look at the mex_matlabXX_winXX folders under the Seagrid folder to see if there is a version ...

nacholibre

You must be defining them on a masked cell if you don't see the discharge comming out. use mask_u or mask_v in Matlab the wet cell at the boundary is the source location e.g. mask_u(439,16) for a river in u direction in ROMS the indices will be one less and swapped e.g. river_Xposition=15, river ...

nacholibre

It is probably a little too late to answer this question, but just not to leave this post unanswered. See:
viewtopic.php?f=23&t=1344

nacholibre

I assume you will still have a problem with the grid points shallower than the minimum of your tidal range. They will go dry and the model will blow up. You will need to set a minimum depth to solve this issue.
Zafer

nacholibre

I would suggest setting your minimum depth to a positive number (say 2 m) and see if it will run this time. It seems to me that you might be having a problem with the depth values. Do you think you might have a grid point that has not been masked properly and has a depth of 0 m maybe?
Zafer

nacholibre

For any of your questions I suggest that you take a look at the ROMS documentation at WikiRoms first. https://www.myroms.org/wiki/index.php/Documentation_Portal . Masked cells are excluded in the calculations therefore masking reduces the computational load. Also it gives user the flexibility of ...

nacholibre

David, Sorry to get back to you so late. But I haven't seen your post earlier. I remember getting that error when I was working on the grids, but I cannot recall what the issue was. It has been a long time since then. I had to modify the seagrid codes myself for my needs and maybe I did not have ...

nacholibre

Seagrid decides on the land cells by automatically connecting the two ends of your coastline array. You can modify the coordinates of these two ends and move them towards the land so that you will get Seagrid to generate a correct polygon for the land.
Zafer

nacholibre

Try zoom in and out by pressing ctrl + [ and ctrl + ] and zoom to extent ctrl + \ Also you can try turning off the mask when you zoom out, so that the grid will draw much faster. You can also try changing your graphics renderer from painters to openGL (if you have openGL), but I haven't experienced ...

nacholibre

Could you tell me please which depth is “h”¿¿??

That is the depth at each grid cell. It is saved in the grid file and all history files with the name "h".

nacholibre

Which version of ROMS are you using?
Did you try a larger NDTFAST? (30 maybe?)
Zafer

nacholibre

What does it really mean? You should probably search on BODYFORCE to see if that code will help you out I am also trying to do a similar thing, but it is not really clear how to use BODYFORCE. Do we need to modify rhs3d.F? I guess that is the dirty way to do it, but I cannot see any other way at the ...

nacholibre

nacholibre wrote:
This one problem that I am having is not related to ANA_INITIAL, but rather to ANA_PSOURCE.

On a second thought it does not have to be limited to ANA_PSOURCE. I think it would happen in case of feeding river information with a netCDF forcing file...

nacholibre

I see. Thanks for your comments. 8) This one problem that I am having is not related to ANA_INITIAL, but rather to ANA_PSOURCE. However, I thought it might fit under this post. I get incredibly high values for velocity where I define my source (almost Inf), which is unrealistic of course. The model ...

nacholibre

You are on the right track. You need to convert that matlab grid file to a netCDF in order to feed into ROMS. Once you run "seagrid2roms" from the command line you will see that the NANs will convert to 2m. s.ClippingDepth in your matlab file contains the information about the minimum and maximum ...

nacholibre

My understanding is that there is a lot of issues with parallel execution in ROMS. Maybe more for ANA_ routines? On the other hand, I did the same thing for the 2D momentum in the same routine and there were no problems with it. e.g. vbar(104,9,1)=-2.0_r8 vbar(104,10,1)=-2.0_r8 ubar(82,16,1)=2.0_r8

nacholibre

Have you read the tutorial at http://woodshole.er.usgs.gov/operations/modeling/seagrid/tutorial.html? Seagrid has produced the "s" matlab structured variable where "s.gridded_ bathymetry" contains NaN for all land cells and some negative values for some sea cells that are close to the shoreline ...

nacholibre

I am trying to define some river inflow in the ANA_INITIAL routine. It is similar to the RIVERPLUME2 test case. No problems with modifying the initial 2D momentum, but I have problems with the 3D momentum. I can insert the following piece of code with no problems. DO k=1,N(ng) DO j=JstrR,JendR DO i ...

nacholibre

Do you define the river forcing with a netCDF file or are you using the ANA_PSOURCE routine?

nacholibre

Using join_cst.m and adding the two points far inland of your coast at the beginning and the end of your coastline should work as Mr. Signell suggested. Have you tried it?

