Ocean Modeling Discussion

tony1230

I am running into a problem these days with LBCs in biological module. Without LBCs (dont use RadNud & Cla conditions) the case can run and the results seem okay. But when i switch the LBC to RadNud or Cla , something strange occurs. I have been strugling on this some days, but no solution. For ...

tony1230

Hi ROMS friends I have been using forcing conditions from ECMWF ERA dataset. I am using the matlab script that Hernan and John provide (i.e. d_ecmwf2roms.m) all the time, but with the STEP selection with "3 6 9 12" and without "0" step. And recently, i found that there are differences between the ...

tony1230

Hi ROMS's friend I am running a real case with biological processes and want to know if the surface/bottom mix layer depth is variable due to seasonal cycles in air-temp ans short wave radiation, etc. The model spin-up from the steady state at Aug 1,2008. In my area of interest, surface waters begin ...

tony1230

Hi ROMS friends These days i have been running a real case with river point source, including T,S and Nutrients. I'd like to test firstly if the river location are right to inflow. My test was: 1. with tides in the open boundary; 2. with rivers; 3. no more other forcing; 4. constant values for T(25 ...

tony1230

Hi John, thanks Here are some further questions. 1.> As for the scale flag for swrad, yes that should be negative to process the accumulation, but swrad must be positive for ROMS. Follow that, the scale flag for swrad should be 1.0 /(3*3600.0). And when it comes here if (F(n).scale < 0) step = rem ...

tony1230

Thank you John for your reply. First, sorry for my misunderstood. if (F(n).scale < 0) step = rem(frc_t,0.5)*24; if step == 3 fieldfinal = field; ... field_previous = field; % Save this accumulation % to on the next step When step = 3, the field_previous equal to field (field at step = 3), so on the ...

tony1230

I have looked through almost all the posts on the topic related to ECMWF products . I got some, but still confused on how to select the TIME and STEP . 35. What are the 'steps' for the surface daily fields in ERA-Interim? The ERA-Interim data server surface archive has a mixture of analysis fields ...

tony1230

A netcdf toolbox is expected in the Matlab when process the *.nc files. You can download the box from website, but i have no idea where it located. Hope that help.

tony1230

Hi, 1. Can the ROMS now tolerant negative values? Primary for temperature in cold winter in initial condition. 2. Why the ROMS always produces negative values to biology variables like NH4,NO3, etc.(under some kind of conditions, also to salinity, say if i add river point sources)? Thank you and ...

tony1230

If i have only the monthly discharge in hand, can the river_time unit in month?

- steve

tony1230

you may want to check the "Qair" in External/varinfo.dat, to confirm the value is 0.01 or 1.0.

tony1230

... 0 00:00:00 0.000000E+00 1.963001E+04 1.963001E+04 1.659940E+17 DEF_HIS - creating history file: ./output/ocean_his_0001.nc rank 447 in job 1 n104_34487 caused collective abort of all ranks exit status of rank 447: killed by signal 9 rank 528 in job 1 n104_34487 caused collective abort of all ...

tony1230

My opinion on "simulating" & "modelling" much agree with ptimko and Hernan but i have own words. As i can understand within my scope of oceanography knowledge, the "Simulating" is an action with which we do the works/jobs repeatedly as our predecessors have already been done and verified by many ...

tony1230

Yes, i know roms can read in BDCs at every grid point. Actually, we can do this for ca. two years by adding a variable in varinfo.dat and corresponding files, and give the values for BDC as a variable of grd.NC file. As in my applications, i have calibrated the BDCs for times, but still dissatisfy ...

tony1230

hi often

I am doing some work by using bio_fennel submodel. You can sent me email via shouweiwei@sina.com or leave yours for me.

thanks

-Shou

tony1230

This is a topic on how to give bottom drag coefficient(s). In standard input file *.in, we have RDRG(RDRG2) and Zob used as bottom drag for momentum calculation. And they also important in tide's computing. As for a region, we firstly want to calculate the tides (usually M2/S2/K1/O1/N2/K2/P1/Q1) and ...

tony1230

I dont know how to figure this out, and i have similar problem when i get AVERAGES defined. I use ROMS version 3.4 and i have no idea if this would happen in latter new versions.

