Ocean Modeling Discussion

d.kobashi

Or could be something like this? I just selected 360 days that is much longer than 90 days at the interior as a placeholder. And obcfac = 90 in ocean.in.

d.kobashi

Dear all, I have a question about clim nudging. I am trying to impose nudging via RadNud along each boundary (west/north/east) as 1 day in and 90 day out within 5 grid points from the perimeter. I used d_nudcoef.m provided by ROMS Matlab package and I attach a plot of the Tnudgcoef. You can see that ...

d.kobashi

Hi, I wonder if someone has encountered slow 2D tidal simulation than 3D one. I set up 2D tidal simulation (tide only no wind, no density change) by turning off #undef SOLVE3D, N=1, NDTFAST=1 and DT=0.5 in ocean.in. The model ran successfully, but it was really slow, even noticeably slower than a 3D ...

d.kobashi

Dear All, Could someone please clarify that the time-dependent values in diagnostic files are averaged values or instantaneous values? I noticed that the timestamp of diagnostic files is not the same for history files, but the same for averaged files. I wonder if the diagnostic values are averaged ...

d.kobashi

John, Thanks for your reply. I modified the river forcing file as follows. dye concentrations to tag are 1. But I am still having the same error. dimensions: xi_rho = 671 ; eta_rho = 191 ; s_rho = 30 ; river = 58 ; river_time = 367 ; variables: float river(river) ; river:long_name = "River index ...

d.kobashi

Hi, I tried to use the water age function built-in ROMS to estimate water age (#define AGE_MEAN and #define T_PASSIVE). For this run, I have 6 dyes: 4 dyes from rivers, 1 dye in deep water, and another passive tracer. River forcing has river_dye_0X (X=1-6). I followed https://www.myroms.org/forum ...

d.kobashi

Thanks for your input, Ivica. I actually did change the coordinate variables from 1D to 2D and the result was the same. The problem about 1e+35 values in the log file comes from interpolate.F below. For Fmin and Fmax on the lines 133 and 134, Finp was empty. So I suspect ROMS did not read the data ...

d.kobashi

Thanks, John. It looks like that the forcing file you used for Sandy test case, i.e. romsforc_NARR_Sandy2012.nc, was interpolated into your parent grids already. Am I correct? Then you used the same file for the child grids without any modifications? I am not sure if this is correct, but I assume ...

d.kobashi

Hi, Can anyone tell me if the interpolation of forcing works? I mean that the interpolation is the interpolation done internally by ROMS. I am trying to create forcing file (parent and child grids); however, due to the large file size, I thought it should be better for ROMS to take care of ...

d.kobashi

Don't know why, but the error is gone after I changed nrrec from 0 to -1. Strange. Now the model is running, but the computational speed seems to be slow.

d.kobashi

Hi, I am trying to run the model with two-way nesting (parent and child grids). I was able to run spinup with lower DT (otherwise the model blows up) and then tried to do another run with larger DT using the restart file from spinup. The model ended up with the error below. PUT_REFINE2D - unbounded ...

d.kobashi

A good catch, John. There was a typo for dstart. Thanks for your help. -DJ

d.kobashi

John, Thanks for your reply. However, after the run with nrrec=0 as you suggested, I now have a new error as follows. It appears that ROMS cannot write time variable to the history file. The reason for the error is not a valid netcdf ID. Not sure why. TIME-STEP YYYY-MM-DD hh:mm:ss.ss KINETIC_ENRG ...

d.kobashi

Dear all, I am trying to run ROMS using the restart file; however, the model asked for a history file to run the model. I wonder if I can override the requirement. NETCDF_OPEN - unable to open existing NetCDF file: /scratch/user/d.kobashi/projects/hindcasts/projects/txla2/outputs/2010/ocean_his ...

d.kobashi

Hmm... I want to setup climatology and nudging for 3d momemtunm and tracers (temp, salt, dye_01) only for the parent grids of my nesting runs. So if I only need nudging for the parent grids , the setup in ocean.in for climatology and nudging is the following? LsshCLM == F F ! sea-surface height ...