nacholibre

Hello Zhou,
Have you found the reason for this? I have a similar issue, where model exits with signal 15 and no error messages. Are you modeling any river inflow?
Zafer

nacholibre

ROMS svn 350 I have seen the following note in the ana_psource.h code. Does it still have the bugs mentioned below? Can it be used in parallel with domain partitions? !----------------------------------------------------------------------- ! Set tracer and/or mass point sources and/or sink ...

nacholibre

I understand that ROMS uses the fill value (spval = 1.0E+37) for dry cells when wetting/drying is activated. I see that there has been a change the way this has been handled (Ticket #297) https://www.myroms.org/projects/src/ticket/297 However, this change was assumed to be only for the wetting ...

nacholibre

There were several reasons for this: The main problem was that the initialization file was missing. I had been overlooking it since ROMS strangely did not throw an error message for that. Also it was not possible to start from the restart file since it is the final step recorded before the blowup ...

nacholibre

it is difficult for me to really see what is going on here. Can i get the Projects folder for this app and try to run it here, and step thru what is happening? Sure, I will share it with you. I was looking at the results today and it is interesting to note that there are very high elevations above ...

nacholibre

You need to figure out the restart problem then figure out the ROMS problem by restarting and seeing what is what. The restart is failing with that posixio issue - which field from which file is it failing to read? The model runs fine when I turn the wet_dry off and set the minimum depth larger ...

nacholibre

Did you check the density field? ROMS looks for outrageous values of both velocity and density. Can you run with a shorter timestep? Sometimes ROMS just needs a shorter timestep to run stably, being happy for months before blowing up, but needing more steps to get through the occasional rough spot ...

nacholibre

not sure. look at all the fields. look at all the forcing data. Can u restart it? Unfortunately I am having a problem restarting my runs. I have been trying to restart from the netCDF restart file, but no luck so far. I have created a post about this very recently... https://www.myroms.org/forum ...

nacholibre

jcwarner wrote:did u look in the restart file? The last time step of that file contains the final fields.

Yes sure. Nothing unusual: the velocity and the water surface elevations are physically acceptable. No large values.

nacholibre

I am using ROMS 3.2 svn 351M. I am modeling a real case and I only have the tidal forcing on. My model blows up after 12 days after 20 tidal cycles. I have checked the depth averaged (ubar, vbar) and depth varying (u, v) values, and also the water surface elevation (zeta), but there are no extreme ...

nacholibre

I am using MPI with 20 nodes and when I try to restart from rst.nc file I get some error related to "Free control buffers" from each node. The model runs for for 15 minutes or so before blowing up, but it does not write any history file or time steps into the output file. I have attached the output ...

nacholibre

I do NOT recommend avoiding the mex files with SeaGrid. Chuck Denham, the author of this tool, tried to make non-mex versions of the elliptic solver and the other mex files, but it didn't work out so well. If you don't use the mex files, you will get a grid, but it may be wildly nonorthogonal. You ...

nacholibre

Did you prepare the forcing file with a word processor in Windows rather than a simple editor. They might sometimes mess up with the end of line characters.
It might be totally unrelated to your problem, but I had a similar problem in the past.
Good luck!
Zafer

nacholibre

Hello Justin,
Did changing the momentum mixing parameters make any change for your case? I am also getting weaker currents in my model than expected and you are right about the bottom drag.
Did you find out any parameters that may help tweaking the results?
Thanks,
Zafer

nacholibre

You need to edit following files:
uncomment '>Mask' in doaddmenus.m
add the following line under the case 'mask' in doevent.m
domasktool(self)

and then simply run seagrid. You can now use the Mask command under <Toggle> menu.

Zafer

nacholibre

Congrats! While it's fresh in your mind, it would be great if you would make a few notes on the problems you encountered and how you solved them. I'd be happy to add them to the WikiROMS section on grid generation. -Rich I followed the instructions in the readme.txt file in the downloaded seagrid ...

nacholibre

Got it

It took more than I thought (getting the Fortran compiler, version problems, manually editing the batch files... etc.), but finally I got it to work! I will be more than happy to help if anybody else ever has a similar problem in the future.

