Ocean Modeling Discussion

leon

Hi there, I ran into some problem when trying to estimate the posterior errors in data assimilation WC13/PSAS case. I'm using the latest version of ROMS while adding two cpp options "POSTERIOR_EOFS" and "POSTERIOR_ERROR_I" to estimate posterior error. An error occurred after the DA run when trying ...

leon

Hello, I found the Normalization case of WC13 tutorial cannot compute the model coefficient even if you turn on the switch in c4dvar.in and set the NADJ to be different form the NTIMES. In short, older version of WC13 Normalization can give us model, initial, forcing and boundary normalization ...

leon

Hi all, I'm using 4DVAR to run a test case. The total iteration number seems odd to me in the output mod.nc file. My understanding is that the total iteration equals Ninner * Nouter. However, the output iteration in mod.nc is larger that Ninner*Nouter. In my case, Ninner = 7 ; Minner = 8 ; Nouter ...

leon

Hi all, I ran the optimal perturbation case for both double_gyre and WC13 case, which give small values at the end (~10^-5). But when I ran the optimal perturbation for my own model, I got extreme large values (~10^5) at the end. I'm not sure why it happens. The time scale for the optimal ...

leon

Hi all,

When I define TLM_DRIVER and NL_BULK_FLUX together (e.g. for the double_gyre test case), I got such error:

NETCDF_OPEN - unable to open existing NetCDF file: ^@^@^@^@^@^@^
call from: inquire.F

If I don't define NL_BULK_FLUX, it would be fine. Any idea? Thanks a lot.

leon

Hi Arango, Thanks a lot for the update. My post (Jul. 9) is before the update (Jul.10). That's the reason. Thanks. I don't know what are you talking about. I checked the code and it already have that correction! I think that you need to update . As you see below, ad_v2dbc_im.F already have the ...

leon

In close_io.F line 69 45 DO i=1,nFfiles(ng) 46 IF ((FRC(i,ng)%Nfiles.gt.1).and.(FRC(i,ng)%ncid.ge.0)) THEN 47 FRCids(i,ng)=-1 48 DO j=1,NV 49 IF (ncFRCid(j,ng).eq.FRC(i,ng)%ncid) THEN 50 ncFRCid(j,ng)=-1 51 END IF 52 END DO 53 IF (model.eq.iADM) THEN 54 DO j=1,FRC(i,ng)%Nfiles 55 IF ((FRC(i,ng)%time ...

leon

Yes, you are right. I ran into the same problem too. It's in mod_boundary.F line1100. isouth should be inorth.

leon

I found this problem too after extensive debugging. But the bug has not been fixed yet. Hope it can be fixed soon, so people like me won't speed too much time on debugging. Thanks a lot. I've found what appears to be a small bug in ad_v2dbc_im.F (svn revision 758). When using the ADM_DRIVER option ...

leon

Hi all, When I do the optimal perturbation run, I got the error info at the first step of model run. PROPAGATOR - Grid: 01, Tangent Initial Norm: NaN STEP Day HH:MM:SS KINETIC_ENRG POTEN_ENRG TOTAL_ENRG NET_VOLUME 0 55136 00:00:00 5.704437E-23 NaN NaN 6.042164E+16 I'm not sure what causes this ...

leon

Hi all, I got an error while run the double_gyre/OP case. The error message is DEF_GST - creating checkpointing file, Grid : ^A^@^@^@ DEF_GST - creating checkpointing file, Grid : gyre3d_gst.nc Fatal error in MPI_Allreduce: Invalid datatype, error stack: MPI_Allreduce(861): MPI_Allreduce(sbuf ...

leon

Hi all, In WC13 R4DVAR_sensitivity case, the Lanczos vector file is needed for the adjoint sensitivity analysis to the observation. However, if we only consider the adjoint sensitivity to the initial/forcing/obcs, is the Lanczos vector files still necessary? If the file is necessary, how can we get ...

leon

Hi all,

I understand that for data assimilation, the objective is to minimize the error covariance related J function. For adjoint sensitivity analysis, are we minimizing the indicator function? During that process, all the observation-related inputs are not required, right? Thank you very much.

leon

Hi all,

There's a too strong surface coastal current for my simulation. Generally, my simulation is OK. What could cause a strong surface coast current? Wind? or anything else? Thank you for any suggestion.

leon

leon

Hi,

It seems that a '&' is omitted in the end of trunk/ROMS/Utility/wrt_tides.F(line 277).

