Search found 29 matches

by cae
Fri Aug 23, 2019 4:52 pm
Forum: ROMS Discussion
Topic: Shortwave and Longwave radiation.
Replies: 3
Views: 294

Re: Shortwave and Longwave radiation.

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 th...
by cae
Mon Jul 29, 2019 9:22 pm
Forum: Job Opportunities
Topic: UCSC/UCLA postdoc in coastal coupled physical/BGC modeling
Replies: 0
Views: 353

UCSC/UCLA postdoc in coastal coupled physical/BGC modeling

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 Po...
by cae
Fri Mar 29, 2019 12:24 am
Forum: Job Opportunities
Topic: UCSC/UCLA postdoc position
Replies: 0
Views: 552

UCSC/UCLA postdoc position

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 the Un...
by cae
Fri Dec 08, 2017 3:02 am
Forum: Job Opportunities
Topic: Postdoctoral Position at UC Santa Cruz
Replies: 0
Views: 1148

Postdoctoral Position at UC Santa Cruz

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 advan...
by cae
Wed Sep 27, 2017 6:23 am
Forum: ROMS Ecosystem
Topic: boundary for biogeochemical-ecological modeling
Replies: 5
Views: 2553

Re: boundary for biogeochemical-ecological modeling

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 eve...
by cae
Thu Nov 10, 2016 1:08 pm
Forum: Job Opportunities
Topic: Faculty position in Physical Oceanography at UC Santa Cruz
Replies: 0
Views: 2045

Faculty position in Physical Oceanography at UC Santa Cruz

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 Sciences...
by cae
Sat Oct 18, 2014 5:57 am
Forum: ROMS Bugs
Topic: tiny nesting/mp_aggregate2d bug
Replies: 1
Views: 1240

tiny nesting/mp_aggregate2d bug

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 simply USE di...
by cae
Fri Sep 26, 2014 3:19 am
Forum: ROMS Ecosystem
Topic: Multiprocessing and coupling
Replies: 2
Views: 2066

Re: Multiprocessing and coupling

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 case...
by cae
Fri May 30, 2014 4:44 am
Forum: ROMS Bugs
Topic: small typo in super_obs.m
Replies: 0
Views: 1021

small typo in super_obs.m

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,
by cae
Thu May 22, 2014 9:55 pm
Forum: ROMS Ecosystem
Topic: nitrate vertical advection versus nitrate*vertical velocity
Replies: 1
Views: 2514

Re: nitrate vertical advection versus nitrate*vertical veloc

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 thi...
by cae
Wed Jul 10, 2013 9:27 pm
Forum: ROMS Bugs
Topic: tiny NEMURO write statement issue
Replies: 0
Views: 989

tiny NEMURO write statement issue

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 phytoplankton ...
by cae
Fri Jun 21, 2013 4:14 pm
Forum: ROMS Bugs
Topic: Possibly 3 nesting-related bugs
Replies: 16
Views: 5439

Re: Possibly 3 nesting-related bugs

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: ! ! Upda...
by cae
Thu Jun 06, 2013 12:05 am
Forum: ROMS Bugs
Topic: Possibly 3 nesting-related bugs
Replies: 16
Views: 5439

Re: Possibly 3 nesting-related bugs

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. !------------...
by cae
Mon Jun 03, 2013 8:15 pm
Forum: ROMS Bugs
Topic: Possibly 3 nesting-related bugs
Replies: 16
Views: 5439

Re: Possibly 3 nesting-related bugs

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 realistic ...
by cae
Sun Jun 02, 2013 5:03 pm
Forum: ROMS Bugs
Topic: Possibly 3 nesting-related bugs
Replies: 16
Views: 5439

Re: Possibly 3 nesting-related bugs

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 not making...
by cae
Sun Jun 02, 2013 5:36 am
Forum: ROMS Bugs
Topic: Possibly 3 nesting-related bugs
Replies: 16
Views: 5439

Re: Possibly 3 nesting-related bugs

Thanks, Hernan.

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

Chris
by cae
Fri May 31, 2013 7:19 am
Forum: ROMS Bugs
Topic: Possibly 3 nesting-related bugs
Replies: 16
Views: 5439

Possibly 3 nesting-related bugs

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+3,JstrR+3...
by cae
Mon Jun 25, 2012 5:40 pm
Forum: ROMS Bugs
Topic: NEMURO bug in GraZS2ZP
Replies: 0
Views: 894

NEMURO bug in GraZS2ZP

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. ! ! Pred...
by cae
Thu May 19, 2011 5:30 pm
Forum: ROMS Bugs
Topic: small bug in lmd_test
Replies: 1
Views: 1290

small bug in lmd_test

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 END IF ...
by cae
Mon Dec 20, 2010 10:59 pm
Forum: ROMS Tools and Techniques
Topic: roms_matlab plotting and analysis routines
Replies: 88
Views: 50039

Re: roms_matlab plotting and analysis routines

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(), are ...
by cae
Thu Aug 05, 2010 7:21 am
Forum: ROMS Tools and Techniques
Topic: plot package: 1 possible bug and 1 question
Replies: 0
Views: 712

plot package: 1 possible bug and 1 question

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 integer file,...
by cae
Thu Aug 05, 2010 6:45 am
Forum: Job Opportunities
Topic: Postdoctoral Position at UC Santa Cruz
Replies: 0
Views: 1325

Postdoctoral Position at UC Santa Cruz

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 (R...
by cae
Tue Mar 30, 2010 5:32 am
Forum: ROMS Problems
Topic: limits on netcdf sizes
Replies: 7
Views: 2469

Re: limits on netcdf sizes

Thanks to both responses. I now have it writing successfully using netcdf-3.6.3.
by cae
Sun Mar 28, 2010 6:35 am
Forum: ROMS Problems
Topic: limits on netcdf sizes
Replies: 7
Views: 2469

limits on netcdf sizes

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_HIS - ...
by cae
Sat Oct 24, 2009 4:08 am
Forum: ROMS Ecosystem
Topic: vertical mixing story
Replies: 6
Views: 3853

Re: vertical mixing story

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 qu...
by cae
Wed Oct 07, 2009 3:25 am
Forum: Meetings/Workshops
Topic: AGU session on connectivity
Replies: 0
Views: 1339

AGU session on connectivity

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 is Oct....
by cae
Tue Aug 26, 2008 12:40 am
Forum: ROMS Problems
Topic: Problem with KPP
Replies: 5
Views: 1882

Re: Problem with KPP

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...
by cae
Mon Jul 07, 2008 8:15 pm
Forum: Job Opportunities
Topic: Postdoctoral position at UC Santa Cruz
Replies: 0
Views: 1623

Postdoctoral position at UC Santa Cruz

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 expl...
by cae
Mon Feb 13, 2006 6:59 pm
Forum: ROMS Problems
Topic: tracer diagnostics
Replies: 5
Views: 3500

tracer diagnostics

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 com...