Ocean Modeling Discussion

seashellingolds

Hi All, I am currently trying to learn how to run a model with tide. On the tidal forcing wiki page, I read this: "Because we run multi-decadal simulations, we have chosen not to include the "nodal corrections" in the external forcing file but to modify ROMS to compute them for the time at hand. The ...

seashellingolds

Hi all, I am running a high-resolution model and having a problem with numerical instability. Attached figure shows the zonal velocity. Strong oscillation appears after several time steps and the magnitude soars into the sky. When reducing the DT, it goes several steps further. It seems an issue of ...

seashellingolds

Thank you so much for your reply Kate.

seashellingolds

Hi All, When using rotated grid, I know the wind stress should be rotated beforehand in the input file. Since "ROMS assumes that all the input vectors are already in (XI,ETA)coordinates.", does this mean that all of the velocity vectors in the climatology file/boundary file/initial condition file ...

seashellingolds

Hi Sasha So glad to see you here. You are one of the persons I am most eagerly waiting for. I have read your previous posts on i7 cpu performance and the presentation of poor man's computing. They are very helpful and instructive. There are still some points that I am not very clear about like how ...

seashellingolds

Hello all, I cannot bear this any longer. My run is too slow with less than 9000 steps per earth day. I read some previous posts in the forum but am still not clear how to accelerate it. Can anybody with such experience help point out which one of my configurations might not be good. Not necessary ...

seashellingolds

Hi All I happened to look at the code in the t3dmix2_s.h and met something I couldnt understand. cff=0.25_r8*(diff3d_r(i,j,k)+diff3d_r(i-1,j,k))*pmon_u(i,j) FX(i,j)=cff*(Hz(i,j,k)+Hz(i-1,j,k))*(t(i,j,k,nrhs,itrc)-t(i-1,j,k,nrhs,itrc)) similar for FE cff=dt(ng)*pm(i,j)*pn(i,j) cff1=cff*FX(i+1,j)-FX(i ...

seashellingolds

Thanks Hernan. Finally got it right... and yes it is the version issue. I was using MATLAB 7.0 (old enough) which cannot open the netcdf output files no matter what version of snctool I use (tried the original old one and the newest one). I just switched to 7.13 and it is working! So do we have ...

seashellingolds

So it's the output from the new ROMS that you can't read? I guess you didn't accidentally get netcdf4 files if you were using the netcdf3 library. When you say "saves the record every 15 days", what kind of output file are you talking about? Could you maybe download new copies of WRT_AVG.F and ...

seashellingolds

tried serial and the same problem...

seashellingolds

2. You admit to having an old version of netcdf - what versions of snctools and ROMS do you have? Old versions of netcdf should still have created files that the new tools can read - tools generally get more accepting in that they should read old and new formats. Could snctools read the old files ...

seashellingolds

Thank you for your reply Kate.
Things are getting more complicated.
Q1: It turned out to be some MPI problem I think. My grid size is 464*194. If I set NtileI=8 and NtileJ=1, it blows up with NaN. If NtileI=4 and NtileJ=2, it doesnt......

seashellingolds

Hi All I ve recently got two problems with ROMS output. 1. I have a climatology forcing run which saves the record every 15 days. After starting from the 15th day, it blows up immediately after saving the first record. Then I restart the model, it blows up exactly just after saving the next record ...

seashellingolds

Hi All

Maybe this is too basic question but I simply cannot get it.
In the Fennel's model, we calculate the new phytoplankton using P(new)=P(old)+cff*(Nnew)
However, the calculation of chlorophyll uses N(old) instead of N(new). Is there any reason about that?
Thanks a lot

seashellingolds

As for the indices, since my left V gave me no problem, I guess the indices could be right btw shouldnt the indices be the same as the rho point below it? It depends. In the ROMS view, the v indices match the rho above. In the netcdf file view, the indices match the rho below. The grid indices were ...

seashellingolds

What would be more helpful to us would be if you could print out that V value from several places in the code to confirm that it's getting set back to zero - and pin down where that's happening. Or else watch in the debugger. Are you sure you have the right i,j? Same as the rho point just above it ...

seashellingolds

Hello All I just got an issue with my river setup. Please look at the grid below ... p-v-p-v-p-v-p-v-p-v-p ... ... u-r-u-r-u-r-u-r-u-r-u ... ... p-v-p-V-p-V-p-v-p-v-p ... .... ------------u-r-u-r-u ... .... ------------p-v-p-v-p ... This is part of a grid. I just labeled the masked points with ...

seashellingolds

no rule to choose this? (I am also doubting if this question is naive?)

seashellingolds

kate wrote:I no longer spin up with climatology - better to just jump into real years and throw away the first one.

