Ocean Modeling Discussion

Hi all,

In fennel.h, the parameter l2mol is used to convert oxygen saturation concentration in mL/L to mmol/m3 and is defined

real(r8) :: l2mol = 1000.0_r8/22.9316_r8 ! liter to mol

But the molar volume of O2 is 22.3916 L/mol (see Garcia and Gordon, L&O, 1992, same source for the equations to ...

Hi Virginia,

As far as I understand it, you don't need to change DSTART when you re-start a run, just NRREC. Hope that helps!

Laura

Hi there,

I have included a remineralization lag in the sediments in a relatively simple way. You can see details of the parameterization and equations in the following paper:

Bianucci, L., K. L. Denman, and D. Ianson (2011), Low oxygen and high inorganic carbon on the Vancouver Island Shelf, J ...

Hi all,

I'm trying to understand what's in the *rate diagnostic output. Take for example nitrate rate: it isn't equal to the sum of advection and diffusion. After going through the code I think it should be the total change with time (ie, include also biological sources minus sinks, fluxes due to ...

Thanks Kate!

from a previous post (https://www.myroms.org/forum/viewtopic.php?f=1&t=709) I had understood that TCLIMATOLOGY (or M3CLIMATOLOGY) was used when a netcdf file was given to provide the climatological data, while ANA_**CLIMA was used when the clim data was an analytical function...
But ...

Hi community,

I'm trying a run with nudging to climatology for tracers and 3D momentum, i.e. cpp options:
#define TCLM_NUDGING
#define M3CLM_NUDGING
#define ANA_NUDGCOEF
#define ANA_TCLIMA
#define ANA_M3CLIMA
#undef TCLIMATOLOGY
#undef M3CLIMATOLOGY

I get the following error:
rhs3d.f90:110.39 ...

Thanks for the reply! This wasn't a restart run (nrrec=0), so I realize now -after your comment- that the DO loop I added is not being used at all! (and probably should be removed)

However, the fix worked and the run is still going on. So it looks like the extra "# ifndef ANA_SEDIMENT" is doing the ...

Hi ROMS community,

I wanted to add sediments to my model. My initial conditions for physics and biology were given in a netcdf file, while I wanted analytical conditions for the sediments. As far as I understand, whenever ana_* is defined, analytical initial fields are used (even if there is an ...

Another thing: Remineralization of nitrogen detritus is now oxygen dependent, but this O2 function has not been included in the remineralization of carbon detritus.

Should the same oxygen function (fac2) be added to the remineralization rates of detrital C?

Best,
Laura

Moreover, I noticed that during night (PARsur=0) there is no oxygen dependence for nitrification. I think it should be included, shouldn't it?

Regards,

Laura

Hi community,

The Fasham module now includes oxygen dependence for nitrification and remineralization rates. I would like to know more about these O2 functions (e.g., where does the half saturation value for nitrification=3 mmol/m3 come from?, etc). Could you point me towards some references ...

I'd be interested...
Thanks in advance, Katja!
Laura

Hi Barbara and hi all,

I'm having the same problem you described in October 15, 2007: An idealized configuration with periodic alongshore conditions and only one open boundary. Even when the VOLCONS option is on at the open boundary, total volume is not conserved. I also tried having a wall instead ...

Hi all,

I would like to use different open boundary conditions for physical and biological tracers (e.g. radiation for temperature and clamped for nitrate). Is there an easy way to do that? (maybe some cpp option that I'm missing to see?)

Thanks for you input in advance!
Best,

Laura

Ups, I missed something :oops: : The 2 radiation bands also represent the distinction between photosynthetically available and not available radiation for P (i.e, PAR or not PAR).

So the 1st problem that I mentioned above should be re-phrased:

1) The attenuation for T and P is the same if we are ...

Hi community,

I think we may have a problem with the physical-biological coupling in terms of light. Please correct me if I'm wrong.

When SOLAR_SOURCE is defined, short wave radiation penetrates the water column and contributes to T. The decay penetration function is based on Jerlov's water type ...

Hi all,

The description in ANA_SRFLUX.h reads:

! This subroutine sets kinematic surface solar shortwave radiation !
! flux "srflx" (degC m/s) using an analytical expression. !

However, when the short wave input has to be given, the title is ...

Hi all,

In my NO3 output I get values very close to zero but negative (~ -10^-7). I added a couple of lines in Fasham.h, so it would tell me when NO3 is zero or less. The funny thing is that it only finds zeros... but I keep getting small negative numbers in my nc file.

Can there be a rounding ...

Hello all,

My question now is about light attenuation, which is given by an exponential: exp[-(kw + kchl . CHL) z],
where CHL is the integrated chlorophyll concentration in the column from surface to level z.

In BioFasham.in, kchl (AttChl) is given in units of 1/(mgChl m^2). In the code, the ...

I'm using analytical fields for my biological initial conditions (ana_biology.h). However, I can't find where I should initialize oxygen (there is no iOxyg in ana_biology). After running the code, it looks like initial oxygen is zero by default, but I would like to know where I can modify that value ...

Hi all,

I'm running ROMS 3.0 with Fasham biology, including carbon and oxygen. I have a question about one of the O2 fluxes:

The flux between zooplankton and ammonium (Z excretion + basal metabolism) produces oxygen... Why is that? I was thinking that maybe these processes could be accompanied by ...

Thanks a lot J, I'll look into this test case.
Laura

Hi all,
I was wondering if anybody knows about 2D (cross shore vs depth) implementations of ROMS (well, probably not strictly 2D, but a 3D model with a few grid nodes in the alongshore direction). I'd appreciate any references you can give me!
Thanks!, Laura
PS: I wasn't sure where to post this ...