Ocean Modeling Discussion

xupeng66

Hello,

I was wondering if I could add more digits to the index of the name of an output file. For instance, changing 'roms_his_0001.nc' to 'roms_his_00001.nc'. I would appreciate it very much if someone could point me to the source code where the filename convention is set.

Many thanks!
Guangyu

xupeng66

Thanks for the detailed explanation, John. To answer your question about the small viscosity and diffusivity computed using MY25, there is no surface or tidal forcing in my idealized simulations. The dynamics are driven by the lateral boundary conditions constructed from daily averaged output of a g...

xupeng66

Here is a follow-up on Parker's questions. While inspecting the vertical eddy viscosity and diffusivity computed by turbulence closures in ROMS, I found that the results were different by several orders of magnitudes between GLS and Mellow-Yamada Level 2.5 in an idealized simulation of the circulati...

xupeng66

Hi All, I am writing this post to let everyone know that the problem with two-way nesting that prompted me to start this thread has been resolved by John Warner after revising the treatment of fine-to-coarse information exchange in nesting.F. The details of those changes are described in this ticket...

xupeng66

Hi All, sorry for taking so long to write back. To answer Stef first, I read your old post and see how that could be problematic. But I do not think that is the cause because that issue seems to affect the input of information from coarse to fine grid and thus the artifacts seen in my results would ...

xupeng66

Hi All, Here are some more test results from a realistic experiment. The model grids include a coarse grid and a fine grid embedded within that is centered at the Axial Seamount in the Northeast Pacific. The top of the seamount is at 1500 m depth. The grids were built using the fine-to-coarse approa...

xupeng66

Hi All, I have done a few more tests over the past couple of weeks. In these new tests, I have removed bottom topography, open boundary, and surface forcing so that the simulations are forced with tides alone. Although this did not solve the problem of those artificial stripes in sea-surface gradien...

xupeng66

As you know time stepping in ROMS is a elaborated and complex beast and exchanging info between grids for fast varying variables is a nighmare. If you are modelling non-tidal, slowly evolving dynamics you are most likely OK. However, if you are in the space of high frequency motions then, I think, ...

xupeng66

Yes, I recall issues with the global attributes. In such cases, I manipulate the global attributes using my matlab/netcdf functions that are distributed in the ROMS Matlab repository: >> Imin=nc_getatt('my_file.nc', 'parent_Imin'); >> Imax=nc_getatt('my_file.nc', 'parent_Imax'); >> Jmin=nc_getatt('...

xupeng66

Building the grids from fine-to-course using an intermediate grid is the way to go! You will have the target bathymetry in the finer grid and can have smooth transitions in the bathymetry gradients when coarsening. You will have all the needed grid variables in the contact points and masked areas: ...

xupeng66

I just updated the ROMS Matlab repository. Check :arrow: trac ticket for more information. Check function roms_metrics.m and study it. Notice that the function grid_metrics.m is deeprecated and will be r emoved in the future :!: Hi Hernan, Here is one quick update. I have just tried roms_metrics.m....

xupeng66

What software did you use to generate your original GRID NetCDF? Many users really miss the fact that although the application has a spherical grid, it is highly recommended to have the associated Cartesian coordinates to compute the metrics pm and pn since ROMS computational grid is in curvilinear...

xupeng66

Yes, that's the way to build complicated grids. One thing that you may consider is to avoid sudden bathymetry changes like seamount and ridges across the contact areas between coarse and fine grids. I have done telescoping grids in the Middle Atlantic Bight, which include the Gulf Stream, with tida...

xupeng66

Thanks for your reply, Hernan. I agree that having the nesting interface go through steep topography is not a good idea. However, in my case, it is hard to avoid abrupt changes in bathymetry since my focus site is on the crest of a linear ridge so the interface is bound to cross the ridge at some po...

xupeng66

I just took another look at my old results and it turned out that the horizontal stripes in eta gradients were also present. I missed that because I did not think to check sea-surface gradients back then. That said, I also reread Arango's post on setting up nesting grids: https://www.myroms.org/foru...

xupeng66

There is approximately 5km between the stripes and the barotropic wave speed is 166m/s, so there is a period of 30s, which is in sync with the baroclinic time step? So assuming the signal is generated at the nesting boundary and propagating into the fine domain, maybe check the effect of the cpp op...

xupeng66

Hi John and Ivica, As Ivica suspected My feeling is we have problem with grids time stepping mismatch and to eliminate this I will run both grids with the same time stepping , I reduced my coarse-grid time step from 30 sec to 10 sec to match the one used for the fine grid. The refinement ratio betwe...

xupeng66

Hello, I have done a couple more tests and found that those artificial stripes in sea-surface gradients only appear when tidal forcing is applied. Those stripes disappeared when I turned off tides. My understanding is that tidal forcing is applied at the open boundary of the coarse grid in a nested ...