BTW: I wanna ask what are the detide fields.

tony1230

I think this topic is still unsolved. Hope some of you to participate in. Thanks.

tony1230

In some applications I am happy with HPGE ~ 7cm/s, however in some cases I try to get them down to 1cm/s.

Here is a question: how do i know that at what magnitude of velocity introduced by HPGE may satisfactory for a region

How to judge? Is there thumb rules?

Regards,
- Shou

tony1230

Hi Kate

I have run into this before, and i do did as you suggested here, but the question is when i turn on the DEBUG the model run smoothly. So, there is nothing message can be follow. It is so tricky. What can i do if this happen again when i need the AVERAGE results.

- Shou

tony1230

Thank you for all the replies. Yes, as Ivica pointed out, these two variables are much important because they not only affect the model stablity, but also related with HPGE which may induce tricky/incredible current velocities. You want to have as real as possible bathy (tides sensitive) so smooth ...

tony1230

After i searched in this forum on "rx0" and "rx1", i can not understand how they affect the roms run. As Kate said https://www.myroms.org/forum/viewtopic.php?f=1&t=2421&hilit=rx1#p9011 , the rx1 is bigger than 14 , but want the rx0 approaching 0.4 . And Mark may want rx0 to ~ 0.2 https://www.myroms ...

tony1230

As we all know that the time for water staying in a semi-close sea or a bay would exerts important influence on many,like matter transport etc..I have searched in ROMS forum for this topic,but find none directly available.I have read some related papers in which they employed the approach of using ...

tony1230

I want to add the ice variable into my application, how to do ? In my real case, i should run years of time to simulate biogeochemistry processes, but during winter time there covers ice on half of the sea ares. I never reach to the ice model and do not know how to use it. I hope someone expertice ...

tony1230

Two possible suggestions. 1> you may want to double-check your input files like initial,forcing,etc. to refirm that no NaN exists. 2> turn Debug on as expect to get more directory info. generally speaking, if model blows up right at spin-up, especially with NaN, you may got it in one/some fields ...

tony1230

Have you got 2D velocities, i.e. ubar and vbar, for you open boundaries? If yes, you used right option with Flather, otherwise you may want to employ Reduced which is more appropriate for the situation without currents.

Regards

- Shou

tony1230

I cannot confirm absolutely that this is a bug report, but i find something... According to Katja's paper/2006, the grazing term on Phytoplankton by Zoop is defined as g*Zoo (page 3), where g is the grazing rate of Phyt. And g is represented by Holling-type s-shaped curve as(refer to P.4) g = gmax ...

tony1230

I'v had the same problem long time ago. I have a extensive shoal as lanerolle said that can be wetting/drying along with tidal flood/ebb. As commonly think the point source/river would be connected to the sea with a permanent water line/flow even when reaching a low tide. But in roms we alway get ...

tony1230

Wow...,big bang. Thank you Larry for your time and carefulness. 1. What are the depths or thicknesses of your 10 vertical levels? If they are e.g. 1 meter each, then even your deepest level will have too much sunlight for net nitrification to occur. So one solution might be to make your levels ...

tony1230

I am now running a biogeochemical case on a well-calibrated-validated hydrodynamic model, but still not run successfully. Stratification seems to me is an important stress that exerts a critical control on biogeochemical processes, say it blocks bottom-layer nutrients be carried upward by vertical ...

tony1230

Thank you Prof. Fennel Before start out on my way to run the realcase physical-biological coupled model, i have successfully run the bio_toy test case. I looded into the results and also the input forcing files, to comprehend the relationships btw variables that on different trophic levels and ...

tony1230

You can open at any (sub)directory with command vi/emacs ~/.bashrc

tony1230

Apparently,model told that you have placed the rivers at points that not should be them. Refer to viewtopic.php?f=14&t=2200&hilit=river. Hope to make your work done.