d.kobashi

Thanks for your input. Hmm... I am a bit confused. I don't understand what's the point of providing climatology file for child grids for online nesting. If we do online nesting (either one way or two way), there should be no nudging for child grids (otherwise, there is no difference between online ...

d.kobashi

Thanks for your help. After I recreated forcing file based on your suggestion, I passed the error on surface fluxes and now I am getting a similar error for climatology file as follow. NETCDF_CHECK_DIM - inconsistent size of dimension: xi_rho 644 1112 in file: /scratch/user/d.kobashi/projects ...

d.kobashi

Hello, Thanks for your input. I tried your suggestion and I had the following error. NETCDF_CHECK_DIM - inconsistent size of dimension: eta_rho 400 872 in file: /scratch/user/d.kobashi/projects/hindcasts/projects/nwgom/inputs/frc/2013/nwgom_frc_2013.nc It seems that the forcing file for the child ...

d.kobashi

Hi, I have a question on nesting. I set up a refined grid and contact file to run a nested model. When I ran the model, I had the following error. NETCDF_CHECK_DIM - inconsistent size of dimension: xi_rho 644 1112 in file: /scratch/user/d.kobashi/projects/hindcasts/projects/nwgom/inputs/frc/2013 ...

d.kobashi

Hernan, Thanks for your input. Now, your second error implies that something is wrong with your coarse grid structure that is used to generate the refined grid. The S and R structures are dissimilar and do not include the same fields. You need to check S and R in the debugger to compare the field ...

d.kobashi

Hi, I am trying to create nested grid and contact netcdf file using ROMS Matlab routine. I made a child grid, but when I tried to create contact file, I had a couple of errors. By the way, I've created a grid file with spherical coordinate. First error is near line 720 in contact.m Undefined ...

d.kobashi

Thanks, Kate. Yes I actually checked the source code already and my reply did not go through for unknown reason. Indeed, in u3dbc_im.F, there are lines, IF (LBC(iwest,isUvel,ng)%nudging) THEN IF (LnudgeM3CLM(ng)) THEN obc_out=0.5_r8* & & (CLIMA(ng)%M3nudgcof(Istr-1,j,k)+ & & CLIMA(ng)%M3nudgcof(Istr ...

d.kobashi

Hi, I would like to set up spatially-varying nudging using netCDF (ocean_nud.nc) and would like to ask you how I can set up outgoing nudging (passive. outflow) when I activate RudNud in ocean.in. I checked d_nudgcoef.m and in d_nudgcoef.m, % In the North Atlantic DAMEE_4 application the nudging is ...

d.kobashi

Hi, I am having a strange error while running ROMS. When I turn off USE_DEBUG in coawst.bash , the compile goes well, but I get the following error while ROMS tries to create a restart file. STEP Day HH:MM:SS KINETIC_ENRG POTEN_ENRG TOTAL_ENRG NET_VOLUME C => (i,j,k) Cu Cv Cw Max Speed 0 14610 00:00 ...

d.kobashi

Yes. I update forecast/nowcast daily and for that, DSTART changes for every run. When I use file splitting function, the initial fields are not included (e.g. 1-year hindcast run), but for short-term runs, file splitting is not necessary for my purpose.

d.kobashi

John, Thanks for checking the code on your side. I appreciate your help (always). As for your comments, I still want to run long-simulation (1+ year) and for the purpose, keeping the file splitting function is necessary as without it, the history file created would be huge.... (FYI. the total size ...

d.kobashi

This is an update to my previous post. The version of ROMS does not seem to be anything do with whether history file includes restart record or not. However, I just found out that if I specify a non-zero value of NDEFHIS (I tested with NDEFHIS = 4320 (that is the same as NTIMES)), the history file ...

d.kobashi

Thanks, John. Attached below are some parameters in ocean.in I use for nowcast. As for NRREC, I use NRREC=-1 and I specify restart file of the previous run as ININAME. I use NDEFHIS=0 as I don't want to split the file, but I don't think that's the problem. When I used an old version of ROMS (COAWST ...

d.kobashi

Hi, I am working on operational forecast/nowcast and use restart file to run forecast/nowcast daily. Now I am in a strange situation that ROMS history file created daily has suddenly started including restart record in history file :? . When we run ROMS with restart file (assuming restart time is ...

d.kobashi

I used to use the following function. Worked fine.
http://www.mathworks.com/matlabcentral/ ... paint-nans
Use with caution.

