Ocean Modeling Discussion

fdaryabor

Dear turuncu,
Hi

You can try "Gra" option for the turbulence kinetic energy (TKE) instead "Cha" and see how's that.

LBC(isMtke) == Cha Clo Clo Clo ! mixing TKE

LBC(isMtke) == Gra Clo Clo Clo ! mixing TKE

good luck to you
Farshid

fdaryabor

Dear Ivica,

Please have a look to "lmd_vmix.F " and the section, regarding to "Sum contributions due to internal wave breaking...", in fact non-breaking wave induced coefficient (Bv(i,j,k); (m2/s)) here is used to enhance the vertical mixing for momentum (Akv(i,j,k); (m2/s)) and tracer (Akt(i,j,k ...

fdaryabor

Yes, it's done by Wang et al., JGR 2010 based on Qiao et al, JPO 2004. I added it as a one of the switches (option) for vertical turbulent mixing :arrow: (lmd_vmix) to the CPP options list (ROMS 3.7), and is running now for the Mid-Atlantic Bight application :idea: . To extract wave induced mixing ...

fdaryabor

Dear,

Alright, use the following linux commands to convert nc2cdl.

:arrow: ncdump -b c myfile.nc > myfile.cdl

by the command "vim" or "gedit" (recommended for you to see as .txt file for edit) open myfile.cdl;

:arrow: gedit myfile.cdl

and also open "frcfile.cdl" from ../trunk/Data/ROMS/CDL ...

fdaryabor

Dear,
Your attached file is completely wrong

and it's not really readable for the ROMS, such attributions, dimensions and time format. I suggest you that follow directory

".../trunk/Data/ROMS/CDL" it can help you to find your questions

. Good luck to you
Farshid

fdaryabor

Dear,
As stated by Katherine and John, such errors :arrow: (GET_2DFLD - error while reading variable: or GET_3DFLD - error while reading variable:) are due to the definition of input variables. To avoid encountering such a problem is essential check consistency of the variables in ".nc" file with ...

fdaryabor

Dear Kate,
I've tried for the two different "timestep" as follow :arrow: ;

NTIMES == 1036800 3110400
DT == 900.0d0 300.0d0
NDTFAST == 30 30

&

NTIMES == 3110400 9331200
DT == 300.0d0 100.0d0
NDTFAST == 50

Second one running too slow. What's your suggestion for having a proper timestep here ...

fdaryabor

Dear users,
I think the problem can be because of the tiling computation :idea: . This is what I have :arrow:;

Architecture: x86_64
CPU op-mode(s): 32-bit, 64-bit
Byte Order: Little Endian
CPU(s): 32
On-line CPU(s) list: 0-31
Thread(s) per core: 2
Core(s) per socket: 8
Socket(s): 2

I have 2 CPU ...

fdaryabor

Dear Users,
Has anybody ever experienced the following problem? it has happened in the sixth year of the model run :!: :evil: . The model is configured with two, one-way nested domains. I don't know really :shock: , but I guess it can be because of the memory process and calculations carried out by ...

fdaryabor

Dear Eugen

I don't think there's actually any difference. Please take a look at ".../Nonlinear/nesting.F" and ".../Modules/mod_nesting.F". I refer you to John Wilkin comment in the following link, https://www.myroms.org/forum/viewtopic.php?f=14&t=4288
Good luck, Farshid :wink:

fdaryabor

Dear Eugen

Referring to the attached header file I recommend you to apply the following suggestions hope it can help you.

1: #define UV_SADVECTION ======> undef "UV_SADVECTION"

2: You have two options for the grid nesting "TWO_WAY, ONE_WAY". When NESTING option is switch ON, the model will run ...

fdaryabor

Dear,

In this case, make sure defined the LD_LIBRARY_PATH environment variables. Use the following command in the home directory that the path of your libraries is defined or not?

[nishtha@localhost oa]$ echo $LD_LIBRARY_PATH

Then you should to have the library path "/usr/local/lib" and "/usr ...

fdaryabor

Dear,

When you use "gfortran" instead of "ifort" compiler, as Kate commented you should be add 'lnetcdf' and 'lnetcdff' together as follow,
'-lnetcdf -lnetcdff'

Hope it can help you,
Cheers,

fdaryabor

Hi
As I look on the domain not defined properly 'land/sea (mask)'.
Cheers

fdaryabor

Dear,

You can use the attachment file.

Hope can help you.

fdaryabor

Did you check time step of the baroclinic and barotropic mode for the both domains. And the time intervals to save data in hisfile and avgfile? You should be careful apply the refinement coefficient for those.

