Ocean Modeling Discussion

cae

Hi. Here are some questions to consider.

1) Does the nested grid run in a stand-alone configuration (i.e., not in a nested configuration)? In other words, is this an issue with the nesting or the domain?

2) Is the value of rx0 given for the nested domain or for the outer domain? I'll assume it is ...

cae

Professor Christopher Edwards in the Department of Ocean Sciences at the University of California, Santa Cruz invites applications for two postdoctoral scholar positions to investigate coupled physical and biogeochemical processes in the ocean using numerical models. One project focuses on ocean ...

cae

I'll echo everyone's heartfelt comments about Dale. Though as a graduate student I knew his papers, I first got to know Dale in the late 1990s when I was a postdoc on a US Globec project with Zack Powell and him. I traveled to Rutgers often (working then with SEOM) and enjoyed many detailed modeling ...

cae

The Department of Ocean Sciences at the University of California, Santa Cruz, invites applications for Postdoctoral Scholar positions in ocean modeling and/or data assimilation in coupled physical/biogeochemical configurations. Various projects revolve around modeling studies of the California ...

cae

POSITION DESCRIPTION
The Department of Ocean Sciences at the University of California, Santa Cruz, and the Institute of Geophysics and Planetary Physics and Department of Atmospheric and Oceanic Sciences at the University of California, Los Angeles, invite applications for the position of ...

cae

Hi. Thanks for the reply.

I have a case that I'm debugging for other reasons and reduced NTIMES lower than it normally might be. In my case, I have

NTIMES == 1536
DT == 225.0d0
NAVG == 384
NDEFAVG == 11520

I only wanted the run to go 4 days, have daily average writes, and want new average files ...

cae

I am only 80% sure that this is a bug, but sufficiently sure that I thought I'd post it. I'm using ROMS version 1005.

In read_phypar.F, lines 3692-3698 read

#ifdef AVERAGES
IF ((nAVG(ng).gt.0).and.(ndefAVG(ng).gt.0)) THEN
OutFiles=ntimes(ng)/ndefAVG(ng)
CALL edit_file_struct (ng, OutFiles ...

cae

Hi.

What John describes is the usual way in which lwrad_down is generated for the LONGWAVE_OUT option. I wonder if there's an error in this approach.

I interpret 'Downward longwave radiation flux' from atmospheric models to mean downward above the ocean surface. Thus, this radiative term includes ...

cae

The Department of Ocean Sciences (https://oceansci.ucsc.edu/) at the University of California, Santa Cruz, and the Institute of Geophysics and Planetary Physics and Department of Atmospheric and Oceanic Sciences at the University of California, Los Angeles, invite applications for the position of ...

cae

Hi.

We're searching for a postdoctoral scientist who will join and collaborate with modeling groups at both UCSC and UCLA.

Thanks,
Chris

============================================================================================

The Department of Ocean Sciences (https://oceansci.ucsc.edu/)at ...

cae

The Department of Ocean Sciences at the University of California, Santa Cruz, invites applications for the position of Postdoctoral Scholar to study coupled physical/biogeochemical processes within the California Current System and broader Pacific Ocean. The project involves the development of ...

cae

Hi. In my experience, a blow-up like this usually results from a physical circulation problem and not from the ecosystem model. Have you configured this model without the biogeochemistry and ensured that it runs?

Also, with only 327 time-steps until a problem, you may be able to output the model ...

cae

Dear All,

The Ocean Sciences Department UC Santa Cruz is searching for a physical oceanographer. Details about the position description can be found at http://apo.ucsc.edu/academic_employment/jobs/JPF00404-17.pdf

Review of Applicants will begin on December 16, 2016.

Regards,
Chris

The Ocean ...

cae

Hi.

In nesting applications without masking, version 741 does not compile due to mp_aggregate2d not being available to nesting.f90.

