Search found 559 matches

by wilkin
Mon Sep 21, 2020 11:38 am
Forum: ROMS Discussion
Topic: scorrection: freshwater flux correction
Replies: 2
Views: 434

Re: scorrection: freshwater flux correction

I believe that code is the boundary condition defined in terms of a freshwater flux given as a velocity being converted into a virtual salt flux for the purposes of imposing the vertical boundary condition on salinity. ROMS does not have a conservation equation for freshwater, only salt.
by wilkin
Sun Sep 20, 2020 3:23 pm
Forum: ROMS Discussion
Topic: Evaporation + precipitation mass conservation
Replies: 4
Views: 536

Re: Evaporation + precipitation mass conservation

I suggest you look at the code for handling river point sources in the LwSrc option. This adds the volume flux as a cell centered divergence. You obviously don't want to create Lm times Mm sources, but a few modifications to omega.F and step3d_t.F might be sufficient. If you look in omega.F at the b...
by wilkin
Tue Sep 15, 2020 11:14 am
Forum: ROMS Adjoint
Topic: How to use ECMWF product
Replies: 4
Views: 440

Re: How to use ECMWF product

The preamble comments in d_ecmwf2roms.m note that it is a "ussr modifiable script" and a "template". You have to configure this for your own purposes - several pieces of the code are examples only. % Path to downloaded ERA data files. Dir = fullfile(getenv('HOME'), ... 'ocean/repository/Projects/gom...
by wilkin
Mon Sep 14, 2020 4:10 pm
Forum: ROMS Discussion
Topic: Appropriate open boundary conditions for tidal forcing
Replies: 11
Views: 1354

Re: Appropriate open boundary conditions for tidal forcing

Guangyu, Nudging to "climatological" (some external information about the ocean) tracers (temp/salt) is common practise to control both components of thermal wind near the boundary (and suppress wave modes that might travel along the boundary). But nudging to 3-D velocity is less common, for the rea...
by wilkin
Sun Sep 13, 2020 12:49 pm
Forum: ROMS Tools and Techniques
Topic: Error in matlab codes
Replies: 5
Views: 774

Re: Error in matlab codes

That error it at the call to nc_interface. Read the help on nc_interface. Your system is having trouble figuring out the best method to read netcdf files. Are you running an old version of Matlab? Have you successfully read and written netcdf files before?
by wilkin
Thu Sep 10, 2020 11:44 am
Forum: ROMS Installation
Topic: Need help to build my application base on riverplume test case
Replies: 2
Views: 305

Re: Need help to build my application base on riverplume test case

I think you might need to define

Code: Select all

./Include/cppdefs.h:** ANA_SPFLUX              if analytical surface passive tracers fluxes      **
and though you don't mention, to turn on the tracers ...

Code: Select all

./Include/cppdefs.h:** T_PASSIVE               if inert passive tracers (dyes, etc)              **
by wilkin
Tue Sep 08, 2020 2:21 am
Forum: ROMS Discussion
Topic: Appropriate open boundary conditions for tidal forcing
Replies: 11
Views: 1354

Re: Appropriate open boundary conditions for tidal forcing

For inflows, ROMS will nudge the interior velocities to match the boundary conditions. Because the 3D velocities in the boundary conditions are from NEMO and do not have tides, I am concerned that nudging in this case will backfire because of the inconsistency between the interior 3D velocities tha...
by wilkin
Mon Sep 07, 2020 12:20 pm
Forum: ROMS Tools and Techniques
Topic: Error in matlab codes
Replies: 5
Views: 774

Re: Error in matlab codes

d_ecmwf2rom.m is adapted from code I wrote a long time ago and may not work nicely with new versions of ECMWF outputs. That said, the particular error you get indicates trouble opening a file, so you should check that it exists and that you've given the correct path. Easiest way is to set a debug st...
by wilkin
Sun Sep 06, 2020 1:34 pm
Forum: ROMS Discussion
Topic: Appropriate open boundary conditions for tidal forcing
Replies: 11
Views: 1354