xupeng66

Hi Ivica, I think the difference in bathymetry between the grid file and the output file you see is the same as what I saw in my previous test. See the quote below from one of my earlier posts. Second, I have compared the fine and coarse grid bathymetries in the corresponding history files to make s...

xupeng66

either way please let us know. would like to figure this one out. Here are my new test results. The first three files shows the flow velocity at 2100 m depth and the last three plots show gradients of sea-surface elevation as suggested by Ivica. I have also attached my grid files and contact file. ...

xupeng66

I never saw anything like you are showing for 2-way nesting (3 grids) in our Mid-Atlantic Bight model. Maybe we need a comparison of what our respective codes generate for the contacts point file. we have a 3 nest of USeast - Carolinas - Outer Banks and i am not seeing this behavior of the currents...

xupeng66

the exterior points of the child grid are replaced with information from the contact file during initialization, in get_grid. At those points, data is interpolated from the parent and the nesting needs characteristics of the parent at those locations. I have found some issues with this for the mask...

xupeng66

Hi All, I have done a few more tests since my last post on this issue. The following are some interesting new findings. First of all, as suggested by Stefan, I did a test wherein the fine and coarse girds share the same bathymetry. Surprisingly, the problem with the nesting interface is still there....

xupeng66

The removal of unnecessary repeated operations in nesting was reported in this ticket: https://www.myroms.org/projects/src/ticket/861 You can find notes like this by going to the search box in trac https://www.myroms.org/projects/src/search I simply entered "nesting" and the ticket was th...

xupeng66

Gents, you are running the latest ROMS version with one/two-way nesting constelations so possibly have the answer from the head; I read long time ago about speedup of nesting algorith in ROMS by excluding some vertical interpolation, masking etc. My question is what are the steps and how to use tho...

xupeng66

If the parent grid discrete stencil for advection and/or diffusion spans, say, 3 parent grid cells then do we need to match bathymetry precisely over this range, which would be refine_factor times the 3 parent cell stencil width. Yes, any insight into this would be great! If I recall correctly, my ...

xupeng66

I have been working on the nesting for a while now. There are some simple steps that i can take to check on a few things. Is your setup easy to share out? what ts_advection are you using? time steps? -j The simulation I am doing has a lot of input nc files that contain information on surface forcin...

xupeng66

I think your suggested test is a good idea. By limiting the fine2coarse contact zone to a narrow band around the nesting boundary, the two-way nesting code may also become more efficient since the costly interpolation from the fine to coarse grid is now done over a much reduced number of grid points...

xupeng66

Thanks for your reply, John. Your point makes sense to me. I initially thought the problem was limited to the bathymetry difference near the nesting interface. But my attempts to relax the fine-grid bathymetry towards the coarse-grid bathymetry at the interface did not make any difference. So the pr...

xupeng66

Hi All, Here is a problem that I have been struggling with for quite a while. I would like to set up two-way nested simulations to study the small-scale dynamics that are influenced by topographic features such as ridges and seamounts. I have done a few experiments so far, but there is one problem t...

xupeng66

Hi John and Stephan, I have finished a new run wherein the bathymetry is refined within the child grid. I did not make any adjustment to the refined bathymetry near the nesting interface since I mainly wanted to see how the nesting works in the presence of the differences in bathymetry across the in...

xupeng66

Thanks for your quick reply, John. I have increased the resolution of the bathymetry for the small grid. I will post the results from this new simulation once it is finished. In the meantime, there is another technical issue that I ran into when I was preparing the nested grids. I found that for som...

xupeng66

Hello, I have recently finished a two-way nested simulation to study the dispersal of tracers from an underwater volcano. The attached is an animation showing the preliminary results. Basically, my grid configuration is of the refinement type with a small fine grid (blue box) embedded inside a big c...

xupeng66

Thanks for explaining, John. I now have a better understanding of how bottom heat/salt fluxes are treated in ROMS.

xupeng66

Hello, I have a question about the CPP option 'scorrection'. In set_vbc.F, that option appears in the lines below. My understanding is that, when 'scorrection' is defined, the surface freshwater flux 'stflx(:,:,isalt) will be corrected by multiplying with the surface salinity. If so, what happens to...

xupeng66

I looked into the source code and found that 'bhflux' is heat flux density in 'watt/m^2' as listed in varinfo.dat. After being read from the external forcing file, 'bhflux' is converted internally to knematic heat flux in 'deg C m/s'. The corresponding variable in ana_btflux.h is kinematic heat flux.

xupeng66

Hello, I have been using ana_btflux.h to define analytical bottom T and S fluxes in my simulations. This is very cumbersome in particular when I need to specify time-varying fluxes at discrete locations. I am thus curious to know if those bottom fluxes can be read from an external NETCDF file like t...

