Ocean Modeling Discussion

You can represent phytoplankton as Lagrangian particles which have biological responses to environmental conditions and active vertical migration behaviors. There is code in the ROMS distribution for oyster larvae which could be converted to phytoplankton with vertical migration. However, this is ...

I have taught an ocean modeling class a number of times over a number of years. My philosophy is that students need to know the basics before working with a publicly available ocean model (any of them). They also need to understand programming and debugging. The class I teach lasts one semester (13 ...

I am using ROMS as part of a GFD class as a way to demonstrate some processes that are hard to show with analytical math. My latest failure is to illustrate baroclinic instability using a periodic zonal channel with linearly stratified (both y and z) initial conditions (matching the setup in G ...

To add to Kate's suggestion, I would run this model for about 10 time steps having compiled with debug on in the compile script (however you compile the model). Run in scalar mode (one processor). Make sure that you turn on array bounds checking. This makes sure that arrays are defined and indexes ...

Given the values in the wind forcing file (10^34), I think these are all "missing values" for netcdf. Are you sure that you assigned variables to the forcing file? I would plot the wind speeds in the forcing file to see that they are what you wanted. If the forcing file is ok, then make sure that ...

John, My thanks to Ivicia. Adding the 4 lines fixed the problem. I can run the upwelling case and the estuary test without sediments. Thanks for the quick response. I am trying to set up an all analytical test ACC/Atlantic overturning model with sea ice (and maybe ice shelves). I will send you the ...

There is a curious difference between COAWST/ROMS(v1175) and trunk/ROMS (v854). The source code for both were obtained last week (July 20 2017). The problem: I am trying to run the upwelling case in COAWST/ROMS to set up the environment. Both scalar and mpi compiles report an incorrect model ...

I think this is an error that I created (sorry to add confusion). I started with the spect_fennel.h model (svn 2232 2012-01-03) in the COAWST distribution (svn 1000, distributed Dec 15, 2014). I changed the spectral light representation in hte code based on GRASSLIGHT (a shallow water optical ...

This error may have been identified before, but I did not see anything in the ecosystem discussion. Depending on how folks develop other ecosystem models, this error might have migrated to other ecosystem codes. At the end of the sinking code in fennel.h, there are statements to remineralize ...

I have figured out how nudging to climatology works, by doing some experiments. Here is my understanding, but I am happy to hear another explanation. The climatology arrays are created (and indexed) in the order in which climatology is processed. In my case, I have 16 tracers (T,S, 4 sediment and 10 ...

The bio input file has the following lines:

LtracerCLM = 12*T
LnudgeTCLM = 12*T

so climatology should be managed and used.

Nudging to climatology does work with the imposed indexes, but the wrong variables are nudged to the wrong values.

John

My "clever" solution to use explicit indexes for the climatology does not work. The climatology arrays don't have the indexes that I expect so the nudging is wrong. I have gone back to the "proper" way to have a climatology. I could not find any example of a biological model that uses a climatology ...

I have an ecosystem model (a modification from Fennel.h) in which I would like to nudge nutrients to climatology. I am trying to define the climatology in ana_tclima.h with statements like those below. I also include "use mod_biology" in the module section which should give access to the biological ...

I am trying to set up roms to represent alternating flow in a uniform depth channel (x-z). It is 40 km long and periodic in y. density is uniform. vertical viscosity is constant. The boundaries are open on east and west ends. I want the flow to have ubar = uo sin(2 pi t/period) for different choices ...

A checkerboard instability pattern is due horizontal diffusion/viscosity. Look at your time step relative to the grid spacing and horizontal diffusivity. With laplacian horizontal diffusivity A dt / dx^2 needs to be less than 1 (maybe 1/2) depending on the time stepping scheme. With variable ...

I was able to set up the source/sink flow based on John's suggestion (Thanks!). I can get a linear abyssal circulation driven by surface sources and sinks using LwSrc=true and LuvSrc=false, and using ana_psource.h to control sources/sinks. The model limits the number of sources to 200. I have a ...

I would like to use roms to demonstrate the abyssal circulation in a homogeneous density model by applying surface mass sources and sinks. Is there a way to add mass to change d zeta/dt? ana_psource seems to be designed as a lateral mass source (rivers) which also adds momentum along with mass. I am ...

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What are the units for the light values (ec_Fobar) in mod_eclight? I am trying to compare this model to the one in Gregg and Carder (1990) where Ho in that paper has units of W/m2/nanometer. These value differ by about 10. Are these values in micromole photons/m2/s? Converting these units don't give ...

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The 4th order milne scheme was tested for accuracy against analytical flow (purely circular flow with oscillating vertical migration). The largest cause for error was the interpolation from the grid points to the particle location. With analytical flow fields (no interpolation) the path error was ...

I have seen this problem with the use of IDT, which is an interactive translator for ncar metacode. I have had trouble installing ncar graphics and getting idt to work. Try the following test ctrans -d X11 gmeta which is the non-interactive metacode translator. This should open a window and show the ...

The requirement of a very short time step must be due to a fast rate in your equations. First order schemes (like Euler) are almost always poor performers. That is, they give bad solutions but are not unstable for a short enough time step. Any of the schemes you mention should behave. The ~1 sec ...

The problem you are having is not clear from your message. Any 2nd order ode can be set up as two coupled 1st order ode. Have you tried solving the ODE with a different solver independent of ROMS? How small must the time step be to get a stable solution? If all else fails, code your own 2nd order ...

Research Scientist in Oceanography. Full-time position: to participate in a National Science Foundation-funded project that is focused on understanding the physical mechanisms controlling cross-shelf exchange on Antarctic continental shelves and how this exchange relates to melting of the base of ...

It looks like the vertical calculation is predictor-corrector unless the random walk is on.

I got lost in the cpp statements.

It should be possible to do the random walk with predictor-corrector. I will think about it, but it will be down my list of things to think about.

Thanks,

John

I have noticed in the step_floats routine, that an Euler forward time scheme is used to calculate the vertical position of the float while the horizontal position uses a predictor-corrector scheme. Is there any reason to do this? Has anyone tried the p-c scheme for the vertical equation? As a second ...

I changed the tiling to by 1x2 and ran with 2 threads. (I have another longrunning job and don't want to interfere).

I get the same result-- abnormal termination during the first step.

John

I am attempting to run the Upwelling test case on a Sun computer with 2 dual core opteron (AMD) chips with openmp. The calculation blows up in the first long step. Has anyone run ROMS with openmp on SUN opteron using the SunStudio 12 compilers? The OS is solaris 10. Thanks in advance for your help ...

1D ice models act in unexpected ways. 1) It is very hard to melt ice with solar radiation, especially with a snow layer. Most ice melts by shortwave heating the water and the water melting the ice. Limit your ice concentration to 90 or 95% and you will see faster melt in spring. 2) We had a problem ...

A baroclinic speed of 3 m/s seems pretty small for strong stratification. Using 320 m depth and a reduced gravity of 2.5 gives an internal wave speed of 28.3 m/s. With a grid spacing of 500 m, I get an internal time step of about 4 sec (making the courant number =1/4, which may not be small enough ...

Hi Hernan and Enrique, I have done more work on the ice shelf startup. The problem with the current setup is that it assumes that the water in which the ice is floating is always rho(zice) , but since the density changes along the base of the ice, this leads to unphysical pressure gradients. Also ...