Ocean Modeling Discussion

johnluick

Just wondered if this was what John Wilkin meant to paste in about negative depths.
GET_GRID - bathymetry at RHO-points: h
(Grid = 02, File: /users/hwang121/scratch/smallinput/ngbay_grd_fine1.nc)
(Min = -1.65801391E+00 Max = 5.26751124E+01)

johnluick

The author of Gridbuilder is on leave this week. Maybe he will have a suggestion, though it does not appear to be a Gridbuilder problem as such.

johnluick

I have updated the TPXO2ROMS Matlab software for creating a ROMS tidal input file from the TPXO tide database. It is now called TPXO2ROMS_v5pt1. Version 5.1 downloads the latest global tidal inversion (TPXO9) from Oregon State University. You will need permission from the authors (Lana Erofeeva and ...

johnluick

ara952, of course Hernan and Kate are right about the time, but if you use TIDE_START=-2 and initialise with GMT phases for a particular time and plan to analyse with t_tide (which assumes all harmonics GMT phase, same as TPXO and all the other global tidal datasets that I know of) you need to think...

johnluick

John W, Thank you very much for the reply and I imagine I am not the only one who will find it useful. I am not in control of the THREDDS service, but I must admit that the idea of configuring my own thredds sounds like acquiring yet another complex skill that will be redundant by the next time I ne...

johnluick

Is there such a thing as a matlab function that lists the filenames in a thredds / opendap catalog? (That is, an equivalent to "ls" for opendap?) Typically the filenames contain a date string, eg http:\\thredds\...\...\xxx20091123T173000Zxxx.nc. Normally I would loop through hour by hour, construct ...

johnluick

Thanks, Mark! I see that ramp is still there.

johnluick

For some reason I was under the impression that RAMP_TIDES had been effectively hardwired in a few years back. From what you (Mark) are saying, I was wrong about that.

johnluick

GridBuilder - see discussion elsewhere in roms forum.
http://austides.com/downloads/

johnluick

Ivica is right of course, but if I had to hazard a guess, I would say ROMS is doing okay in the interior,and the problem is with OTPS in shallow coastal water. But then, we don't know if those interior points are in shallow coastal water.

johnluick

Yadu, I'm not sure when I'll get in to the office where the code you requested is located. Until then you might try following some more recent notes I made to myself after downloading HYCOM data (obviously your times and lats and lons will be different, and I only downloaded the surface data (level ...

johnluick

My suggestion would be to assume your tides are ok, and move on to whatever process you are really interested in. At some point, use t_tide or something to analyse the ROMS hourly data for a point near where your harmonics are from, but don't get too hung up on an exact match to amplitude or phase. ...

johnluick

My second suspicion would be that there is something wrong with the tide gauge. Do you have a reliable set of harmonics? If the amplitudes of the two major harmonics (probably M2 and S2) sum to about .15 m, then the data is in error.

johnluick

Giannis, It might be timely to mention that I have not updated TPXO2ROMS.m since before 19 April 2017, when Hernan updated the way ROMS keeps time (I haven't updated my ROMS yet either). It isn't obvious to me, from ticket 724, whether TPXO2ROMS.m actually requires updating. First, the ticket says t...

johnluick

My apologies. The link at the end of this contains LatLonTopo.mat (as well as the matlab functions). It is simply a mat-file version of: http://tds.hycom.org/thredds/dodsC/datasets/GLBa0.08/analysis/topo/GLB_depth_2d.nc ...which is what HYCOM uses for seafloor topography. I cannot remember why I cre...

johnluick

Here is a link to some somewhat dated Matlab functions - two are for downloading HYCOM reanalysis, one is for preparing a boundary file. Beware that I wrote them in 2013 and I would probably do the boundary file function differently if I did it now (I'm including it as you may find it a useful start...

johnluick

Hi Rocky, You have: DSTART = 56228.5d0 56228.5d0 ! days TIDE_START = 52866.0d0 ! days TIME_REF = 18581117.0d0 ! yyyymmdd.dd 1. Why do you have two values of DSTART? 2. Did you mean to have DSTART=TIDE_START? Just checking, because the digits are similar but not the same. 3. You seem to have three di...

