Ocean Modeling Discussion

rduran

John, Thanks for sharing your code. Is it fair to say the subversion branch has been discontinued? If so, I will move my local repo to download from github. svn up Updating '.': At revision 606. I was able to update Hernan's code with svn (Updated to revision 1208), but perhaps these are old updates ...

rduran

pressure gradient: the averaged value tends to the instantaneous value as the averaging period tends to zero, six-hourly averages may not be much different than the instantaneous value you need. you can hack the code to not average pressure: you can compute the pressure by integrating density ...

rduran

If the cold water originates at the boundary as it seems that it may, perhaps your BCs are the problem. I saw very intense upwelling when using monthly BC and that was resolved when using daily BC, it had to do with the continuity equation, the model wants outflow and the BC is still stuck at inflow ...

rduran

Not related to tropical cyclones, but I also found momentum advection terms that tend to cancel each other in my doctoral thesis on a poleward undercurrent, in case that is of interest:
https://ir.library.oregonstate.edu/conc ... /cj82kf17c

rduran

35 sigma layers over 30cm? Hopefully, someone that knows can chip in but I would be concerned about numerical problems because there may be way too many layers for such a shallow water column. Is there any stratification at all? Just curious. " I think that the problem lies in the fact that bustr ...

rduran

For flux and transport, you need a velocity. I don't see that in A. By including the velocity you account for stuff leaving, not just stuff entering.

rduran

If you have a place where you can put a noisey server, you can get very good and relatively cheap performance for a dual 16 core epyc server style machine. The biggest issue is the noise they make... I am sure someone has tried to put in in a desktop form factor, but am not sure. Reach out if you ...

rduran

Also, if you are concerned with the representation of the gradient, linear interpolation is C^0 (derivatives are discontinuous at cell edges), and using higher-order interpolation can introduce spurious results such as "unrealistic water masses". I am not an expert in the vertical interpolation of ...

rduran

I know, that is why I mentioned that I see his point, and that m_vec may solve the problem. in m_quiver help it says Note that we do not scale arrows with respect to map coordinates! Instead, the arrows will correspond better to actual motions over some time step. The tradeoff is that a single scale ...

rduran

I see your point, but reading he manual still applies since reading the help for m_quiver I am directed to m_vec for this type of problem. Hope that helps.

rduran

When everything else fails, read the manual. From Matlab's quiver documentation: By default, the quiver function shortens the arrows so they do not overlap. Call axis equal to use equal data unit lengths along each axis. This makes the arrows point in the correct direction. A simple axis equal ...

rduran

I know this is not done often, but how about saving the velocity and eddy diffusivity often enough to do the Eulerian computations offline? It will require some coding of course but given the lack of better options ... is there a reason this will not work? (Especially if only interested in the sea ...

rduran

the endpoints are not differentiable, the definition of derivative at a point requires a continuous function in the vicinity of the point, in this case, the function to be differentiated is not even defined in the vicinity of the point, let alone continuous and with a well-defined slope. The best ...

rduran

However, in this strategy results in seemingly erroneously faster velocities in the shallower nearshore part of the domain. Another problem to keep in mind when using periodic alongshore boundaries, is that next to the coast, whatever signal is generated will propagate right back to where it is ...

rduran

Can ROMS track passive tracer through nested grids? If so, another option is three passive tracers with physical diffusion set to zero—each tracer being a label for each coordinate of each parcel's initial position. For examples see Kuebel Cervantes, B. T., J. S. Allen, and R. M. Samelson, 2004. ...

rduran

Here are some Matlab tools that are based on ideas that seem to be along the same lines. It should be relatively straightforward to test them so it's probably worth the time. I was happy with gridfit when I used it back in the day. Gridfit offers "diffusion", "gradient" and "springs" options to fit ...

rduran

Are these low temperatures related to a vertical velocity?

rduran

Ed, they are not using cygwin. I don't have any help for your question, sorry to say. But wanted to mention that an alternative that will allow one to use a display is to instal Xming free software, double click that and that is it, you will be able to run your apps with display (so far tested ...

rduran

just wanted to update that windows subsystem for linux is now fully released: Another key upgrade is that the Windows Subsystem for Linux (WSL) is now fully released. Once again, there are several steps involved: enable the feature, install your preferred distro from the Store, run the app to ...

