Search found 33 matches

by kfennel
Fri May 31, 2019 11:39 am
Forum: ROMS Discussion
Topic: Fennel model nutrients accumulate in lower minimum depth
Replies: 1
Views: 293

Re: Fennel model nutrients accumulate in lower minimum depth

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.
by kfennel
Fri Oct 12, 2018 4:52 pm
Forum: Job Opportunities
Topic: MSc and PhD Positions at Dalhousie University
Replies: 0
Views: 1172

MSc and PhD Positions at Dalhousie University

MSc and PhD Positions in Marine Biogeochemistry, Oceanography and Climate at Dalhousie University The Departments of Earth Sciences and Oceanography at Dalhousie University seek candidates for multiple, fully funded MSc and PhD projects on long-term climate impacts to the marine environment and fis...
by kfennel
Wed Apr 25, 2018 1:56 am
Forum: Job Opportunities
Topic: Professor Position in Physical Oceanography - Dalhousie Univ
Replies: 0
Views: 1244

Professor Position in Physical Oceanography - Dalhousie Univ

Tier 2 Canada Research Chair in Physical Oceanography The Department of Oceanography at Dalhousie University is seeking applicants for a Tier 2 Canada Research Chair in Physical Oceanography. Applicants must hold a PhD in Physical Oceanography or a closely related discipline, and have a strong recor...
by kfennel
Wed Dec 13, 2017 1:10 pm
Forum: ROMS Discussion
Topic: Problems about output vertical pCO2 into dia.nc from Fennel
Replies: 1
Views: 664

Re: Problems about output vertical pCO2 into dia.nc from Fen

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 alk...
by kfennel
Wed Jan 18, 2017 7:26 am
Forum: ROMS Discussion
Topic: Biological tracers coupling with currents
Replies: 2
Views: 1181

Re: Biological tracers coupling with currents

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
by kfennel
Sat Dec 10, 2016 8:01 pm
Forum: ROMS Ecosystem
Topic: a question about the chlorophyll growth term in fennel.h
Replies: 2
Views: 1877

Re: a question about the chlorophyll growth term in fennel.h

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 ce...
by kfennel
Thu Oct 27, 2016 3:51 pm
Forum: Job Opportunities
Topic: Faculty Position in Physical Oceanography at Dalhousie Uni.
Replies: 0
Views: 7891

Faculty Position in Physical Oceanography at Dalhousie Uni.

Dear All, The Department of Oceanography at Dalhousie University is looking for a new faculty member in Geophysical Fluid Dynamics with application to Physical Oceanography. The complete ad is attached and pasted below. Please don't be deterred by the stated preference for Canadians -- we have many ...
by kfennel
Thu Jan 07, 2016 9:35 pm
Forum: Job Opportunities
Topic: Assistant Professor in Physical Oceanography, Dalhousie Univ
Replies: 0
Views: 4569

Assistant Professor in Physical Oceanography, Dalhousie Univ

Department of Oceanography, Dalhousie University Diversity Faculty Award (This position is restricted to candidates who self-identify in one (or more) of the following groups: Aboriginal; racially visible; or persons with a disability.) The Department of Oceanography at Dalhousie University invites ...
by kfennel
Fri Oct 09, 2015 12:10 pm
Forum: ROMS Discussion
Topic: Solar radiation, Jerlov water types and plankton feedback
Replies: 3
Views: 1096

Re: Solar radiation, Jerlov water types and plankton feedbac

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
by kfennel
Thu Jul 23, 2015 12:23 pm
Forum: Meetings/Workshops
Topic: Two more sessions at 2016 AGU Ocean Sciences meeting
Replies: 0
Views: 1473

Two more sessions at 2016 AGU Ocean Sciences meeting

This is to inform you of two more sessions at the upcoming AGU Ocean Sciences meeting in New Orleans (21-26 February, 2016). One is related to coastal hypoxia (session ID #7828) and one related to physical and biogeochemical processes in coastal and shelf seas (session ID #9277) . Please consider su...
by kfennel
Fri Jun 12, 2015 7:09 pm
Forum: ROMS Usage
Topic: Questions about bio_fennel simulation
Replies: 3
Views: 1930

Re: Questions about bio_fennel simulation

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 id...
by kfennel
Fri Jun 12, 2015 12:47 pm
Forum: ROMS Usage
Topic: Questions about bio_fennel simulation
Replies: 3
Views: 1930

Re: Questions about bio_fennel simulation

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
by kfennel
Thu Aug 28, 2014 5:36 pm
Forum: Job Opportunities
Topic: Postdoc in Biogeochemical Modelling at Dalhousie University
Replies: 0
Views: 1605

Postdoc in Biogeochemical Modelling at Dalhousie University

Postdoctoral Fellowship in Biogeochemical Modelling Dalhousie University, Oceanography Department Marine Environmental Modelling Group The Marine Environmental Modelling Group (MEMG, http://memg.ocean.dal.ca/) at Dalhousie University in Halifax, Canada, has an immediate opening for a postdoctoral p...
by kfennel
Sun Nov 25, 2012 1:07 pm
Forum: ROMS Discussion
Topic: questions for coupled roms-fennel model
Replies: 4
Views: 2390

