Search found 40 matches

by seashellingolds
Thu Jan 28, 2016 4:56 pm
Forum: ROMS Discussion
Topic: nodal correction for long simulation
Replies: 0
Views: 2750

nodal correction for long simulation

Hi All, I am currently trying to learn how to run a model with tide. On the tidal forcing wiki page, I read this: "Because we run multi-decadal simulations, we have chosen not to include the "nodal corrections" in the external forcing file but to modify ROMS to compute them for the time at hand. The...
by seashellingolds
Sun Nov 22, 2015 3:37 am
Forum: ROMS Discussion
Topic: numerical instability and CFL violation
Replies: 1
Views: 860

numerical instability and CFL violation

Hi all, I am running a high-resolution model and having a problem with numerical instability. Attached figure shows the zonal velocity. Strong oscillation appears after several time steps and the magnitude soars into the sky. When reducing the DT, it goes several steps further. It seems an issue of ...
by seashellingolds
Sat Aug 15, 2015 12:00 am
Forum: ROMS Discussion
Topic: rotated grid setup
Replies: 2
Views: 1068

Re: rotated grid setup

Thank you so much for your reply Kate.
by seashellingolds
Fri Aug 14, 2015 9:19 am
Forum: ROMS Discussion
Topic: rotated grid setup
Replies: 2
Views: 1068

rotated grid setup

Hi All, When using rotated grid, I know the wind stress should be rotated beforehand in the input file. Since "ROMS assumes that all the input vectors are already in (XI,ETA)coordinates.", does this mean that all of the velocity vectors in the climatology file/boundary file/initial condition file sh...
by seashellingolds
Sat Sep 01, 2012 4:24 am
Forum: ROMS Problems
Topic: how to determine the optimal tiling
Replies: 2
Views: 1662

Re: how to determine the optimal tiling

Hi Sasha So glad to see you here. You are one of the persons I am most eagerly waiting for. I have read your previous posts on i7 cpu performance and the presentation of poor man's computing. They are very helpful and instructive. There are still some points that I am not very clear about like how t...
by seashellingolds
Fri Aug 31, 2012 12:44 am
Forum: ROMS Problems
Topic: how to determine the optimal tiling
Replies: 2
Views: 1662

how to determine the optimal tiling

Hello all, I cannot bear this any longer. My run is too slow with less than 9000 steps per earth day. I read some previous posts in the forum but am still not clear how to accelerate it. Can anybody with such experience help point out which one of my configurations might not be good. Not necessary t...
by seashellingolds
Fri Jul 06, 2012 7:18 am
Forum: ROMS Discussion
Topic: A simple question about the t3dmix2_s
Replies: 2
Views: 905

A simple question about the t3dmix2_s

Hi All I happened to look at the code in the t3dmix2_s.h and met something I couldnt understand. cff=0.25_r8*(diff3d_r(i,j,k)+diff3d_r(i-1,j,k))*pmon_u(i,j) FX(i,j)=cff*(Hz(i,j,k)+Hz(i-1,j,k))*(t(i,j,k,nrhs,itrc)-t(i-1,j,k,nrhs,itrc)) similar for FE cff=dt(ng)*pm(i,j)*pn(i,j) cff1=cff*FX(i+1,j)-FX(i...
by seashellingolds
Wed Mar 14, 2012 8:40 pm
Forum: ROMS Discussion
Topic: netcdf output file cannot be open
Replies: 9
Views: 2557

Re: netcdf output file cannot be open

Thanks Hernan. Finally got it right... and yes it is the version issue. I was using MATLAB 7.0 (old enough) which cannot open the netcdf output files no matter what version of snctool I use (tried the original old one and the newest one). I just switched to 7.13 and it is working! So do we have chan...
by seashellingolds
Wed Mar 14, 2012 7:59 pm
Forum: ROMS Discussion
Topic: netcdf output file cannot be open
Replies: 9
Views: 2557

Re: netcdf output file cannot be open

So it's the output from the new ROMS that you can't read? I guess you didn't accidentally get netcdf4 files if you were using the netcdf3 library. When you say "saves the record every 15 days", what kind of output file are you talking about? Could you maybe download new copies of WRT_AVG.F and frie...
by seashellingolds
Wed Mar 14, 2012 3:33 pm
Forum: ROMS Discussion
Topic: netcdf output file cannot be open
Replies: 9
Views: 2557

