Ocean Modeling Discussion

kfennel

Hello,

Mjfconan is correct. They are the same unit.

Cheers, Katja

kfennel

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kfennel

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kfennel

Hi Eugen, Please look at these papers: Moriarty et al., Impact of seabed resuspension on oxygen and nitrogen dynamics in the northern Gulf of Mexico: A numerical modeling study, Journal of Geophysical Research-Oceans 123, 7237-7263 (2018) https://agupubs.onlinelibrary.wiley.com/doi/full/10.1029 ...

kfennel

Hi Stlaur,

Thanks for raising these excellent points -- indeed these and other updates should be made and are, in fact, long overdue.

We're working with Hernan to get a number of updates (including PO4 as additional variable) into the trunk.

Stay tuned and have a nice weekend,
Katja

kfennel

Looks to me like the change in your grid file affected the circulation in your shallow bay with longer flushing time leading to more trapping of nutrients. Note that your salinity has changed as well.

kfennel

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kfennel

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kfennel

Hi Kent, There is no problem. The behavior you are describing is to be expected since pCO2 is only calculated in the surface layer. During ROMS time-stepping, knowledge of pCO2 is only required at the surface for the calculation of the air-sea CO2 flux. Since the calculation of pCO2 from DIC and ...

kfennel

Hi Haiyun,

I would recommend you try a sponge/nudging zone along the open boundaries and nudge your NO3 variable to the WOA climatology in the nudging zone.

Best, Katja

kfennel

Dear Mingshun, I was about to answer to your post, but you beat me to it. You are correct that there is a discrepancy in notation with the Geider et al. (1997) paper. Geider et al. (1997) describe the factor rho_chl, i.e. the factor that determines synthesis of chlorophyll in viable phytoplankton ...

kfennel

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kfennel

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kfennel

Bronwyn Cahill had also implemented this a few years ago. Here is a link to her 2008 article: http://onlinelibrary.wiley.com/doi/10.1 ... 33595/full

kfennel

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kfennel

Dear Shuwen, It looks like your fall mixing is not bringing enough nutrients into the euphotic zone to trigger a fall bloom. It may help to plot the mixed layer depth on top of your time series plots (at least to illustrate the reasons for the lack of a fall bloom). If this is meant to be just an ...

kfennel

Hi Shuwen,

It would be helpful if you could post some plots of your results. For the bio-toy case it would be useful to see time series of nutrient and phytoplankton profiles.

Cheers, Katja

kfennel

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kfennel

I don't see a problem with your Test 2. Nitrification is inhibited by light. If you impose constant light (without a day/night cycle) you effectively shut off nitrification in the sunlit layer, ammonium will accumulate and nitrate will run out. You can activate DIURNAL_SRFLUX to switch on a day ...

kfennel

Hi tony1230, I'm surprised to see PO4 as one of your model outputs. The BIO_FENNEL module does not include PO4 as state variable. Did you add this yourself? In any event, there seems to be a problem with your PO4. PO4 has essentially disappeared in your simulation after about 100 days. I would ...

kfennel

Are all initial concentrations for your biological variables positive?

kfennel

Phytoplankton is calculated using the implicit scheme as described in the comments right before the start of the ITER LOOP. This is done to avoid negative concentrations, in the case of phytoplankton growth, of the nutrients that are being consumed in the process. Chlorophyll synthesis is different ...

kfennel

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kfennel

Most likely the model is trying to write a diagnostic term related to denitrification that doesn't exist because denitrification is switched off. I would check the logic in the DIAGNOSTICS_BIO portion at the end of the biology subroutine (the section dealing with sediment fluxes).

kfennel

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kfennel

Hi Kate, Note that some of the other bio models don't clip bio tracers (I know for a fact that BIO_FENNEL does not). Instead a local variable inside the biology routine is clipped temporarily for calculating source and sinks terms, but when written back into the tracer array the biological sources ...

kfennel

Just to confirm John Warner's point above: we decided to not "chop off" negative values to ensure mass conservation. Problems should be greatly reduced with TS_MPDATA.

-Katja

kfennel

Hi Laura and Barry,

Please download here:
http://memg.ocean.dal.ca/memg/pubs/Fenn ... L_2008.pdf

Cheers, Katja

kfennel

Hi Wen, The correct unit for P_Production and NO3_uptake is mmol N/m3/diag-period, where diag-period is the duration over which the fluxes are accumulated or, in other words, the period between writing diag-files (nDIA as specified in ocean.in). If dia-files are written once per day, the units thus ...

kfennel

Hi, For a description of the Fasham option as implemented in ROMS you can check out: Fennel , K., Wilkin, J., Levin, J., Moisan, J., O'Reilly, J., Haidvogel, D., Nitrogen cycling in the Mid Atlantic Bight and implications for the North Atlantic nitrogen budget: Results from a three-dimensional model ...

kfennel

Hi Laura, In the equation exp[-(kw + kchl . CHL) z] CHL represents the mean chlorophyll concentration between z and the surface (the chl integral divided by z). The correct unit for kCHL is 1/(mg CHL m^{-2}). Also note that the factor 1/z in front of the chl integral is missing in equation 5 in ...

kfennel

It's a typo. You should change the sign to minus to make this process an oxygen sink.

kfennel

You got me on the right track. Many thanks! I inserted $(if ,, $(warning ROMS_CPPFLAGS: $(ROMS_CPPFLAGS))) in line 212 of the makefile. Turns out that my ROMS_CPPFLAGS was empty: [fennelk@dell-rack]$ make makefile:212: ROMS_CPPFLAGS: Compilers/make_macros.mk:1: *** missing separator. Stop ...

kfennel

I have:

Code: Select all

[fennelk@blue]$ more Compilers/make_macros.mk
   CPPDEFS - Choose an appropriate ROMS application.
  USE_ADJOINT :=
  USE_TANGENT :=
  USE_REPRESENTER :=
  USE_WRF :=
  USE_SWAN :=
  USE_REFDIF :=
  USE_ARPACK :=
  USE_MCT :=
  USE_ESMF :=

kfennel

I'm compiling with ifort on Linux. I typed "make clean" between compilation attempts. I'm using svn revision 126 from this morning.

kfennel

Hi,
I can compile the UPWELLING case fine, but when I try to compile BIO_TOY I get the following error message:

Code: Select all

[fennelk@blue ]$ make
Compilers/make_macros.mk:1: *** missing separator.  Stop.

Does anybody have an idea what I'm missing?
Thx, Katja

kfennel

Hi, we're trying to build ROMS with OpenMP on a Linux (centOS 4.4 X86_64) system for testing purposes, and are having problems with OpenMP in particular Initial build attempts without OpenMP were successful using either gfortran or g95 fortran compiler. Most recent attempts now with openMP enabled ...

kfennel

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Ocean Modeling Discussion

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Re: Questions about the ROMS-fennel model nitrogen units.

Senior biogeochemical modeller/group leader

Project Manager

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Re: Suggestions for Nonlinear/Biology/fennel.h

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Professor Position in Physical Oceanography - Dalhousie Univ

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Re: Questions about bio_fennel simulation

Re: Questions about bio_fennel simulation

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Re: some problems about fennel bio model

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OS 2012 session on biogeochemical data assimilation

Re: Denitrification in Fennel model

Graduate and Post-doc Fellowships at Dalhousie University

Re: vertical mixing story

Re: negative tracer and preserving negativity in fennel.h

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Re: unit inconsistency in DiaBio3d outputs in fasham.h?

Re: qestion about biogeochemical model of roms

error: Compilers/make_macros.mk:1: *** missing separator.

Research Assistant sought