Re: Appropriate open boundary conditions for tidal forcing

#define ADD_FSOBC is typically used to introduce slowly varying non-tidal sea level (e.g. from a larger domain model, or climatology) at the boundary. The TIDES are added separately. It's probably helpful to look at the code. It's easy to find that ADD_FSOBC is only active in one subroutine, set_tid...
by wilkin
Fri Sep 04, 2020 2:11 pm
Forum: ROMS Discussion
Topic: Appropriate open boundary conditions for tidal forcing
Replies: 11
Views: 1354

Re: Appropriate open boundary conditions for tidal forcing

You definitely should not use VOLCONS. Your 300 km wide domain is much smaller than the wavelength of the barotropic M2 tide (about 7000 km in 2500 m water) so the sea level should be heaving up and down almost in unison across your domain and constantly changing volume. It's fine to use 3-D radiati...
by wilkin
Thu Sep 03, 2020 2:51 pm
Forum: ROMS Discussion
Topic: swrad and lwrad not reading properly in ROMS
Replies: 6
Views: 398

Re: swrad and lwrad not reading properly in ROMS

Because I have noticed that the peak of swrad is around 18hrs in the data but it's actually supposed to be around 12hrs I am not mistaken. When you convert data that are accumulations into rates, the natural time to use would be the center of the accumulation interval. So a quantity accumulated fro...
by wilkin
Tue Aug 25, 2020 1:26 pm
Forum: ROMS Sediment
Topic: Lake_jersey test case error at first time steps
Replies: 4
Views: 312

Re: Lake_jersey test case error at first time steps

Code: Select all

 Minimum Z-grid spacing, DZmin = -3.07148846E+02 m     Water points = -5.80559302E+00 m
 Maximum Z-grid spacing, DZmax =  7.34847624E+02 m     Water points =  7.34847624E+02 m

 
You have negative vertical grid spacing. Check your bathymetry and initial zeta.
by wilkin
Fri Aug 21, 2020 3:58 pm
Forum: ROMS Discussion
Topic: River Sinks
Replies: 7
Views: 600

Re: River Sinks

The existing LtracerSrc functionality is to give the option to have selected tracer concentration data applied at all rivers, or none . If I understand what you are asking, it is to break down that choice so that you specify inflow tracer concentration for some rivers (presumably where you have thos...
by wilkin
Thu Aug 06, 2020 12:33 pm
Forum: ROMS Discussion
Topic: River Sinks
Replies: 7
Views: 600

Re: River Sinks

Did you read the description in wikiroms? https://www.myroms.org/wiki/River_Runoff I would hope if you simply followed the protocols for a reversed sign for a sink it would work. The code was originally conceived that way long, long ago, but you are in novel territory on this as a user. I did not te...
by wilkin
Tue Aug 04, 2020 1:22 pm
Forum: ROMS Discussion
Topic: Lagrangian floats
Replies: 2
Views: 391

Re: Lagrangian floats

What's the typical value of zeta (sea level). Might be something to do with depth being with respect to z=0.

Did you verify the depth was correct at initialization and then changed? Or is it starting out wrong.
by wilkin
Sun Jul 26, 2020 1:49 pm
Forum: ROMS Discussion
Topic: My boundary condition is not working.
Replies: 4
Views: 445

Re: My boundary condition is not working.

Check the log file to verify you have radiation and nudging activated for oxygen on the correct boundaries. For example, my model shows Rad+Nad on my 3 open boundaries: Lateral Boundary Conditions: NLM ============================ Variable Grid West Edge South Edge East Edge North Edge --------- ---...
by wilkin
Tue Jul 21, 2020 9:42 pm
Forum: ROMS Discussion
Topic: time-dependent bottom fluxes in roms?
Replies: 3
Views: 547

Re: time-dependent bottom fluxes in roms?

ana_btflux.h sets the bottom boundary condition to the vertical turbulent flux of tracer, like a heat flux. It has no associated volume flux of water, so it is not the same thing as using LwSrc which adds water of a given tracer concentration. It's like the difference between warming the ocean by bl...
by wilkin
Sat Jul 11, 2020 8:43 pm
Forum: ROMS Documentation
Topic: Updated LwSrc rivers documentation
Replies: 0
Views: 272