Hi Kate

This is interesting to me. Can you tell me the reason (related paper?) or your experience on that.
Is this particular for some cases but not for others? It really saves time

Y

seashellingolds

Hello

I am wondering if there is a quick way to estimate the sponge layer width and the multiple of visc in ROMS according to the resolution and velocity etc

thanks very much

seashellingolds

Hi, In the vorticity.F file, should the last dRde be dRdx here when computing PV? pvor(i,j,k)=orho0* & & (cff*dRdz_pr*(fomn(i,j)+ & & dVdx(i,j)-dUde(i,j))+ & & 0.125_r8*(dUdz_pr*dRde_pr-dVdz_pr*dRde_pr)) Moreover, I am wondering what the 3D relative vorticity means here. It looks the sum of 3 ...

seashellingolds

Hi all I may be asking a simple question but I really need confirmation Does it numerically make sense to release Lagrangian floats at between the first W layer and RHO layer as shown below ********* *** w *** . ^^^\ ^^^ free surface ********* . \ . . . . HERE :?: . ********* / . *** r ...

seashellingolds

Hi All I just made a test with both original code and my corrected code. I think the root of the problem is right as I mentioned above. But I am not sure the way I modified the code is the most optimal but kind of direct. Moreover, as the thread I posted in the ROMS Discussion several days ago ...

seashellingolds

Thanks for the replies Tonight is so hot that makes me wake up -_-!. So I was starting to think this problem. I guess the problem comes out of the double periodic boundary condition. Assume there is a 2*2 partitioned domain, a particle originally in the Northwest tile goes to Southeast tile in the ...

seashellingolds

It will be better if they synchronize.
Is it a good idea to separate float output from the output.F?
Any better suggestion will be appreciated

seashellingolds

Hi Has this problem ever been met or reported? Description : Lagrangian floats get lost at the periodic boundary Details : I put floats uniformly on a square domain with periodic boundary condition After several time step, some floats close to the boundary disappeared and even more with the model ...

seashellingolds

Hi all

I have a quick question about writing float file. Take main2d.F as example, output is before the float initialization. Does this mean the info in float output is always 1 step after the ocean_time?

Thanks

seashellingolds

If adding FB feedback as wikiroms says, the maximum step can reach about 1.4 sec, still very short, how can I improve this? The only two ways I can think out are 1, doing iteration, 2, separate this time step from momentum timestep. Is there anyone can give me professional suggestion. Thanks very ...

seashellingolds

Thank you for your reply John I used predictor-corrector method to solve these two first order ODEs and tried different predictors and correctors. I think 2nd RK is one kind of them but I didnt try. Let's say the equations are dx/dt=u, du/dt=RHS. The RHS comes from the instantaneous result of ...

seashellingolds

I am wondering if there is a module that plays with second order ODE in ROMS
I made one but have difficulty in stability. I tried many methods but the time step is still too small
Any suggestion will be appreciated

seashellingolds

well, I see, many thanks. It seems we have no pre-knowledge about that and therefore no better choice.

seashellingolds

Actually the answer can be no. I am just starting to learn bio model in ROMS and doing my class project. I think it is better to set bio Akt the same as salinity (means do nothing). I realized new ROMS is designed to seperate bio model part, which really simplify the work of adding a new model. That ...

seashellingolds

Maybe I need extend the length of Akt from NAT to NT, so I might be free to define Akt for bio tracers
But I guess this is not the original intention of bio model design

seashellingolds

just see this old thread with new reply by chance. I guess the problem is the difference between window and linux text system Windows follows the rule of old-style typewriter. Two steps is needed to get to the next line \r (return) \n (jump to next line), while linux just has \n doing this ...

seashellingolds

Hi All In ROMS 3.0 I used before, the variable Akt is dimensioned by total tracer number NT, so I can simply use Akt_bak for TS from stardard input and for bio tracers from bio input file or I can redefine them using ANA_VMIX Now I am using new ROMS, Akt has dimension of NAT which usually is 2. It ...

seashellingolds

Hi everyone Has anybody managed to apply UV/TS_U3ADV_SPLIT? I tried to use both and either of them but they keep making Blowing-up. This option can cause stability problem as cautioned in output script. Generally speaking, by which way can I reduce this risk. Is there any requirement or restriction ...

seashellingolds

Thanks Kate I know where the problem is. In fact there is something wrong with libmpichf90nc.a. It is not an archive file... Maybe I need to ask admin to rebuild it. However, this problem would not happen if I use -Bstatic flag with both ROMS 3.0 and 3.3. It does not seem to contain this static ...

seashellingolds

Plus : Anybody tells me the difference between
FFLAGS += -Bstatic -fastsse -Mipa=fast
and
FFLAGS += -O3
I used to use the former. Is the latter better?

seashellingolds

Hi everyone I just got a compiling problem with new ROMS. I ve been using ROMS 3.0 before and everything is fine. Does anybody meet the same problem or help me out. Here is the error msg. ...... ar: creating Build/libUTIL.a ranlib Build/libUTIL.a master.f90: /usr/local/mpi/bin/mpif90 -O3 Build/esmf ...

seashellingolds

Hi everyone I am new with ROMS and I am trying to make a run with daily wind forcing. I made my climtology file and boundry file with the cycle length 365. But in the wind forcing file, the leap year has 366 days. So how do they match with each other? I mean probably there is a flag variable which ...

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