DJ@TAMU

d.kobashi

You don't need to define TS_FIXED for tide-only modeling. Just constant tempe/salt as you specified. It looks to me that your problem may be something to do with open boundaries. What's your cppdefs and ocean.in? Also, why did you edit ana_tobc.h? I don't think I did that for tide-only modeling ...

d.kobashi

Splitting time step is a way to run a full 3D ocean model more computationally efficiently as baroclinic mode is much slower than barotropic mode. It is used for recent ocean models: structured, unstructured models alike. GETM, MOM, FVCOM etc. By the way, what I suggested was to identify the problem ...

d.kobashi

A few comments aside from what Kate suggested. 1. Turn off Wet/Dry and see if the model still blows up. 2. You said you turned on TS_SADVECTION, but your ROMS log says TS_C4VADVECTION. So I am confused. Don't use TS_SADVECTION. 3. Try other GLS mixing like k-omega, not k-e. 4. You max courant number ...

d.kobashi

However, with my new installation I don't have netcdf.mod or typesizes.mod anywhere, so I am back to my original error What OS do you use? Linux? If so, type >> locate netcdf.mod and see if you can find it somewhere. Or maybe the installation was not completed? I installed netCDF3/4 many times and ...

d.kobashi

In my build script I have now specified the following, but I still get the same error. export NETCDF_INCDIR=/apps/netcdf/4.2.1.1/include/Intel export NETCDF_LIBDIR=/apps/netcdf/4.2.1.1/lib/Intel Which version of ROMS do you use? A recent version of ROMS uses NC-config so for netCDF4, you don't need ...

d.kobashi

Why don't you use COADS or ICOADS dataset? I personally don't think you need atmospheric model outputs (e.g. ERA interim) to create dqdsst. Climatology should be fine. Some use a constant dqdsst over their entire model domain. COADS http://iridl.ldeo.columbia.edu/SOURCES/.COADS/ ICOADS http://icoads ...

d.kobashi

I don't think a python tool equivalent to the John's one exists. I searched for it before because I switched to Python. There are few python tools on tidal analysis as far as I know. I found the following. http://sourceforge.net/projects/tappy/ You can possibly write python scripts to create ROMS ...

d.kobashi

Ok. Hernan answered a part of my question in a different post related to appending additional variables to the existing tidal forcing file (see https://www.myroms.org/forum/viewtopic.php?t=3553). Google did not catch this one. I am still digging in more to understand why I have to manually specify ...

d.kobashi

Hi, I am a bit confused about tidal forcing file. I created tidal forcing netcdf file and when I ran ROMS for the Texas-Louisiana Shelf (actually COAWST, but Rutgers ROMS inside), I got the following error. GET_IDATA - incosistent restart and harmonics time: When I looked at tidal forcing file, ROMS ...

d.kobashi

Thanks John and Kate for input. Always helpful. tile!? :shock: my bad. Why didn't I think of that... Yes. the single core run worked and so did the modification that Kate mentioned for multiple core run. Thanks a lot. When I re-ran my analytical model, I saw abnormally high concentration at the ...

d.kobashi

Dear all, I am trying to run a simple analytical model (a rectangular-shape domain with uniform depth). I put M2 tidal elevation and current along the eastern boundary and radiation OBC along western boundary so that tides are radiated out. The northern and southern boundaries are closed. The grid ...

d.kobashi

My understanding is that COAWST is based on ROMS 3.4. The function you mentioned was introduced after ROMS 3.5. So I don't think you can use the function yet. I tried that before with an old version of COAWST and it did not work (revision 711). John is working on updating COAWST with a new version ...

