Ocean Modeling Discussion

lcbernardo

Looking through your original post again though, perhaps the resolution is simpler. I think I agree with Kate, that you try to download the ssh file directly to check if it really exists on the server. You might also try to check the corresponding HYCOM page for Glbv0.08 for information on missing ...

lcbernardo

While the GitHub site also contains some Matlab scripts, in the ROMS_Prep repository, there are codes written in Fortran that can be used to download and process HYCOM data for use as initial and boundary conditions. I have been able to use them with gfortran on Cygwin, but I suppose they also can ...

lcbernardo

You can probably try the tools available from this GitHub page:

https://github.com/NakamuraTakashi

lcbernardo

Hi Charles. Thank you for the detailed explanation of the functionality in the currently uploaded version. And as you said, I think the latest update which gives the option of using the mask or not when making smoothing and other bathymetry changes may indeed make possible what I wanted to achieve ...

lcbernardo

I'd like to report what seems to be a bug in the Gridbuilder MATLAB toolbox. I have been using it in Matlab R2019b, and I noticed that when I set a minimum depth and then perform some smoothing, within Gridbuilder it seems to be okay. But when I export to a netcdf file to create a ROMS grid, it ...

lcbernardo

Thank you so much for your explanation and suggestions Dr. Wilkin. Indeed it must be quite a task for Dr. Warner, and I've really grateful for the times he's been able to reply to me regarding concerns with the COAWST model. Now that my ROMS is up to date and I've been able to get it to work ...

lcbernardo

I finally got to work on this issue after focusing on other stuff. I had been using COAWST, but I then tried using the latest version of Rutgers ROMS and with this change somehow the issue I previously had did not occur (NaNs suddenly appearing in the outputs). I guess this question is off topic ...

lcbernardo

Thanks for replying Kate. My original intent was to add coastal river sources, but even with these turned off, the model output values for the BGC tracers seem to be going bad quickly. I tried both with a boundary conditions netcdf file (with values for all incoming tracers), and also with the open ...

lcbernardo

Thank you for your comments. To observe the output, I focused on the first hour or so of the calculation and set the output of the history files to print out data every timestep. What I observed is that while temperature and salinity look fine, all of the NEMURO related parameters were either ...

lcbernardo

Hi Kate, Thank you for your comments. To observe the output, I focused on the first hour or so of the calculation and set the output of the history files to print out data every timestep. What I observed is that while temperature and salinity look fine, all of the NEMURO related parameters were ...

lcbernardo

Hi Kate, Thank you for your reply. I'm trying to investigate the varinfo.dat entries, but now have come across more issues, this time even with the river sources turned off. For my test run with NEMURO activated, the 11 biological tracer variables are written to the output netcdf file, but when I ...

lcbernardo

Dear ROMS users, Although I have been using ROMS (particularly through the COAWST modelling system) for some years now, I recently attempted to start using the Nemuro ecosystem model. So far I have been able to get it to run using test values for the 11 biological tracers used in the model for both ...

lcbernardo

patrickm wrote: ↑Fri Dec 04, 2020 9:18 am NEW_S_COORD in CROCO corresponds to Vstretching=4 in ROMS/COAWST (first introduced in ROMS-UCLA in 2010)

Thanks Patrick! I really hoped to clarify this. I think I can with more confidence now look deeper into how I may be able to use both versions for my work.

lcbernardo

Thank you so much for your responses. They give me an initial idea at least of some of the options that I can look into. I don't know what the capabilities of PISCES is, but my ROMS "master" branch has the COBALT model. The person who put it into ROMS has moved on, taken a different job, and I'm ...

lcbernardo

Dear all, I had been a using Rutgers ROMS/COAWST for a number of years, but due to a recent change in my work place, I have now also been assigned to use the CROCO system. And though my previous experience has allowed me to understand the general usage, I'd like to ask for any advice or help ...

lcbernardo

Thank you so much for the clarification Dr. Wilkin! I think that I can indeed use this feature to try what I have in mind.

lcbernardo

Dear ROMS users, Lately I've been looking into creating a file for spatially varying nudging coefficients, to see if this approach can help improve my model results. By looking through some older posts, it seems that modifying the d_nudgcoef.m script is one way to do this, but then I've become ...

lcbernardo

I have somehow "resolved" my blowing up problem, but since I still haven't fully confirmed the main cause, I will continue to look into it. But to properly close this topic, I'd like to share what did and didn't work. Firstly, I attempted to decrease the time step DT and NTDFAST to the recommended ...

lcbernardo

After checking more closely, I found that the blowup occurred at a time very close to when a typhoon passed my study area. In my initial simulation, the blowup occurred just a few days after my start time, during which the approaching typhoon already seemed to be influencing the conditions in my ...

lcbernardo

Dear Kate, Zafer, and hpd14thu, Thank you for your additional suggestions and my apologies for the delayed response. I went into the New Year vacation and then had to work on something else these past two weeks. Anyway, going back to this issue... After checking more closely, I found that the blowup ...

lcbernardo

venuscheung wrote: ↑Wed Dec 25, 2019 6:08 am Thank you for your reply.