Good Luck!

fdaryabor

Dear Chaos4u2,

What kate suggest you is the one way to resolving problem. I recomend you, please try to avoiding option "Output Diagnostics File: ocean_dia.nc" for Output/Input Files in your simulation, and see how. Few reason can be for "BLOWS UP".

1- Input data, such as forcings and boundary ...

fdaryabor

safoora,
Pls send your questions via my email;
farshiddaryabor@gmail.com
TQ

fdaryabor

Dear Safoora,
About what you ask me, is depend. Currently use the data what you have now. Then verify your results with observation/SODA.

Hope help you

fdaryabor

Hi, Safoora,

If you looking for matlab code to make forcing file, pls refer to following link and register as user, then through download link you able to download ROMS_TOOLS package. You can find matlab cosde as "make_forcing.m".

"http://www.romsagrif.org/index.php/download"

Hope can help you ...

fdaryabor

Hi,Taowang,

For your case after make surface forcings and boundary conditions of domain, add tidal elevation (m) and tidal currents (m/s) to sea surface height and 2D momentum climatologies, respectively. Furthermore, you must be careful when add tidal forcings, since tidal forcings (TPXO6/TPXO7 ...

fdaryabor

Dear Dr
Hi

For tide simulation using ROMS (one-way nested domain) used TPXO.6 (25 km) as boundary condition for the parent domain (with 50 Km resolution), so that the parent provides boundary condition for the child ( with 9 Km resolution). Compare RMS (amplitude and phase) of the parent, child and ...

fdaryabor

Dear All
During compilation I faced to following massage
mv a.out roms
make:warning: Clock skew detected. Your build may be incomplete.
I know by "make clean" for the other compiler can fix above massage, in the roms case is not correct.
is anybody know how can I solve this warning massage.
High ...

fdaryabor

Dear all
I have to use MPI, so I need know how can I set compiler "jobcomp" and the path variables for compiler.
Actually I set compiler as follow:

#!/bin/tcsh
####################################################
# COMPILATION JOB #
####################################################
#
# set ...

fdaryabor

Hi
In order to the arango guide for ignore wind stress don't touch to subroutine. You have to zero all of the array of wind stress matrix for this case if you refer to 'make_forcing.m' in ROMSTOOLS in line that is for writing of wind stress in netcdf file you put u=0 and v=0 after 'horizontal ...

fdaryabor

Hi kate
I checked again the model input (the looks is attached) in my idea should be right, but problem is still for figure out temp and salinity profile from the model output (the looks is attached. I will send you the all configurations for climatology run. Really appreciate for your guide.
Best ...

fdaryabor

Hi kate
Thanks for your response, what I want to say is the model's output for SST, Currents and SSH, are acceptable but the problem is with the vertical section of temperature and salinity in interior layers which has to be horizontal but what I got was vertical that's not right. since the model ...

fdaryabor

Hi kate
Thanks for your response, actually I run model climatology and got real results from model (SST, Currents, SSH), but I face to problem for figure out vertical section of temperature in the interior,in first survey I check vertical mixing scheme,I using Large, W.G., J.C. McWilliams, and S.C ...

fdaryabor

Dear all
I use "Roms_Agrif" for Peninsular of Malaysia and sunda shelf ((99E 115E),(5S 10N)), horizontal resolution (1/6 deg), Number of layer 25, (theta_S=5, theta_b=0.4, hc=40),(hmin=50m, hmax=1000) and level of reference for geostrophy calculation is 100m. I face to problem to figure out vertical ...

fdaryabor

Hi dhtjtks
Dear my friend best guide for set netcdf library for your machine refer to downloading "toolboxes" in following address,
http://roms.mpl.ird.fr/download.php in "Roms_Agrif"
download "mexnc" and "mex60" and set netcdf library in "/home/.../Roms_tools/mexnc/mexopts.sh" and make sure path ...

fdaryabor

Hi
Also you can use matlab toolbox in Roms_Agrif following address:
1) http://roms.mpl.ird.fr/Data/Preprocessing_tools_08_04_2009.tar.gz
2) http://roms.mpl.ird.fr/Data/Tides_2006_10_05.tar.gz
Best Regards
F.Daryabor

Center for Tropical and Climate Change System
Faculty of Science and Technology ...

