Ocean Modeling Discussion

osean

Do you want to do this with Lagrangian particles, or Eulerian tracers? With tracers: You can do this with the sediment model. Configure it with just a single sediment class and set the sinking velocity you want. Turn off all the options for resuspension etc. (unless you ultimately those). You can t...

osean

Hi All I am trying to implement a simple tracer with a constant settling velocity in ROMS. So far I am able to set up a simple Lagrangian fluid particle by the FLOAT flag. But I don't know if there is a way I can set a settling velocity for it. Any guidance on how to do it / where to find the right ...

osean

Hi All I am attempting to calculate vertical eddy energy flux (<w'p'>) from my ROMS outputs. One trouble I am facing now is how to calculate pressure (p) that is needed for calculating the flux from output variables in roms_avg.nc or roms_his.nc Of course I would then need to interpolate to have w a...

osean

I am trying to find an efficient way to identify internal waves from variables in either roms_avg and roms_his files.

Wondering if there is any publicly available code that can search for IWs, mostly those at near inertial frequencies.

Cheers

osean

I am currently trying to set up a field of floats at initial condition. My thought is to have in total 8000 floats, filling up an 2D field with 200 x 40 floats along x and y direction. However it is not so clear in float.in file how I can set up something like this. ! Number of floats to release in ...

osean

I am attempting to implement Lagrangian floats into my idealised simulations. However after getting my head around the FLT_TEST case and playing with it a bit, I still cannot get my runs to work once I have the floats input set up. Here is the log - Operating system : Linux CPU/hardware : x86_64 Com...

osean

Where did you get vorticity and pvorticity outputs?

Curious

osean

Hi All I am trying to navigate through wiki roms to figure out what options I have for horizontal mixing of momentum and tracers. Currently I find there are four - which are UV_VIS2, UV_VIS4 - these two are well commented - and perhaps also TS_DIF2 and TS_DIF4 that have zero information provided? UV...

osean

Thanks for the information. After some digging I found it But I wonder if you know why in the flt_test.h there is no FLOATS flag, but the test case still runs normally and produces float output?? ** svn $Id: flt_test.h 1100 2022-01-06 21:19:26Z arango $ **********************************************...

osean

Is there a way to seed particle floats in ROMS?

I see that there is a float tracking test case, but the wiki page for it is nonexistent: https://www.myroms.org/wiki/FLT_TEST_CASE

Is a tutorial somewhere that can help me set up particle tracking in ROMS? Very lost in this

Thanks

osean

Similarly, Ur and Vr (bottom velocity above bed) writing also don't appear to be activated Qout(idUbur) == T ! Ur bottom U-velocity above bed Qout(idVbvr) == T ! Vr bottom V-velocity above bed Do they also need to activate some options? I can't find any info on this

osean

thanks - never done this before - If I activate GLS_MIXING, do I need to activate all the 'related' ones as well that are described on this page? ==> https://www.myroms.org/wiki/GLS_MIXING For LMD - do I simply activate it or is there anything I should be aware of? I can't find any instruction mater...

osean

I am trying to make use of the logical switch for 'depth of bottom boundary layer' - i.e. Hbbl switch in the roms.in file. I have set the following switches under the Logical switches (TRUE/FALSE) to activate writing of fields into HISTORY output file section to the following - Hout(idDano) == F ! r...

osean

Hello All, This might seem like a very basic question. Where can I find the exact linear equation of state used in ROMS? I see that in roms.in one can set Tcoef and Scoef (for thermal expansion and haline contraction coefficients) for linear EoS. But I am wondering if somewhere the isothermal compre...

osean

jpringle wrote: ↑Tue Oct 12, 2021 1:42 pm I have a python code to compute these from history file that is based on the ROMS Fortran code; ask if interested.
Jamie

Hello Jamie,
thanks - if you could share the python code that would be immensely useful
Sean

osean

I am in the process of doing some diagnostics of an idealized experiment which turned out pretty well. On the Wiki ROMS page, it looks like I should be able to get 3D relative and potential vorticity diagnostics in the diagnostic .nc file if I turn the logical switches on for pvorticity and rvortici...

osean

kate wrote: ↑Sat Sep 04, 2021 1:18 pm You can run for a bit with one output frequency, then restart with a different output frequency. Anything more fancy is going to take hacking the code.