xupeng66

Many thanks for all your explanations, John. I now have a much better understanding of the use of tidal forcing and associated boundary conditions. My idea of nudging to climatology for 3D velocities is that I am hoping such nudging can dampen the waves (e.g., baroclinic tides) not present in the op...

xupeng66

Hello John and All, After some more digging, here is my latest understanding of open boundary conditions of 3D velocities in the presence of tidal forcing. It appears to me that there is no need to add tides to the 3D non-tidal velocities used as boundary conditions even when nudging is on. This is ...

xupeng66

I did the test John suggested. It turns out that changing the boundary conditions for 3D variables from 'RadNud' to 'Rad' has backfired in a big way. As shown in the attached diagram. The simulated flow field is completely overwhelmed by the rim currents. This sharp contrast with the previous result...

xupeng66

Thanks again, John. In my ROMS simulation, the non-tidal variations in sea level and velocities (both 2D and 3D) are introduced from the daily reanalysis product of the global ocean model NEMO. I created the boundary condition file by interpolating the NEMO outputs onto the ROMS grid points on the f...

xupeng66

Many thanks to your replies, Miguel and John. I did a little bit more fiddling and found that the a lot of the rim currents were caused by forcing volume conservation at the four boundaries as John pointed out. I now see that conserving volume no longer makes sense for a regional simulation when the...

xupeng66

Hello, I have a few general questions about adding tidal forcing in a realistic simulation. The attached diagrams show the flow velocities at 1500 m depth near Axial Seamount in the Northeast Pacific from two simulations: one without tidal forcing and one with it. The open boundary conditions used a...

xupeng66

Thanks a lot, Kate. I added ANA_BSFLUX to my cpp list and it solved the problem. I had thought the ANA_BTFLUX flag covered both temperature and salinity, but apparently an additional flag is needed for the latter. Cheers!

xupeng66

Hello, I have a question about the variable 'bwflux', which according to the metadata in varinfo.dat is the bottom freshwater flux. I suppose that variable is used for simulating offshore groundwater discharge. However, I could not find where that variable is used in the source code. The problem I h...

xupeng66

Hello, I have a question about the direction of the bottom fluxes specified in ana_btflux.h. When the variable 'btflx' is assigned a positive value for temperature at a given location on the bottom, does that make that location a heat source or sink? I did some idealized simulations to test this. I ...

xupeng66

Hello, I think I have found the cause of problems. It turns out that I forgot to specify the horizontal and vertical advection schemes for temperature for the fine grid. I feel frustrated that it took me so long to spot such a simple mistake in the model setup. The roms.in file I used for the nested...

xupeng66

Thanks again for your feedback, Arango. Those animations were generated from a serial run that finished without apparent blow up. The error message was actually from a debug run, which I now realize was in barotropic mode by default. So I now see that the error message is not related to the numerica...

xupeng66

Hello, Here is follow-up on a problem I posted previously. I did a two-way nested simulation of the outward propagation of surface gravity waves from the a collapsed sea-surface mound (see attached animation). The horizontal resolutions of the small domain is 5 times that of the large domain. There ...

xupeng66

Thanks a lot! I have finally found time to come back to the simulations. Yes, changing to use different grid points in X and Y directions did the trick. The simulation now runs without a hitch in both serial and parallel modes. This is an important lesson for me going forward. I will also remember t...

xupeng66

Any idea?

xupeng66

Hello, I have done an idealized simulation to test the performance of two-way nesting in allowing surface waves to propagate across the nesting interface. As shown in the attached animation, my domain includes a small grid embedded in a large grid. The grid spacing (800 m) in the small domain is fiv...

xupeng66

Hello,

Here is a simple question. I am wondering if there is a way to assign different numbers of processors for different grids in a nested simulation. If not, does it mean that all nested grids have to have the same number of segments?

Thanks!

xupeng66

Thanks for the useful tip, John. I will look into the distributed soliton case.

xupeng66

Thanks to all of you for your replies and sharing your exiting results. I will go read the references you recommended.

Lars, I am curious to know if the two-way nesting method you implemented available in the latest public version of ROMS? Or is it a custom build that needs modified source code?

xupeng66

Hi Kate and All, I am working on setting up a new simulation to test the ability of the various open boundary conditions to let external information enter the domain. My test case features a geostrophic surface eddy that moves into the domain from one open boundary and leaves at another. For the sta...

xupeng66

Hello, I have done a couple of more tests. As Kate said, the Chapman+Flather and Chapman+Shc combos both work better than the radiation boundary condition+nudging. I have attached the new animations that show almost zero reflection from the boundaries. My nest step to add stratification and do some ...

xupeng66

Thanks a lot for both of your replies. My simulation is essentially barotropic but the setup is in 3D with the cpp flag 'SOLVE3D' on. I did that because the 2D mode did not work due to a bug in the source code, which has been fixed by the developer. I will try the other conditions that you recommend...