- Shou

tony1230

I am now using coupled ROMS-BIO_FENNEL to do some ideal tests. I ran into a problem with vertical diffusion. I started from a simple cubic domain with horizontal dimension 32x64 and vertical 10 layers, with constant temp(10) and salt(28), no tide , nor flow. Bio_variables are also initialize with a ...

tony1230

Thanks for all your reply Yes, John, you are right. I have mentioned in my first post I have simply got the SH from NECP file in unit kg/kg and have seen values both LT and GT 2.0(g/kg). , but i neglected to take RH(values in percentage) into account. The RH in % could never less that 2(2%). In this ...

tony1230

Yes,i think you are right that roms needs SH for calculate the other term, but roms wants RH from input in uint % (am i right?). And i dont follow why you did that for multiply the sh from NECP by 1000 to transform into g/kg unit. That dose not make any sense. I think so as follows. 1、As i can learn ...

tony1230

hi roms friends Recently i have been thinking about what i mentioned in the subject. It's Kate's post in a earlier thread https://www.myroms.org/forum/viewtopic.php?f=31&t=2673&hilit=rho0#p9996 that reminded me this. I have never taken this into practice, but after saw that, i want to know the ...

tony1230

Okay, on this topic, Kate have mentioned in a earlier thread in 2008 https://www.myroms.org/forum/viewtopic.php?f=4&t=1032&hilit=RH , but it's remain unresolved. :?: :cry: I have been looking into this (bluk_flux.F) the couple days and still confused with the terms, say RH,Qair,Hair,Q and their ...

tony1230

Hi roms's friends Simplified: How to give the values for theta_s and theta_b according to different kinds of Vstretching = 1,2,3,4? Here and follows i would use 1,2,3,4 to represent. Narrate: Now there are four schemes for we to choose on vertical stretching, and as i know the 2 and 4 were hingly ...

tony1230

Hi kate,

We use Chapman/Flather for all frequencies of boundary conditions. This requires both the outside zeta and the ubar/vbar through the boundary.

Then, what would be the suggestion if we have only zeta but without ubar/vbar?

-shou

tony1230

Is there any odd symbol in your path?

tony1230

Hi Zhiqiang,

Thank you so much.

Happy mid-autumn.

Diaoyu islands are belong to China!!!

-shou

tony1230

Hi Zhiqiang,

You can tell explicitly what you think that may cause those kind of problems, or give some clear directions/guidance.

I would also like to know more about that.

Regards.

-shou

tony1230

Hi l_fr

I have post in thread viewtopic.php?f=14&t=2454

John gave a detailed illumination on this. It may help you.

-shou

tony1230

Thank you mashinde, for your reply. Is that mean that the "Surface thermal radiation" is the Net radiation from surface atmosphere into the water and the later one stands for just the short wave radiation downwards and without net longwave? If that is the case, how it cause such a negative ...

tony1230

hi mashinde

I'd like to hear what is the problem with the input radiation flux and why you did that.

thank you

-shou

tony1230

Yes, i remember that Hernan said many times in some threads that we have to set LBC for every state variable on every boundary in ocean.in. In my New code, i have these as follow, ! W S E N ! e o a o ! s u s r ! t t t t ! h h ! ! 1 2 3 4 LBC(isFsur) == Clo Clo Cha Clo ! free-surface LBC(isUbar ...

tony1230

Hi rduran Thanks for your suggestion. As i mentioned in the earlier thread, i'd gave one set of input files to the two runs but the CPP .h file, since there had updated more times for many CPP options, say *_WALL etc. As far as i can remember(i can open the files because the cluster was powered off ...

tony1230

Hi all, I was confused by the results from two version (Old:V.549, New:V624) of roms code, running with all the same input files. The attached are three plots that with model results comparison and data validation. As i dont know what's wrong with the new code, i set two parallel runs with one set ...

tony1230

Firstly, you would like to delete the Land-points and make your masking subsequently(to produce a variable,mask_rho or what you like,contains the value 1 for wet and 0 for land); Secondly, you could use you undeleted grid file to generate the NetCDF grd file. But here, you should have your mask ...

tony1230

Yes Tomasz, before try to modeling biological we much simulate the temp well since it is a critical factor that influence the biological process. The 4 plots in the previous post were from two different version of ROMS run, explicit say, the upper most two plots(the temp and salt plot and the ...

tony1230

Thank you Tomasz and Prof. Wilkin Yes, it is odd that ROMS yielded the negative temp as reach to about -7C after few days of the run. I have took notice of that but i dont know why and how to figure it out. Some suggestion? I have check the initrial input file and no value smaller that zero exist ...