Updated LwSrc rivers documentation

Following the release of the corrected LwSrc code (see ticket https://www.myroms.org/projects/src/ticket/860)
the documentation in WikiROMS for river Runoff has been updated.
https://www.myroms.org/wiki/River_Runoff
by wilkin
Wed Jul 08, 2020 4:16 pm
Forum: Meetings/Workshops
Topic: AGU 2020: Ocean Modeling in Support of Blue Economy
Replies: 0
Views: 371

AGU 2020: Ocean Modeling in Support of Blue Economy

Dear Coastal Modellers NOAA Office of Coast Survey and its academic partners teamed up to host a session at the 2020 AGU Fall Meeting (Dec 7-11, 2020), to explore how the ocean modeling community would be able to support marine navigation and the Blue Economy. We specifically encourage oral and post...
by wilkin
Mon Jul 06, 2020 2:45 pm
Forum: ROMS Discussion
Topic: disagreement between ouput ubar and calculated values
Replies: 2
Views: 454

Re: disagreement between ouput ubar and calculated values

Remember that ROMS uses a vertically stretched s-coordinate system (set by your choice of Vtransform, Vstretching and the parameters theta_s, theta_b etc.). These determine the layer thicknesses you need to use to correctly calculate a vertical integral. The time varying sea surface height, zeta, en...
by wilkin
Thu Jun 25, 2020 7:40 am
Forum: ROMS Discussion
Topic: Budgell vs. CICE sea ice model with ROMS
Replies: 7
Views: 805

Re: Budgell vs. CICE sea ice model with ROMS

Some enhancements to the Budgell ice code are reported here: "A high-resolution coupled ice-ocean model of winter circulation on the bering sea shelf. Part I: Ice model refinements and skill assessments", by Durski and Kurapov, 2019, Ocean Modelling https://www.sciencedirect.com/science/article/pii/...
by wilkin
Wed Jun 24, 2020 2:28 pm
Forum: ROMS Adjoint
Topic: Offline Heat Budget calculations from ROMS model output
Replies: 13
Views: 8521

Re: Offline Heat Budget calculations from ROMS model output

Your plots seem to indicate the mismatch in your budgets is only at the Antarctic coast. So that does rather implicate the ice shelf as a possible issue - perhaps some term not added to the diagnostics, or that needs to be separately explicitly taken account of in your analysis. I don't follow what ...
by wilkin
Mon Jun 22, 2020 2:33 pm
Forum: ROMS Adjoint
Topic: Offline Heat Budget calculations from ROMS model output
Replies: 13
Views: 8521

Re: Offline Heat Budget calculations from ROMS model output

temp_rate = temp_hadv + temp_vadv + temp_vdiff + temp_hdiff + shflux You shouldn't have shflux here because it was applied as the surface boundary condition to temp_vdiff and so is already included in the vertical divergence d/dz*(K_v*dT/dz) (i.e. shflux/(Cp*rho0) = K_v(dT/dz at z = zeta; notice th...
by wilkin
Wed Jun 17, 2020 12:03 pm
Forum: ROMS Discussion
Topic: Boundary condition problems
Replies: 4
Views: 412

Re: Boundary condition problems

The Shchepetkin boundary conditions needs ubar and vbar so you have to provide them in the boundary conditions file. If you have u,v and are using the myroms Matlab tools then the function uv_barotropic.m will do the calculation. It can work on both boundary and initial conditions files.
by wilkin
Tue Jun 16, 2020 1:50 pm
Forum: ROMS Usage
Topic: How do I input my own netCDF grid file for the ROMS Upwelling test case?
Replies: 10
Views: 874

Re: How do I input my own netCDF grid file for the ROMS Upwelling test case?

