Ocean Modeling Discussion

jacopo

http://www.cmre.nato.int/ ---> Employment ---> current vacancies

jacopo

Please consider submitting an abstract to

OS4.1 Open session on Operational Oceanography

We welcome contributions in the area of Operational Oceanography which demonstrate skill assessment, error analysis and uncertainty estimation. This might be through the use of a range of metrics comparing ...

jacopo

with this options compile without complaints about waves.

yes, because you are using a currents-only BBL (either UV_LOGDRAG or UV_LDRAG). Waves are required instead by SSW_BBL.

Looking at your CPPdefs, I see that you have all OBC for passive tracers. But I guess you have to define also T ...

jacopo

i found in varinfo.dat

'Dwave' ! Input
'wind-induced wave direction'
'degrees' ! [radians]
'Dwave, scalar, series'
'wave_time'
'idWdir'
'r2dvar'
0.017453292519943295 ! pi/180

'Hwave' ! Input
'wind-induced significant wave height'
'meter' ! [m]
'Hwave, scalar, series'
'wave_time ...

jacopo

dnavidad wrote:i've inserted

#define ANA_WWAVES.h

wait: this must be 'ANA_WWAVES', not 'ANA_WWAVES.h'

jacopo

SSW_BBL is meant for bottom boundary layer wave-current interactions (mostly due to sediment transport).
If you define this, you have to provide several wave parameters:
- running ROMS-SWAN coupled online
or
- running SWAN uncoupled and later (i.e., offline) providing ROMS with forcing file ...

jacopo

congratz!

jacopo

wilkin wrote: Then also set SOLAR_SOURCE so that the radiation is absorbed over some depth range set by the WTYPE options in ocean.in.

jacopo

Post title: Principal Scientist - Physical Oceanographer
NURC is seeking a qualified physical oceanographer as Head of the Environmental Modelling and Prediction Team within the Applied Research Department. This post is offered at the Principal Scientist (NATO grade A-4) level.

for details, see ...

jacopo

Courtney,

the easiest option I see is the following:

1) estimate (offline) the momentum stress using simple parameterizations that require only the wind field. An example parameterization is here
http://woodshole.er.usgs.gov/operations/sea-mat/RPSstuff-html/wstress.html

2) Create a netcdf ...

jacopo

try using MPDATA

jacopo

where did you install ncdump?
If it is not in a standard path (e.g., /usr/bin/), you have to export the path netcdf-4.1/bin in your .profile

jacopo

Yes. However, sometimes, it is safer if you replace the cpp def MY_OPTION with the name of your application (RIVERTEST1?) in order to prevent having unwanted pieces of code used because MY_OPTION could be used somewhere else.

jacopo

Thanks. I didn't provide an initial field for the passive tracer except giving a constant value to the variable 'stflx' in the ana_stflux.h file as below."
!
!-----------------------------------------------------------------------
! Set kinematic surface flux (T m/s) of passive tracers, if any ...

jacopo

did you provide the initial field for the passive tracer?

if not, you want to modify Functionals/ana_passive.h

Jacopo

jacopo

For the second problem, try using the solution with PWTAIL=5
https://www.myroms.org/forum/viewtopic.php?f=20&t=1311

For the first problem (current along the boundary), I'm not sure I can help. Maybe there is an issue with the radiation stress over there? Try defining DIAGNOSTIC_UV and check if ...

jacopo

your code?!? did you get ROMS via SVN or what?

Let's assume you did (If you didn't, go here https://www.myroms.org/wiki/index.php/Subversion )

In ROMS/Include/upwelling.h you have

#if defined GLS_MIXING || defined MY25_MIXING
# define KANTHA_CLAYSON
# define N2S2_HORAVG
#else
# define ANA_VMIX ...

jacopo

PATH=$PATH:home/thingumajig/netcdf_dir/bin
export PATH
home/thingumajig/netcdf_dir/bin is the dir where your ncdump/ncgen are, so modify the name according to where you put netcdf.
Add these lines to your:
$HOME/.profile if you are a ksh or sh user
$HOME/.bashrc if you are a bash user
export ...

jacopo

add the path where ncdump is in your ~home/.profile

jacopo

kate wrote:You can check Build/analytical.f90 during the build to see if it got the right ana_wind.h.