Re: blow up everytime after writing the record

tried serial and the same problem...
by seashellingolds
Wed Mar 14, 2012 6:49 am
Forum: ROMS Discussion
Topic: netcdf output file cannot be open
Replies: 9
Views: 2557

Re: blow up everytime after writing the record

2. You admit to having an old version of netcdf - what versions of snctools and ROMS do you have? Old versions of netcdf should still have created files that the new tools can read - tools generally get more accepting in that they should read old and new formats. Could snctools read the old files a...
by seashellingolds
Mon Mar 12, 2012 8:05 pm
Forum: ROMS Discussion
Topic: netcdf output file cannot be open
Replies: 9
Views: 2557

Re: blow up everytime after writing the record

Thank you for your reply Kate.
Things are getting more complicated.
Q1: It turned out to be some MPI problem I think. My grid size is 464*194. If I set NtileI=8 and NtileJ=1, it blows up with NaN. If NtileI=4 and NtileJ=2, it doesnt......
by seashellingolds
Sat Mar 10, 2012 6:29 pm
Forum: ROMS Discussion
Topic: netcdf output file cannot be open
Replies: 9
Views: 2557

netcdf output file cannot be open

Hi All I ve recently got two problems with ROMS output. 1. I have a climatology forcing run which saves the record every 15 days. After starting from the 15th day, it blows up immediately after saving the first record. Then I restart the model, it blows up exactly just after saving the next record. ...
by seashellingolds
Tue Dec 20, 2011 8:33 pm
Forum: ROMS Ecosystem
Topic: question on chlorophyll
Replies: 1
Views: 2377

question on chlorophyll

Hi All

Maybe this is too basic question but I simply cannot get it.
In the Fennel's model, we calculate the new phytoplankton using P(new)=P(old)+cff*(Nnew)
However, the calculation of chlorophyll uses N(old) instead of N(new). Is there any reason about that?
Thanks a lot
by seashellingolds
Mon Nov 21, 2011 7:23 pm
Forum: ROMS Discussion
Topic: river issue
Replies: 5
Views: 1356

Re: river issue

As for the indices, since my left V gave me no problem, I guess the indices could be right btw shouldnt the indices be the same as the rho point below it? It depends. In the ROMS view, the v indices match the rho above. In the netcdf file view, the indices match the rho below. The grid indices were...
by seashellingolds
Mon Nov 21, 2011 7:10 pm
Forum: ROMS Discussion
Topic: river issue
Replies: 5
Views: 1356

Re: river issue

What would be more helpful to us would be if you could print out that V value from several places in the code to confirm that it's getting set back to zero - and pin down where that's happening. Or else watch in the debugger. Are you sure you have the right i,j? Same as the rho point just above it?...
by seashellingolds
Sun Nov 20, 2011 11:02 pm
Forum: ROMS Discussion
Topic: river issue
Replies: 5
Views: 1356

river issue

Hello All I just got an issue with my river setup. Please look at the grid below ... p-v-p-v-p-v-p-v-p-v-p ... ... u-r-u-r-u-r-u-r-u-r-u ... ... p-v-p-V-p-V-p-v-p-v-p ... .... ------------u-r-u-r-u ... .... ------------p-v-p-v-p ... This is part of a grid. I just labeled the masked points with lette...
by seashellingolds
Wed Nov 10, 2010 2:32 pm
Forum: ROMS Discussion
Topic: sponge width
Replies: 2
Views: 1286

Re: sponge width

no rule to choose this? (I am also doubting if this question is naive?)
by seashellingolds
Sat Nov 06, 2010 2:38 pm
Forum: ROMS Discussion
Topic: about forcing
Replies: 7
Views: 1807

Re: about forcing

kate wrote:I no longer spin up with climatology - better to just jump into real years and throw away the first one.
Hi Kate

This is interesting to me. Can you tell me the reason (related paper?) or your experience on that.
Is this particular for some cases but not for others? It really saves time

