Ocean Modeling Discussion

stef

think of the beach, and the tide (or surge) coming in and out. what is the horizontal distance from the high tide line to the low tide line - that is the what you should think about.

Good point, thanks again for your help!

stef

I think at 12km your spacial scales are probably not resolving those wet-dry processes. Thanks for the reply, that makes sense. I have a nested toy setup and tried to keep the processing of the grids identical as far as possible. So I have not used a minimum depth at all, even in the coarsest grids...

stef

I have a grid with 12km resolution and dcrit=0.1. Is this reasonable? I have been looking at a specific blowup and I'm wondering if there is an instability caused by the combination of wet-dry flux-inhibitor and the multiple time levels used in the predictor-corrector scheme. The "three-time" Adams-...

stef

Update: note that there is a problem with the patch in that the wet/dry flux limiter (i.e. suppress outflow from a dry cell) does not work at the boundary. An already dry cell adjacent to the boundary may still export water out of the domain, depending on the boundary condition. It could be fixed si...

stef

I should say that the "mod_stef.F" is very messy. Sorry.

The only variables needed are the ones used in step2d.

stef

Hi, Thanks for your email, I'll respond tomorrow, meanwhile I attached the patch. Please note: *) Some (much?) of this may be incorrect. I'm a beginner. My approach was "if I get a reasonable result, it's good enough for now". *) I have not really understood MPI yet, in particular, in the end of ste...

stef

I wrote a blog post [1] about my experience using ROMS in 2d setups with grid nesting and wetting/drying. Very early stage, but if anybody is interested in this, I appreciate comments/suggestions, in particular if you are working on new code that is being pushed to the repository in the near future....

stef

In the first post of this thread it says: u(XI,ETA)=u(LON,LAT)*cos(angle(i,j))+v(LON,LAT)*sin(angle(i,j)) v(XI,ETA)=u(LON,LAT)*sin(angle(i,j))-v(LON,LAT)*cos(angle(i,j)) shouldn't this instead be u(XI,ETA)=u(LON,LAT)*cos(angle(i,j))+v(LON,LAT)*sin(angle(i,j)) v(XI,ETA)=-u(LON,LAT)*sin(angle(i,j))+v(...

stef

Another question about the boundary condition for barotropic flow for nested grids. This applies to 3d setups. In 'u/v2dbc_im.F', there are lines like: cff=0.5_r8*GRID(ng)%on_u(Istr,j)* & & (GRID(ng)%h(Istr-1,j)+zeta(Istr-1,j,kout)+ & & GRID(ng)%h(Istr ,j)+zeta(Istr ,j,kout)) cff1=GRID(ng)%on_u(Istr...

stef

So maybe in a 2d setup, one could store the volume flux of the donor after each barotropic corrector step, and impose that during the 3 (or 5 etc...) time steps made in the receiver grid? Hmm, I guess one should store two time levels of the donor volume flux along the boundary, and then do a tempor...

stef

I guess that we never accounted for a User needing nesting in a 2D application. The motivation would be to do storm surge modelling, in a way that is roughly consistent with other storm surge models such as SLOSH or ADCIRC (both mostly 2d, at least until a couple of years ago...I'm not sure about t...

stef

I see, thanks. That DU_Avg field is actually appearing in u2dbc_im.F, for the "nested" type boundary conditions (in a 2D application). I substituted it there by a dummy value to test, and then the dummy value appears in my history file. Unfortunately I can only continue testing on Monday. Anyways, t...

stef

Thanks for your replies! I work on a 2d application, and another potentially relevant thing I just noticed is that the nesting boundary conditions for the refined grid use fields called e.g. REFINED(cr)%DU_avg2(1,m,tnew) I think this is the case even in 2d applications. However, I think that this fi...

stef

Hi,

I read wetdry.F, and was wondering if the index boundaries should account for the contact regions in nested applications? Currently, there are ranges like "JstrR,JendR" etc., but shouldn't they be "JstrT,JendT" instead?

Thanks!