rduran

It seems the key word is conservative interpolation or conservative remapping, I hope ROMS folks can chip in re what ROMS does when interpolating but in general this paper answers your question http://journals.ametsoc.org/doi/pdf/10.1175/1520-0493(1999)127%3C2204:FASOCR%3E2.0.CO%3B2 The software ...

rduran

There are other places where to learn matlab, and that is probably a good place to start.

rduran

hslope.m version % svn $Id: hslope.m 796 2016-05-11 01:45:21Z arango $ %===========================================================================% % Copyright (c) 2002-2016 The ROMS/TOMS Group % % Licensed under a MIT/X style license % % See License_ROMS.txt Hernan G. Arango ...

rduran

Hi, Looking much much better (as far as spurious velocity is concerned), glad I could help. Possibly, you have reduced both terms on the right hand side of vel = PGE + stuff so who knows, perhaps a bit of a steeper topography is ok, probably a good idea to test with higher r. Ocean models are simply ...

rduran

1.Is it means wave reflection,or momentum diffusion term? :?: 2.Can I set TNU2 == 0 and VISC2 ==0 to minimize momentum diffusion term if it is the "stuff"? Its been some time since I last checked for a pge, but I do have a plan for next time I check for it and I can share it with you, just keep in ...

rduran

What do the horizontal currents from the pge with no forcing look like? ROMS vertical velocity is related to the horizontal velocity, it is computed diagnostically by integrating the continuity equation. It seems that somehow near the slope you are getting divergence/convergence of horizontal ...

rduran

Hi johnluick thanks for your response. I have good news, starting with an update that is currently (also slowly) making its way to windows 10 users, you no longer need to be in the windows insider club. Ubuntu is still beta (not everything is functional) and you will need to have developer mode ...

rduran

The latest windows 10 update provides native linux ubuntu. Its supposed to run just like ubuntu you can find plenty of demos by googling it. It would therefore seem if ubuntu users can do it that windows 10 users could do it as well ... but there is only one way to know for sure. I hope those that ...

rduran

Hi Hernan, Depth integrated is m2/s and is consistent with the definition you give; in that case this is what may need revising: units = "meter second-1" Edit: however if both sides are divided by D before writing to netcdf then the units are correct and that would be depth-averaged by definition.

rduran

I guess it could be understood from the context but just to be clear, it seems that vertically averaged was intended instead of vertically integrated: float ubar_eastward(ocean_time, eta_rho, xi_rho) ; ubar_eastward:long_name = "eastward vertically integrated momentum component at RHO-points" ; ubar ...

rduran

A very appealing option is just becoming available: run ubuntu natively within windows 10. Search for "ubuntu windows 10" you will find plenty of info for example https://blogs.windows.com/buildingapps/2016/03/30/run-bash-on-ubuntu-on-windows/ It will be interesting to see how this option handles ...

rduran

They found that KPP did better than MY2.5 for a coastal environment in this study, except during a downwelling episode -- see fig 9.

http://onlinelibrary.wiley.com/doi/10.1 ... 8/abstract

Circumstantial evidence is as good as it gets it seems, so the more of it the better.

rduran

Thanks John. Your conclusion is similar to the paper I posted which also uses ROMS' implementations, that's good.

rduran

My comment was on the ROMS implementation of MY, not the algorithm itself. Thanks Kate I can see that now. It would be good to know if ROMS implementation has problems. At OSU ROMS is used quite a bit with MY, not sure what ROMS or MY for the matter. Edit: In fact that paper uses ROMS and is over ...

rduran

I was told probably ten years ago now that the MY2.5 scheme in ROMS is broken and should not be used. Instead, it is recommended to use either the GLS or the LMD schemes. Anyone know if the MY2.5 scheme was ever fixed? Or why it wasn't simply deleted? There may be researchers that are not fond of ...

rduran

ROMS doesn't solve vorticity equations, solve primitive equations.

rduran

Vertical velocity at the surface tends to be much smaller than vertical velocity in the interior. Did you check different layers? (Just making sure it's not that). Vertical velocity in ROMS should be decent enough to, say, simulate upwelling and downwelling as long as they correspond to the ...

rduran

I recall my undergrad adviser (physical oceanography) saying: I am sure you can find a square wave in the ocean. That actually makes sense if one thinks in terms of representing waves as a linear combination of trigonometric functions (Fourier series) -- you get a square with two step functions and ...

rduran

Sorry I meant to say increase horizontal resolution, as Kate said.