johnluick

A few years ago we got interested in this and we simply copied the oceanM, ocean.in, and input data files up to Amazon and had it running in about ten minutes from go to whoa. The oceanM was an mpich2/mpif90/ifort/netcdf4 compile on an HPC system. The next step would be to re-compile on Amazon in or...

johnluick

Hopefully/probably Kate's approach will help you solve it. But I'm also wondering what sort of dynamics you are using. Can you post the cppdefs? Also, what are the values of Lm, Mm, and N? Ad do you mean by "SST difference"? PS the 16x16 solution looks to be going mentally unstable or something. Or ...

johnluick

Thanks Rodrigo. I hope to give it another try (next week, inshallah). John

johnluick

rduran, after reading your comment, I decided to look into the Ubuntu that comes with Windows 10. A Ubuntu website explained that you must first join Windows Insiders, which I did. The next step is to sign up for receiving Windows Preview Builds. When you go to do that, you receive a warning that yo...

johnluick

Thank you for spelling that out Kate (and John W). I saw a comment once which made me think that your usual procedure was to have your boundary file temporally resolve the tides, so that is what I thought you meant by suggesting "ADD_XXOBC". But now I understand from your last comment that you would...

johnluick

I should clarify - I thought Kate was suggesting that tides could be added using ADD_FSOBC and ADD_M2OBC as an alternative to using SSH_TIDES and UV_TIDES - in other words, by adding tidal time series to the subtidal 2D sea level and velocity time series at the boundary (outside of ROMS). My point w...

johnluick

Here are the cpp defs I use for tides ONLY runs. I think Kate adds tides differently to the way I do - I don't define ADD_FSOBC and ADD_M2OBC. Either approach works but probably it will fail if you try to use both together. Note - be sure to set N == 1 in your inputs file, (the line after where you ...

johnluick

Hard to say, but it appears to be a Chrysler product.

johnluick

I am responding to Kate's remark that the standalone MY mixing scheme may not be as reliable as the one in GLS. I did a simple test, which was two restarts of a well-tested coastal/shelf model, ran each for two years, saving five-day averages. One had the standalone, one had the GLS version. I looke...

johnluick

I will point out your question to the author (Charles James). I'm pretty sure we can find a solution. Actually we have the same rule here, but we are allowed to install some freeware (like GridBuilder) if we get permission. Also, many of us bring in our own Windows machines for this sort of thing. T...

johnluick

What I will say is that if you use GridBuilder (http://austides.com/downloads/) instead of seagrid it will be like going from a bicycle to a Ferrari. An old bicycle with innumerable broken parts, to a new Ferrari.

johnluick

I'm overseas at the moment but I will answer as best I can from memory. TPXO2ROMS 4.x is designed to run with TPXO 8.1 not TPXO 7.x.. You should download 8.1. I believe you cannot accurately simulate tides for more than one year with ROMS because it doesn't allow the nodal factors (f and u) to vary ...

johnluick

Bear in mind that the ocean adjusts to atmospheric pressure gradients through long waves and currents generated by wind stress. Both pretty easy to model if they are within your domain but you imply your domain is small and you want to model remotely-generated effects to enter at the boundary. Becau...

johnluick

Great work! Thanks very much. Also a good example of how the forum can be helpful to many.

johnluick

Restarts may fail with an error message like: GET_CYCLE - ending time for multi-file variable: sms_time is less than current model time. TMAX = 15196.5000 TDAYS = 15862.0000 (could be srf_time, etc. rather than sms_time). Multi-part files are when you break up forcing (or climatology or boundary) in...

johnluick

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

johnluick

I have not gone back and looked at the code, but from curiosity I did try doing a quick run with AVERAGES_DETIDE turned on, and then a second run which tried to use the same tide forcing file. I also got an error message that it cannot find the variable Hcount. As you probably know, ROMS writes some...

