Ocean Modeling Discussion

kee

ok, thanks!

kee

dear Kate,

I have used roms_tools to prepare input datasets. these days I try to use roms own matlab scripts to do the thing, and met with many problems that still unresovled. I felt terrible these days. I wish you can help me.

<1> I obtain grid.nc using gridpak, then I turn to matlab scripts to ...

kee

dear Kata,

Thanks for your help!
The compiler I use is ifort, and it did go wrong. I followed what you suggested, added idx = MAX(i,1) into Utility/blktri.F, and now it goes through.
Now I have other questions:
1) how to use bathsuds and bathsoap to get a good r-Value?
---------
In the Caribbean ...

kee

the grid.h file
cat grid.h
#include "griddefs.h"
#include "bathy.h"
integer ITMAX, IBIG
parameter ( ITMAX=6, IBIG=500 )
! ITMAX is the number of iterations to perform
! IBIG is the largest number of points to be read in for one
! boundary.
!
! original distribution of x,y points is preserved on ...

kee

Hi,

I tried to use Gridpak to generate a grid, and simply used the two given examples, namely Carribean and USwest . The first case was successfully duplicated, while I failed in the USwest case.
The error messages are

[gridpak]$ gridG < Include_USwest/grid.in
rectangularity error in mapped ...

kee

hi kate,
after last poster, I did some work.
Now I met with new problem, i wish the problem can be solved soon.
the following is the description.
sorry for its length.

I found out that the boundary conditions I made the first time is seriously wrong, all seems OK except "zeta" with all NaNs. So I ...

kee

hi kate,

you are right. its most due to myself.
I check out the standard output carefully and found that there are NaNs in the inputs, like

GET_2DFLD - sea surface salinity climatology, t = 15 00:00:00
(Rec=0000001, Index=2, File: roms_frc.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = 1.79227009E ...

kee

FYI, it's blowing up at the surface not the bottom. What are you using for surface forcing fields?

Hi Kate,

thanks for your reply.
COADS05 (surface marine climatology 1945-89) 0.5deg resolution data was used.
I tried to use it to have a climatology run, and I have done that before.

what is the ...

kee

I just wondering if there is some CPP flags that I set improperly!

kee

hi,

when i set dt to 120s, the Courant number is less than 0.1, the result is the same.
any idea is appreciated!

bing

kee

hi,

I made a 1/6deg grid, with 20 levels in vertical and 1151x0734 in horizontal.
Dt was set 600s. it blow up at the beginning of calculation. But I do not think it is much related with dt, since

Minimum barotropic Courant Number = 1.38934555E-02
Maximum barotropic Courant Number = 4.67089096E ...

kee

hi simion,

which tools did you use to create your datasets to start your 2-way nesting model?
I want to use it. Could you tell me about it?
thanks.

Cheer!

kee

hi kakearney,
Im sorry I cannot help you, since I am new to ROMS and have not test the two-way nesting yet.
However, I am curious about how did you created your datasets(eg.ini/frc/grd/bry) that are used in your 2-way nesting model.

Could you tell me about that?
I want to learn it.
thank you in ...

kee

... The problem was solved by specifying a GLS mixing model in the model options during the build process. It may not be the probelm you have but it might be a starting point to look at...

Hi ptimko,

Thanks for yr kindly reply.
I did specify a GLS mixing model in the APPLICATION.h, like
#define ...

kee

Did it blow up because of a large velocity or because the tracer fields got weird? Where did it happen? At the surface, bottom or in the middle?

Kate, thanks a lot!
I checked the output and some information is pasted below

STEP Day HH:MM:SS KINETIC_ENRG POTEN_ENRG TOTAL_ENRG NET_VOLUME
C => (i ...

kee

Hi all,
I am very confused that the model blow up at the 9966 timestep. I am sure the CFL creteria is satisfied.
I think that if the DT is not small enough, the model can blow up shortly after the starting. Now it blowup at the 9966th timestep, it is more likely that waves shorter than 4*DX cause ...

kee

The problem has been solved by the administator
thanks

kee

Hi all,

I am carrying out an application. After 3816 time steps the model stoped. I checked the logfile, the error information is

... ...

3816 26 12:00:00 8.009553E-03 2.085246E+04 2.085247E+04 1.348033E+16
(276,031,14) 3.500503E-02 6.354667E-03 5.346894E-01 2.668803E+00

NETCDF_PUT_FVAR_1D ...

kee

Hi Wilkin
Thanks a lot!

kee

is there any suggestion?

kee

Hi all,

I downloaded Arango's Matlab packet , and tried to make my own grid file.
The MEX is also needed when using SeaGrid. As told by the instruction, I typed 'make_seagrid_mex' in matlab prompt, and errors came out like
>> make_seagrid_mex

Warning: You are using gcc version "4.4.6". The ...

kee

Hi all,
I got the answer from https://www.myroms.org/wiki/index.php/seagrid .
The matlab scripts should be written in this way
>> [xbathy,ybathy]=meshgrid(xbathy,ybathy);
>> xbathy = xbathy(:);
>> ybathy = ybathy(:);
>> zbathy = -zbathy(:);
>> save bathy_seagrid.mat xbathy ybathy zbathy

the ...

kee

Hi all,
I tried to get the bathy data via read_srtm30plus.m , and it returned wrong mesages like below.
can anyone tell me why?
and how to fix it?
thanks a lot.
I feel bad these days since always having problems...

>> [lon,lat,z]=read_srtm30plus([-5 30],[95 135],60,1);

url =

http://onearth.jpl ...

kee

Hi all,
I tried to obtain the Bathymetry data through below way, but it doesnot work.
I donot know how to do.
can anyone help me?
thank you!