I have solved it by using ANA_INITIAL in my header file.

I'd like to clarify what you meant as you seemed to be using an initial condition file earlier. So instead of using an initial condition file, you edited ana_initial.h to input your desired initial conditions?

lcbernardo

Thanks for the reply Kate. I think they are indeed always dry, so I guess that the -100 values are most likely unrelated to the blowup. Actually, ALBEDO_CLOUD did have bugs, relating to fortran syntax. I reported it to Dr. Warner through email, and also was able to fix it. And the fix seemed to work ...

lcbernardo

Dear all, I'm now investigating some frequent blowing up in a model I've been running. It used to work without too much difficulty before, but after activating ALBEDO_CLOUD, for some reason it ends up blowing up after a few simulation days. Investigating the log file hasn't been helpful as the last ...

lcbernardo

I have recently build a ROMS grid using RGFGRID and QUICKPLOT, from Delft3D's Graphical User Interface (GUI), and pyroms ( https://github.com/ESMG/pyroms ). The main idea is to convert a delft3d grid (.grd) created with RGFGRID into .mat using QUICKPLOT. This will give you the grid vertices in a ...

lcbernardo

venuscheung wrote: ↑Wed Dec 18, 2019 8:39 am Sure. Would you mind to leave your email here?
As I want to double confirm the python code before posting it on here openly to prevent any misleading.

Thanks for double confirming the code. You can reach me at: bernardo.l.aa@m.titech.ac.jp

lcbernardo

Thanks all, I think i have solved the problem successfully by using a python code. I create my d3d grid and make bathymetry in delftdashboard and generate _roms.nc. Then I use my python code to generate the ROMS readable _roms.nc and convert it to swan.grd using COAWST matlab script. Let me know if ...

lcbernardo

You could read lon_rho, lat_rho, and h from the _roms.nc then use mat2roms_rps.m to generate a *.nc file. One issue I notice when using Delft3D to output the grid as *_roms.nc is that a line of zeros is added on all four sides of the variables 'lon_rho' and 'lat_rho'. So perhaps these segments need ...

lcbernardo

Hi,

Recently I've been needing to look into this too as I've been looking through some of my old Delft3D simulations, although I use mostly ROMS and COAWST now. I'd also appreciate information on how such a grid conversion can properly be carried out. I'm using Delft3D version 4.01.

Lawrence

lcbernardo

Hi Lizhicheng, Your rx0 and rx1 values are still too high I think. But I think it would be better to show your complete log file to see what other possible problems the model may have. As for bathymetry smoothing, you can try to use GridBuilder (https://austides.com/downloads/) or other tools which ...

lcbernardo

Hi Charles, I'd just like to share that I've been able to use GridBuilder for my relatively small domain without any issues after using the updated getDefaultBathymetry.m I'm finding though that the default coastline even at highest resolution seems to have some mismatch with some commonly used ...

lcbernardo

I've made a small fix to getDefaultBathymetry.m which is hopefully attached, if too few eTOPO points are found in the model domain this should ensure that the nearest array of depths that include the model domain are still returned. I'm not sure if this will help with the polar grid yet I'll have ...

lcbernardo

After looking through recent posts in this thread, I thought I'd try posting about some grid generation related issues I've been having. Though I've tried using Gridbuilder a few times before, it's only this week that I really started using it for an application I'm setting up. It works great for ...

lcbernardo

Thanks for the reply Kate! So scaling isn't so good for floats. I guess I'll have to be more strategic in my use of this option then.

lcbernardo

Thank you for the reply Dr. Warner. I'll look into these previous posts to see what may be helpful. But just basing on the explanation you provided, if the problem is the added time exchanging information among tiles, will this be particularly true for the floats option? Because if I don't use ...

lcbernardo

Dear ROMS users, I have encountered a strange situation when I use floats in ROMS (or in my case, COAWST using only ROMS). My application's grid size is 300 x 300, with 15 vertical layers. And I am trying to run a 60-day simulation with floats, and the total number of floats released is 149975. I ...

lcbernardo

Thank you for the bug fix. With this modification, the peaks in swrad in my application now occur at the expected times.

lcbernardo

Thank you so much Kate! Indeed, adjusting to the new style was able to solve the issue. Now cawdir_eval.F seems to be working as it was designed to do. I greatly appreciate everyone's kind assistance on this issue!