The code compiles if the CPP lines 2831 and 2833 of nesting.F are removed. Thus:

# ifdef MASKING
USE distribute_mod, ONLY : mp_aggregate2d
# endif

becomes ...

cae

Hi. Just to add to Kate's good advice:

In cases that I'm familiar with, the terms governing biological dynamics involve only local fields (e.g., uptake in a grid cell depends on nutrients and phytoplankton in that grid cell and not in a grid cell from somewhere across the ocean). If this is the ...

cae

Hi.

In Release 736, lines 309-311 are

Code: Select all

if (isfield(Sinp,'origin_flag_values'));
  Sout.origin_flag_values = Sinp.state_flag_values;
end,

but should (I think) be

Code: Select all

if (isfield(Sinp,'origin_flag_values'));
  Sout.origin_flag_values = Sinp.origin_flag_values;
end,

cae

Hi Fanny.

For a tracer, C, the vertical advection term in the tracer equation is wdC/dz or in flux-conservative form d(wC)/dz. It is the flux divergence that causes changes to a tracer value in a cell, not the flux across any cell boundary alone.

ROMS is written in a flux conservative form and I ...

cae

Hi.

This bug is inconsequential except for writing information to the output log. On lines 556-557 of nemuro_inp.h (revision 671), it reads:

WRITE (out,80) MorPS0(ng), 'MorPL0', &
& 'Large phytoplankton mortality rate', &

but should read

WRITE (out,80) MorPL0(ng), 'MorPL0', &
& 'Large ...

cae

Hi.

Thanks so much, Hernan, for developing this nesting code and continuing to fix it. As you say, it's very complicated, but it will a great capability for everyone once it's working. We all appreciate it.

I've found what may be another bug. In nesting.F (revision 671), lines 221-227 read ...

cae

Hi.

I have another section of code that may be in error. In mod_nesting.F (revision 668), lines 487-534 read:

!
!-----------------------------------------------------------------------
! Deactivate boundary condition switches if contact point lay on the
! physical nested grid boundary ...

cae

Hi. Excellent. I'm glad if these are on the right track.

I'm sure you'll find this with the debugger, but there's similar logic (with the SOLVE3D CPPDEF and Zt_avg1) in lines 2154-2164 and 2190-2203 of nesting.F (revision 668). Note also that an END IF on line 2163 should be an END DO.

My ...

cae

Hi again,

Thanks for correcting contact.m. There's still one spot that needs fixing:

Line 1695 in contact.m:
C.mask_v = G(rg).mask_u(IN);

should be
C.mask_v = G(rg).mask_v(IN);

Another issue that I'm seeing with a refinement nesting arrangement is that the free surface of the fine grid is ...

cae

Thanks, Hernan.

I was least sure of the change to inp_param.F. Thank you for clarifying.

Chris

cae

In ROMS revision 667, I found what may be 2 bugs in contact.m and one in inp_par.F. Apologies if these are correct as they are.

1) Lines 1608 and 1664 in contact.m:

C.mask_v = G(rg).mask_u(IN);
should be
C.mask_v = G(rg).mask_v(IN);

2) Lines 792 to 800 in contact.m:

R.lon_rho(IstrR+3:IendR ...

cae

It looks to me like there's a small bug in line 673 of the current nemuro.h code. This occurs in the HOLLING_GRAZING section of the GraZS2ZP section. In the last line of the following code snippet, cff depends on cff3 raised to the power cff4. I think this should be cff3 multiplied by cff4 ...

cae

In LMD_TEST, I believe the wind stress should follow Equation 36 in the Large et al (1994) paper.

In ana_smflux.h, the relevant line for sustr currently reads:

IF (time(ng).le.57600.0_r8) THEN
windamp=-0.6_r8*SIN(pi*time(ng)/57600.0_r8)* &
& SIN(2.0_r8*pi/57600.0_r8)/rho0
ELSE
windamp=0.0_r8 ...

cae

Hi.

closest.m from the roms_wilkin set of routines is a useful routine for trying to find the nearest grid point to a lat/lon position. I find a tiny issue when a desired point is exactly mid-way between roms grid points. The following section of code crashes when ii and jj, returned by find ...

cae

Hi.