fdaryabor

Hi
Tanks so much Kate
I have following data by following metrics, I need script or command for convert them to same metrics.
size(u) size(v) lon_rho lat_rho
104x102 103x103 104x103 104x103
could you please guide me.
Best Regards
F.Daryabor

fdaryabor

Hi Everybody
I want convert dimension of variables for example variable of 'u' recognized by dimension of 'time', 's_rho', 'eta_rho' and 'xi_u' to 'time','depth','lon_rho' and 'lat_rho',could you please help me.
Best Regards
F.Daryabor

fdaryabor

Hi my friend
Thanks so much for your guide.
I have model output to following form for 5 years.
roms_avg_Y1M1,roms_avg_Y1M2,...,roms_avg_Y1M12
roms_avg_Y2M1,roms_avg_Y2M2,...,roms_avg_Y2M12
roms_avg_Y3M1,roms_avg_Y3M2,...,roms_avg_Y3M12
roms_avg_Y4M1,roms_avg_Y4M2,...,roms_avg_Y4M12
roms_avg_Y5M1 ...

fdaryabor

Hi Everybody
ROMS is in xi,eta,sigma
coordiantes. I want to convert sigma co-ordinates to
depth coordinates. I will get the output nc file in
the following form. Everybody could help me for guide or have script for converting thanks so much.
netcdf roms_avg_Y1M1 {
dimensions:
xi_rho = 103 ;
xi_u ...

fdaryabor

Hi
I want model output file obtained from long simulation in a specific form for example I want run model for 5 years thus I want output file be to following form:
roms_avg_Y1M1.nc, roms_avg_Y1M2.nc, roms_avg_Y1M3.nc,...
Everybody can help me thanks so much.
Best Regards
F.Daryabor

fdaryabor

Hi
when I want show salinity and temperature vertical profile from 'roms_gui' vertical profile of salinity and temperature is wrong near coast. could you please guide me for solve this problem.
Best Regards
F.Daryabor

fdaryabor

Hi
When I choice 'tide' option in cppdef.h I face to following error, could you please help me for solve problem.
Best Regards
F.Daryabor

GET_TCLIMA -- Read climatology of tracer 1 for time = 345.0
GET_TCLIMA -- Read climatology of tracer 1 for time = 15.00
GET_TCLIMA -- Read climatology of ...

fdaryabor

Hi Kate
I attach for you 'romstools_param.m' file, this is alone the file for edit by user, you will see that I must edit only grid parameters for building the grid, surface forcing parameters for getting the wind and other surface fluxes and getting the initial and the lateral boundary conditions ...

fdaryabor

Hikate
I attached temperature vertical profile yield of Roms output near coasts I'm looking for near coast looks should be wrong, because depth is inversely proportional to temperature. Could you please tell me why are wrong?
Best Regards
F.Daryabor

fdaryabor

Hi Kate
Thank so much, I face with following error. Please you guide me for resolve it.
Best Regards
F.Daryabor
******************************************
ABNORMAL JOB END
USER TERMINATED
******************************************
VMAX = 0.630E+39 IMAX,JMAX = 187 78
IINT,IEXT = 28 1

MAIN ...

fdaryabor

Hi
I want Run model for South China Sea with Lonmin=98, Latmin=0 and Lonmax=125, Latmax=30.
I tried find optimum values, dl,theta_s, theta_b, hc and N for my domain but I can't find
optimum values.
Everybody could help me thank so much.
Best Regards
F.Daryabor

fdaryabor

Hi
When I run 'make_clim' I face following error:

Compute geostrophic currents
time index: 1 of total: 12
??? qhull precision warning:
The initial hull is narrow (cosine of min. angle is 1.0000000000000002).
A coplanar point may lead to a wide facet. Options 'QbB' (scale to unit box)
or 'Qbb ...

fdaryabor

Hi
Thank So Much Kate
I use Agrif ROMS and in this ROMS version I have STATION, FLOATS and SEDIMENT options, but I don't selection them. The model resolution is:

Resolution: 1/6 deg

Create the grid file...
LLm = 95
MMm = 84

Fill the grid file...

Compute the metrics...

Min dx=18.1122 km ...

fdaryabor

Hi
I have changed 'theta S', 'theta b' and 'hc' for my domain few time and time step but every time I run model face to following error (BLOWUP:
South China Sea
1080 ntimes Total number of timesteps for 3D equations.
2400.00 dt Timestep [sec] for 3D equations
45 ndtfast Number of 2D timesteps ...

fdaryabor

Hi kate
I have question, when I checked up Roms_Agrif directory I saw some of scripts was undefined for my case 'REGIONAL' and some of parameters for tracers (Temperature and Salinity) and baroclinic and barotropic mode was undefine thus I defined them for model ans so in main.F for example was ...

fdaryabor

Hi
When compile I face to following error:

OPERATING SYSTEM IS: Linux
PROCESSOR IS: i686
cp: No match.
/bin/rm -rf core *.o AGRIFZOOM/AGRIF_YOURFILES/*.o *.i *.s *.f *.trace *.mod
/bin/rm -rf roms mpc cross_matrix cppcheck srcscheck checkkwds partit ncjoin ncrename ./rii_files
fpp -free -P -I ...