Best,
Lawrence

lcbernardo

Hi Kate, thanks for sharing a bit of history on the code. I think indeed other choices may have some problems. As a follow up to this issue, I think I found the source of the inconsistency and it was in the Nonlinear/bulk_flux.F of the COAWST version I'm using, in particular the lines: # if defined ...

lcbernardo

Thank you Dr. Wilkin for directing me to these sections in the code! I think I can see now how the inconsistency arises, though I'm also curious as to the reason/basis for the kludge. As you mentioned, it's something for me to look into further and to tweak.

Best,
Lawrence

lcbernardo

Dear ROMS users, I've encountered some confusion simulating water temperatures for my site. I have been running both Rutgers ROMS (circa October 2018) and ROMS-only COAWST (version 3.3) and there was a striking difference in the results (more than 1 deg C temperature difference), even when using the ...

lcbernardo

Dear ROMS users, I'd like to ask if this issue regarding the possible bug in ana_srflux.h has already been resolved. I ask because I'm using ROMS code updated up to circa 2018, and I find that if I convert the model outputs for solar radiation flux and surface net heat flux to local time, the peaks ...

lcbernardo

Thank you for your reply Christie! I appreciate the short explanation. I'll also try to use the Nautical convention instead for my runs as you recommended.

Lawrence

lcbernardo

The first few lines of my swan.in input file are: MODE NONSTATIONARY TWODIMENSIONAL SET DEPMIN 0.10 INRHOG CARTESIAN COORDINATES SPHERICAL Also, later in the file, I use BOUNDSPEC to define boundary segments, and use CONSTANT FILE to specify time series wave data. And in the data file, I provided ...

lcbernardo

Hi John, thank you for your reply. Actually I already sent you an email before and have already been using the COAWST system. So this question actually refers to the COAWST framework, even as I continue to use Rutgers ROMS for other applications. In my swan.in, I have been using CARTESIAN instead of ...

lcbernardo

Hi! Lately I have been coupling ROMS with SWAN and have selected some of the wave parameters for output and I'm confused about the units for Dwave, defined as the 'wind-induced wave direction'. It says 'degrees' (but it also has [radians] next to it, which is also confusing) in varinfo.dat, but is ...

lcbernardo

Dear ROMS users, I'm not sure if this is a simple question with an obvious answer. Lately I've become a bit confused regarding the vertical sigma layer configuration in ROMS, especially since I've been outputting the z_rho variable in my runs. When plotting temperature using the depth information ...

lcbernardo

Thank you for the link Dr. Warner. I'll see if I can use this when I get a chance to consult with our technical staff on the issue.

Lawrence

lcbernardo

Dear ROMS users, We've had this problem for around half a year already and have attempted working with the technical staff in our institution. However, the problem persists and I thought I'd try asking here in the forums. We're running ROMS on a parallel computing cluster, and when we use only 1 ...

lcbernardo

Thanks again for your thoughts. Since things haven't been really working well for me, I've been trying to nudge to a climatology now, in addition to using daily HYCOM data as lateral boundary conditions. I've had the best results so far when I set my *NUDG==1.0d0 and OBCFAC=100.0d0. And since I don ...

lcbernardo

Thanks for your thoughts on this Kate. I don't think I mentioned in on this post, but the grid cell size is 1.5 km on a side. But indeed, I guess I'll have to consider using more resolution. I've also come across your bathymetry tools on GitHub, which I would like to look into more, even if I'm not ...

lcbernardo

Thank you for your reply Dr. Warner. I have wetting and drying turned on, but the cells with a -100 are part of the permanent land mask. Even so, will it be useful to still change the value to something like 5 or so? But anyway, I did try to turn off WET_DRY, but the model still blew up, and at a ...

lcbernardo

Thanks for the clarification Kate! Nevertheless, determining the most appropriate values for my application is turning out to be quite a challenge.

lcbernardo

Thank you for your reply. I see. I guess that's what "inverse scales will be computed internally" implies. Anyway, even so, I'd like to verify using a concrete example. If I have TNUDG == 30.0d0 30.0d0, and my OBCFAC = 30.0d0, does this mean that my outflow (tracer) nudging time scale for is 30 days ...