277 20 FORMAT (6x,'WRT_TIDES - wrote time-accumulated tide harmonics, ',
278 & 'Grid ',i2.2)

Best,

X

leon

Thank you for the advice. The weird thing is that when I just run the circulatio part without sediment submodel, everything is fine. And the false TS only occur at the bottom layer when running the sediment model. Anyway, thank you for your suggestion.

leon

Hi John,

Thank you for the reply. I just tried to not use sed_dens, but I got the same problem. The TS are totally wrong. Do you have any suggestion? Thanks

leon

Hi all, I'm using ROMS-SWAN-Sediment coupled model to simulate river sediment transport on continental shelf. However, at the river mouth, the T goes too high, about 300, and the salinity goes to low, about -300, after 7 months running. The river sediment concentration is really high, about 50 kg/m ...

leon

Dear all,

I'm using WWIII to interpolate the OBC for my ROMS-SWAN model. However, I can't
find any information about the fifth values in the TPAR files (the
directional spreading values). Does anybody have such experiences? Thank
you very much.

Best,
leon

leon

In file "varinfo.dat", 'river_dye_' ! Input 'river runoff dye concentration' 'kilogram meter-3' ! [kg/m3] 'river_dye, scalar, series' 'ocean_time' 'idRtrc(inert(i))' 'nulvar' 1.0d0 I think the "ocean_time" should be "river_time" . Am I right?

leon

Dear all, Recently, I'm doubtful about the number of sediemnt bed layers. You can set three bed layers or five bed layers or some else. Is there any difference? I read the paper Warner et al. wrote in 2008. What I got is that 3 bed layers maybe ok. So what's the effect of setting more bed layers ...

leon

Hi,Kate. Thank you very much for your reply.

How did you determine the nudging coefficients? By expericences?

And do you use the coefficents for all the simulation time scales? For exmaple, the real time scale and the climatological time scale.

Thanks~

leon

Dear all, Sometimes, I'm not sure about the nudging time scales in the *.in file of ROMS. Actually, different settling about them will get different resluts. The current around the boundary may not flow out or fully radiated when the nudging time scales are set appropriately. For exmample, when a ...

leon

Hi, I'm confused about the formulas you give in your document.

What dose the 'Fu' painted in the attachfile represent in the formula?

Actually, I'm confused about the horizontal mxing treatment of ROMS. Could you please recommend some papers abouth that?

Thank you very much~

leon

Dear all, The model is running well before updated to r444. But when updated to r444, the model exits after the first step. I run the model in our cluster, the message is' signall 15 recieved'. I did not change anything, but just update to r444. The previous well-running model just exits without ...

leon

Dear all, How is the cohesive sediment treated in the latest ROMS? Is the cohesive sediment and non-cohensive sediment treated the same way? I have read Warner's several articles. The cohesive and non-cohensive sediment is treated the same. Actually, the cohesive and non-cohesive sediment is really ...

leon

First, thank you very much~ I update the code and there are still some errors. In the previous verison, there is no Ltracer option for mud or sand in the sediment.in file. The model is running ok. After updating to the latest version, the model runs well when the Ltracer option is F in sediment.in ...

leon

Sorry for that. Actually, the error is about the river sediment. The files are all the same, But it is right in the ROMS version 399 and wrong in the verison 429 or the lastest one. The north south east and west boundary sediment condition all exist in the bry file. Log files are below: Time is date ...

leon

Dear all, I am using the sediment model now. However, I'm confused about the value of surface erosion rate in the sediment.in file. Actually, a lot of factors influence the surface erosion rate, such as sediment diameter, current speed and so on. Other values can be caculated using the Sediment ...

leon

Dear fellows, In the sediment model,there has to be at least one bed layer so that the sediment can settle onto the sea floor. One interesting thing is that it will still produce sediments even you have set the thickness of the only one bed layer to be 0, whether you set the bed porosity to be 0.5 ...