fdaryabor

Hi
This is Roms_Agrif version
Best Regards
F.Daryabor

fdaryabor

Hi
Could you please explain for me following parameters exiting in ana_initial.F include: 'Z0','THKNSS',and 'STRAT'

Best Regards
F.Daryabor

fdaryabor

Hi
1- do you defined your grid from 30m under surface to 1000m?
2- Is shallow water your study region ?
3- Is concept of h, study region depth?
when I want set teta_s and teta_b for 5000m depth and switch index=0 for both column section and row section I face following error:
>> [z,sc,Cs]=scoord ...

fdaryabor

Hi
Thanks so much my friend.
I defined function parameters
[z,sc,Cs]=scoord(h,theta_s,theta_b,Tcline,N,kgrid,column,index,plt)
but when I want plot S-coordinate I face with following error:

>>[z,sc,Cs]=scoord(40,6,0.4,10,15,0,0,1,1)
??? Error using ==> set
Bad value for axes property: 'XLim ...

fdaryabor

Hi
Thanks so much for your guide.
Could you explain me, how can I use from this tool (scoord.m) for test theta_s,theta_b,hc and N?
Best Regards
F.Daryabor

fdaryabor

Hi
I'm going to test the effects of theta_s,theta_b,hc and N by using '../Preprocessing/test_vgrid.m', but doesn't exist this script in directory.
Could you guide me

Best Regards
F.Daryabor

fdaryabor

Hi
Could you more explain following concept of each parameters and those function in model:

Roa, theta_s, theta_b, hc, hmin, hmax_coast, rtarget, n_filter_deep_topo, n_filter_final, tini,Yorig , SPIN_Long
concept of tini=0 is 1st Jan, tinni=1 is 2st Jan,..., etc
if Day of initialisation for ...

fdaryabor

Hi
When I execute 'jobcomp' automatically create 'Makedefs' in Compile directory you say me, 'Just find this file and save if for your records'. I don't understand concept of this sentence. Please kindly could more explain me.
I found your paper and was very useful for me
Thanks so much for ...

fdaryabor

Hi
I can't downloading full text your paper, namely 'A method for computing horizontal pressure-gradiant force in an ocean model with a non-aligned vertical coordinate. Journal of Geophysical Research 108 (C3),3090,2003' please kindly Could you send me
I need understand concept of 'hereafter SH91 ...

fdaryabor

Hi
Could you specify me, which executable files must place into ../bin directory?
After place executable files into ../bin directory.
I must place ../bin path into PATH in .cshrc?

I check .cshrc that is include:

# .cshrc

# User specific aliases and functions

alias rm 'rm -i'
alias cp 'cp -i ...

fdaryabor

Hi
Thank so much for anythings. I need use of ROMS_AGRIF results for my ph.d thesis for South China Sea.
In ROMS exist twin Compile directory '/home/ROMSTOOLS/Compile'
and
'/home/ROMSTOOLS/Roms_tools/Compile'
I find 'Makedefs' file within both of them.
I don't understand your aim 'saving the ...

fdaryabor

Hi
1- I typed "make tools" in '../Roms_tools/Roms_Agrif' directory for creates executable files but I face to this message:
Makefile:5: Makedefs: No such file or directory
make: *** No rule to make target `Makedefs'. Stop

I have only following execute files in Roms_Agrif directory
Makedefs.generic ...

fdaryabor

Hi
I go to ncrename.F in Roms_Agrif but I can't do your guide, can you more explain me following guide

'Do do so, you MUST DESTROY netCDF variable "time_step" in you
restart file which you want to treat as initial. Rename it to be
something else, say use

ncrename restart_file_name.nc time_step ...

fdaryabor

Tank so much
I need understand, how can I manually replace climatology data and wind forcing myself.
For example I need replace COADAS05 and QUIKSCAT, which file or code can do this way.
Best Regards
F.Daryabor

fdaryabor

Hi
Tank so much
Can you explain this cod 'NRREC' in initial: NRREC filename
1

Best Regards
F.Daryabor

fdaryabor

Hi
I check my file size,I have a 2 GB limit on system, my out put files 'roms_avg.nc','roms_his.nc' and 'roms_diags_avg.nc' are more 2 GB size, around 2.9 GB, How can I to exceed that?
can you guide me?