It is also specified in the ROMS log file once you make it to run

jacopo

Make sure your makefile point to the right ana_wind.h specifying the dir

MY_ANALYTICAL_DIR ?= /home/the_pat_to_the_folder_with_your_ana_files

jacopo

good news, I was going to implement the same thing, but it's already there

jcwarner wrote:However, for 3D this perhaps should be some weighted average over a depth ~ Hsig, with an exponential decay.

Indeed, but including TKE from wave breaking makes this OK anyway.

jacopo

in mct_roms_swan.h I see:

CASE ('Ubar') ! 2D U-momentum

CALL ROMS_export2d (ng, tile, &
& id, gtype, scale, add_offset, &
& LBi, UBi, LBj, UBj, &
#ifdef SOLVE3D
& OCEAN(ng)%u(:,:,N(ng),NOUT), &
#else
& OCEAN(ng)%ubar(:,:,KOUT), &
#endif
& Fields(id)%ExpMin, Fields(id)%ExpMax, &
& Asize, A ...

jacopo

try

Code: Select all

BINDIR ?= .

note that there is a 'dot'. I don't see the 'dot' in your post.

slvester wrote: BINDIR ?=

It should be there.

jacopo

slvester wrote:first,I can't find the file :oceanM,maybey there are not this file.

ok, then forget my tip

slvester wrote: Second,/usr/bin/ld,what's this mean?

it's the linker you run in the last step in compiling. Did you get any error before that point?

jacopo

I believe you have to just rename (or remove) the old oceanM.

jacopo

in addition to Mathieu's list, using k-epsilon can cause instabilities. try out something else (MY2.5, k-w) or use half the timestep

jacopo

Hi all ROMS users!))))
Please, help me with my application for compute sediment transport in seashore with input real grid and forcing from SWAN.
I have installed MCT and have run his examples. All works well. When I start ROMS with mpif90, assign next error:

[xxx@host] roms3 # mpirun -np 2 ...

jacopo

Thanks for explaining zo. I have found that in the code,but I don't know whether the value is trnasferred to wave code or not, I found swan still uses PBOT(5) (0.05) in the coupling code.

did you comment out

&& KEYWORD TO CREATE BOTTOM FRICTION GRID &&
INPGRID FRIC CURVILINEAR 0 0 76 71 ...

jacopo

well, digging a little bit into the model (ROMS - ssw_bbl.h), I see:

zoMAX=0.9_r8*Zr(i,j)
zoMIN=MAX(absolute_zoMIN,2.5_r8*d50/30.0_r8)
!
! Initialize arrays.
!
zoN(i,j)=MIN(MAX(2.5_r8*d50/30.0_r8, zoMIN ),zoMAX)

[...]
bottom(i,j,izNik)=zoN(i,j)

and, in mct_roms_swan.h

CASE ('ZO') ! bottom ...

jacopo

When you couple the two models (def SWAN_COUPLING) and in the coupling_inlet_test.in you specify to exchange UBAR and VBAR from the ROMS into SWAN, SWAN actually computes wave based on 'apparent wind', instead of the exact input wind. This is the way SWAN takes into account currents.

Zo is used as ...

jacopo

rempoints.m is supposed to be in the roms_tools package.

I have it in

Visualization_tools\rempoints.m

Did you add in the matlab pathdef or startup the Visualization_tools dir along with subdirs?

-J

jacopo

This post is primarily targeted on those of you using SWAN, but since it is associated to ROMS/SWAN wave-current interactions, I think is a good idea to post this here.