lcbernardo

As the nudging parameters seem to be important for my current modeling runs, I've been looking at this more closely. !------------------------------------------------------------------------------ ! Nudging/relaxation time scales, inverse scales will be computed internally ...

lcbernardo

I'd like to post an update on this problem, after trying out some of the suggestions. First, after checking the log file, I found that the blowup occurs at a grid cell which is at the westernmost tip of an island, and at the surface level (NaN values appear). The depths in the immediate area are ...

lcbernardo

Dear Dr. Warner and Dr. Wilkin, Thank you for sharing your thoughts and suggestions regarding how to possibly resolve this issue. Indeed my modeling domain includes some relatively steep bathymetric features, and I'll try to investigate the blowup more closely using the restart file as basis, and ...

lcbernardo

Dear ROMS users, I'm encountering a problem using the GLS mixing option (k-epsilon in my case). In most ROMS configurations I've seen in the forums and other sites, if GLS mixing is used, the following combination of options is usually set in the header file: # if defined GLS_MIXING #define KANTHA ...

lcbernardo

Hi everyone. I have been working on my ROMS simulation for a part of southwestern Japan for quite some time now, but I could not seem to properly reproduce the vertical stratification, at least in comparison to the Global HYCOM model I use for the boundary forcing (please see attached PDF file, as ...

lcbernardo

Thank you for sharing the link to the manual, and for explaining the choices for your Arctic case. I see. So I guess selecting the parameter values is in a large part application-dependent, and you need to work towards the most realistic solution possible. I greatly appreciate your help!

lcbernardo

Thank you for the explanation on the use of nudging and the implications for the model output. I'll think about the points you mentioned to help guide me through the numerical experiments I'm conducting. Also, I'd like to get a more quantitative sense of "strong" and "weak" nudging in terms of TNUDG ...

lcbernardo

I am now running a simulation for the southernmost Ryukyu Islands in Japan, forced mainly by Global HYCOM, tides, and an atmospheric model. And to test the model performance, I have been comparing time-series outputs to field observations of temperature. And although there is reasonable reproduction ...

lcbernardo

Thanks for your advice Kate! I'll study the paper then for starters, and see how I can proceed.

lcbernardo

Hi everyone. As my modelling study sites often feature complex bathymetric features, I would like to learn more about properly running a pressure gradient error test. And although I have a general idea after reading many posts about it, I'd like to clear up some of my confusions about it, which are ...

lcbernardo

Hi Kate, Thank you for your reply. I have been conducting tests as you have suggested, and indeed there comes a point where even doubling the amount of processors hardly has any improvement on performance. I have been going about this blindly previously, so thanks for pointing me in the right ...

lcbernardo

Hi all, I am a PhD student with an interest in physical oceanography and ecological modeling. Though I am able to perform modeling runs using ROMS, there are still many aspects that I do not fully understand and would like to know more about. Like most members, I'm trying to find the best ...

lcbernardo

You could also use Python pyroms module which can be found in following link, https://github.com/kshedstrom/pyroms it also has option for linear programming approach to smooth bathymetry and as i know, it also supports Vstretching = 4. I hope it helps. Thank you turuncu! I haven' done much Python ...

lcbernardo

rtopper wrote:A linear programming matlab code can be found here.
However, these matlab scripts seem to be 6 years old already. For instance, Vstretching = 4 is not supported.

Hi rtopper, thank you for pointing me to this link! I'll give the scripts a try.

Lawrence

lcbernardo

Dear ROMS users, As proper bathymetric smoothing is necessary for model stability, I've been looking to experiment more on testing different smoothing algorithms. While looking through the repositories and other public sites, I've been able to find matlab tools for applying the Shapiro and Laplacian ...

lcbernardo

Lawrence have you considered doing the particle tracking in ROMS? While I am asking, I wonder if anyone has compared the accuracies of the two approaches. I have always assumed the ROMS approach could be more accurate, since the positions would usually be updated more frequently than one would save ...

lcbernardo

Yes, that would do it. I believe the code will only reflect a particle 3 times before it gives up and calls it out of bounds. If you would like to ignore these particles, you can change the error flag towards the bottom of LTRANS.data to 3. It will set those particles out of bounds, but continue to ...

lcbernardo

Hi Ian, Thank you for your reply, and for the clarification on how LTRANS uses the grid information. I think I can now understand what seems to be happening. I can run make successfully, and the error I get upon running LTRANS.EXE is the following: ****** BEGIN ITERATIONS ******* write output to ...