Either decrease vertical resolution (e.g. Decreasing number of sigma levels) or increase horizontal resolution, or both.

You have to see what is required for your application, what error is acceptable and what error is not.

rduran

I would not be surprised if the currents were substantially less if the boundaries were closed at the same time the signal can move around the domain when the boundaries are closed adding momentum each time it does, need to watch for that. the rx parameters are not the whole story they are apriori ...

rduran

Excellent, thank you very much Ryan, Patrick.

rduran

Hi,

I would like to track down any papers using/describing the full vorticity equations (2D and/or 3D) say from cross-differentiating ROMS diagnostics or any other method.

Does anyone know the details for such references?

thanks.

Rodrigo.

rduran

If you search for netcdf.mod or the error you get youll probable find a number of people already asked a similar question and you'll probably find some helpful answers as well.

HTH

rduran

A few grid points at a river mouth were plain wrong. I thought that all grid cells had to add up to zero. So once you identified the cells that were wrong, you removed them from your analysis? Yes, momentum terms adding up to zero (whatever zero means) should be pointwise. I guess it is possible to ...

rduran

Hi, A few grid points at a river mouth were plain wrong. Checking for balanced momentum in an integrated fashion might be a good first step but I needed to look at the details to see where things went wrong. Your case seems to be different. Perhaps the question "what is zero?" is a relevant one. One ...

rduran

Do your vshapes add up to one?

I got very weird salinities at a river mouth with a vshape that did not.

Another thing to check in your trial and error list.

rduran

I was looking at the wikiroms page that Hernan posted, and found that the donor/receiver grid exchange information through a bilinear interpolation The horizontal interpolation weights are as follows: Hweight(1,:) = (1.0 - p) * (1.0 - q) Hweight(2,:) = p * (1.0 - q) Hweight(3,:) = p * q Hweight(4 ...

rduran

Notice they are giving you the max values for r0 and r1 so its not surprising that you get the bigger of the values reported for the nested grids when using only one grid. You can look up how they are computed in the code by using grep.

rduran

That's right. as you discovered everything but accel is on the rhs

rduran

I wish all errors were as explicit, did you check what the error suggests you check?

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CHECK_MULTIFILE - Error while processing Climatology multi-files: 
data does not include initialization time = 0 00:00:00

rduran

I believe that the bottom boundary condition

-w + \vec{v} \cdot \nabla h = 0

should be

w + \vec{v} \cdot \nabla h = 0

https://www.myroms.org/wiki/index.php/E ... Conditions

rduran

Did not know that thanks to all for sharing.

rduran

Yes, i found it very interesting, I'm not sure if there is a paper out yet because it seemed a very recent result, but he might have a poster or something like that. Turns out that the Columbia river output is very important to get SST right off the norther US West coast. But that is a very big ...

rduran

If there is a river in your region of study you might want to contact Dr. Alexander Kurapov from Oregon State University. He has recent research showing the effect of a river on the sea surface temperature of a ROMS model off the Oregon and Washington coasts. It has to do with how deep radiation ...

rduran

Here is a doctoral thesis (methematics) dealing with PDEs and negative times -- in particular they work with Navier Stokes and Burgers equation as t --> -Inf http://repository.tamu.edu/bitstream/handle/1969.1/4940/etd-tamu-2005C-MATH-Dascali.pdf?sequence=1 Radu, the author, came to OSU as a ...

rduran

There is a recent article for the hydrological modeling literature that reads (section 3): There is considerable confusion in the literature about the use of the terms simulation, prediction, projection, forecasting, and hindcasting; the usage in hydrological modeling in some cases conﬂicts with u ...

rduran

do you mean that a daily BC will do better for a ten year model ? Mybe I will try a daily BC... in my small amount of experience daily boundary conditions work very well. If you can get data at the same times when ROMS asks for a BC you might not even need nudging at the boundaries at all... that ...