leon

I'm afraid there are still some problems with the variables, maybe with the bry file varibles. Pls check out~

leon

The error is in checkvar.F, when set the sediment on. The mud_01 and snad_01 are considered as mud_ and sand_

error information：

NLM:checkvar unable to find model variable : mud_

leon

There has to be at least one bed layer so that the sediment can settle onto the sea floor. So set Nbed = 1, and init the thickness =0. That is fine. I suggest you set porosity = 0.5, not 0. In the future the porosity will be computed by the model. If you start the model with zero concentration in ...

leon

Dear all,
I　find the kinetic energy in the model log file is very small. For exmaple, there is only 0.02 in the model domain 24N-41N, 117E-131E. Of course I did not find the unit. SO what's the unit?

Thank you ~

leon

Thank you very much~ I made the tidal forcing file before, I'm just not sure the way I define the tidal options in *.h file. Because when I add tidal forcing, the current just go disorderly, I mean not so good as the no tidal case. Maybe there are some problem with the tidal harmonics, I'll check it ...

leon

Dear all, I'm still confused about the tidal forcing. Actually, my model domain is East China Sea. At first, I get the OBC data--zeta,u,v, from OCCAM ( a global ocean model). And there is no tidal forcing. The model rusult is fine. But when I add tidal force, the currents just become disorderly. I'm ...

leon

Thank you very much. You really do me a favor. In my case, I use add_fsobc and add_m2obc. One more question, If I add tide using SSH_TIDE UV_TIDE ADD_FSOBC ADD_M2OBC, the model will generate tidal information such as amplitude, right? But how to output the tidal information? I didn't find settings ...

leon

Dear all, After learning ROMS for several months, I'm really confused about the so called 'add tidal forcing. Q1: I have run a model with OBCs, which the OBC data are getted from some global ocean model such as HYCOM. There's no tidal forcing here. The result is good. If I want to simulate sediment ...

leon

Dear all. Why can't the number of bed layers be set to be zero? Actually, when the number of layers (Nbed) is set to be zero, there is an error says that the Nbed can not be zero. I want to know why. I want to see how the river sediments transport over continental shelves. If I set the Nbed to be ...

leon

Cool~ You are totally right. I have tried to define the river sediment as river transport, then I got such errors: NETCDF_GET_FVAR_1D - error while reading variable: river_sand_01 in input file: /dcfs2/users/leon/Documents/roms_examples/sediment/sediment-forc.nc call from: get_cycle.F GET_NGFLD ...

leon

Fist, thank you very much. I still have a question. Is the river sediment defined as the river runoff river_transport or the river_salt? For example, if as the river_salt, it should be N layers, but not for the river_transport. Which one is right? Thank you~

leon

I understand, I should add 'river_sediment' to the cpp*.h. But I'm not sure that if I must give the wave condition after I define the bottom boundary layer closure.
Any body?
Any suggestion?
Thank you~

leon

Dear all, I want to add sediment to a river mouth. But I am not sure about the cpp defines. Is it ok if I set 'UV_PSOURCE TS_PSOURCE Q_PSOURCE'? I find there are 'river_mud_. river_sand_' in the file varinfo.dat. So is it ok? Or what should I set in the cpp defines if I want to add sediment to the ...

leon

Hi, I get the same problem, I try to add variables to 'varinfo.dat', but have not successed. But I am a little confused about what I do, because what arango said in https://www.myroms.org/forum/viewtopic.php?f=30&t=1450 . Any way, I have to try. Can anybody give me some useful suggestion about this ...

leon

Dear all, I got a problem. When I didn't plus tide, my model can run for a long time. But when I plus tide, it just blows up after a few time steps. Why? I add my *.h file with 'UV_TIDES, SSH_TIDES, ADD_FSOBC, ADD_M2OBC'. Am I right? What's the most possible problem? Any suggestion is ok. Thank you ...

leon

Hi, John, I will use the ROMS-SWAM Coupled System to do some research on the sediment transport.

leon

Hello all, I got an odd problem with hc. Actually, the probelm is NETCDF_CHECK_VAR-inconsistent value of variable:hc 3.000000E+00 2.999994E+00 in/users/leon/nest-init.nc. But I check the init file and grid file, the value of hc are all equal 3. What's the problem? By the way, I just update my ROMS ...