Y
by seashellingolds
Wed Nov 03, 2010 10:26 pm
Forum: ROMS Discussion
Topic: sponge width
Replies: 2
Views: 1286

sponge width

Hello

I am wondering if there is a quick way to estimate the sponge layer width and the multiple of visc in ROMS according to the resolution and velocity etc

thanks very much
by seashellingolds
Sun Jul 18, 2010 12:39 pm
Forum: ROMS Bugs
Topic: vorticity.F
Replies: 0
Views: 1008

vorticity.F

Hi, In the vorticity.F file, should the last dRde be dRdx here when computing PV? pvor(i,j,k)=orho0* & & (cff*dRdz_pr*(fomn(i,j)+ & & dVdx(i,j)-dUde(i,j))+ & & 0.125_r8*(dUdz_pr*dRde_pr-dVdz_pr*dRde_pr)) Moreover, I am wondering what the 3D relative vorticity means here. It looks the sum of 3 compon...
by seashellingolds
Fri Jul 16, 2010 8:32 pm
Forum: ROMS Discussion
Topic: question about the first half layer
Replies: 1
Views: 741

question about the first half layer

Hi all I may be asking a simple question but I really need confirmation Does it numerically make sense to release Lagrangian floats at between the first W layer and RHO layer as shown below ********* *** w *** . ^^^\ ^^^ free surface ********* . \ . . . . HERE :?: . ********* / . *** r *** . ___/ **...
by seashellingolds
Sun Jul 04, 2010 6:06 am
Forum: ROMS Bugs
Topic: problem with Lagrangian floats
Replies: 6
Views: 2364

Re: problem with Lagrangian floats

Hi All I just made a test with both original code and my corrected code. I think the root of the problem is right as I mentioned above. But I am not sure the way I modified the code is the most optimal but kind of direct. Moreover, as the thread I posted in the ROMS Discussion several days ago, http...
by seashellingolds
Thu Jul 01, 2010 9:21 am
Forum: ROMS Bugs
Topic: problem with Lagrangian floats
Replies: 6
Views: 2364

Re: problem with Lagrangian floats

Thanks for the replies Tonight is so hot that makes me wake up -_-!. So I was starting to think this problem. I guess the problem comes out of the double periodic boundary condition. Assume there is a 2*2 partitioned domain, a particle originally in the Northwest tile goes to Southeast tile in the n...
by seashellingolds
Wed Jun 30, 2010 8:25 pm
Forum: ROMS Discussion
Topic: Quick question about float output
Replies: 2
Views: 933

Re: Quick question about float output

It will be better if they synchronize.
Is it a good idea to separate float output from the output.F?
Any better suggestion will be appreciated
by seashellingolds
Wed Jun 30, 2010 8:21 pm
Forum: ROMS Bugs
Topic: problem with Lagrangian floats
Replies: 6
Views: 2364

problem with Lagrangian floats

Hi Has this problem ever been met or reported? Description : Lagrangian floats get lost at the periodic boundary Details : I put floats uniformly on a square domain with periodic boundary condition After several time step, some floats close to the boundary disappeared and even more with the model go...
by seashellingolds
Sat Jun 26, 2010 8:50 am
Forum: ROMS Discussion
Topic: Quick question about float output
Replies: 2
Views: 933

Quick question about float output

Hi all

I have a quick question about writing float file. Take main2d.F as example, output is before the float initialization. Does this mean the info in float output is always 1 step after the ocean_time?

Thanks
by seashellingolds
Thu Jun 24, 2010 1:18 am
Forum: ROMS Discussion
Topic: second order ODE in ROMS
Replies: 4
Views: 1042

Re: second order ODE in ROMS

If adding FB feedback as wikiroms says, the maximum step can reach about 1.4 sec, still very short, how can I improve this? The only two ways I can think out are 1, doing iteration, 2, separate this time step from momentum timestep. Is there anyone can give me professional suggestion. Thanks very mu...
by seashellingolds
Tue Jun 22, 2010 4:49 pm
Forum: ROMS Discussion
Topic: second order ODE in ROMS
Replies: 4
Views: 1042

Re: second order ODE in ROMS

Thank you for your reply John I used predictor-corrector method to solve these two first order ODEs and tried different predictors and correctors. I think 2nd RK is one kind of them but I didnt try. Let's say the equations are dx/dt=u, du/dt=RHS. The RHS comes from the instantaneous result of previo...
by seashellingolds
Mon Jun 21, 2010 4:46 pm
Forum: ROMS Discussion
Topic: second order ODE in ROMS
Replies: 4
Views: 1042

second order ODE in ROMS

I am wondering if there is a module that plays with second order ODE in ROMS
I made one but have difficulty in stability. I tried many methods but the time step is still too small
Any suggestion will be appreciated
by seashellingolds
Wed May 05, 2010 1:49 am
Forum: ROMS Ecosystem
Topic: Quick question for vertical mixing
Replies: 6
Views: 3990