tony1230

Thank you Prof. Fennel Yes exactlly, we added the PO4 in the BIO-model. And i have run cases as you suggested that run without the PO4,but why i still got the similar results.Here attached two results with(you say the PO4 eventually vanished,but in this case,there still PO4 be left and why other ...

tony1230

Hi,guys. Dose the Fennel BIO-module work? I am recently run a bio-physical coupled model in a semi-closed shelf sea to simulate some species of nutrient and primary production. The model spin up on Jan 1 and end-up on Dec 30,namely a whole year. As i know,i should have to get a rational results,e.g ...

tony1230

Thank you so much John That is exactly what i want and extremely useful to me(and others).In my previous post,i really confused by these so much kind of OBCs and even their awesome combinations.I am sure we have to specify all the state variables a designated type of condition at each of the ...

tony1230

Hi kate, thank you for yr reply. I have been running a two-boundary domain nested in a bigger domain with only eastern OBC posed there. I configured them as follows. To the big domain,i just have elevation(using 8 tidal constituents)imposed on OBC without any currents(say 2D or 3D). Note that when i ...

tony1230

Hi prof. Arango On mention the OBCs, i was always confused by their combination of so many state variables. On Wikipage , we can find 6 types of OBCs Gradient,Clamped,Flather,Chapman,Radiation and Wall .But in the ocean.in file,there also exists Nested,Nudging,periodic and Reduced Physics types of ...

tony1230

hi, First, to Kate's post. Its latitude ranges from N40-43, with a skip of 3 degs. If this, with a resolution of 0.5 deg, it should have 6 cells along the N-S boundary, thus makes 6 point sources. Also, along the W-E direction. Second, to Mathieu's post. I think you are right and its a accurate ...

tony1230

hi jihene,

can you compile all the Roms versions older than 607 with the same ifort compiler ?

steve

tony1230

Minimum X-grid spacing, DXmin = 1.20130955-310 km Maximum X-grid spacing, DXmax = 1.20130955-310 km Minimum Y-grid spacing, DYmin = 0.00000000E+00 km Maximum Y-grid spacing, DYmax = 0.00000000E+00 km Minimum Z-grid spacing, DZmin = 5.78056806-322 m Maximum Z-grid spacing, DZmax = 5.82997462-322 m ...

tony1230

There must be NaN value in you netcdf input files. eg temp or salt initial values that you interp by the grided Rho points.
Check them and also the bottom drag coefficient.I think one of them cause the blowup!

w.shou

tony1230

Hi mathieu I can run the .m script and the location-pic shown me where the river-sources are. But, something i still can not understand. 1. What's the two type of hint-points mean created by plot(LonDot,LatDot,'ro'); % arrow "tail" plot(LonStar,LatStar,'*'); % arrow "head" i see, if my point loc is ...

tony1230

ok i know

. it's the geometric mean . Under my MATLAB version, the function is

geomean

!

tony1230

Hi mathieu
Thank you for your .m script. But one question : what's the function for gmean

Code: Select all

lat=gmean(LAT_rho(:));

on the line 218 .
when i try to run the script , it collapsed.

tks anybody who reply me.

tony1230

Thank you arango Yes, it's my carelessness result in the problem forementioned, the second one, but i still have the first problem. And these days, i was runing a real-application on Biological with Fennel CPP options on. It brings me blowup: without BIO_FENNEL on, model can goes on smoothly, but if ...

tony1230

Hi kate Thanks very much.I want to use non-point source for Nitrate, Phosphate, etc. But till now, im not sure whether equivalent to non-point model if i use much individual points. That is to say, what's different between the two concepts "non-point source" and "source by putting much single points ...

tony1230

Two ploblems: 1) if i use a packege of bland-new code of ROMS 3.6, the upwelling case can goes to end with USE_DEBUG ?= on(oecanG) , but can not going on with that option off(oceanM). Show me the following awful notice: STEP Day HH:MM:SS KINETIC_ENRG POTEN_ENRG TOTAL_ENRG NET_VOLUME C => (i,j,k) Cu ...