johnluick

I should have mentioned that with Charles' Seagrid, I'm pretty sure you won't need seagrid2roms.

johnluick

My colleague, Charles James, has just completed writing a version of Seagrid in Matlab 2014b. I have no doubt that his version will suffer none of the issues (bugs, infuriating complexity, etc.) that plague Seagrid. I have seen it, and it looks great. I think the GSHHG coastlines and etopo 1 or 2 or...

johnluick

I look forward to trying this myself!
Thanks Thomas.
John

johnluick

You are quite right of course. Thanks for pointing this out.
I do not know of any python script for this.
John

johnluick

Would it be useful to add a variable NTSHIS to ocean.in (similar to NTSAVE)? Seems like it might be handy for debugging a crash (could start outputting every time step for the final few timesteps) or for looking at tides (to save only the last couple of weeks of hourly data).

johnluick

Thank you again, Kate. What I have found is that the speed-up for running in 2D as opposed to a 3-level 3D model was less than a factor of two (on my test grid). If that is true in general then many people will probably find it isn't worth the bother to go to 2D (simpler just to reduce the number of...

johnluick

Thank you, Kate. Yes, ANA_SSFLUX was the culprit. For those who might be wondering, what I think comes down to is that the same variable name (stflux) is used to mean "surface tracer flux" in the context of the ana_stflux.h subroutine, whereas it specifically refers to "surface heat flux" in the con...

johnluick

When I undefined SOLVE3D (let's just say out of morbid curiosity), it would not compile. The first error was easy to fix (minor coding issue at around line 846 in inp_par.F). The second fix is less obvious to me but I think it may be obvious to ROMS programmers (if not I will provide more info). Pre...

johnluick

Thanks for the prompt response, Hernan. Well here is the error message: CHECK_MULTIFILE - Error while checking input Lateral Boundary file: ../DATA/bry_AD_1_Nsig3_01Mar14_09Mar14.nc last data time record available is for day: 0 04:38:46 but data is needed to finish run until day: 16726 00:00:00 Here...

johnluick

Just updated to 724M. Wouldn't run until I added a line
Tmax=Tmax*day2sec
to check_multifile.F right after Tmax is defined (approx line 117).
Puzzling because this should have been a problem for others long before today, at least since 713M. My apologies if this is a false lead.

johnluick

TPXO2ROMS_v4pt0.zip This new version of TPXO2ROMS (TPXO2ROMSv4pt0) reads from the new TPXO 8 atlas. The most important harmonics in TPXO8 are at 1/30 degree resolution (as opposed to 1/4 degree for version 7.2 and earlier). There are other improvements in TPXO 8 as well (see http://volkov.oce.orst....

johnluick

A week or two ago I posted an update of TPXO2ROMS and some comments about the new Matlab netcdf interface commands ncread, ncwrite, etc. Since I did so by editing a previous post, there was no notification sent out (as far as I know). TPXO2ROMS users are advised to download this update. I would be i...

johnluick

I happened to notice that (at least with version 3.7) ROMS did not write out the name of the tidal forcing file for a purely tidal-forced run until I changed line 4597 in read_phypar.F from #if defined FRC_FILE to #if defined FRC_FILE || defined TIMELESS_DATA Not sure if that was the best fix but it...

johnluick

This version (3.1) should be used. The one I put up a couple of weeks ago saved transports instead of velocities (my apologies). I also made a number of lesser changes which noted are at the start of the function. 23 October note - the new Matlab/netcdf interface commands ncread, nccreate and ncwrit...

johnluick

Please send your next response to john.luick@austides.com, so we can go offline and thereby not annoy everyone with a troubleshooting exercise. Also, in your email, can you confirm that you are not plotting phase (rather than amplitude) in that first plot you sent?

johnluick

Looks good. Before I go further, what version of Matlab are you using? Must be R2012 or later.

johnluick

Please pause Matlab right after the line: TPXO=readTPXOdata(TPXOfile_elev,TPXOfile_vel,TPXOfile_grid,lonR,latR); Then enter: zz=squeeze(TPXO.h.z(:,:,8)); contourf(abs(zz)) colorbar This will show if the values you are reading in are in correct units etc. What I get are numbers which are typical open...