ROMS computes on all points, even the land, and then masks the result afterward. So you can't have h < 0 anywhere - including in the land. There are many places where terms in the ROMS equations involve a division by zeta+h, so if this is zero or close to it then there's your problem. Where you have...
by wilkin
Mon Jun 15, 2020 1:34 pm
Forum: ROMS Discussion
Topic: BODYFORCE-transform acceleration to stress
Replies: 2
Views: 353

Re: BODYFORCE-transform acceleration to stress

There is a different approach to imposing an effective horizontal acceleration that is uniform throughout the vertical water column. This is to introduce a horizontal gradient in the air pressure (e.g. within ana_pair.h) and impose this force via #define ATM_PRESS. I use this method to impose a time...
by wilkin
Mon Jun 15, 2020 1:09 pm
Forum: ROMS Usage
Topic: BLOWING UP during nesting
Replies: 11
Views: 1842

Re: BLOWING UP during nesting

When updating your source code remember you may need to update the roms.in (ocean.in). New options may have been introduced to manage file input/output that your old set-up does not have. It is not difficult to diff your input script with the trunk version it was based on to highlight possible missi...
by wilkin
Sun Jun 14, 2020 4:27 pm
Forum: ROMS Discussion
Topic: the defination of density rho
Replies: 16
Views: 1451

Re: the defination of density rho

I see your point. Then you might have to code some workaround, like ... # if !defined BODYFORCE ! the original code ... DO i=Istr,Iend cff=om_v(i,j)*on_v(i,j) cff1= svstr(i,j)*cff cff2=-bvstr(i,j)*cff rvfrc(i,j)=rvfrc(i,j)+cff1+cff2 ... #else ! the code you want, whatever that is ... But before you ...
by wilkin
Sat Jun 13, 2020 2:14 pm
Forum: ROMS Discussion
Topic: the defination of density rho
Replies: 16
Views: 1451

Re: the defination of density rho

Code: Select all

    cff1= 0.0_r8
    cff2= 0.0_r8
    rufrc(i,j)=rufrc(i,j)+cff1+cff2
I can't find that code anywhere in my version of rhs3d.F.
by wilkin
Thu Jun 11, 2020 1:52 pm
Forum: ROMS Discussion
Topic: the defination of density rho
Replies: 16
Views: 1451

Re: the defination of density rho

(But I modify sbstr code, I don't want to transform it to bodyforce, it is still used in 2d equation), as shown below: All you need to do to prevent the bottom stress also being applied as a bodyforce is make LEVBFRC = 0 in roms.in: !-----------------------------------------------------------------...
by wilkin
Wed Jun 10, 2020 11:45 am
Forum: ROMS Usage
Topic: How do I input my own netCDF grid file for the ROMS Upwelling test case?
Replies: 10
Views: 874

Re: How do I input my own netCDF grid file for the ROMS Upwelling test case?

When ROMS runs it writes the grid information to the output netcdf files. Everything is in there to actually use the history file as a grid file. So test this out. Run UPWELLING with the ana_grid option for a brief simulation. Then #undef ANA_GRID and instead point GRDNAME to the history file. Does ...
by wilkin
Wed Jun 10, 2020 11:39 am
Forum: ROMS Discussion
Topic: the defination of density rho
Replies: 16
Views: 1451

Re: the defination of density rho

It seems that the forcing term ru on the right hand side of the equation euqals τ*A*Hz/Wrk,which has a force (N) dimension (Pa*m2*m/m). No, at this point in the code sustr is a kinematic stress tao/rho0 and has units m2/s2. It is not Pascals. See in bulk_flux.F and ana_smflux.h that Tau gets divide...
by wilkin
Tue Jun 09, 2020 4:20 pm
Forum: ROMS Discussion
Topic: the defination of density rho
Replies: 16
Views: 1451

Re: the defination of density rho

Where ROMS expresses anything in kinematic units (per unit mass), such as converting stress to friction velocity (tau/rho0), or heat flux (W/m2) to degrees meters/s (Hf/(Cp*rho0) in the surface temperature boundary condition, it always uses the constant parameter rho0. Likewise, to calculate Brunt-V...
by wilkin
Sun May 24, 2020 12:59 pm
Forum: ROMS Discussion
Topic: roms river LwSrc problem
Replies: 8
Views: 2658

Re: roms river LwSrc problem

I have corrected code that passes my simple tests for all tracer advection schemes. Contact me if you want to test it in advance or its addition to the public code.
by wilkin
Wed Apr 29, 2020 11:36 am
Forum: ROMS Discussion
Topic: Why ROMS does not read the provided swflux?
Replies: 2
Views: 385

Re: Why ROMS does not read the provided swflux?