lcbernardo

Dear all, Lately I have become interested in using the LTRANS model to run particle tracking simulations. I've been able to get it to run successfully using a ROMS simulation with wetting and drying turned off. However, when I tried a similar simulation with wetting and drying turned on, I received ...

lcbernardo

Hi everyone, Up until recently, I had been using the ROMS Plotting package to visualize my modeling results. However, when I started doing modeling runs with WET_DRY turned on, the plot outputs became strange, especially when plotting velocity vectors and magnitudes. It seems that previously there ...

lcbernardo

Thanks for the reply Kate! At least now I know that TIME_REF and DSTART are set properly. As for the tides, I followed the instructions (with a few modifications due to the differences in matlab versions, etc.) described for OTPS tides in https://www.myroms.org/wiki/index.php/Tidal_Forcing . The ...

lcbernardo

Hi everyone, I have been able to successfully run ROMS but have gotten a little bit confused with the time stamp variables DSTART, TIDE_START, and TIME_REF. I created a boundary conditions file which runs from May 15 to September 30, 2013, with a daily time step. Suppose I want to start the model ...

lcbernardo

I see! Thank you for clarifying, and for directing me to the get_coast.m script. Creating the file manually does not seem trivial indeed. I have worked with the GSHHS shoreline dataset before using a different application, and my sites do appear when using the full resolution global dataset. If I ...

lcbernardo

Thank you for the explanation Prof. Arango. I will initially attempt to make simplified coastline files for my study domains. In one of my modeling runs however, parts of Taiwan make up some of the land areas. I assumed that perhaps the global_inter.cst would represent Taiwan even coarsely. But I ...

lcbernardo

Hi everyone, I only recently got to compile the ROMS Plotting Package on my system and have enjoyed using its plotting features. However, as my domain is quite small, it doesn't seem to appear in any of the coastline selections. If I want to create a custom coastline file, are there any available ...

lcbernardo

Hi everyone, Today I tried compiling ROMS on a new computer system in our laboratory. It was a challenge finding all the system prerequisites, but somehow I got it to compile. The netcdf I am using is netcdf-4.1.3, which would not compile properly unless I set the options --disable-netcdf-4 and ...

lcbernardo

Hi DJ and all, Thank you for the explanation of the time-splitting feature. I'll try to look more into the details as I become more familiar with the model. I'd like to report that with my recent runs, the early blowing up problem stopped occurring after doing some bathymetry smoothing. Now I'm ...

lcbernardo

Hi Kate, Thank you for the guidance on selecting the proper timestep. In numerical models I've tried before, ocean or other, selecting the proper timestep indeed involved something similar to what you have suggested. What's new to me is the use of not one but two (barotropic and baroclinic), which I ...

lcbernardo

Hi lanerolle, Thank you for your suggestions. I'll try not using the spline-related schemes in one of my test configurations. As for the timestep, I was of the thinking that it was already very small given that the horizontal grid resolution is greater than 1 km. But maybe it is necessary to handle ...

lcbernardo

Hi DJ, Thank you for the additional comments and suggestions. So far, doing some bathymetric smoothing seems to have changed the results somewhat, but indeed, I have to be careful about overdoing it. I'll also turn on the diagnostics for my succeeding tests. I also want to maximize the available ...

lcbernardo

Hi Kate, Thank you so much for pointing this out, and I'll remember it as I continue my learning. I'll attempt some bathymetry smoothing and see what difference it can make. In relation to this, when I was simulating smaller domains using other models, I would start with a relatively "simple ...

lcbernardo

Hi everyone, I am quite new to ROMS and would like to know how to use it properly. So far, I have successfully run some of the test cases, and also tried running simple coastal applications for some of my study sites. For these cases, I did not really need to have 3D boundary and initial conditions ...

lcbernardo

Hi Kate,

Thank you for your reply and advice. I'll look more closely into the _FillValue attribute. I'll also try getting rid of the wonky values and see what happens with the model run.

Lawrence

lcbernardo

Hi everyone, I have a simple question regarding land boundaries/land masking in the ROMS model. I have been modifying some of the ROMS matlab scripts for creating initial and boundary conditions for my study site, and I notice that in the temperature and salinity fields, the value 65535 is inserted ...

lcbernardo

Hi everyone, I think this is a very basic question for many users, but it's been on my mind for quite some time now and I've yet to find a satisfactory answer for my better understanding. I have been using Delft3D to run hydrodynamic simulations for several years now and have been able to have some ...

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