johnluick

The tide extraction software (TPXO2ROMS.m) I wrote and posted here last year has been updated. It requires at least R2012a but now uses the native Matlab netcdf interface instead of snctools. It also has improved interpolation (offers a choice between TriscatteredInterp.m and scatteredInterpolant.m/...

johnluick

Hernan, did you ever get around to enabling the use of multiple input files for climatology?

johnluick

rduran, thanks very much for your comments. I have brought this up before on the forum but am still wondering about it. It would be handy if your test was something that could be easily run for any new application any time one wanted to decide whether to use inline or offline tracking. liyizhen: my ...

johnluick

I meant to say: 18 cpus

johnluick

liyizhen:
LTRANS v1
It speeds it up a LOT though the testing was not thorough. A normal run formerly took around 30 hours. With mpich it took an hour and a half or so.

johnluick

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. Another freely available program that ...

johnluick

I don't think they make six-hour data available. But you're asking in the wrong place. You should ask ECMWF via that website. If you want six-hour data you could go with NCEP. I think that you would then lose some spatial resolution however. Some of those ERA 12 hour fields are not instantaneous; th...

johnluick

John, thanks for your comments which are always very helpful. I guess I should not have used the term "fluxes" as it was misleading - what I was referring to was the averaging (looks like averaging to me) done in the equation in my first post on this thread (averaging of Qsrc*Tsrc above and below th...

johnluick

John, sorry could not get back to this sooner. Thanks very much for explaining that FC is defined at the w-points. In practical terms, since the fluxes are required at rho points, and this is done by taking a vertical average of the flux above and below each rho-point, the consequence of defining a ...

johnluick

I find that performance is improved tremendously if the following change is made in step3d_t.F (in the part where mass point sources are applied)... FROM: DO k=1,N(ng) FC(i,k)=FC(i,k)+0.5_r8* & & (Qsrc(is,k )*Tsrc(is,k ,itrc)+ & & Qsrc(is,k+1)*Tsrc(is,k+1,itrc)) END DO TO: DO k=1,N(ng)-1 FC(i,k-1)=F...

johnluick

I think that in read_phypar.F: # ifdef T_PASSIVE DO i=1,NPT itrc=inert(i) WRITE (out,185) LtracerSrc(i,ng), 'LtracerSrc', itrc, & & 'Processing point sources/Sink on tracer ', itrc, & & TRIM(Vname(1,idTvar(itrc))) END DO # endif LtracerSrc(i,ng) should be changed to LtracerSrc(NAT+i,ng) It only affe...

johnluick

Kate, thanks for that - indeed I did not always have ana_spflux and/or ana_bpflux defined before, and it took me some while (and with some help) to realise they were required (and indeed this was my main problem, since I do not provide surface and fluxes using netcdf files). I was going to add this ...

johnluick

Thanks, Hernan, for this explanation, and for your post yesterday. You are quite right; I did think that there was a connection between the 3D state variable and the point source. This now makes much better sense. This also explains why it ran when T_PASSIVE was turned off. I also got rid of all ref...

johnluick

Thank you, Kate, for asking this. I started to experiment with adding it to varinfo.dat, but HOW to do it wasn't obvious because of the way "_sflux" is tacked on within the program after the 01, 02, etc., so I gave up and when home feeling rather frustrated. Nice to see your post this morning.

johnluick

This is an oddity...but then, so is everything until someone explains it, I suppose... ROMS stops with the following message from inquire.f90: INQUIRE - unable to find requested variable: in files: ...etc. (then it lists all the netcdf forcing files). Notice that the variable field is blank! What is...

johnluick

I'm in a hotel room somewhere and unable to check my facts, but you have reminded me of a question so will take the opportunity to reply. As I recalled there was one (and I think only one) realistic coastal application a few years ago when I first started using Rutgers ROMS, called NJ_BIGHT or somet...

johnluick

Hi Ivica,

thanks for the explanation and offer of scripts. I could use all the ones you mentioned. Not sure of the best way but one way is to email them to john.luick@sa.gov.au.