xupeng66

Hello, I have done some tests to investigate the performance of various open boundary conditions available in ROMS. The setup of my simulation is pretty simple, which starts with a Gaussian-shaped mound that collapses at t0, which generates outward-propagating surface waves. There is no stratificati...

xupeng66

Thanks a lot for the quick fix. I have just tried the new code and it works for the barotropic case now

.

xupeng66

I think I have solved the problem. It turns out that I did not turn on the logical switch "Lm2CLM" in my ocean.in file. I had thought that that switch only needed to be turned on when reading climatology data from an external netcdf file. I now see that that switch needs to be on when usin...

xupeng66

Hello, Here is a problem I have with using analytical climatology. I got the following error message when I set 'LnudgeM2CLM == T' in ocean.in. "Attempt to use pointer UBARCLM when it is not associated with a target". It seems that the analytical climatology defined in ana_m2clima.h is not...

xupeng66

Thanks a lot! Glad to know there is an easy fix.

xupeng66

Hello, I tried to run the 2D Canyon example but got the following error in compilation: inp_par.f90(107): error #6911: The syntax of this substring is invalid. [HADVECTION] ThreeGhostPoints=ANY(Hadvection(:,:)%MPDATA).or. & ---------------------------^ This error seems to only occur in the 2D ba...

xupeng66

Thanks for explaining, John. I will set up a test run and keep you posted on how it works.

xupeng66

Kate, I agree that the proof of the pudding is in the eating so I will have to try and find out how those open boundary treatments work. John, thanks for your reply. On page 17, lines 5-7, the authors state that "Perkins et al. (1997) suggest that continuity at the open boundary is improved by ...

xupeng66

Thanks, Kate. I am trying to build a regional simulation using the global reanalysis products from NEMO as open boundary conditions/forcing (i.e., one-way nesting). In this case, should I use the radiation+nudging open boundary conditions and radiate out only the difference between the interior solu...

xupeng66

Hello, I have a question about the radiation boundary condition that is currently implemented in ROMS. For the example shown in Marchesiello 2001, the authors mention that only the difference between model and climatology is radiated out at the open boundaries. I looked into the latest source code o...

xupeng66

Hi All,

I have a question regarding the tidal ellipse inclination angle "tide_Cangle" in the forcing file. I am wondering if "tide_Cangle" is the angle between the semi-major axis and east or it is the angle between the semi-major axis and the xi direction.

Thanks

Guangyu

xupeng66

Got it. Thanks a lot!

xupeng66

Hi All, I found that the coordinates in the output netcdf files (e.g., ocean_his.nc) of my simulation are lat/lon despite that I only defined the x/y coordinates of each grid points in the grid file. The lat/lon coordinate variables in the output files are all zero matrices. I am wondering if the th...

xupeng66

I use Matlab so I guess the dimensional order of the grid variables has to be (xi, eta).

xupeng66

Hi All, I managed to solve the "exceeds dimension bound" error mentioned in my previous post by switching the dimension order of the variables (e.g., x_rho) in my grid file from (eta_rho,xi_rho) to (xi_rho,eta_rho). I am wondering if this means ROMS actually requires a fixed dimension orde...

xupeng66

Hi All, I have been having the following error message when running my simulation: GET_GRID - error while reading variable: x_rho in grid NetCDF file: MEF_grid.nc ERROR: Abnormal termination: NetCDF INPUT. REASON: NetCDF: Start+count exceeds dimension bound My grid is 370 by 210 (eta, xi). The corre...

xupeng66

Yes, the baroclinic waves are slower. The 3-D timestep is more costly than the 2-D timestep. The purpose of the time splitting is to save computer time - otherwise you compute everything at the barotropic timestep limit. Yes, ROMS can model things at 5 m resolution. It has successfully simulated a ...

xupeng66

Yes, that's a good guess for barotropic timestep. If the timestep ratio is 10-20, then you try that and see what happens. ROMS will report Courant numbers during initialization - and a lot more besides. Best is to just make some guesses and see what you get, then adjust as needed. Hi Kate. Thanks a...

xupeng66

Hi All, I have a question about determining the time-step size. For example, my grid has a uniform 5 m spacing in both xi and eta directions. The water depth is about 2000 m. The CFL condition for 2-D advection equation is Cdt/dx<1/2. Assuming C is the shallow water wave phase speed C = sqrt(gH) ~ 1...

xupeng66

Thanks a lot for the prompt reply Kate. I have another question about setting the time step size. I will post it in a separate post.

xupeng66

Hi All, I am fairly new to ROMS and have several questions regarding setting up the grid file. First, I want to know if I need to define the sigma-coordinate parameters: theta_s, theta_b, Tcline, Hc, etc., in the grid file? Second, do I also need to define the s-coordinate and the value of the stret...

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