rduran

A monthly BC is not a good idea, imagine following scenario to illustrate: a relatively strong flow coming in, you have that more or less fixed for a period of time because of the low frequency BC, but your model has higher frequency stuff going on the interior and it wants flow to go out. Strong ...

rduran

The reason dimensions do not agree is because you are doing a matrix multiplication of a single value and a matrix instead of an element-wise (or point-wise) multiplication of the matrix with the element {sqrt(1)}

not true

rduran

Hi all, I am not persuaded that you are not simulating when modeling, take a box model for example. A much simplified model but I still see it as simulating say a very basic physical principle or the likes. Nor am I persuaded that you are not modeling when simulating. What I do agree is that giving ...

rduran

Perhaps they are being used interchangeably. I think one could argue that if you are doing a simulation you are surely modeling (whatever you are simulating you are using a model to simulate it) and if you are modeling ... well you are certainly simulating something (if not reality then some ...

rduran

Hi! Here is a copy-paste of what I get with ncdump -h RST00.nc :NLM_LBC = "\n", "EDGE: WEST SOUTH EAST NORTH \n", "zeta: Cha Cha Clo Cha \n", "ubar: Fla Fla Clo Fla \n", "vbar: Fla Fla Clo Fla \n", "u: RadNud RadNud Clo RadNud \n", "v: RadNud RadNud Clo RadNud \n", "temp: RadNud RadNud Clo RadNud \n ...

rduran

Hernan, The command :set invlist in editor Vim shows any invisible characters, the $ is for "enter" (or next line), the point there is that there are no other characters in the in file, if you read a previous post in this thread I have checked that carefully. Re netcdf, then I do not know how to ...

rduran

HI just want to mention that I tried to restart with a restart file that was created with ROMS 3.6 and again, as above, I am getting problems with characters that don't exist: LBC_GETATT - inconsistent northern boundary for variable: tke Keyword = Gra<90>§ß^N in input file: /home/server/student/h ...

rduran

I verified the results in different matlabs, different computers and using matlab's official way to read netcdf (i.e. ncread in matlab R2012B) instead of using ncload and makenan. I did this for a run made with ROMS revision 571 and in run made with a revision 656 I am getting same results as above.

rduran

Hernan,

Thank you for your answer. In the first post of this thread you can see that the 2D diagnostics also look suspicious. You can also see I added the code for the sum of 2D momentum terms (I did include bottom and surface stress).

rduran

Parker, Thank you very much for taking a look at this! Are you using "nudging to climatology" in your domain? I do not have M2CLM_NUDGING nor M3CLM_NUDGING defined (I found that with daily boundary conditions there was no need for nudging). This was done with ROMS 3.6 revision 571, but I am getting ...

rduran

I wrote a simple matlab code to check if momentum diagnostics add to zero, turns out that the u-momentum does and v-momentum do not. Here is the code I used so you can see it is not a bug (typo or so) from my part: for kk=1:tot file=files{kk}; ncload(file) vmom=makenan(v_accel-(v_cor+v_hadv+v_vadv+v ...

rduran

You should have noticed that all cpp options that are defined have

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#define XXX

while all options that are undefined have

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#undef YYY

.

# is not used to comment a line.

rduran

depends on your application, if you want to do momentum balances for a current with typical velocities of 10 cm/s then 7 cm/s of PGE doesn't sound good. A few 2 cent points to keep in mind: less vertical levels means less convergence although it will help with PGE, there are a few parameters that ...

rduran

thanks for sharing! it's always good to earn in experience

rduran

I would very much appreciate if model developers and advanced users could chip in to answer:

If you were to pick one ocean modeling book, which one would it be?

thanks many,

Rodrigo.

p.s. I hope this will result in a nice reference list, I haven't found one already.

rduran

the proper diagnostic test is to run your model with zero everything (ie no forcing no initial velocities) and only a horizontally-constant vertical (stable) profile of density. perhaps constant salinity and a typical temperature profile will do if temperature controls density in your region. any ...

rduran

with such dx,dsigma and total depth it is possible you bathymetry would need much smoothing, do you have a slope? how do your r-factors look? a false pressure gradient certainly produces currents.

rduran

I'm wondering if changing the vertical profile of the river discharge would help?