Thanks a lot,
Zafer

nacholibre

Yes, you can recompile it using a larger dimension. Or even better, you could rewrite it to use dynamic memory allocation so people wouldn't have to do this in the future! -Rich I have never done it before, so I would be happy if you could please direct me in the correct direction. I am assuming ...

nacholibre

I increased the size to 1200x1200 and recompiled. If you replace your win32 mex files with these, does it work? http://stellwagen.er.usgs.gov/rps/share/seagrid_mex2.zip -Rich Is it possible to have seagrid handle a much larger grid like 2000x2000? The latest version I got from the web page gives ...

nacholibre

I get the following error when I try to get the results output at selected points: "Read_StaPar inconsistent number of points..." ...change input script values" I have checked the number of points in the station.in file that I am using and the point numbers match with NSTATION. I changed the number ...

nacholibre

Well things got messier now. I downloded netCDF 3.6.2 and tried building it but the files in folder usr/local didn't seem to update. Then I downloaded the pre-built binary files and put them in the relted folders in usr/local and I get the following error message now. (which is pretty ...

nacholibre

I agree, that might be the case. I remember moving the ROMS directory to a different HARD DISK on the same computer a month ago. Do you think the problem might be related to that? I did the svn update after that, and I tried some of the old cases that I ran before , they worked all right. I have a ...

nacholibre

Finally my desktop crashed down! Well, I cannot say I am surprised!!! :lol: Last thing I was doing was trying to find the version information for netcdf. I am using a Linux desktop, an intel compiler and netcdf 3.6.1 I guess? I am not very confident with the file structure of ROMS. How can I tell ...

nacholibre

kate wrote:Did you step into nf_fread3d? I asked about values there, before the call to nf90_get_var.

Code: Select all

What is Lm and Mm in the model?

Lm=298
Mm=398

nacholibre

Hello Kate, The values I have are as follows: start 7 0 0 0 total 1 0 0 0 That is in IF (Lgrided) THEN loop, therefore, before status=nf_fread3d(ng, model, ncid, Vid, 0, Vtype+4, & & Vsize, LBi, UBi, LBj, UBj, 1, Irec, & & Fscale(ifield,ng), Fmin, Fmax, & & Fmask(LBi,LBj), & & Fout(LBi,LBj,1)) It ...

nacholibre

start and total read the ng (nested grid number) and it is equal to 1. So I have start(1)=Trec total(1)=1 where Trec =7. The 7 tidal constituents that i am using in my model. I don't know if this is what you were asking Kate. I hope I did not lose you completely at this point. :? Thank you for your ...

nacholibre

Hello Kate, The problem is at IF (status.ne.nf90_noerr) THEN IF (Master) THEN WRITE (stdout,70) TRIM(Vname(1,ifield)), Trec END IF exit_flag=2 ioerror=status RETURN END IF at the very end after the comment ! Read in 2D-grided or point data. Notice for special 2D fields, Vtype ! is augmented by four ...

nacholibre

Thank you for your reply Kate. I have a 400x300 grid with 8 layers. I thought that the errror mesage was straight forward so did not use a debugger. Do you mean debugging the f90 code in the Build folder? Thanks a lot! %% ncdump('clyo_tide.nc') %% Generated 30-Oct-2007 19:31:06 nc = netcdf('clyo ...

nacholibre

Hello, I am getting the following error. Apparently the get_2dfld.f90 cannot read the variable. GET_2DFLD - error while reading variable: tide_Eamp at TIME index = 7 ROMS/TOMS - Input error ............. exit_flag: 2 ... Analytical header files used: ROMS/Functionals/ana_initial.h ERROR: Abnormal ...

nacholibre

Thank you very much for the quick reply. I just realized that there are actually two different addresses for Seagrid. http://woodshole.er.usgs.gov/operations/modeling/seagrid/index.html and http://woodshole.er.usgs.gov/operations/modeling/seagrid/seagrid.html I downloaded Seagrid again and used the ...

nacholibre

Barbara, I increased the size to 1200x1200 and recompiled. If you replace your win32 mex files with these, does it work? http://stellwagen.er.usgs.gov/rps/share/seagrid_mex2.zip -Rich Hello, I am having a similar problem to what Barbara had. I would like to increase the grid size (say 400x400). I ...

nacholibre

I wonder if it is possible to get some more information about the cppdefs.h options? I have already read the page about the cppdefs.h options on WikiROMS (or the information in cppdefs.h file itself) and it was very helpful. :) However, there are still many options that I do not fully understand ...

nacholibre

Mr. Warner, When transferring my model from ROMS 2 to 3, I simply overlooked the fact that some of the parameters in mod_param.F are now included in the *.in input file. In order to prevent riffraff information, I wanted to delete my previous posting, but it was not possible. I tried to change my ...

nacholibre

I've recently switched to ROMS 3.0 and I am trying to do the same run that I did with the previous version.:D I copied the part from the cppdefs.h to a new header file. I modified the 'Upwelling' input file according to my previous input file. However, I get a segmentation error. I read the messages ...

nacholibre

Dear all, I am planning to model the entire Georgia and SC coast in detail. I used Seagrid for a few small areas I studied on, but I thought Gridgen might be a better option since it had more flexibility. I have read the bulletin board, but I am still unclear about following things: 1. is it ...

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