Best Regards
F.Daryabor

fdaryabor

Hi

1- I want run model for 1 year (2005), I decrease the time step but I have following error:

4175 2.41609 7.509198465E-03 1.3246625E+01 1.3254135E+01 4.8568477E+15 0
4176 2.41667 7.508518509E-03 1.3246628E+01 1.3254136E+01 4.8568477E+15 0

NF_FWRITE ERROR: nf_put_vara netCDF error code = 22 ...

fdaryabor

Hi
when execute ' ./jobcomp' I face to follow error:

gmake: *** No rule to make target `ropigrid.o', needed by `roms'. Stop.

please you guide me for solve this problem

Best Regards
F.Daryabor

fdaryabor

Hi
when execute './roms roms.in' I have follow error

READ_INP ERROR while reading block with keyword 'auxiliary_history_fields'.

READ_INP ERROR: A total of 1 configuration errors discovered.

please you help me for solve this problem

Best Regards
F.Daryabor

fdaryabor

Hi
In page 21 of user guide line "ROMS can be compiled by running the UNIX tcsh script ~/Roms_tools/Run/jobcomp. Jobcomp should be able to recognize your system. It has been tested on Linux, IBM, Sun and Compaq systems. On Linux PCs, the default compiler is the GNU g77, but it is possible to ...

fdaryabor

hi
I have error in create make_bry but I skip of it and when I execute './jobcomp' in shell script I will have follow errors:

AGRIF_FILES/modinitbis.F:27: error: keys_agrif.h: No such file or directory
AGRIF_FILES/modinitbis.F:60: error: include_agrif.h: No such file or directory
AGRIF_FILES ...

fdaryabor

hi
I have error in create make_bry but I skip of it and when I execute './jobcomp' in shell script I will have follow errors:

AGRIF_FILES/modinitbis.F:27: error: keys_agrif.h: No such file or directory
AGRIF_FILES/modinitbis.F:60: error: include_agrif.h: No such file or directory
AGRIF_FILES ...

fdaryabor

Hi

when I execute make_bry after make_clim,
my computer will restart and unable to create 'xxx_frc.nc', 'xxx_ini.nc' and 'xxx_clm.nc' in '/root/ROMSTOOLS/Roms_tools/Run/ROMS_FILES'. matlab will only create 'xxx_grd.nc' , another time when I test make_bry in matlab I have follow error:

>> make_bry ...

fdaryabor

Hi, subs is the name of a variable in the program, but is also the name of a matlab function.
"which subs" will tell you if you have the subs function and in which directory it is. If you do, try removing that directory from your matlab path.

Tank you my friend for your guide.

Best Regards
F ...

fdaryabor

hi
When I execute make_grid in matlab for Linux system I have follow error:
make_grid

Making the grid: ../Run/ROMS_FILES/roms_grd.nc

Title: Benguela Test Model

Resolution: 1/3 deg

Create the grid file...
LLm = 23
MMm = 31

Fill the grid file...

Compute the metrics...
??? Error ...

fdaryabor

Hi

When I execute make_grid in matlab I see follow error:

>> make_grid

Making the grid: ../Run/ROMS_FILES/roms_grd.nc

Title: Benguela Test Model

Resolution: 1/3 deg

Create the grid file...
LLm = 23
MMm = 31

Fill the grid file...

Compute the metrics...
??? Error: File: subsref.m ...

fdaryabor

You are compiling svn from sources? Is there any binary available for your system? What system is it, anyway? You'd probably get more helpful replies from the svn site than from the ROMS site.

Thankful Kate, I try doing your guide.

Best Regards
F.Daryabor

I cant solve problem my svn error ...

fdaryabor

kate wrote:You are compiling svn from sources? Is there any binary available for your system? What system is it, anyway? You'd probably get more helpful replies from the svn site than from the ROMS site.

Thankful Kate, I try doing your guide.

Best Regards
F.Daryabor

fdaryabor

Hi
When I execut './configure' for subversion-1.4.6 I have following error:

'configure: error: no suitable apr found'

Please anyone confronting this problem guide me.

Best Regards
F.Daryabor

fdaryabor

Hi
Please anyone confronting following problem guide me.
In launch a Matlab session in the directory: ~/Roms_tools/Run, when I Run the 'start.m' script, I confronting following message:

>> cd Roms_tools/
>> cd Run/
Add the paths of the different toolboxes
/bin/bash: .mysystem: Permission denied ...

fdaryabor

User Dear & Lady
I am new user ROMS. When I installing libdap after Type './configure' and 'make' I confronting this message after Type 'make check

'make[3]: *** [check-TESTS] Error 1
make[3]: Leaving directory `/home/farshid/libDAP/libdap-3.7.10/tests'
make[2]: *** [check-am] Error 2
make[2 ...

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