rduran

How about seeding some Lagrangian floats to see if any left and came back? There is another Lagrangian technique that quite frankly I find a tremendous tool, I believe it will become a very popular with time. It might be useful in your applications since it allows you to measure total volume of ...

rduran

then of course going through your output is always a good idea: GET_NGFLD - temperature western boundary condition, t = 1 00:00:00 (Rec=0002, Index=1, File: cefs_upwelling_bry.nc) (Tmin= 0.0000 Tmax= 183.0000) (Min = 0.00000000E+00 Max = 2.75380093E+01) GET_NGFLD - salinity western boundary ...

rduran

your Maximum barotropic Courant Number = 6.22825707E-01 is not that far from one, from browsing the forum it seems the first things to check are lowering your time step and Nans in input files as well of zero bathymetric values which u already looked into.smoothing the bathymetry is for numerical ...

rduran

nan in input files or the need to reduce the time step are probable culprits

rduran

Anything with a T for true can have an F for false i.e. your choice. There is no way (that I know of) around sensitivity tests when starting a new application, you should not expect to get it right the first time because you probably wont. You may want to design an experiment to test the parameters ...

rduran

in my Experience every six hours worked ok, it depend on the timescales u are interested in. I don't think any post-processing particle tracker can be expected to produce the exact same solution as the ROMS calculations, unless run for every ROMS time step...but the advantages come in being able to ...

rduran

Is anyone aware of any studies that compare this "offline" tracking approach, with letting ROMS do the tracking? Assuming ROMS updates the positions at each timestep, the two results must diverge noticeably at some point. For example in shallow water with wind. Rivas and Samelson (2011) did some ...

rduran

Did you try navg = 120 and nhis = 120?

rduran

120 nHIS Number of timesteps between the writing fields into history file. 0 ntsAVG Starting timestep for the accumulation of output time-averaged data. 60 nAVG Number of timesteps between the writing of Well, the diagnostic terms involve a time-integral like the averages files. I usually recommend ...

rduran

This is an interesting discussion, are there any news regarding the discussed inaccuracies?

thanks,

Rodrigo

rduran

many thanks Kate, that all makes sense.

rduran

I am looking for details of ROMS' floats, I would like to put together a brief description. So far I have found in the manual (Figure 11: Flow chart of the model main program) that floats are stepped in time every baroclinic time step. Presumably the latest time-stepped 3D velocity is integrated to ...

rduran

Shou

Could you please let us know what differences you find in your Build/*.f90 files?

It is interesting to learn what configuration change would cause the differences.

thanks,

Rodrigo

rduran

Shou,

One place to start with would be comparing the CPP defs, do you have them available?

Rodrigo.

rduran

I dont think THE baroclinic pressure gradient(bpg) is included in a vertically averaged pressure gradient. It would need to have vertical dependence to be THE bpg. Rather there is a term of baroclinic nature included in the uv_bar_prsgrd terms to make the barotropic-baroclinic coupling work.

rduran

Reminds me when I was starting out with matlab: you need to pay attention to the error messages. In this case the dimensions are not working out. type whos to see the size of your variables. type help horzcat to see what it means. Another option is copy-paste the error message into google, youd be ...

rduran

how bout sign(y_1)*geomean(abs(y_i))? (need y_i < 0 for all i)

rduran

If you are running without forcing and just an arbitrary horizontally-constant stratification then it is the pressure gradient error - not necessarily surprising. If this is a regular run, you have baroctropic flow following f/h contours - not necessarily surprising. Granted that 0.5m/s 3km deep is ...

rduran

that's what happens in realistic simulations of ice!

rduran

I would continue asking before spending too much time creating grid files with different resolutions. Other possibilities are sensitivity to boundary conditions. What is your vertical resolution? In general, the finer the resolution the longer the spin up time (allows for (more) higher mode waves ...

rduran

Possibility:

by reducing your time step you are able to resolve different types of waves possibly related to spin up.