leon

Yes,it's the land mask computing which cousts a long time. But the seagrid I use is from the RNT toolbox( http://eros.eas.gatech.edu/RNT/ ). Maybe there are some different. I usually load the coastline first, then setup the grids and computing land mask. Finally, adding bathyment and editing land ...

leon

Actually, when I　use the seagrid in RNT toolbox to compute the land mask, it always costs such a long time. Why does it cost such a long time? I know it depends on the number of grids and the computing domain. Are there other reasons? Which process costs the longest time? Can we improve it ?

leon

Thank you very much, rich. I know what's the problem. The seagrid that I use is from the RNT toolbox. Maybe it's different or old, so the spacer is not working. I download the one you told me. And the spacer works well. The RNT users should remeber that the RNT seagrid is to some extent different ...

leon

It is said that seagrid can change the space of the grid by change the position of the spacer. I did as the seagrid tutorial, but the spacing is not changing. What's wrong with the seagrid spcaer? Can someone tell me why it doesn't work for me? Thank you very much~

leon

leon

You'd better use the RNT in the Linux OS. And if you use RNT in the 32bit systerm, you need to recompile the mex files as the complie.txt said in the RNT website. By the way, RNT is really a good tool for ROMS beginners. Good luck.
leon

leon

Thanks all of you very much. Actually, RNT toolbox is also a useful tools for ROMS. You can get it from http://www.o3d.org/RNT/ . And there are also some tutorials on http://www.o3d.org/ROMS-Tutorial/ . Thanks a lot for Mr. E. Di Lorenzo. He really does a good job~

leon

Dear all,
Can ROMS do nesting right now? And how?
Are there any tutorials or tools or examples for ROMS nesting?

Any information is OK. Thank you very much~

leon

I learn a lot from :http://sauron.urban.eng.osaka-cu.ac.jp/%7Emori/research/ROMS/roms_obc.pdf. But I am still confused about the wikiROMS said in https://www.myroms.org/wiki/index.php?title=Frequently_Asked_Questions What are the ways that ROMS can receive tides on the boundaries? 1. You can specify ...

leon

hi, I think it's the problem of netcdf.
Maybe you should choose the appropriate mexnc netcdf snctool for your version of matlab.
You can check follow link for more details.
https://www.myroms.org/wiki/index.php/MEXNC

Good luck!

leon

Dear all, I'm really confused about the different OBCs. There are several options in the cppdef.h,for example: ** Eastern edge open boundary condtions OPTIONS: ** ** ** ** EAST_FSCHAPMAN use if free-surface Chapman condition ** ** EAST_FSGRADIENT use if free-surface gradient condition ** ** EAST ...

leon

Dear all, I am a little confused about the RNT toolbox(http://www.o3d.org/RNT/). There are some readmes in the toolbox, But still not enough. Now I am confused about the matlib/misc directory. I don't know what the files in the /misc diretory are used for. There are no any explanations. If you konw ...

leon

Hi~ There is some information about the bounday conditons.Hope this is useful. http://www.oceanwave.jp/tmp/roms_obc.tgz https://www.myroms.org/forum/viewtopic.php?f=17&t=930&p=3232&hilit=nobuhito#p3232 I have the similar problem. I am cofused with the different boundary condtions, especially the ...

leon

First, thank you very much. I have the roms_obc.pdf already. It just said some codes of the obc. But I still don't know the details mean of the obc options. I mean the physical means. Anyone can tell me that? Thanks~

leon

Dear all, In the cppdef.h of ROMS, we can see some open boundary condtion options. For example: ** Eastern edge open boundary condtions OPTIONS: ** ** ** ** EAST_FSCHAPMAN use if free-surface Chapman condition ** ** EAST_FSGRADIENT use if free-surface gradient condition ** ** EAST_FSRADIATION use if ...

leon

thx for reply first, Acturally，the output files are all less than 200M. But I still got the problem: MPI process terminated unexpectedly Exit code -5 signaled from node48 Killing remote processes...DONE real 9862.22 user 0.02 sys 0.01 + exit 0 I am not familiar with the MPI. Wish someone can tell me ...

