Ocean Modeling Discussion

aryansafaie

I believe it's about time I post an update: After reexamining Warner et al 2005 (OM), it seemed like a good idea to reconsider the surface boundary condition for TKE (equation 51 in that paper). The file gls_corstep.F contains code to implement the surface BC for TKE; from my prior simulations, it ...

aryansafaie

Hi John, Thanks for the advice. Now this is interesting: I was inspired by what you mentioned regarding my use of the k-epsilon closure; so I ran another quick simulation, this time using KPP instead. A comparison of vertical profiles of alongshore velocities and eddy viscosity at various cross ...

aryansafaie

Hi John,
1 for levbfrc.

aryansafaie

Dear all, My grid is a wedge-shaped f -plane domain with a constant bottom slope, initialized with uniform temperature and density fields, and zero u,v,w velocities everywhere. The only forcing is a constant alongshore surface momentum flux (via ana_smflux), using BODYFORCE to distribute it to all ...

aryansafaie

Dear all, This question is in regards to motivating the damping time of the Laplacian viscosity used in horizontal mixing. I know that we want to have that time scale be resolved by our model time step but large enough to resolve features of interest. For some context, my application is concerned ...

aryansafaie

Hi All, Thank you very much for your insights. In response to John, Sasha, and Jamie: Essentially we are envisioning a 2D problem with negligible alongshore gradients, so we want any alongshore flows to be fully developed as they enter/exit the domain. We are also trying to keep our model as simple ...

aryansafaie

Thank you for the reply, Alexander.

That makes sense, except where within ROMS am I supposed to supply my inflow density field?

Cheers,
-aryan

aryansafaie

Hi Kate,

Thanks for the quick reply.
Indeed, my next tactic is to make the surface stress a function of depth.
I'll report back on an successes/insight.

Cheers,

aryansafaie

Dear ROMS community, I've been searching for good way to do this for a while now, and the answer has thus far evaded me. I'm trying to implement an alongshore current, with periodic alongshore boundaries. The goal is to have the flow fully developed over the alongshore direction (my domain can be as ...

aryansafaie

Hi Virivarola,

Can you explain how you prescribed an alongshore current with periodic boundaries? I'm trying to do something similar.

Thanks,

aryansafaie

Thanks for the heads up Dr. Warner. I think I'm on the right track now. If it's any help to anyone, here's what I did: My CPP defs were modified to include ana_wave.h and all the necessary dependencies therein to specify wave height, length, top period (bottom period is for moveable bed i.e ...

aryansafaie

Hi Nirnimesh, Thank you for your reply. I'm using ROMS, and I'm trying to figure out the least complex (in terms of model coupling) method of simulating the effects surface gravity waves in my simulations. ANA_WWAVE seemed promising, though I realize now I need to pay more attention to the bottom bl ...

aryansafaie

Dear ROMS Community, I'm using ana_wwave.h to specify significant wave height, direction, and bottom period. However, I can't seem to figure out the correct CPP def's to activate; simply defining ANA_WWAVE fails at compilation, because the variables within ana_wwave.h of Hwave, Dwave, and Pwave_bot ...

aryansafaie

Oh boy do I feel like a dummy; I see my error.

As usual, thank you very much for your help Kate!

Best,
-aryan

aryansafaie

Thank you for the quick reply, Kate.
Would using seawater density make a difference, since all I'm doing is
setting the value of Cd*V^2 to svstr?

Thanks,
-aryan

aryansafaie

Dear all, I'm trying to force my model with an analytical surface heat flux (which by itself works fine), and a surface V-wind component of 10 m/s. However, I don't want to use the bulk flux algorithm, as that would alter my surface heat flux forcing (right?). Therefore, I'm not defining ANA_WINDS ...

aryansafaie

Dear Gustavo, Thank you very much; this paper is exactly what I needed. And just for the general community, here's an oldie but a goodie: Marshall, J., Hill, C., Perelman, L., & Adcroft, A. (1997). Hydrostatic, quasi‐hydrostatic, and nonhydrostatic ocean modeling. Journal of Geophysical Research: ...

aryansafaie

Dear all, I know this is a broad question, and I apologize in advance for my ignorance, so I would be very grateful if you can just direct me to any appropriate reading material/literature. My question is: when confronted with a non-hydrostatic process, such as the front of a gravity current ...

aryansafaie

Thanks for the guidance John. Yes, the BC values are being set to their initial values. We will be adding other forcing mechanisms, such as alongshore currents with tidal variability, and indeed we would like perturbations generated inside the model domain to leave offshore without influencing the ...

aryansafaie

Dear All, Perhaps I'm overthinking this, but I'm having trouble understanding what the purpose of the ana_Xobc.h files are (i.e. ana_fsobc.h, ana_m2obc.h, ana_m3obc.h, and ana_tobc.h), and whether I'm using them correctly. In short, I'm running an idealized model forced only by analytical surface ...