Convergence also depends on spatial grid refinement, what is your spatial resolution?

rduran

Off topic comment/question: When doing a pressure gradient test (i.e. all forcing and initial fields zero except for an arbitrary stratification), initially velocities are due to pressure gradient error but eventually the advection and difussion of T,S will also be involved in the development of ...

rduran

Could someone recommend me literature regarding numerical conservation of PV, density... etc ? Books, articles, related to ROMS, or in general regarding numerical ocean models are all welcome. Thank you very much in advanced!! R. p.s. lagrangian context is specially welcome but eulerian also very ...

rduran

Along-path relative and potential vorticity saved as output into the FLT00.nc file for any and all kinds of floats (just as temp, salt, lon, etc are saved). Planetary is straightforward from lat so no need for that one.

rduran

do you have to recompile every time you edit them? Seems you should always stick to the bry conditions when you are restarting at least: https://www.myroms.org/forum/viewtopic.php?f=17&t=2411&hilit=NLM_LBC But as far as running different experiments with the same executable and different BC in the ...

rduran

Thank you very much!

rduran

I dont want to allow the bustr term to change the sign of u_new. This is unphysical. How can the extraction of energy make the current go the other way? Greg Holloway would argue that: We consider eddies interacting with bottom topography. It is seen that traditional ‘‘eddy viscosity’’ and/or ‘‘topo ...

rduran

I would like to reference the new Stretching function (Vstretching =4) which is referred to as Shchepetkin 2010 but I cannot find this paper. Please advise.

thanks!

rduran

Thank you very much, all of this is good to know. My dissertation's first two parts are 1) a kinematic description of the Eulerian and Lagrangian flow for a poleward undercurrent off the US West coast (41 to 48 N) as seen through a ROMS simulation and 2) a follow up dynamical description. Mean ...

rduran

Dr. Arango, Thank you for your answer. I understand the discontinuity problem you mention, that is why the solution ended involving either keeping the Lagrangian Labels continuous by nesting in bigger domain or by using an alternative method (regular floats in this case). Regarding the meaning of ...

rduran

This does not make any physical sense to me That might be because these are relatively unusual dyes, really they are Lagrangian Labels giving the initial position of all water parcels in the domain defined and advected as passive tracers. There is not a way in ROMS to have computations with NaNs or ...

rduran

Hi, I would like for my dyes to get nudged to NaN values with incoming flow. I tried nudging with boundary dye values set to 1e37 but they get read as 0 (zero). I also tried reducing boundary conditions to only radiation with no nudging, but that was not good enough, I need incoming water parcels to ...

rduran

I found a work around that worked following https://www.myroms.org/forum/viewtopic.php?f=19&t=2356 I commented ! Report input parameters. !----------------------------------------------------------------------- ! ! IF (Lwrite) THEN ! DO ng=1,Ngrids ! IF (Lfloats(ng)) THEN ! IF (ncount(ng).ne.Nfloats ...

rduran

I am using latest ROMS (svn 583). For some reason my floats.in file is not being read properly: READ_FltPar - Inconsistent number of floats to process: 0 888 change input script. But I have checked by floats.in and everything looks right, I even checked for tabs that would not allow for the number ...

rduran

Hernan, Recap: When I build -noclean after commenting the lines as suggested above things work fine. Follow up experiments: I updated the code and compiled the same case and tried running with no further modifications, now I get the following error: LBC_GETATT - error while reading global attribute ...

rduran

Thank you Alexander!

rduran

In the current cppdefs ( svn $Id: cppdefs.h 572 2011-10-18 17:56:01Z arango $ ) the pressure gradient options are: ** Pressure gradient algorithm OPTIONS: ** ** ** ** If no option is selected, the pressure gradient term is computed using ** ** standard density Jacobian algorithm. Notice that there ...

rduran

Hernan, will do in about two weeks.

rduran

I believe the answer (at least partial) to your question is here:

viewtopic.php?f=17&t=2411

rduran

John, thank you very much! If I do svn up I get: At revision 571 The varinfo.dat I am using is the one that came with revision 571 however it reads: svn $Id: varinfo.dat 567 2011-09-19 22:43:36Z arango $ Yeah that makes sense (of course ... again!!), now it reads: LBC(isTvar) == RadNud RadNud Clo ...

rduran

John, thank you very much! You are right, I should be checking my stdOut more carefully and it does make sense it would be something to do with the bry conditions (of course!)... For some reason ROMS is only reading the bry conditions for the first dye and it is invoking ROMS/Functionals/ana ...