Regards, Stefan

stef

I wonder if in 2d applications, the multi-valued mask can just be converted to a binary mask like so

I mean only in fine2coarse2d(), not elsewhere....

stef

Hi, This is unrelated to the incorrect netcdf header reproduced in the wiki (as reported earlier in https://www.myroms.org/forum/viewtopic.php?f=17&t=5425 ), but it's related to nesting in general. In 2-d applications with wetting/drying, the u/vmasks supplied to fine2coarse2d() are in their multi-v...

stef

I think that we, as ROMS developers, have freely provided a very sophisticated modeling framework to the ocean community without asking anything in return. I highly appreciate your effort and that of your team, and the appreciation and admiration grows every day I work with the software you provide...

stef

Hi, I was able to do a refinement using 2 grids, using a self-written python script to generate the contact file. It's a 2d application and although I hit a bug with the wet masks using wetting/drying, I was able to patch it and proceed. However, now I want to use 3 refined nests (i.e. one telescopi...

stef

Thanks, that sounds perfect! I have never heard about this!

This way I don't have to set up the server, plus it occurred to me I would have needed to set up a VPN too. Much simpler!

stef

Wow, thanks for this! Looks great! I like the zooming with the mouse wheel and the panning.

I'm not sure if I need a time axis with calendar units, but maybe I can tweak it. I'll read the docs! Thanks!

stef

Also, I just found a paper on "Accessing HDF5 Files via SSHFS".

https://support.hdfgroup.org/pubs/paper ... -final.pdf

They say it's comparable to NFS, and useful for subsetting remote files. So it may be comparable to using the THREDDS server anyways.

stef

Thanks for your response! Yes that would be great, but does THREDDS have an option to deliver a UI to the clients so they can browse data, in the sense that they can specify e.g. which x-y slice at fixed z and t they want to look at? This way only the figure would be sent over the internet, not the ...

stef

I was wondering if anybody has experience with visualtization tools for remote work over the internet (WWW, not LAN). I used to mount remote directories on my local machine via sshfs, so any netcdf browser will work. However, now I sometimes make larger simulations, and the UI of the browser becomes...

stef

Also, there is a typo in the computation of the radiation stress component derivative for the vbar forcing: >> git diff master mybranch ROMS/Nonlinear/nearshore_mellor08.h ... @@ -1116,9 +1116,9 @@ DO j=JstrV,Jend DO i=Istr,Iend cff=(Syyl(i,j )- & - & Syyl(i,j-1))*on_v(i,j)+ & - & (Sxy_psi(i+1,j)- &...

stef

I tested the spurious wetting of high elevation grid points now with the 3d version of COAWST. No spurious wetting occurred in my test, neither using WEC_VF nor WEC_MELLOR. Browsing through the source code and Warner et al. (2013) I currently think the following (unverified/untested hypothesis): In ...

stef

Thanks for your reply! Yes, I should have mentioned it's a 2d application. I'm trying to simulate storm surges. At some point I want to have at least a bottom boundary layer, but having 2d simulations for reference and comparison is interesting. (also I just noticed that I have the WET_DRY_LIMIT dir...

stef

I have tried ROMS+SWAN coupling with wetting/drying and the model blew up. jcwarner already had told me to use the COAWST version for ROMS+SWAN coupling, but I wasn't able to compile it (see below for the error. Also, I'm not sure where to report errors.). So I kept working with the Rutgers version....

stef

I'm interested in modeling storm surges in the context of probabilistic risk assessment, e.g. using the Joint Probability Method as described e.g. in [1]. See also ROMS forum post [3]. I just found a paper [2] describing an efficient alternative to SWAN. The authors of [2] note that, as opposed to S...

stef

Thanks John, I sent the email! Sooner or later I wanted to learn about COAWST anyways, so that's great. For the near future, I have to keep it simple as I'm still learning nearshore processes, wind waves and small scales in general. I looked for the most simple method to compute wave setup. SWAN has...

stef

I'm trying to set up a minimal storm surge model and hit the same bug. It seems to affect any 2d application using both NEARSHORE_MELLOR0*. I don't know much about wind waves yet, still reading literature. But this is still a bug, isn't it?

stef

I should add that an example for the 1D transects can e.g. be found on page 25 in: Federal Emergency Management Agency, 2013: Flood Insurance Study (preliminary). City of New York, New York. https://hazards.fema.gov/femaportal/prelimdownload/prelim/ProductsDownLoadServlet?pfiProdId=16353 This public...

stef

Hi, May I kindly ask for your opinions on using ROMS for storm surge modelling? I'm particularly interested in risk assessment, similar to what has been done by FEMA for coastal flood hazard studies. Here is a link to the New York - New Jersey region: http://www.region2coastal.com/ They are using AD...

stef

Just a quick warning in case anybody (like me) considers making oblique Mercator projections with Proj version (4.9.3): be careful

stef

It turns out that "oblique Mercator projection" is exactly what I need, I think. It lets you define two points in lat,lon coordinates through which the central line for the cylindrical projection goes (that's the line at which the projection cylinder touches the sphereoid), and this can be tilted wi...