Apologies if these 2 items have been discussed already or are wrong.

1) I find the gfortran fails to compile the slevels.F routine in the plot/src/Utility directory, with the variable tindx already defined.

Compile works if I change line 35 as follows:

! integer file, nc_gid, tindx ...

cae

The Department of Ocean Sciences at the University of California, Santa Cruz (UCSC), invites applications for the position of Postdoctoral Scholar to develop and explore data assimilation methods for ecosystem processes within the California Current System using the Regional Ocean Modeling System ...

cae

Thanks to both responses. I now have it writing successfully using netcdf-3.6.3.

cae

Hi.

I'm running into a netcdf problem trying to define a history file for a high resolution run with many tracer variables. The code works fine at (a) lower resolution or (b) fewer tracer variables.

Here's the error message:

0 1 00:00:00 9.967519E-04 2.013537E+04 2.013537E+04 7.714335E+15
DEF ...

cae

I don't know if this is helpful or not, but it seems to me that clipping alone is not sufficient to prevent a blowup. The diffusion process conserves total nitrogen between cells, but clipping does not. The process then acts as a local source of nitrogen, which can continue indefinitely.

A second ...

cae

We would like to draw your attention to a special session at Ocean Sciences which will be held February 22-26, 2010 in Portland, Oregon.

IT39: From field observations to modeling connectivity in the nearshore and back again: Circulation, dispersal, and settlement

Abstract submission deadline ...

cae

With coastal simulations, we've experienced a nearshore checkerboard pattern using KPP during periods of weak wind stress. This pattern was reduced some with horizontal smoothing, but still was disturbing. We've had better luck from this perspective with gls. Not exactly the same issue that you have ...

cae

UNVERSITY OF CALIFORNIA, SANTA CRUZ
DEPARTMENT OF OCEAN SCIENCES
POSTDOCTORAL SCHOLAR

The University of California, Santa Cruz (UCSC), seeks a Postdoctoral Scholar to develop and explore numerical models of the California Current System (CCS) focused on marine microbial communities. Through the ...

cae

Hi.

I was able to get the tracer budgets to work along with MPDATA by making 4 changes to step3d_t.F. It seemed to me that the diagnostic tracer work arrays were not being fully updated for MPDATA. I'm not 100% sure this is right, but I believe it's consistent. The lines are listed below between ...

Ocean Modeling Discussion

Search found 36 matches

Re: Blow up in nested version

postdoc positions at UCSC

Re: Dale B. Haidvogel (1949-2023)

modeling postdoc at UC Santa Cruz

UCSC/UCLA postdoc in coastal coupled physical/BGC modeling

Re: average file count logic

average file count logic

Re: Shortwave and Longwave radiation.

UCSC/UCLA postdoc in coastal coupled physical/BGC modeling

UCSC/UCLA postdoc position

Postdoctoral Position at UC Santa Cruz

Re: boundary for biogeochemical-ecological modeling

Faculty position in Physical Oceanography at UC Santa Cruz

tiny nesting/mp_aggregate2d bug

Re: Multiprocessing and coupling

small typo in super_obs.m

Re: nitrate vertical advection versus nitrate*vertical veloc

tiny NEMURO write statement issue

Re: Possibly 3 nesting-related bugs

Re: Possibly 3 nesting-related bugs

Re: Possibly 3 nesting-related bugs

Re: Possibly 3 nesting-related bugs

Re: Possibly 3 nesting-related bugs

Possibly 3 nesting-related bugs

NEMURO bug in GraZS2ZP

small bug in lmd_test

Re: roms_matlab plotting and analysis routines

plot package: 1 possible bug and 1 question

Postdoctoral Position at UC Santa Cruz

Re: limits on netcdf sizes

limits on netcdf sizes

Re: vertical mixing story

AGU session on connectivity

Re: Problem with KPP

Postdoctoral position at UC Santa Cruz

tracer diagnostics