Re: Quick question for vertical mixing

well, I see, many thanks. It seems we have no pre-knowledge about that and therefore no better choice. :(
by seashellingolds
Sun May 02, 2010 9:46 pm
Forum: ROMS Ecosystem
Topic: Quick question for vertical mixing
Replies: 6
Views: 3990

Re: Quick question for vertical mixing

Actually the answer can be no. I am just starting to learn bio model in ROMS and doing my class project. I think it is better to set bio Akt the same as salinity (means do nothing). I realized new ROMS is designed to seperate bio model part, which really simplify the work of adding a new model. That...
by seashellingolds
Sun May 02, 2010 7:18 pm
Forum: ROMS Ecosystem
Topic: Quick question for vertical mixing
Replies: 6
Views: 3990

Re: Quick question for vertical mixing

Maybe I need extend the length of Akt from NAT to NT, so I might be free to define Akt for bio tracers
But I guess this is not the original intention of bio model design
by seashellingolds
Sun May 02, 2010 7:10 pm
Forum: ROMS FAQ
Topic: build.bash problem
Replies: 10
Views: 11469

Re: build.bash problem

just see this old thread with new reply by chance. I guess the problem is the difference between window and linux text system Windows follows the rule of old-style typewriter. Two steps is needed to get to the next line \r (return) \n (jump to next line), while linux just has \n doing this altogethe...
by seashellingolds
Wed Apr 28, 2010 7:37 pm
Forum: ROMS Ecosystem
Topic: Quick question for vertical mixing
Replies: 6
Views: 3990

Quick question for vertical mixing

Hi All In ROMS 3.0 I used before, the variable Akt is dimensioned by total tracer number NT, so I can simply use Akt_bak for TS from stardard input and for bio tracers from bio input file or I can redefine them using ANA_VMIX Now I am using new ROMS, Akt has dimension of NAT which usually is 2. It s...
by seashellingolds
Wed Apr 14, 2010 4:01 pm
Forum: ROMS Discussion
Topic: Problem with UV/TS_U3ADV_SPLIT
Replies: 0
Views: 638

Problem with UV/TS_U3ADV_SPLIT

Hi everyone Has anybody managed to apply UV/TS_U3ADV_SPLIT? I tried to use both and either of them but they keep making Blowing-up. This option can cause stability problem as cautioned in output script. Generally speaking, by which way can I reduce this risk. Is there any requirement or restriction ...
by seashellingolds
Tue Apr 13, 2010 4:21 am
Forum: ROMS Installation
Topic: compiling problem (libmpichf90nc.a)
Replies: 4
Views: 1651

Re: compiling problem (libmpichf90nc.a)

Thanks Kate I know where the problem is. In fact there is something wrong with libmpichf90nc.a. It is not an archive file... Maybe I need to ask admin to rebuild it. However, this problem would not happen if I use -Bstatic flag with both ROMS 3.0 and 3.3. It does not seem to contain this static libr...
by seashellingolds
Sun Apr 11, 2010 10:05 pm
Forum: ROMS Installation
Topic: compiling problem (libmpichf90nc.a)
Replies: 4
Views: 1651

Re: compiling problem (libmpichf90nc.a)

Plus : Anybody tells me the difference between
FFLAGS += -Bstatic -fastsse -Mipa=fast
and
FFLAGS += -O3
I used to use the former. Is the latter better?
by seashellingolds
Sun Apr 11, 2010 5:20 pm
Forum: ROMS Installation
Topic: compiling problem (libmpichf90nc.a)
Replies: 4
Views: 1651

compiling problem (libmpichf90nc.a)

Hi everyone I just got a compiling problem with new ROMS. I ve been using ROMS 3.0 before and everything is fine. Does anybody meet the same problem or help me out. Here is the error msg. ...... ar: creating Build/libUTIL.a ranlib Build/libUTIL.a master.f90: /usr/local/mpi/bin/mpif90 -O3 Build/esmf_...
by seashellingolds
Mon Oct 12, 2009 6:48 pm
Forum: ROMS Discussion
Topic: quick question on model time
Replies: 1
Views: 1758

quick question on model time

Hi everyone I am new with ROMS and I am trying to make a run with daily wind forcing. I made my climtology file and boundry file with the cycle length 365. But in the wind forcing file, the leap year has 366 days. So how do they match with each other? I mean probably there is a flag variable which w...