tony1230

Its a tricky thing. I can run my applications smoothly, but UPWELLING test case.Everything is left as they are, just use the upwelling.h instead of my file , then it can not work.So i dont think something worng in file Compilers/Linux-ifort.mk.Also i got something tricky analytical.f90(394): error ...

tony1230

Thanks kate for your reply I konw, for common use, i can specify some more individual points connected together instead of the role as plane-source. That can be done, but actually the non-point source is not the gathering of individuals so simple.Between every two single point, there must exists ...

tony1230

Did you have the NetCDF Lib included in the Matlab working path?

tony1230

I have found for papers on web of science、science direct and etc,accounts for non-point sources.
But hardly did i find some papers.For simplicity, i can specify number of cells of grid that gathering together
as so-called non-point, indeed it's not.

tony1230

Hi kate Its a feasible way that you said,but in my mind it suitable in the situation with incoming flow on one side and outgoing flow on the other side.Like the ECS Black-Tide or the Gulf-Stream.I dont know how to keep the net volume of a modeling domain and at the same time apply the incoming and ...

tony1230

Hi Roms users as we know,we can specify a mesh grid with active or passive point-sources at the river where the sources can be carried into our simulating system.we can do this without effort.And recently,i was attempting to setup an application with plane- or area-sources at intertidal area,in ...

tony1230

Hi dschaffer
Can the coupled WRF/ROMS model work now?
Im usually have the WRF run first and then ROMS.
Im really want a trying on.

tony1230

hi phamsymt you mean in your orthogonal-curvilinear mesh, the resolutions are Min dx=16.34 km - Max dx=18.5221 km Min dy=16.3735 km - Max dy=18.5221 km in x and y direction respectively. What is the "ROMS resolution:17.9km" ? It seems no data in the vector "x" , so is the "xx".check them first.

tony1230

Hi simion Thank you very much.Now basically i can follow what you said.But:?::why you have to do So basically only the velocity fields are periodic, and both the tracer fields and sea surface elevations are not periodic. I have no idea and can not imagine on the situation(velocity fields periodic ...

tony1230

hi prof A and friends
I have some questions:
1> what is the

periodic boundary conditions

exactly mean
and 2> the meaning for

negative pressure gradient

.
I can not understand very well.

thanks for reply

tony1230

hi
do you wanna run a new simulation from the previous one? and start from 00:00:00 on the 16th day?
i think so from your "15*24*3600=1296000".if so ,you must set the ocean_time from zero.

tony1230

hi guys
as to the frist problem, you should check your initial netcdf file,
to see if some 'NaN' in temp, salt, depth or bottom drag cofficient values.
I'v get the similar prob times, every time i see the 'NaN', there muse be
odd values.

tony

tony1230

hi mashinde
there is a *.m matlab script used to creat the river runoff netcdf file.
the only you must have in your hand is time-series runoff data.

best regards

tony

tony1230

hi kate
It's the first time i have seen 'modulo'. i have absolutely no
idea about the 'lon:modulo = 360'.would you explain to me what's
the equation mean or how to operate it!
Best regards!

tony

tony1230

hi buddies its a nice topic.i have questions with regard to arango‘s comments. 1.you said that if we have a squared grid the Fortran and Matlab would transposed arrays (X,Y) into (Y,X) .the point i want to know is that the event you mentioned going to happen in any rate or by chance？ 2. This can giv ...

tony1230

And can the 'hc' be set to a negative value?

hc can be any positive value , but negative ones!

tony1230

hi kate, why would you say"If positive u is to the east, then you have strong downwelling flow in a very narrow band." i wanna know how you identified the "downwelling flow"! thank you !

tony1230

just to use "isfinite" instead of "finite", i think. have a try...

tony1230

hi susonic and kate i got a same return from the run.yes,without the PERFECT_RESTART option, run can go on wheels, but with it turn on, run blowup within some steps. till now, even no one idea rocks me.seeing susonic reported it to all,i deem it's not a problem to me only. [quote="susonic"]Hi all ...

tony1230

which one is good to generate the grid for ROMS, delft3d or seagrid ? i used to use the 3d and , i know that the seagrid also can generate the grid , but i never used that. someone used both of them?

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