Search found 23 matches

by LauraB
Tue Oct 07, 2014 6:10 pm
Forum: ROMS Bugs
Topic: typo when converting oxygen units from mL to mmol
Replies: 0
Views: 1263

typo when converting oxygen units from mL to mmol

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 calcul...
by LauraB
Tue Oct 29, 2013 12:56 pm
Forum: ROMS Ecosystem
Topic: Restart with biology
Replies: 5
Views: 3816

Re: Restart with biology

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
by LauraB
Fri Apr 13, 2012 12:29 pm
Forum: ROMS Ecosystem
Topic: BIO_SEDIMENT time delay of remineralisation
Replies: 12
Views: 7908

Re: BIO_SEDIMENT time delay of remineralisation

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. Geo...
by LauraB
Mon Nov 30, 2009 11:14 pm
Forum: ROMS Information
Topic: What is the output of DIAGNOSTICS_TS/UV?
Replies: 6
Views: 4624

Tracer rates in diagnostics file

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 nu...
by LauraB
Thu Jul 09, 2009 12:32 am
Forum: ROMS Problems
Topic: Error when compiling with M3CLM_NUDGING and ANA_M3CLIMA
Replies: 2
Views: 1588

Re: Error when compiling with M3CLM_NUDGING and ANA_M3CLIMA

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 wit...
by LauraB
Wed Jul 08, 2009 4:38 pm
Forum: ROMS Problems
Topic: Error when compiling with M3CLM_NUDGING and ANA_M3CLIMA
Replies: 2
Views: 1588

Error when compiling with M3CLM_NUDGING and ANA_M3CLIMA

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: & CLI...
by LauraB
Sat Mar 28, 2009 7:45 pm
Forum: ROMS Sediment
Topic: When ana_sediment is defined & there is an initial nc file..
Replies: 3
Views: 2523

Re: When ana_sediment is defined & there is an initial nc file..

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 ...
by LauraB
Fri Mar 27, 2009 10:35 pm
Forum: ROMS Sediment
Topic: When ana_sediment is defined & there is an initial nc file..
Replies: 3
Views: 2523

When ana_sediment is defined & there is an initial nc file..

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 init...
by LauraB
Wed Feb 18, 2009 10:47 pm
Forum: ROMS Ecosystem
Topic: Oxygen dependence for nitrification and remineralization
Replies: 2
Views: 2235

Re: Oxygen dependence for nitrification and remineralization

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
by LauraB
Fri Feb 13, 2009 12:42 am
Forum: ROMS Ecosystem
Topic: Oxygen dependence for nitrification and remineralization
Replies: 2
Views: 2235

Re: Oxygen dependence for nitrification and remineralization

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
by LauraB
Thu Feb 12, 2009 12:37 am
Forum: ROMS Ecosystem
Topic: Oxygen dependence for nitrification and remineralization
Replies: 2
Views: 2235

Oxygen dependence for nitrification and remineralization

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? Thanks...
by LauraB
Wed Nov 19, 2008 12:49 am
Forum: ROMS Ecosystem
Topic: qestion about biogeochemical model of roms
Replies: 4
Views: 3630

Re: qestion about biogeochemical model of roms

I'd be interested... :)
Thanks in advance, Katja!
Laura
by LauraB
Wed Oct 08, 2008 7:23 pm
Forum: ROMS Discussion
Topic: ROMS 3.0 possible bug with volume conservation
Replies: 6
Views: 2596

Re: ROMS 3.0 possible bug with volume conservation

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 ...
by LauraB
Fri Jun 20, 2008 2:06 am
Forum: ROMS Problems
Topic: different OBC for different tracers?
Replies: 0
Views: 764

different OBC for different tracers?

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
by LauraB
Tue Feb 12, 2008 10:01 pm
Forum: ROMS Ecosystem
Topic: Light issues when Biology is defined
Replies: 3
Views: 2793

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 car...
by LauraB
Tue Feb 12, 2008 8:25 pm
Forum: ROMS Ecosystem
Topic: Light issues when Biology is defined
Replies: 3
Views: 2793

Light issues when Biology is defined

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, wh...
by LauraB
Fri Feb 08, 2008 10:25 pm
Forum: ROMS Problems
Topic: Units problem in ANA_SRFLUX
Replies: 1
Views: 1019

Units problem in ANA_SRFLUX

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: !---------------------------------------------------------...
by LauraB
Wed Jan 30, 2008 2:08 am
Forum: ROMS Problems
Topic: Negative nitrate concentrations
Replies: 1
Views: 964

Negative nitrate concentrations

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 probl...
by LauraB
Thu Jan 24, 2008 7:17 am
Forum: ROMS Ecosystem
Topic: Light attenuation in Fasham
Replies: 2
Views: 2732

Light attenuation in Fasham

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 computa...
by LauraB
Wed Jan 23, 2008 6:50 pm
Forum: ROMS Ecosystem
Topic: Initial conditions for Oxygen
Replies: 4
Views: 3299

Initial conditions for Oxygen

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...
by LauraB
Wed Nov 28, 2007 12:34 am
Forum: ROMS Ecosystem
Topic: Oxygen in Fasham model
Replies: 1
Views: 2229

Oxygen in Fasham model

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 a ...
by LauraB
Thu Aug 02, 2007 8:06 pm
Forum: ROMS Discussion
Topic: 2D (cross shore vs depth) applications...?
Replies: 2
Views: 1185

Thanks a lot J, I'll look into this test case.
Laura
by LauraB
Thu Aug 02, 2007 6:40 pm
Forum: ROMS Discussion
Topic: 2D (cross shore vs depth) applications...?
Replies: 2
Views: 1185

2D (cross shore vs depth) applications...?

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 mess...