Digging the SWAN forum, I found an interesting post by Rogers (with reply by John) about the use of curvilinear grids in SWAN ...

jacopo

I forward this to whom it may concern.

Jacopo

############################################################
Postdoctoral position opening:

Physical Oceanography With Experience in Numerical Modelling. The Marine
Technology and Operational Oceanography Department is looking for two
year position in ...

jacopo

looks like tide_period is not present in 'oslo150m_tide_zero.nc'.
Then ROMS seeks it throughout all the forcing files (last is oslo150m_wind_zero.nc) -without luck-

check with 'ncdump -h oslo150m_tide_zero.nc' if tide_period is there.

jacopo

you may be interested to read the post

https://www.myroms.org/forum/viewtopic.php?f=14&t=1191&p=4159&hilit=sponge#p4159

2. what is the relationship between VISC2 from ocean_*.in and visc2_r from ana_hmixcoef.h?
This question can be asked in another way: Is it true that the visc2_r is used in ...

jacopo

oops,

first, the worst heat wave ever in the last century,

now the tropical cyclone Hamish

I hope you will survive the 2009 Asia-Pacific workshop

J.-

jacopo

I have been running MPDATA in the last days as well. Indeed, results are much better compared to UH3/C4V.

http://img205.imageshack.us/img205/5961/results3tp5.png

http://img205.imageshack.us/img205/7964/results4rq1.png

I think I can finally converge now to a solution with some adequate ...

jacopo

It is intriguing to see the results from this experiment.

I used the 'workaround' cited before: set minimum depth 30 m and insane stretching at the surface of the s-levels. The vertical grid in the surface layer is now this:

https://www.myroms.org/links/t_1193/newgridge5.png [/url]

This comes at ...

jacopo

Guys,

thanks for replying.

The idea of composed grid is nice, even if a little bit tricky given the morphology of the basin.
thanks for suggesting. I might consider this if I fail with simpler approaches.

Ivica, you don't want to know the actual rx0, rx1 values. As Kate said somewhere in this ...

jacopo

Dear all,

I’m searching for the correct representation of mixed layer with stable stratification and (generally) moderate to low wind condition in a realistic basin/application. I would like to hear from you any useful comment, if any.

Application:
The sea is enclosed, with two straits at opposite ...

jacopo

Hi,Jacopo, Thanks. I got your point.
In my case, I will never set the horizontal viscosity to zero.
[...]
In my understanding, if not define the sponge layer, the horizontal viscosity is set to TNU2(which is given in the ocean.in file)

yeah, you can set whatever value you need, of course, and ...

jacopo

if define VISC_GRID, they set the horizontal viscosity according to the grid size:
cff=visc2(ng)/grdmax(ng)
DO j=JstrR,JendR
DO i=IstrR,IendR
visc2_r(i,j)=cff*grdscl(i,j)
END DO
END DO
I suppose the variable visc2_r should be the horizontal varied viscosity.
Then I just wonder, if not define ...

jacopo

In many application the viscosity is simply zero because numerical schemes for advection may already include implicit mixing.
Of course, I suppose you can set whatever viscosity value you want.
Does it make sense to you?

cheers,

Jacopo

jacopo

I experienced too that k-e is less stable than others schemes. In several realistic applications I did, the model runs OK if using MY25, k-w, gen but it blows up with k-e using the very same time step. With a reduced time-step, k-e works fine. This problem occurs mostly during spin up periods.

jacopo

If you need to figure out what a variable name means, you want to look into ROMS/External/varinfo.dat.

There you find:

'bhflux' ! Input
'bottom net heat flux'
'watt meter-2' ! Input: [Watt/m2]
'bottom heat flux, scalar, series' ! [Celsius m/s]
'bhf_time'
'idTbot(itemp)'
'r2dvar'
1.0d0

The ...

jacopo

For those of you which are struggling with Matlab plotting without a display, there is a way to by-pass this.