I noticed that there's a restart file option. How does one go about restarting with a different output frequency from a restart .nc file?

osean

Hello All, I am trying to produce a year-long simulation, with high output frequency over a particular period of time. At the moment, I only manage to increase output frequency for the entire simulation duration through NHIS in roms_.in file: Output history, average, diagnostic files parameters. LDE...

osean

In this case, I am trying to figure out which variables go into m2obc and m3obc. For velocity field, would that be m2obc or m3obc?

Thanks

osean

Hello I am trying to figure out how to set up an open boundary condition for a domain I am attempting to create. It is a channel where N/S walls are closed, E boundary closed/radiation TBC, and W boundary open with a time-invariant flow prescribed, as attached in the figure below: BC.png Essentially...

osean

If you are using the latest version of the code, which I recommend using, you need to be sure that your roms.in is up to date. Compile with debugging flags so you get more information about the division by zero. We can get such errors when the arguments to MOD are zero or uninitialized. There are l...

osean

I don't think that is an I/O error: Note: The following floating-point exceptions are signalling: IEEE_DIVIDE_BY_ZERO ERROR STOP Something is wrong in your configuration in roms.in that you get a division by zero . I updated the code yesterday to remove those confusing I/O errors when you have a co...

osean

Hello ROMS experts I am moving back into office so now I have a Ubuntu linux workstation. I was running ROMS previously on my Macbook, which has been pretty smooth. Now switching to Ubuntu linux, I am running into some unexpected issues when I try to re-run some stuff. I have set up ROMS from scratc...

osean

HI Osean, our application has a vertical grid like the one you are aiming at. We achieved this with the vertical transformation formulation 2 and the vertical stretching formulation 3 with theta_b = 1.5 and theta_s = 1.0. Our vertical resolution ranges from 0.3m in places at the bottom and surface ...

osean

jcwarner wrote: ↑Mon Apr 12, 2021 5:08 pm here is a good start:
https://www.myroms.org/wiki/Vertical_S-coordinate

there is also an m file "roms_getnplot_grid_rutgers" that you can use to see what an adjustment to the various parameters will do to the vertical stretching.
-j

Oh this is very helpful, thank you!

osean

Hello ROMS experts I am currently looking for a way to modify the vertical grid scheme so that I can have increased bottom vertical grid numbers to resolve the bottom mixed layer, for example. Ideally, I would like to have a grid that has high resolution for the surface mixed layer and the bottom mi...

osean

Dear all ROMS experts I am very new to modelling and am trying to start from the very basics by modifying the bathymetry, grid domain, and wind forcing of the UPWELLING test case to an idealized exercise for my ROMS learning. My intent is to modify the UPWELLING test case: (1) the domain becomes big...

osean

You appear to be using a combination of Homebrew and anaconda so perhaps that is contributing to your issues. That said, in older versions of ncl/ncarg there was a separate library ( libncarg_gks_cairo.a) that had several added dependencies ( -lcairo -lfontconfig -lpixman-1 -lfreetype etc.). Some t...

osean

Try installing cairo and freetype (probably called freetype2) libraries. If they are already installed, make sure they are the 64-bit versions and are in the library search path. Thanks. I have installed cairo and freetype. But I don't know how to find out where they are located / how to add librar...

osean

Following up on the post above, I then made edits to FFLAGS in Darwin-gfortran.mk to allow argument mismatch. This then leads to a new error: cd /Users/sean/Documents/ROMS/plot/src/Bin/Build_plt; /usr/local/bin/gfortran -c -fallow-argument-mismatch -O3 cnt.f90 cnt.f90:1273:58: 1155 | CALL streamline...

osean

The plotting package still seems all very confusing to me. I tried multiple ways but still failed. Instead of using the makefile in src to make, I am now trying to build_plt.sh. I changed the USE_MY_LIBS to ON, and the following: case "gfortran" setenv NCARG_ROOT /Users/sean/opt/anaconda3/...