leon

I change the dt value, but it still bolws up. This is my first application, I hope someone can help me. Thank you in advance. Information: Physical Parameters, Grid: 01 ============================= 86400 ntimes Number of timesteps for 3-D equations. 36.000 dt Timestep size (s) for 3-D equations. 50 ...

leon

I want to known that whether the CFL condition for ROMS is dt<sqrt(((min(min(dx))^2)+(min(min(dy))^2)) / (9.8 * (min(min(h))^2))) or not.
leon

leon

Thanks all of you. I　ｒｅａｌｌｙ　ａｐｐｒｅｃｉａｔｅ　ｉｔ．And I want to known that whether the CFL condition for ROMS is dt<sqrt(((min(min(dx))^2)+(min(min(dy))^2)) / (9.8 * (min(min(h))^2))) or not.
leon

leon

I just use ROMS for my own application, But it blows up when just runs several steps. When I check the history file and restart file, I find the value of zeta as fllows(only a part of zeta values): zeta = _, _, _, _, _, _, _, _, 0, 0.256860918381414, 0.254291715215559, 0.248481492553035, 0 ...

leon

Dear all, I'm new to ROMS. When I run my own application, I got model configuration error. I am not familiar with the ROMS model configration. Can someone tell me what's wrong with my model configuration? Thank you very much. My model configuration is as follows: Time is date cat ${PSB_NODEFILE ...

leon

I run the DAMEE application download from http://www.myroms.org/index.php?page=Datasets. What I do is just as the readme file tells me. But the program just exit when run at step 16320. The log file got such error: MPI process terminated unexpectedly Exit code -5 signaled from node46 Killing remote ...

leon

I did as arango said here(https://www.myroms.org/forum/viewtopic.php?f=3&t=45&p=70&hilit=bath&sid=4942beaa5724be5be7366aed7f299d07#p70).Then I use the seagrid to caculate the depth and mask of the gird area. But I think the result of depth is actually wrong. My area is 24N-41N 117E-131E. The related ...

leon

yes,you are right.
I think
region =[min(grd.latr(:))-1,max(grd.latr(:))+1,min(grd.lonr(:))-1,max(grd.lonr(:))+1]
is ok.
Thank you very much

leon

Dear all, When I use the RNT toolbox(http://www.o3d.org/rnt/) to get my topography as the MAIN_grid.m said, I got problem when I run code of MAIN_grid below: %========================================================== % topography %========================================================== %EDIT ...

leon

There are two mat2str functions, one is in the mexcdf5 directory of ROMS matlab tool, and the other one is in matlab/toolbox/matlab/strfun/ directory. The two mat2str functions are different. The first one is : function s = mat2str(x) % MAT2STR String equivalent to a matrix. % MAT2STR(X) converts ...

leon

Lm == 200 ! Number of I-direction INTERIOR RHO-points
Mm == 3 ! Number of J-direction INTERIOR RHO-points
N == 20 ! Number of vertical levels

I　think the value of Mm is wrong in the ocean_estuary.in

leon

That's the piont! It's ok now. You are really cool! Great! Thank you very much!

leon

Dear users,
I am new for ROMS, and when I learn ROMS, I get a lot of problems. I want to know if there are some groups like QQ or MSN for the users to discuss problems when they use the ROMS.
I really want to jiont if possible.
Or any one can create it?
Thanks!

leon

Dear all, I am a new user of ROMS. I run the upwelling test, it's ok. But when I run the ESTUARY_TEST , after 'make',I get such problem: cd Build; /usr/bin/gfortran -c -frepack-arrays -O3 -ffast-math -ffree-form -ffree-line-length-none analytical.f90 analytical.f90:256.32: BOUNDARY(ng)%zeta_west(j ...

leon

thx,kate.I download the package again, then there is no problem. I think it must be something wrong in my previous packge. Anyway, thank you very much.

leon

Dear users, I saw from wikiroms that we can use the plotting package for visualizing ROMS model output. But when I install the package as the wikiroms, I get such problems: leon@leon-desktop:/media/disk/linux/romstools/plot/src$ make /usr/bin/cpp -P -traditional -DLINUX -I/opt/g95soft/s_netcdf4 ...

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