aryansafaie

Dear ROMS Community, I suppose this is more of a C-header file question, but: I'm computing the total water depth at any horizontal location as abs(z_w(i,j,N(ng))-z_w(i,j,0)) If, for example, I wanted to do this inside the body of ana_smflux.h, how would I import the z_w variable? I've trying ...

aryansafaie

Hi Kate, Thanks again for your assistance; you work wonders! I just wanted to share that the free surface no longer appreciably drops (first and last time step transects attached), and my volume is approximately conserved (first time step volume = 6.422130E+08; last time step volume, 28 days later ...

aryansafaie

From my understanding, the ROMS experts recommend a configuration such that your max Courant # is .8 to .85. You can check how ROMS computes these (3D and 2D) in Nonlinear/diag.F.
Best,

aryansafaie

Hi again, just a kind of philosophical question; In order to implement the Shc boundary condition, after looking at files like u2dbc_im.F and v2dbc_im.F, I either have to define SSH_TIDES or UV_TIDES, or have to have some exterior value; I'm not yet ready or comfortable (i.e. I have no justification ...

aryansafaie

Thanks for the suggestion.
I'll try these different BC's and share any successes/failures.

aryansafaie

Thanks for the heads up. After looking at the log file, the volume is indeed decreasing; it starts at 642,213,000 m3 and ends at approximately 615,710,000 m3 before the blow up. This makes me curious then: am I loosing water because my (offshore) boundary condition is set to radiation, and I ...

aryansafaie

Thanks Kate, good to know about the test problem. As far as I can tell, the u, v, w velocities, as well as temperature field, are not behaving abnormally. The only striking thing I can say for now is that somewhere down the line, the depth in the nearshore-most cells become inverted (pictures of the ...

aryansafaie

Dear ROMS community, Can ROMS handle a grid resolution (rho points) where dx = dy = 10 m, but dz is as small as 0.14 m in the very nearshore-most cells (30 vertical levels)? A transect image of the first ~100 m of my grid (an idealized 3D wedge shape, with a bottom slope of 0.05, and everything ...

aryansafaie

Thank you very much Kate.
That helps!

aryansafaie

Dear ROMS Friends, In setting values for the harmonic and biharmonic horizontal diffusion and viscosity coefficients (TNU2, VISC2, etc), I'm taking guidance from the following page (the one Kate refers people to) : https://www.myroms.org/wiki/Horizontal_Mixing I have a couple questions based on the ...

aryansafaie

Alright, so the simulation ran to completion after adding #define WET_DRY to the CPP defs.

Thank you both very much for your help.

aryansafaie

Quick update: with the WET_DRY CPP option defined, and a minimum depth of 10 m (which I could probably reduce), the GLS simulation has lasted longer than ever: 8 days 20 hours and counting! Thank you both for your assistance. When this is all said and done, I'm still very curious as to why the BVF ...

aryansafaie

Thank you both for your quick replies. "#define WET_DRY" ---> wow, silly me, I could have sworn I already activated this. Thank you so much for pointing that out! I'm investigating GLS parameters that will hopefully bring the model to stability; I'll post when I find a set that works. With regards ...

aryansafaie

Hi again, I've included an image of the surface temperature and the mid-depth salinity from the restart file of another similar run. Nearshore (the left side) is full of NaNs. I've also included a transect of the temperature field through time. Just before the blow up, the nearshore region cools at ...

aryansafaie

Dear ROMS Community, I'm running an idealized simulation of an along-shore uniform, wedge-shaped (simple linear sloped bottom) coastal region, to hopefully observe a thermally-induced exchange flow. I'm aiming for a 4 week simulation time, with a time step of 5 seconds. My primary forcing is an ...

aryansafaie

Thank you Kate.

Yes, I'm also exploring/manipulating the exponential decay of solar radiation with depth. So many interesting options!

Best,
-aryan

aryansafaie

Dear all, If I understand correctly, the default setup for ROMS traps all heat flux arriving at the bottom cells in those cells. Would defining a bottom flux in ana_btflux make the model behave differently? For example, if I wanted 50 degC m/s to pass through those bottom cells, is that what I would ...

aryansafaie

An update: This time I tried running the oceanG executable with lldb instead of gdb. The last few lines of the output are: NL ROMS/TOMS: started time-stepping: (Grid: 01 TimeSteps: 00000001 - 00001440) STEP Day HH:MM:SS KINETIC_ENRG POTEN_ENRG TOTAL_ENRG NET_VOLUME C => (i,j,k) Cu Cv Cw Max Speed 0 ...

aryansafaie

No, the directory and .f90 files are still there. The build folder gets replaced everytime I run a new build though.

aryansafaie

The compilers listed in build.bash are ifort, pgi, and gfortran. I don't know if this helps, but I also have gcc and g++ installed: Aryan-Safaies-MacBook-Pro:Upwelling aryansafaie$ which gcc /opt/local/bin/gcc Aryan-Safaies-MacBook-Pro:Upwelling aryansafaie$ which gcc43 /opt/local/bin/gcc43 Aryan ...

aryansafaie

I'm using gfortran.