If you print the plots in *.ps with -cymk -painters options, it works even without a display.

Then you can convert your *.ps in whatever format you want outside Matlab (I personally use ...

jacopo

Hi Rob,

I actully downloaded the movie.

Just let me know where I can upload it and I'll do that.

cheers,

Jacopo

jacopo

yep, it worked!

tnx

J.-

jacopo

did you find out anything relevant?
I'm having the very same problems when running SWAN on more than 1 proc with ROMS version 116

jacopo

Hernan,

I would like to submit more than one poster, but the web form doesn't seem to allow for this.

what should I do

thanks,

J.-

jacopo

add in the forcing netcdf file the attribute 'cycle_length':

for example:

double sms_time(sms_time) ;
sms_time:long_name = "surface momentum stress time" ;
sms_time:units = "day" ;
sms_time:field = "sms_time, scalar, series" ;
sms_time:cycle_length = 360.0 ;

This generates a 360 days ...

jacopo

some simple checks:

Remember you have to feed ROMS with 'net' shortwave, i.e., albedo effect already taken into account.

Remember to define DIURNAL_SRFLUX if you are using daily values of shortwave radiation

Remember to adjoust the values (in mod_scalars.F) of

real(r8) :: blk_ZQ = 10.0_r8 ...

jacopo

There are nowadays 3 actually different version of ROMS -as far as I know-

1) ROMS "eastern coast" mainly managed by RUTGERS but with substantial contributions by several other groups worldwide.

http://www.myroms.org/

2) ROMS "western coast" (developed independently since ROMS-2.1?) by UCLA

http ...

jacopo

read this

viewtopic.php?t=141

the input file is in the directory External/

You will find several ocean_*****.in
Pick up one, figure out what's in (everything in the *.in file is explained at the end of the very same file) and develop your own.

jacopo

To answer to this question is a little bit a pain in the ass :lol:

check this out first:
https://www.myroms.org/forum/viewtopic.php?t=63

Of course what you need to provide in the input NetCDF files strictly depends on your application.

You have to provide al vectors ALREADY rotated onto ROMS ...

jacopo

the only difference between roms-2.1 and roms 2.2 is that some variables have been renamed for CF compliancy. In particular, s_rho and s_w. But this is an easy fix. Not really relevant differences.
The preprocessing tool is somewhat outside ROMS, in the sense that it is not released within each ...

jacopo

I'm not sure to see your point, meanwhile keep in mind that it is a standard when writing NetCDF that the dimensions are somewhat 'reversed': if you have a matrix(i,j,k,time), in NetCDF it is supposed to be written as matrix(time,k,j,i). So, what you are having doesn't sound incorrect to me.

If ...

jacopo

the version of depths.m you are using is old, and consistent with ROMS-2.1.
While using ROMS 2.2, for NETCDF compliancy, s-coordinate parameters have been renamed.

replace the the following in depths.m

%----------------------------------------------------------------------------
% Read in S ...

jacopo

new version.

now using roms 2.2 and reinitialized in Aug 2006 from CTDs

http://www.arpa.emr.it/sim/?mare

jacopo

the heights of measurements are, by default (from mod_scalars.F)

#ifdef BULK_FLUXES
!
!-----------------------------------------------------------------------
! Constants used in surface fluxes bulk parameterization.
!-----------------------------------------------------------------------
!
! blk ...

jacopo

Hi all,
When I give NRREC value to -1 then it is running freshly i.e., from the first time step onwards. :?:

This actually happens if you set NRREC=1. NRREC=-1 means restart from the latest available field in the ININAME file. I didn't experience any weird behaviour on this using both ROMS-2.1 ...

jacopo

ROMS expects you to provide the NET shortwave radiation.

Looking in bulk_flux.F...