John

johnluick

Good article. I have been using your method "1"; now I will try your method "2". Have you written a script to do the tidal analysis and create the child BCs? If so I (and probably others) would appreciate a copy. Otherwise I'll write something that fits in with the new boundary condition scripts Ara...

johnluick

Eli, thanks for pointing these things out. I haven't updated snctools in a long time and clearly it is time to do that. I think that the Marchesiello/Penven/Gambon team will be revising make_tides soon, and perhaps now also you will be making your tide software extraction software simpler to use. Wh...

johnluick

Hi Chilequan, thanks for your interest. I'm unable to reproduce this error, and to tell the truth, I can't see how it could arise (since min(min.. only seems to return a single value even there are two equal minimums), but your solution appears reasonable. If you like, when your exams are finished, ...

johnluick

I'm glad you mentioned this Patrick. I used to use make_tides and am indebted to it's authors - thank you! The main reason I wrote this was (as I recall) at the time, at least, make_tides required the use of a tidal database (provided with ROMS_Tools) derived from TPXO 6.x, rather than directly usin...

johnluick

The problem is with your unzipping software. Here is a link to an evaluation version of WinZip that does work: http://download.cnet.com/WinZip/3000-2250_4-10003164.html There is plenty of other free compression software. Yes, I tried WinRAR and it failed. Or you can go to my rather dusty and moth-ea...

johnluick

I have attached my matlab script for extracting the tidal harmonics from the TPXO 7.2 netcdf files and creating a forcing file for ROMS. I've put everything required (I hope) in the zip file. It also does some plots to check the results. My goal, in writing it, was to simplify the process provided i...

johnluick

Interesting - but mine is stable with TS_DIF2, MIX_S_UV, and MIX_GEO_TS. Same as yours with the addition of MIX_S_UV (unless you have that and didn't mention it). I just mention it in case it helps you track down the problem. John

johnluick

Mark, I had the same problem until I restricted the inflow to the top bin or few bins (I forget just now). I would be interested to know the outcome if you were to try this (top bin only).

But what if inflow is at or near the bottom, like the brine from a desal plant. Has someone sorted this out?

johnluick

Kate, thanks for your reply. Now that I have actually implemented a source in them model interior, I understand a bit better how it works, and will put some hints on a more active and relevant thread. But as to what I was asking about, it turns out this was implemented with 3.5 using LtracerSRC (for...

johnluick

Regarding the internal waves generation problem mentioned by John Wilkin in an early post on this thread... how difficult would it be to add an option, and modify the code, to set the river T and S to the ambient ocean values at each vertical level? Would that solve the problem? Seems like this woul...

johnluick

Ban, did you resolve this issue? I've been hoping to hear you did. I think Hernan spelled it out clearly - and it wouldn't matter much whether you are talking about 13 days or 40 days. You need more days. Also, for a given number of days, you may get very different harmonic amplitudes depending on t...

johnluick

BAN,

probably my arithmetic is wrong, but if I am correct, you only ran the model for 23 days or so, and since you don't use the first ten days, that would mean you only analysed only 13 days. If so I am surprised the results are so good!

John

johnluick

Ban

can you tell us some more about your adcp data, in particular - how many days went into the analysis behind the profiles?

John

johnluick

I think Gouillon's idea to run for M2 only is good, but perhaps I'd make a slight change (or do both). Rather than adding M2 "analytically", consider using a netcdf file. (Easy to create because you just modify the script you are currently using to create TPXO tides input.) If you do it analytically...

johnluick

Thank you Gildas for that explanation! Given that I previously recommended using TIME_REF=-2, I should mention that if you do so (i.e. if you use TIME_REF=-2 in the Rutgers code) then time and phase lag will not be referenced as described near the end of Gildas' explanation. Rather, they will be ref...

johnluick

Was there ever a question on the forum that was not urgent? If you want to forecast tides, I suggest you use something like: DSTART=14652 !Modified Julian Days since 1968-05-23 00:00:00 GMT TIDE_START=14652 !Se equal to DSTART TIME_REF=-2 This example will start the model running at 0000 Hours on 4 ...

johnluick

Do you have any data that you can check your OTPS elevations and currents against? Ultimately if you decide the OTPS amplitudes are too small at the open boundary you may have to construct a larger grid out to deep water to run your tidal model on. Then, take the open boundary conditions for the sma...

johnluick

I second the motion to have the next meeting in Alaska (Fairbanks).