stef

Wow, Lambert conformal conic! On Wikipedia it says: By scaling the resulting map, two parallels can be assigned unit scale, with scale decreasing between the two parallels and increasing outside them. This gives the map two standard parallels. In this way, deviation from unit scale can be minimized ...

stef

figure_grid_rotation_tutorial_mercator.png I'd like to show off a figure about one way to correctly (?) rotate the grid, where I'm trying to follow the steps from above post: For pm, pn, I have an initial value based on the flat projection space. Then I later remap to the sphere so that I can assig...

stef

Very good, thanks for your patience and the information, it helped a lot. I will try to process all of this during the next couple of weeks

stef

Ok, but ROMS doesn't care whether it's orthogonal on the sphere, right? What it wants is orthogonality in the plane. And this cannot be fulfilled if we measure pm and pn on the sphere and then use it on the plane. Is this right? Or is there a conformal projection that can do that? The way I see it, ...

stef

Thanks for the help! Now I also found a presentation , where you explain this on page 4 (may be helpful for other readers). However, strictly speaking, when we measure pm, pn on the sphere and use it in the horizontal plane, we don't get an orthogonal grid, right? So if we computed the ds quantities...

stef

Ok thanks a lot for your time Kate. Let me see if I understand correctly: The real question to ask is what to use for pm and pn in the first place. This reflects how the projection is made from the sphere to the plane. It already involves a trade off: If one chooses Mercator, one doesn't conserve vo...

stef

After spending some time today browsing through the SCRIP manual, I think I should better explain the motivation of my initial question. If I understand correctly :? none of the bilinear and bicubic methods take into account the sphericity, neither in SCRIP nor in ROMS. What they do is interpolate i...

stef

Very good, thanks! Meanwhile I also found some Python code, specific to ROMS: https://github.com/ESMG/pyroms/blob/master/pyroms/pyroms/remapping/remap.py with "conservative" and "bicubic" remapping. It seems they use the "SCRIP" library you linked to, so that starts to make sense to me :) Cheers, St...

stef

I'm trying to configure a model to practice data assimilation, but stumbled across a very basic question about interpolation (maybe embarrassing for a geophysicist :oops: , but I never had to do with that problem before.). When I interpolate data on an equidistant lat/lon grid, do I need to do some ...

stef

met_c48xlarge.png Hi, I'm tinkering with benchmarks on Amazon Web Services (AWS). The attached figure shows time (in seconds) spent per process for the ROMS ”large” benchmark test (benchmark3.in), as function of the number of processes. Axes are logarithmic with base 2. Computations are performed o...

stef

Yes I'm trying AWS. At the moment I'm doing some benchmark testing, see https://github.com/poidl/awsroms and https://poidl.github.io/awsroms/ . I still have few results, and they are not interpreted properly. I'd like to become an independent (sub-) contractor, so I'm also very interested in estimat...

stef

That's it, thanks. Setting the right path in the platform dependent file solves it!

On a side note, this still leaves me wondering why the line after the prerequisites is executed (sfmakedepend), if the prerequisites are not fulfilled? Not urgent, though.

stef

I'm trying to run the upwelling example, and make gets caught in an infinite loop. To reproduce: I change the compiler and netcdf paths in the makefile: >> diff makefile path/to/original/makefile 142c142 < FORT ?= gfortran --- > FORT ?= pgi 312,313c312,313 < NETCDF_MODFILE := ../../include/netcdf.mo...

stef

Thanks for the guidance! I'll try that.
--stefan

stef

Hello! We use a grid generated with 'Roms Tools', and we changed the code in the m-files to have constant, user defined coriolis acceleration. Everytime we make a run with different f we have to generate a new grid, although the rest is the same as before. Is there an easy way to analytically define...

stef

Relating to this discussion I want to point to a different post. The following is *very* instructive:
viewtopic.php?t=622
Thanks!

stef

Thank you for the replies! Ok, we will try to isolate the user-modified parts of the code and avoid using svn for anything else than checking out a working copy from the roms/toms-group repository for every user. This seems to be easy and gives every user a chance to learn how to use svn. When we ge...

stef

We are in the process of switching to the new ROMS version and I have some questions concerning administration: Imagine that on a cluster of our university, there are three people using ROMS and making setups, all working on the same project, but all going into a slightly different direction (one is...