# if defined NL_BULK_FLUXES && !defined BULK_FLUXES (read EminusP) # elif !(defined ANA_SSFLUX || defined FRC_COUPLING || \ defined EMINUSP || defined SRELAXATION) (read swflux) # endif || is a logical "OR", and since defined SRELAXATION is "TRUE" the expression in () is TRUE, and the "!" is a logi...
by wilkin
Thu Apr 23, 2020 1:22 pm
Forum: ROMS Discussion
Topic: tidal phase mismatch between ADCP data and ROMS output
Replies: 4
Views: 775

Re: tidal phase mismatch between ADCP data and ROMS output

I am very surprised that TPXO currents would be so out of agreement with an open ocean current meter time series. Are you sure you have the correct time base for both, and that you are interpreting phase correctly?
by wilkin
Tue Apr 21, 2020 12:28 pm
Forum: ROMS Discussion
Topic: tidal phase mismatch between ADCP data and ROMS output
Replies: 4
Views: 775

Re: tidal phase mismatch between ADCP data and ROMS output

Did you try computing the tidal harmonics from the data directly and comparing them to TPXO? This to take ROMS out of the loop and be sure you've got the correct interpretation of phase for both data sets.
by wilkin
Mon Apr 20, 2020 9:06 pm
Forum: ROMS Discussion
Topic: Computing advection using 'utemp' vs 'temp_xadv'
Replies: 4
Views: 547

Re: Computing advection using 'utemp' vs 'temp_xadv'

HuonT is dimensioned (i,j,k). It still has k dependence. It's just that it has already been multiplied by the elemental layer thickness "Hz" prior to time averaging, but it is not summed over k. That's why it has units m^3*tracer/s, not m^2*tracer/s The vertical integral of HuonT is just the sum k=1...
by wilkin
Mon Apr 20, 2020 1:46 pm
Forum: ROMS Discussion
Topic: Computing advection using 'utemp' vs 'temp_xadv'
Replies: 4
Views: 547

Re: Computing advection using 'utemp' vs 'temp_xadv'

No, these things won't be exactly the same. The _xadv and _yadv terms (and their divergence which is already saved for you in the companion _hadv diagnostics) are the fluxes through the faces (time averaged) exactly as ROMS computed them according to the selected advection scheme. In the case of the...
by wilkin
Tue Mar 31, 2020 3:04 pm
Forum: ROMS Discussion
Topic: Question about radiation boundary condition
Replies: 7
Views: 734

Re: Question about radiation boundary condition

Yes, Perkins et al. (1997) choose to radiate "Q_inner minus Q_outer" in their nested model application, but this is not what Marchesiello et al. (2001) do and it is not implemented in ROMS. Radiating the difference between model and climatology - as opposed to the difference in nested grids as in Pe...
by wilkin
Mon Mar 30, 2020 7:45 pm
Forum: ROMS Discussion
Topic: Question about radiation boundary condition
Replies: 7
Views: 734

Re: Question about radiation boundary condition

...the authors mention that only the difference between model and climatology is radiated out at the open boundaries. Where do you see this in Marchesiello et al (2001)? My reading of it says the radiation calculation is based on the prognostic variables u,v,T,S separately, and the active/passive d...
by wilkin
Wed Mar 25, 2020 12:09 pm
Forum: ROMS Discussion
Topic: Artificially strong surface velocities (BODYFORCE?)
Replies: 5
Views: 683

Re: Artificially strong surface velocities (BODYFORCE?)