rduran

Thank you for you answer Lyon. I do have a river but the problems happen with and without point source for the dyes. The boundary conditions (double-checked to be right) are given by the definition below. The max min values for my dyes are: -129<dye_01<-123.7 (Longitude) 48<dye_02<41 (Latitude) min ...

rduran

I am advecting three dyes one looks great, one is terrible and the third is less than acceptable. This is during the same run and all options for the three dyes are the same. I had done a similar run before and it worked nicely. I have double checked my bry and ini and forcing files it is all as it ...

rduran

Im not sure whether this would introduce a character (as mentioned above) but I got this warning when compiling ROMS 3.6 so I thought I would mention it in case it is helpful: ROMS/Utility/state_addition.F > /home/server/student/homes/rduran/ore/Build/state_addition.f90 ROMS/Utility/state_addition.F ...

rduran

there is something called VOLCON (volume conservation) I believe there is info somewhere in the forum for VOLCON (and bry conditions associated with it) .. or was the info in the .in file? I'm not sure

rduran

thank you very much Hernan.

Just for the record my case is a realistic simulation of the Oregon coast (simulating 2005).

R.

rduran

Should I add an item to the wish list?

rduran

I have a few questions regarding spurious mixing in ROMS-Rutgers: 1) Is the cppdefs option TS_U3ADV_SPLIT something similar to what is described here: Marchesiello, P., Debreu, L., Couvelard, X. 2009. Spurious diapycnal mixing in terrain-following coordinate models: The problem and a solution. Ocean ...

rduran

Good to know, thanks!

rduran

Im just curious how the solution of imposing a pressure gradient via barotropic velocities would compare with imposing a pressure gradient via sloping isopycnals in the boundary conditions or even how about both. Any thoughts?

rduran

First I tried erasing all spaces and introducing them one by one with spacebar in the boundary conditions of my .in file, and I got the same error, it does seem that the character has been introduced somewhere else. Please note I have exclusively used vi editor in linux to work with my .in file ...

rduran

Thanks for the tip I will change from using Rad for TKE.

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wyam.OCE.ORST.EDU 104: uname -a
Linux wyam.OCE.ORST.EDU 2.6.9-55.ELlargesmp #1 SMP Fri Apr 20 16:46:56 EDT 2007 x86_64 x86_64 x86_64 GNU/Linux

rduran

Hernan, Thank you for your time/answer. Both the HIS and RST files I used were created with ROMS 3.6. This has been an "all-ROMS3.6" run. Indeed this new global attribute is found with ncdump here is what it looks like: Restart file :NLM_LBC = "\n", "EDGE: WEST SOUTH EAST NORTH \n", "zeta: Cha Cha ...

rduran

Im using ROMS 3.6 revision 571 I followed the instructions for restarting as in https://www.myroms.org/forum/viewtopic.php?f=14&t=599, in different ways: 1.a) Using a history file with NNREC = -1 1.b) Using the fields of a history file to write a netcdf file using the same script I used for my ...

rduran

I think that this might be a relatively easy and quite useful feature: There are several good reasons why one would want to plot time series of kinetic or potential energy, volume, or maximum velocities ... all that info is available in the out file but it is not straightforward to put it into ...

rduran

For sure you would need to change the initial conditions. This post might help:

viewtopic.php?f=14&t=599

rduran

Andre, Mathieu,

thanks for the helpful replies.

rduran

It is well known that the bathymetry should be smoothed to avoid fictitious pressure gradients and that is where the conditions 3 < rx1 (Haney) < 7 0 < rx0 (Beckman and Haidvogel) < 0.4 come from. in Robert Miller's "Numerical modeling of Ocean Circulation" 2007 Cambridge University Press, one can ...

rduran

Kate thank you, as usual you have been very helpful. Reducing the time step seems to be working. I had considered this possibility but I thought my Courant numbers to be small enough so I (prematurely) discarded that option. Here are my previous and new values: 364,366c384,386 < Minimum barotropic ...

rduran

My model blew up in first step ... after inspecting the initial conditions (first file to be written out by roms) I noticed all my 3D array for initial salinity was nan (or more precisely whatever that _fill_value was (I did salt(salt>1e10)=nan in matlab to plot and inspect file) I also noticed that ...

rduran

Then again it could refer to the other non-linear juicy stuff ...