Should I try using any of the others in build.bash?

aryansafaie

What I'm guessing is that the problem is either:
-I have a hardware issue
-I need to use NetCDF 4 instead of 3
-Somewhere along the way, using MacPorts went wrong.

But that still doesn't explain why gdb won't give me line numbers.

aryansafaie

Running a backtrace or where gives me question marks: 0x0000000100e2799c in ?? () (gdb) bt #0 0x0000000100e2799c in ?? () #1 0x000000005fbf8920 in ?? () #2 0x00007fff00000000 in ?? () #3 0x0000000100000001 in ?? () #4 0x0000000000000000 in ?? () (gdb) where #0 0x0000000100e2799c in ?? () #1 ...

aryansafaie

Hi Kate I've been running it with the following limits: core file size (blocks, -c) 0 data seg size (kbytes, -d) unlimited file size (blocks, -f) unlimited max locked memory (kbytes, -l) unlimited max memory size (kbytes, -m) unlimited open files (-n) 256 pipe size (512 bytes, -p) 1 stack size ...

aryansafaie

Hi Kate, I was being foolish in hitting escape...I saw it on another forum post, and thought it might lead me to a clue as to what's going on in my situation. So never mind that. Now in ocean_upwelling.h I've tried setting NHIS, NAVG, and NDIA each form 72 (their defaults) to something large like ...

aryansafaie

Hello again Kate, You were exactly right; the NetCDF directory on the HPC was in a directory I wasn't able to access yet, so I changed some things around and resolved that issue. Apologies for the side-issue; perhaps I should have posted that in another thread. Getting back to the main issue at hand ...

aryansafaie

Hi again, This time I'm trying to run ROMS on my university's HPC cluster; It compiled, and I have an oceanS executable. Now when I run it with ocean_upwelling.in, I get the following error: (I've copied and pasted the relevant part of the output): STEP Day HH:MM:SS KINETIC_ENRG POTEN_ENRG TOTAL ...

aryansafaie

Hi Kate, I was worried it would come to this; I have a feeling I did something iffy earlier on (in terms of preparing netcdf and fortran), and I remember some of the other forums making mention of different compilers giving different segfault errors. I'll dig around some more and hopefully make a ...

aryansafaie

cd /Users/aryansafaie/ROMS/Projects/Upwelling/Build; /opt/local/bin/gfortran -c -frepack-arrays -mcmodel=medium -g -fbounds-check master.f90 /opt/local/bin/gfortran -frepack-arrays -mcmodel=medium -g -fbounds-check /Users/aryansafaie/ROMS/Projects/Upwelling/Build/esmf_roms.o /Users/aryansafaie/ROMS ...

aryansafaie

Doing that results in: 0x0000000100fd299c in ?? () (gdb) where #0 0x0000000100fd299c in ?? () #1 0x000000005fbfa200 in ?? () #2 0x00007fff00000000 in ?? () #3 0x0000000000000001 in ?? () #4 0x0000000000000000 in ?? () I don't understand why I'm getting the ??; perhaps it's an issue with my ...

aryansafaie

Hi again, Using the where command gives me the following: #0 0x000000010047399c in ?? () #1 0x000000005fbfca90 in ?? () #2 0x00007fff00000001 in ?? () #3 0x0000000000000001 in ?? () #4 0x00007fff5fbfcbbf in ?? () #5 0x0000000000000000 in ?? () I also tried lowering Lm to 10, but it made no ...

aryansafaie

Hi Kate, Thanks again for being so speedy! Pardon my novice ineptitude running gdb. Ok, this time, after running it properly, I received the following (I'm pasting the last few lines from the terminal) STEP Day HH:MM:SS KINETIC_ENRG POTEN_ENRG TOTAL_ENRG NET_VOLUME C => (i,j,k) Cu Cv Cw Max Speed 0 ...

aryansafaie

Hi Kate, Thanks for getting back to me. My stack size is 65532 KB; when I enter the following in the terminal: gdb ./oceanS < ocean_upwelling.in the terminal prints out many (worrisome) messages. I've attached them as a txt file if that helps. However, there doesn't seem to be any mention of a ...

aryansafaie

Dear ROMS community, I recently installed and compiled ROMS on my Mac (64-bit Yosemite, GNU 3.8.1); I followed (mostly) the tutorial here: https://www.myroms.org/wiki/index.php/ROMS_Mac After compiling ROMS with ./build.bash and getting an oceanS file in my Projects/Upwelling directory, I entered ...

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