stef

Hi Zhou Wei!
If it's because of the blank, mybe you can try type your username 'Zhou\ Wei'. the backslash is use in linux (and I guess unix) to mark a blank.
good luck
--Stefan

stef

Hi Mark! Yes, I will read the manual for ifort to see what kind of options it has. I also will ask our sysadmin to install g95 and idb. SALINITY is undefined. I think the error was caused by my altering the files over and over again and making some copy-paste error with emacs, because the error show...

stef

Hi!
The post I was referring to is the one from Mon May 28, 2007 10:34 pm in:
viewtopic.php?t=538

There seem to be a lot of other posts on this topic, but I haven't read them yet...

stef

Hi! I recently ran into troubles with segmentation faults and it was the first time that I tried the debug option. I'm using ifort on Linux. As m.hadfield suggested in another post, I also added a '-traceback' option the the '-g -check bounds' in the Linux-ifort makefile. Now when I start oceanG, th...

stef

Concerning the pressure gradient: I'm looking at prsgrd31.h (probably not good, but maybe for flat ocean bottom it's ok) and there is a term called fac2 that is multiplied by a gradient of z_w(i,j,N). It looks like the shallow-water-part of the prsgrd. z_w(i,j,N) is set in set_depth (called at the l...

stef

I see. So the baroclinic mode is effectively doing nothing. I'm not sure, but my guess is that is has to do with the time-filtering of the barotropic mode in the coupled system. I don't know if time-filtering is used in the standalone 2d-code, but I guess not, since it serves to remove instabilities...

stef

Hi!
Sorry, I don't know the answer, but I wonder how the vertical velocity-profile looks like? Is v z-independent, like it's supposed to be?

stef

I think that what I wrote above only makes sense for 2nd order centered advection, both for velocity and tracers.

stef

Hi! I still use version 2.2, and don't know if anything has changed in the new version. In mod_grid.F there are some variables defined, three of them are: Hz: Thickness of vertical rho-Points Huon: Total u-Momentum Flux term: interpolated(Hz)*u*dy (dy is the same as 1/pn, at least for a rectilinear ...

stef

I just reread the scrum manual and there it just says "finite diffences", not finite volume. I looked at the 2d-momentum equation and if I did everything right, then for a rectilinear grid the finite-volume and centered finite difference formulation is the same thing. But for a curvilinear grid you ...

stef

Hello! Thanks for the reply! I am also searching for information on ROMS finite volume formulations on the c-grid. Specifically, I have troubles understanding how the variables on the boundary of the gridcells are reconstructed to do the integration of the fluxes. It seems like there are many ways t...

stef

Hi! I was wondering if someone could give me hints about where to find documentation of the 3d momentum time-stepping (Adams-Bashforth 3) used in version 2.2. I tried to understand the Shchepetkin-McWilliams paper, and could extract some info about the barotropic LF-AM3, but I think they don't cover...

stef

I'm going to try that as soon as I can. My most stable setup so far is: Everything clamped in north, m3, m2 and tracer clamped in south, with free surface radiation.

stef

Hi! Hmm, that's interesting. When I define m2 to be zero and define a m3 profile, e.g. u=w=0 and v=v(z), with all values negative from zeta down to the bottom (so vbar should be negative), the entry in the history files for the first calculated baroclinic timestep (NHIS=2) containes a vertical v pro...

stef

Thanks Kate, In my version (2.2) there is only one possibility to define 3d velocity initial conditions analytically: ANA_INITIAL. If I define it, I have to insert analytical initial fields for BOTH m2 and m3 velocities (and tracers). That's why I don't think that there is a call to any routine that...

stef

My configuration is a flow-channel with open boundaries in north/south and closed walles in the east and west. I want to have velocity boundary conditions identical to velocity initial conditions. All of these conditions are analytically defined. If I want inflow from the north with u=w=0 and a vert...

stef

I see. Thanks. Another question: In my mathematical model, I will have water flowing in a channel from north to south, with u=w=0 and a vertical shear in v (just like in the paper above). This implies a horizontal density gradient wich I want to impose by using a linear equation of state. A tilted f...

stef

In the vertical boundary conditions for z=zeta there should be the total time derivative of zeta for the w condition. If I understand correctly, the advective terms are missing.

stef

I would like to set up a thermal wind balanced channel flow. The channel will have flat bottom for now, later I will put a cylinder or an island into the domain. I basically follow the setup in the article "Island Wakes in Deep Water" by Changming Dong. http://www.atmos.ucla.edu/~cdong/papers/iswake...

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