d.kobashi

What are DSTART and TIME_REF in ocean.in? I had a similar situation recently for bry netcdf files. My problem was that I did not properly set time units in boundary netcdf files. I set time units as "bry_time:units = days since 1970-01-01 00:00:00" and that did the trick. DSTART was consistent with ...

d.kobashi

Thanks for your reply, John and Kate. I downloaded the code this February so I guess that was in the middle of transition .... I confirmed that the latest trunk (rev 736) does not have TCLIMATOLOGY in the code. Also, thanks for the link, John. I actually have been looking all over for a list of ROMS ...

d.kobashi

cd /scratch/saud/Projects/Upwelling/Build; /scratch/saud/ROMS/Compilers/Linux-ifort.mk -c -heap-arrays -fp-model precise -ip -O3 -free mod_kinds.f90 As Kate said, you need to know where ifort or mpif90 of intel fortran is located, not Linux-ifort.mk. The above line is supposed to be >> ifort -c ...

d.kobashi

I did that using COAWST for the East Australia coast and it worked fine. You just need to create separate input files for ROMS and SWAN. COAWST comes with user manual and matlab tools to create child grids and other forcing files. If you want to get source code of COAWST, you need to ask John Warner ...

d.kobashi

Thanks for your reply, Kate. I attach output of my grep. There are lots of hits. >> grep TCLIMATOLOGY */* My version of ROMS is a recent one (ROMS 3.7 rev 715). I downloaded it a couple of months ago. >> cat Version ROMS/TOMS Framework: Feb 10, 2014 =================== Copyright (c) 2002-2014 The ...

d.kobashi

Hi, I understand that some of the cpp options have been migrated from cppdefs.h into ROMS parameter file, ocean.in (e.g. open boundaries, TS_PSOURCE to LtracerSrc. etc.). When I checked a example of cppdefs.h and ocean.in, I saw some options seem to be on both cppdefs.h and ocean.in. I checked ...

d.kobashi

If you are after a GUI tool easy to use and if you use Windows, Delft3D RGFGRID may be your best option so far. You can create detailed curvilinear grids using the tool. Now you can even save grids as ROMS netcdf grid file with RGFGRID. But you will need to tweak a bit after you create a ROMS grid ...

d.kobashi

Hi mengqingjun First, you can check the post I just submitted. I am wondering how you gave the values of dQdSST to ROMS ? I meet a similar problem like yours. Without BULK_FLUXS,ROMS need only sstr,svstr,shflux,swflux,swrad.But like yours, I followed what Dr. Mark Hadfield did. Check the following ...

d.kobashi

Hi John, Many thanks for your comment. Sorry for the late response. I've just come back from an oversea trip. I have now a better understanding of heat flux on ROMS. I did some test about surface heat flux and got the result which I attach as a figure. Three cases were tested. (1) No surface heat ...

d.kobashi

Thanks for letting me know that wtype-grid has been included in your branch, Kate. I modified my version of ROMS based on your sea ice model and the model is now being tested (it is at least not giving an error so far). I agree with you and Hernan that it would be a good idea to associate water type ...

d.kobashi

Dear ROMS users/developers I am trying to use spatially varying gridded Jwtype in ROMS. I found a couple of days ago that in pyroms (https://github.com/kshedstrom/pyroms), there is a script, add_Jwtype_map.py, which creates a parameter, "wtype_grid" based on bathymetry. I am curious to know how this ...

d.kobashi

Thanks for your comments, Kate and John, I learned a lot about what ROMS does on ALBEDO thanks to your comments. Reading a comment from John, I am a bit confused about how ROMS reads forcing files. As with all forcing fields in ROMS, if an analytical option is not active then the default is for the ...

d.kobashi

Dear Rduran, Thanks for your comment. Not sure if you are aware of this, but after some search, I've just found his manuscript submitted to JGR (SST variability influenced by river plume). You can download it from the following link. http://ingria.coas.oregonstate.edu/pdf/cr_sst_2013_08_06.pdf ...