I further move that a prize be given to the participant that traveled the greatest distance to get there.

johnluick

jivica, thanks very much, that fixed the problem...which is strange because I am not, in fact, adding tides at the boundary. If you read my email carefully, you will see that things were fine, it was just that when I turned the tides on, the tides were fine, but the subinertial waves disappeared. I ...

johnluick

Can anyone suggest why the sea level and velocity boundary conditions, which are read in by my nested model (nested in the "offline" sense), appear to be ignored when I add tides to it? Here are the relevant switches used prior to adding tides: #undef SSH_TIDES #undef UV_TIDES #define WEST_FSCHAPMAN...

johnluick

Vinay, I am not sure, but I think the error is actually because make_clim.m uses the Chuck Denham set of tools, as I have noticed some similar limitations in the past with them. One solution is the following. Where there is a line such as var=nf{'wind'}(:); replace it with the new netcdf commands av...

johnluick

Well, in case anyone has a clue, here is a snapshot of what happens at the boundary. sarom.png The aberrant velocities are at column Iend-1. (The ubar BCs at the eastern boundary are calculated at Iend+1; they are not plotted). ubar is too small at Iend; vbar is too big at Iend-1. The colours here a...

johnluick

Thanks Kate and John W for your responses. The Chapman paper makes the point that there is no universally best method in all the types he tested, and that the choice can have profound effects on the solution well away from the boundary. In my tests (which are similar to the Kelvin test case, but wit...

johnluick

It looks to me like the combination FSCHAPMAN/M2FLATHER/M3RADIATION are not radiating fully. I am experimenting with a barotropic model driven only by a free surface boundary condition on a western boundary in the southern hemisphere. The northern boundary is a coastal wall (the depth shoals). The w...

johnluick

I believe there is a minor error in scoord.F. It only affects writing to stdout. (Version 348 2009-04-17). The line near the end that reads cff1=hc(ng) *(SCALARS(ng)%sc_w(k)*hc(ng)+ & & SCALARS(ng)%Cs_w(k)*hc(ng))/(hc(ng)+hc(ng)) should read cff1=hmin(ng) *(SCALARS(ng)%sc_w(k)*hmin(ng)+ & & SCALARS(...

johnluick

I agree with Wilkin, but if you insist on trying this (i.e. you don't care about accurately reproducing the tides, just want some tidal dispersion) just drive one boundary the way the kelvin test case does. Your tides are in phase all around the boundary! You are driving it like an eskimo blanket to...

johnluick

If you just want to check if you are understanding the phase correctly, use a single purely solar constituent like S2 that is not affected by the nodal modulation. Then worry about the nodal modulation later. It modulates the amplitude and phase of the lunar constituents. You can write yourself a li...

johnluick

Since the topic is being discussed, perhaps it is worth mentioning that the kelvin case boundary conditions presently only work in the northern hemisphere. Down here where f changes sign the exponential blows up. (I added an "ABS" to the exponential.) Also as I recall the combination of COS and SIN ...

johnluick

Kate, thank you for the response to my question. I realise you have suggested this metric in a previous posting. After reading your response I went back and found that it was in fact violated (despite that I thought I'd smoothed sufficiently). So I took a different approach this time - starting from...

johnluick

Before I waste any more time attempting the impossible, can someone advise me if my problem is simply unsuitable for ROMS? I want to model upwelling over a complex (coral reef) topography. The grid goes from the coast, across a coral-studded shelf about 40 m deep, out to deep water. There are numero...

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