>> y=nc_varget('etopo5.nc','topo_lat',[1020],[421]);
>> x=nc_varget('etopo5.nc','topo_lon',[1140],[481]);
>> z=nc_varget('etopo5.nc','topo',[1020 1140 ...

kee

Hi all,

I made the atmpheric forcing file in my own way, and tried to run the model.
However, it doesnot work, and the messages is below.
Can anyone give some ideas?
Thanks in advance!

GET_VARCOORDS - Cannot find "coordinates" attribute for variable: uwnd
in file: ./Inputs/roms_blk.nc

This ...

kee

Hi,

adding more information here.

The results I obtained were simulated using Roms_Agrif version. The odd is that I can't visualize them via the tools provided by Myroms.com, just like the above discribtion.

So the questions are:
1)what's the similarities and differences bewtween these two ROMS ...

kee

Hi,

I carried out an experiment, in which the ini and bry conditions , as well as the atmosphere forcing , were made on my own .
At last, I obtained several nc files, namely the his.nc and avg.nc .

I checked the file, and the header part is below:
>> nc_dump('roms_his.nc')
NetCDF roms_his.nc ...

kee

You can make the same plots that you saw in ROMS manual by using John Wilkin's plotting tools:

http://www.similarsites.com/goto/romsmatlab.tiddlyspot.com

I think Roms_Islice is the one you want (figure 19 in roms manual).

thank you!
I draw the same figure with MATLAB.
I will try the plot later ...

kee

Hi Zhao,
You can not expect that vertical temperature profile to be similar with the one illustrated in the WikiROMS, since you didn't plot it in the right way.

You should use h.*s_rho in MATLAB to find out the yaxis in the figure you demonstrated.

Good Luck

thank you!

I draw the same figure ...

kee

Hello Kee,
I'm new in ROMS and in ocean modeling so i can't really help you. I wanted also to run the Latte test case but i found the following discussion saying that latte needs to be updated so i didn't even try to run it.... Check this and good luck
https://www.myroms.org/forum/viewtopic.php?f ...

kee

Hi Kee,

try to compile your code by enabling the MPI
option on the build.bash/build.sh script, specifically
uncomment USE_MPI and USE_MPIF90 commands. Now if your
machine have, for example, the mpich2 library after your
compile is finished type this

echo MPD_SECRETWORD=roms > ~/.mpd.conf
chmod ...

kee

kate wrote:Those names are placeholders for files you may or may not need. I have used a boundary condition file and a climatology file, but not any of the rest. Cases like UPWELLING need none of them.

Yeah, I also noticed that. but still confused.
Anyway, I will figure it out.

kee

The true geometry has a flat center with a shelf to both the south and the north. Depending on your plotting software (and what you tell it of your geometry) you may or may not see the shelves. Logically, the computer has a rectangular grid of points on which is it computing and that is the easiest ...

kee

Hi all,

I found that nearly all the *.in file has the following INPUT section :
____________________
! Input NetCDF file names, [1:Ngrids].

GRDNAME == *.nc
ININAME == *.nc
ITLNAME == ocean_itl.nc
IRPNAME == ocean_irp.nc
IADNAME == ocean_iad.nc
CLMNAME == ocean_clm.nc
BRYNAME == ocean_bry.nc ...

kee

Hi all,

I managed to run the UPWELLING case, and drawed some figures.

The question is that there is difference between my results and those showed on the web : https://www.myroms.org/wiki/index.php/UPWELLING_CASE .
My day-1's T-field is showed in the attachment.

My results did not have the ...

kee

Hello Kee,
I'm new in ROMS and in ocean modeling so i can't really help you. I wanted also to run the Latte test case but i found the following discussion saying that latte needs to be updated so i didn't even try to run it.... Check this and good luck
https://www.myroms.org/forum/viewtopic.php?f ...

kee

Hi,

I tried to run the LATTE case, and it's Ok during the compiling, but broke during running.
Some information is as the following:
_______________

CHECKDEFS - cannot activate option: TS_MPDATA
in serial with partitions or shared-memory...
Use distributed-memory (MPI) in parallel runs ...

kee

is there any cue ?

I guess someone else also met with this problem.

kee

The trunk ROMS does not have the Apps directory, nor a sea ice model. My branch has both. To get my branch you either have to ask Dave Robertson for access to my svn branch or go to github: https://github.com/kshedstrom/roms

I should warn you that this is a development code with various warts ...

kee

I went to 'http://coast-enviro.er.usgs.gov/models/Latte/in/', and downloaded all the files except "varinfo.dat" (it goes wrong when download it). The same thing happened when dealing with ./original/ file.

I want to know if the 'varinfo.dat' file here is the same with that used in the UPWELLING ...

kee

can anybody help me?

kee

Hi everyone,

I want to do the Arctic example . But I donot have the Apps/ file, and I didnot find it on the web, too.

What's the matter?
Where can I get it?
if there is no for now, can anyone send a copy to me ?
paste on the web or email to me: zhaoyuanbing88@126.com
I need it.
Thank you very ...

kee

Hi arango,

Thank you very much.
I have already known how to do

zhao

kee

On page 79 of the <DRAFT Technical Manual for a Coupled Sea-Ice/Ocean Circulation Model (Version 4)>, there is a paragraph written as the following:

++++++++++++++++++++++++++++++++++++++++++

7.1.2 Case-specific Include File

... ... ... ...
Note that any undefined variable need not be ...

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