d.kobashi

Dear Kate and Rduran, Thanks for your comments. They are helpful. Kate, As far as I checked, ALBEDO cpp option is used in Bulk_flux.F and ana_srflux.h (I use COAWST which is based on ROMS 3.4). So if I need to include albedo, I also need to define BULK_FLUXES and ANA_SRFLUX . If that is correct ...

d.kobashi

Dear ROMS users/developers, This may be a 101 question, but I have a question about surface heat flux for my ROMS modelling. I am studying internal tides and mixing in shallow coastal waters. I saw some posts on myroms.org that the inclusion of surface heat flux from weather forecast/reanalysis ...

d.kobashi

Dear all, I am having a problem running ROMS for internal wave modelling. Compiling the ROMS code went well. But when I run ROMS, I've got the following error (x 12 times as I use 12 cores I think). At line 73 of file set_ngfld.f90 Fortran runtime error: Array reference out of bounds for array ...

d.kobashi

Many thanks for your prompt fix. I use ROMS 3.5. I replaced the old one with the corrected one as you suggested and then the 2d model runs like a charm.

Sincerely,

DJ

d.kobashi

Dear all, I have encountered an error when I tried to run a 2-D ROMS tide model for my study area. A 3D tide model run without problems and I am now trying to run 2D version of the 3D model. I use TPXO to get open boundary conditions along each boundary. After checking other ROMS community posts on ...

d.kobashi

Dear all I also had similar errors while compiling inlet_test case (revision 566), but mines are associated with MCT, which I compiled using the same compiler as the one I used for ROMS compile (intel fortran 11.1). I checked the website which Kate indicated (Errors at link time), but my errors do ...

d.kobashi

Oops. Why didn't I think of multiple TPAR files to set up OBC..... :oops: Many thanks, John. I will write some matlab script to automatically create TPAR files for operational forecasts. Will let you know how it works. Just one last quick question. We indeed need to include Hs, Tp, Dir and ...

d.kobashi

Dear John, Many thanks for your prompt comments, which are helpful and my apologies for that I did not provide enough info for you to comment. What I am trying to do now is to test operational capability of the ROMS-SWAN coupled models using NCEP operational forecast products as forcing and OBC data ...

d.kobashi

Dear ROM users/developers I have a question regarding how to create input files for the ROMS-SWAN coupling. What I am trying to do is to get wave parameters from NOAA NCEP global WW3 and to use them as open boundary condition for the ROMS-SWAN coupling to the domain of my interest (East Australia ...

d.kobashi

Yep. I saw the thread discussing OBC tidal forcing too. Following your comment, I wrote a script to check all grid data for all constituents and found that a few grids contained NaNs for Q1 constituent. :shock: As Q1 tide does affect little to my domain so I took it out and the model run without the ...

d.kobashi

Thanks for your input, Kate. I used OSU tidal prediction software (matlab version. otps2frc_v3.m). I followed the steps articulated on the ROMS tidal forcing page. (https://www.myroms.org/wiki/index.php/Tidal_Forcing) and run the following script. t=datenum(2007,1,1); tpred=datenum(2008,1,1); base ...

d.kobashi

Dear all, I would like some help from ROMS users to resolve a problem that I have for my custom ROMS run. Hope someone could help me resolve the problem. I run a barotropic current model for testing (by intel fortran compiler 10.1 for linux). I used tide (tidal elevation and currents) as OBC (using ...

d.kobashi

Thanks Hernan for your input,
You were absolutely right! My cpp option included "TIDES".

I changed it to something else and it worked like a charm...

Good to know how ROMS works. Still learning.

Thanks again for your help.

Kind regards,

DJ

d.kobashi

Dear ROMS users, I am a bit struggling to figure out the problem I am encountering on ROMS compiling. I have successfully compiled the upwelling example and recently yellow sea example. When I tried to compile my own model (barotropic model with winds and tidal elevation/current as OBC), I ...

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