rduran

Thanks Kate, good to know globaldefs.h does these kind of things. Im not sure how

Code: Select all

#ifdef TS_U3ADV_SPLIT

would prove positive (and that was the only define TS_C4VADVECTION part that I found) , but I did find the problem to be solved when I commented the diagnostics_uv line properly ...

rduran

I have a weird thing going on. It does not happen with roms 3.0 but it does with roms 3.5 My cppdefs.h is: ================================ #define OREGON_OBC /* Oregon, open boundary conditions (AK: 7 #if defined OREGON_OBC /* ** Options for the Oregon case: Open BC */ #define UV_ADV /* turn ON ...

rduran

Yes there was a tab, thanks.

rduran

Hi, This is what I have put in my .in file: ! Grid dimension parameters. See notes below in the Glossary for how to set ! these parameters correctly. Lm == 248 ! Number of I-direction INTERIOR RHO-points Mm == 294 ! Number of J-direction INTERIOR RHO-points N == 31 ! Number of vertical levels In ...

rduran

Can someone help me understand what I need to do: if i try running: ./oceanS < ./User/External/RomsInit_03_Jul1.in I get this error: Tile partition information for Grid 01: 0000x0000x0000 tiling: 001x001 tile Istr Iend Jstr Jend Npts 0 1 0 1 0 0 INP_PAR - domain decomposition error in input script ...

rduran

Might want to read this post:

viewtopic.php?f=14&t=1702&p=6157&hilit= ... ries#p6157

rduran

I heard someone that wanted to have a continuous release of dye used biological tracers by de-coupling them (i.e. no phytoplancton eating nutrients; make the nutrient a conservative tracer I guess). I'm not sure of the details. I have a question of my own: If you have an open boundary with positive ...

rduran

Hi,

Remind me how you defined continuous die?

rduran

Does this mean that my forcing netcdf files need to be modified if I want to start running my model latter in the year? In other words: I have been running a model starting Jan 1st 2005, now I want it to start Apr 1st 2005, does setting DSTART = 90 (instead of 0), without changing the forcing file ...

rduran

Rachael, That what indeed useful information thanks, and it came just hours after I started wondering why my model had crashed too. By day 148 output garbage from dye_03 (depth label) was too much for the writing routine to handle. Similar to what happened to you. Im curious to learn more about ...

rduran

Thanks for you reply. I am using MY25_MIXING I changed AKT values as suggested. My .out file now gives me 0.0000E+00 Akt_bak(03) . . . 0.0000E+00 Akt_bak(05) Which are the values for dye_01 through dye_03. Am I good to go? If I change into another closure (LMD or GLS) scheme, then I would have to ...

rduran

Thanks for the replies, I have a couple of doubts, As for horizontal mixing, Im not sure how I can set TNU2 to zero only for the passive tracers but not salinity or temperature. I saw the tutorial for ocean.in but don't understand [1:NAT+NPT,Ngrids] Is the first value for NAT and the second for NPT ...

rduran

Hi, I would like to do some experiments with lagrangean labels, i.e. 3 dyes defined as follow: X (x,y,z,t=0)=x Y (x,y,z,t=0)=y Z (x,y,z,t=0)=z where x is longitude, y is latitude, z is depth, t is for time of course. I would like to see where these labels are advected to, but I would not want them ...

rduran

I like em. Pretty cool.

Excuse my ignorance though, what were the strings for?

Rodrigo.

rduran

Hernan, With regards to the juicy non-linear stuff, I believe that's what Rivas & Samelson were describing in their paper (which I mentioned above) when they said: "Note that the presence of diffusion and mixing in the model introduces an in- evitable ambiguity into any attempt to analyze Lagrangian ...

rduran

Val`ere, I'm not sure what it was Petrovsky was showing with this example but I'm sorry to say that it is certainly not true that the solution "explodes" for -epsilon<0. Assuming you meant k>0 (so that your arguments make more sense), you can in fact, choose any t<0 whatsoever as long as it is in IR ...

rduran

Zhaoqian and Valere: You can solve the equations (i.e. run the model) make sure you get all the components of velocity in all of your domain. Once finished you can choose a 'particle' that interests you and trace it back. First find the velocity at each particle's location (interpolate from your ...

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