osean

make: /opt/gfortransoft/serial/netcdf4/bin/nc-config: Command not found If you have a modern netcdf-c and netcdf-fortran correctly installed, nc-config should be on your search path. Did you install them? What operating system is this? Your laptop or a major computing platform? Hello kate, thanks f...

osean

Hello I am following https://www.myroms.org/wiki/Plotting_Package_Installation page in an attempt to plot the output from the Upwelling test case. I don't know if this page is outdated or whether I am doing something wrong, I am a little lost at this step: Machine Dependent Include File Next you sho...

osean

1. I used homebrew, not macports, and had success. So if you're more familiar with homebrew take that route. 2. Looking through my notes, I believe I got the same (or at least a similar) netcdf error as you. I tried a bunch of different things but it looks like the fix came from altering the trunk/...

osean

That is correct. I thought I had replaced all the occurrences of 'ocean*' with 'roms*' in the wiki but I clearly missed some. I corrected several more pages this morning but, out of curiosity, on which page did you find the reference to 'oceanS'? Thank you so very much for your help. It is the wiki...

osean

Having gone through a rather tedious process of setting up ROMS, I think a new manual for installing ROMS on Mac OS would be extremely useful, for someone like me who is new to the modelling community and has very little clue what is going on, especially since the ROMS Mac page on WikiROMS is very o...

osean

I'm not sure where homebrew is getting their patches but they are missing some important things and are actually further from a usable product than the netcdf-fortran 4.5.3 release is. I believe home brew puts symlinks to all libraries in /usr/local/lib so, if you have the proper permissions, I wou...

osean

Your error is still in the linking. Those object files with no symbols are normal and most of them relate to the 4D-Var system which isn't used for the upwelling test case. From the paths you have shared, I'm assuming that you are using a Mac with Homebrew. What appears to be the issue is the 'nf-c...

osean

Having taken a more thorough look, it looks like the problem started after producing all the .f90 and .o files; the longer, more comprehensive version below, from the point where I think shows errors: ar: creating archive /Users/sean/Documents/ROMS/Projects/Upwelling/Build_roms/libUTIL.a /Library/De...

osean

I've run on Catalina. I haven't tried on Big Sur though. I'm very curious about ROMS performance on the new M1 chip so if you get one of those machines please keep us updated. Works fine for me on Catalina. You likely have to update macports. Hello both, thanks for your info. On Catalina I keep enc...

osean

At the start of your output from the build script, which 'my_build_paths.sh' does it say it's loading and does it match the path to the one you have updated. From your latest post of the ROMS link line it looks like there aren't any NetCDF libraries linking at all now. What is returned when you typ...

osean

At the start of your output from the build script, which 'my_build_paths.sh' does it say it's loading and does it match the path to the one you have updated. From your latest post of the ROMS link line it looks like there aren't any NetCDF libraries linking at all now. What is returned when you typ...

osean

In your build script enable "USE_NETCDF4". This will allow the build system to get the proper library locations and names to link your executable. I did turn on USE_NETCDF4. But somehow the problem still persists. I have attached below my my_build_paths.sh code for the gfortran section- I...

osean

Even I had a similar issue a few months back. For me what worked was checking my netcdf file, it's location where it's installed and passing on the same as exact location in the netcdf portion in makefile and buildfile. Then try to recompile it. FYI I was working on UBUNTU WSL for windows . Typical...

osean

I've run on Catalina. I haven't tried on Big Sur though. I'm very curious about ROMS performance on the new M1 chip so if you get one of those machines please keep us updated. Thanks! Interesting... I am currently on Catalina. Perhaps once I get it to work for the test cases, if I manage to set it ...

osean

I am at the step of building ROMS using build_roms.sh, with the new bash file that was updated on svn recently. But I encounter the following issue (see the end of quote) (base) XXX-MBP:Upwelling XXX$ ./build_roms.sh :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::...

osean

Hello ROMS community I am new to this, as a graduate student, starting on a project that involves ROMS. I currently work on MacOS environment (MacOS v.10.15.2 Catalina), and I plan to buy a new macbook for research use. The only information available on ROMS wiki was for MacOS X 10.5.4, which was th...

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