# elif defined LONGWAVE_OUT
!
! Treat input longwave data as downwelling radiation only and add
! outgoing IR from model sea surface temperature.
!
LRad(i,j)=lrflx(i,j)*Hscale- &
& emmiss*StefBo*TseaK(i)*TseaK ...

jacopo

1) define
#define TCLIMATOLOGY
#define TCLM_NUDGING

2) create a climatology file with your salinity fields

3) go into set_nudgcoef.F and define the region in which the relaxation has to take place, setting wrk (see below) different from zero ONLY where you want to relax. Units of wrk are [1/s ...

jacopo

when trying to write rain in a station file, I see (l. 602)

! Write out precipitation rate (kg/m2/s).
!
IF (Sout(idrain,ng)) THEN
scale=1.0_r8
CALL extract_sta2d (ng, Cgrid, idrain, r2dvar, &

I believe it should be

! Write out precipitation rate (kg/m2/s).
!
IF (Sout(idrain,ng)) THEN ...

jacopo

LATIN?!?!?

jacopo

the URL is changed:

www.smr.arpa.emr.it/prodotti for the pass-protected website

www.arpa.emr.it/sim/pagine/previsioni/adriaroms for the free access website (same as before)

Jacopo

jacopo

Are ppt presentations of the meeting available anywhere?
tnx
Jacopo

jacopo

The system is finally up again.
Expect to find the current forecast published on either sites in 1.5 hours .
Jacopo

jacopo

Hi Rich,
My workstations here are down due to severe maintenance. The last forecast I produced ran last monday only. In the site you check, only 3 days time-window is preserved (starting backward from the current date), so monday run is no longer present, therefore the flag "missing data" is shown ...

jacopo

Tide_start is not necessarily equal to dstart, while you should use the same convention.
Tide_start represent the reference time you used in the estimates of Ephase when creating tidal_frc.nc (or whatever you have as tidal forcing file).

jacopo

Hi,
seek for "roms_tools" and download it. There is a GUI ("Visualization tool") that allows you to do pretty much everything. In addition, you can get inspiration looking there and there amongst subroutines if you want to build your own scripts.
cheers
Jacopo

jacopo

Hi folks (whoever you are, I don't know who is involved in this specific forum, :shock: ),

for those of you interested in, ROMS is now operational in the Adriatic Sea

check this out if interested

http://snoopy.smr.arpa.emr.it/prodotti/

login adriaroms
passwd WillCode

no documentation yet, sry ...

jacopo

I never had problem with BULK_FLUX
Do you have maybe NaNs in your *_frc.nc file?
Jacopo

jacopo

you need to define
TS_PSOURCE for salinity and/or temperature sources/sinks
and/or
UV_PSOURCE for mass sources/sinks
due to river runoff.

You can either add discharge data analytically (in analytical.F) or writing a full NetCDF forcing file. You can find examples on how to write such a river ...

jacopo

David,

thanks

Jacopo

jacopo

Are presentations available somewhere?
I would grab a couple of them if possible...

thanks

Jacopo

jacopo

In clm_tides.F, omega is estimated in this way:

omega=2.0_r8*pi*time(ng)/Tperiod(itide)

time(ng) is the "ocean_time", that is, non necessarily zero (especially in realistic application) at the zeroeth timestep.
Ephase should be referenced to the value of "ocean_time" = 0.
However, if the actual ...

jacopo

Well, this is not a *real* bug. However, in the "official" downloadable ROMS tar file, the time ramping parameter in clm_tides.F has a default value not equal to 1.
While the default setting
ramp=tanh (tdays(ng)-dstart)/1)
may be fine for spinning up at rest, it can be misleading when doing ...

jacopo

why not simply replace with
"1st Europen Workshop, Venice, 2004" ?
Jacopo

jacopo

Dear Al,
Hotel Marconi is really close to the conference site: approx 3 mins walking.
In any case, hotels in the SAN POLO (or SANTA CROCE) area are recommended. SAN MARCO or CANNAREGIO locations may take a while to get to the conference (up to 15-30 mins with probably a few vaporetto stops).
If you ...

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