Re: questions for coupled roms-fennel model

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/nigh...
by kfennel
Sun Jun 17, 2012 11:16 am
Forum: ROMS Ecosystem
Topic: BIO_SEDIMENT time delay of remineralisation
Replies: 12
Views: 7507

Re: BIO_SEDIMENT time delay of remineralisation

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 sugge...
by kfennel
Mon Jan 02, 2012 2:24 pm
Forum: ROMS Discussion
Topic: some problems about fennel bio model
Replies: 11
Views: 3400

Re: some problems about fennel bio model

Are all initial concentrations for your biological variables positive?
by kfennel
Wed Dec 21, 2011 12:45 pm
Forum: ROMS Ecosystem
Topic: question on chlorophyll
Replies: 1
Views: 2236

Re: question on chlorophyll

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 ...
by kfennel
Fri Sep 16, 2011 3:06 pm
Forum: Meetings/Workshops
Topic: OS 2012 session on biogeochemical data assimilation
Replies: 0
Views: 1616

OS 2012 session on biogeochemical data assimilation

Dear Colleagues, Please consider submitting an abstract to our session on biogeochemical modelling and data assimilation at the 2012 Ocean Sciences Meeting (20-24 February 2012, Salt Lake City): 041: Methods and Applications of Data Assimilation for Ocean Biogeochemistry Organizers: Katja Fennel, Da...
by kfennel
Fri Jan 07, 2011 1:25 pm
Forum: ROMS Ecosystem
Topic: Denitrification in Fennel model
Replies: 1
Views: 2750

Re: Denitrification in Fennel model

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).
by kfennel
Tue Jan 26, 2010 1:29 pm
Forum: Job Opportunities
Topic: Graduate and Post-doc Fellowships at Dalhousie University
Replies: 0
Views: 1588

Graduate and Post-doc Fellowships at Dalhousie University

Graduate and Post-doctoral Fellowships at Dalhousie University Graduate and post-doctoral fellowships in ocean observation, modeling and data assimilation are available at Dalhousie University through a newly funded NSERC Strategic Network Grant (SNG). The SNG builds on the Ocean Tracking Network, ...
by kfennel
Sat Oct 24, 2009 11:19 am
Forum: ROMS Ecosystem
Topic: vertical mixing story
Replies: 6
Views: 3862

Re: vertical mixing story

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 a...
by kfennel
Thu Jul 02, 2009 12:16 pm
Forum: ROMS Discussion
Topic: negative tracer and preserving negativity in fennel.h
Replies: 3
Views: 1620

Re: negative tracer and preserving negativity in fennel.h

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
by kfennel
Thu Nov 20, 2008 11:21 pm
Forum: ROMS Ecosystem
Topic: qestion about biogeochemical model of roms
Replies: 4
Views: 3495

Re: qestion about biogeochemical model of roms

Hi Laura and Barry,

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

Cheers, Katja
by kfennel
Wed Nov 19, 2008 1:25 pm
Forum: ROMS Bugs
Topic: unit inconsistency in DiaBio3d outputs in fasham.h?
Replies: 3
Views: 2239

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

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 ...
by kfennel
Tue Nov 18, 2008 1:18 pm
Forum: ROMS Ecosystem
Topic: qestion about biogeochemical model of roms
Replies: 4
Views: 3495

Re: qestion about biogeochemical model of roms

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...
by kfennel
Fri Jan 25, 2008 2:39 pm
Forum: ROMS Ecosystem
Topic: Light attenuation in Fasham
Replies: 2
Views: 2617

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 Fenn...
by kfennel
Thu Nov 29, 2007 1:24 pm
Forum: ROMS Ecosystem
Topic: Oxygen in Fasham model
Replies: 1
Views: 2139

It's a typo. You should change the sign to minus to make this process an oxygen sink.
by kfennel
Sun Nov 18, 2007 12:56 am
Forum: ROMS Problems
Topic: error: Compilers/make_macros.mk:1: *** missing separator.
Replies: 13
Views: 9112

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. Inspectio...
by kfennel
Fri Nov 16, 2007 8:17 pm
Forum: ROMS Problems
Topic: error: Compilers/make_macros.mk:1: *** missing separator.
Replies: 13
Views: 9112

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 :=
by kfennel
Fri Nov 16, 2007 8:01 pm
Forum: ROMS Problems
Topic: error: Compilers/make_macros.mk:1: *** missing separator.
Replies: 13
Views: 9112

I'm compiling with ifort on Linux. I typed "make clean" between compilation attempts. I'm using svn revision 126 from this morning.
by kfennel
Fri Nov 16, 2007 7:15 pm
Forum: ROMS Problems
Topic: error: Compilers/make_macros.mk:1: *** missing separator.
Replies: 13
Views: 9112

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

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
by kfennel
Wed Dec 13, 2006 6:08 pm
Forum: ROMS Installation
Topic: ROMS OpenMP with gfortran?
Replies: 5
Views: 3853

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 a...
by kfennel
Mon Nov 13, 2006 6:36 pm
Forum: Job Opportunities
Topic: Research Assistant sought
Replies: 0
Views: 1675

Research Assistant sought

Dalhousie University's Marine Environmental Modelling Group is seeking Research Assistant/Associate Research Assistant/Associate sought for emerging marine environmental modeling group within Dalhousie University’s Department of Oceanography ( http://oceanography.dal.ca ). The marine environmental ...