It's not obvious to me why you would be getting that surface shear effect, and quickly looking at the BODYFORCE code I don't see any problems with the k indexing. Maybe try stripping out a lot of the options you have that you don't need. In particular, MIX_GEO_UV (and MIX_GEO_TS) - you have no densi...
by wilkin
Tue Mar 24, 2020 11:40 am
Forum: ROMS Discussion
Topic: Artificially strong surface velocities (BODYFORCE?)
Replies: 5
Views: 683

Re: Artificially strong surface velocities (BODYFORCE?)

What do you have for LEVBFRC?
by wilkin
Fri Mar 13, 2020 8:52 am
Forum: ROMS Usage
Topic: Confusion with d_nudgcoef.m script
Replies: 2
Views: 520

Re: Confusion with d_nudgcoef.m script

Does this mean that if I want to apply spatially varying nudging coefficients, I have to provide the boundary conditions as a climatology file instead (specified by CLMNAME)? Yes, if you want to use 3-D nudging to help constrain the solution near to the boundary then you must have a 3-D file of val...
by wilkin
Tue Mar 03, 2020 12:31 pm
Forum: ROMS Discussion
Topic: Inundation Blowing Up
Replies: 2
Views: 399

Re: Inundation Blowing Up

Your log file shows you have set "nested" open boundary conditions for some variables but you have only one grid. You have also mixed "gradient" and "closed" along the same boundary, so that can't be right. Your initial conditions show a starting ubar and vbar of 4.5 and 5.7 m/s which is very fast s...
by wilkin
Sun Mar 01, 2020 9:34 pm
Forum: ROMS Source
Topic: Typo in roms.in following overhaul of advection schemes
Replies: 4
Views: 732

Re: Typo in roms.in following overhaul of advection schemes

Well this is something that needs some testing and experimentation. In our model "Doppio" for the Mid-Atlantic Bight and Gulf of Maine we know that the MPDATA scheme tends to foster a poor separation of the Gulf Stream. The 3rd-order upwind (U3) or 4th-order Akima (A4) schemes give better performanc...
by wilkin
Sat Feb 22, 2020 2:09 pm
Forum: ROMS Bugs
Topic: WET_DRY and Gridbuilder Problem
Replies: 21
Views: 2195

Re: WET_DRY and Gridbuilder Problem

Keep in mind that the rx0 value is guidance only with respect to bathymetry steepness than might introduce truncation errors in the baroclinic pressure gradient. In shallow tidal flats that wet and dry it is unlikely you will see sufficiently large vertical stratification to introduce baroclinicity ...
by wilkin
Sun Feb 02, 2020 2:03 pm
Forum: ROMS Problems
Topic: A ROMS nesting question
Replies: 10
Views: 1318

Re: A ROMS nesting question

I don't think your problem is with nesting. The logfile info you show ... 1257 GET_2DFLD - surface u-wind component, 2013-01-01 00:00:00.00 1258 ( Grid=01 , Rec=0000001, Index=1, File: nwgom_frc_2013.nc) 1259 (Tmin= 15706.0000 Tmax= 16101.9583) t = 15706.0000 1260 ( Min = 1.00000000E+35 Max = -1.000...
by wilkin
Wed Jan 01, 2020 4:31 pm
Forum: ROMS Source
Topic: passive tracer: decay term added but not working
Replies: 2
Views: 524

Re: passive tracer: decay term added but not working

Check your step3d_t.f90 in Build. The first DO and its closing ENDDO begin in column 6 which compilers should interpret as a continuation. But if that were so you would get an error. But check that you got what you intended. As written, your RHS term is positive and is a source, not a decay (you mul...
by wilkin
Thu Dec 05, 2019 12:31 pm
Forum: ROMS Discussion
Topic: doubts about BULK_FLUX
Replies: 3
Views: 497

Re: doubts about BULK_FLUX

You can #define ANA_PAIR and ROMS will go to your code in Functionals/ana_pair.h where you can set a default constant value. It will read all others from the file - which is the default if no 'ANA' is defined. At runtime you should see the variables it reads from your netcdf file, but not get an err...
by wilkin
Fri Nov 15, 2019 3:01 pm
Forum: ROMS Discussion
Topic: Is it a must to use VolCons if RadNud activated?
Replies: 8
Views: 981

Re: Is it a must to use VolCons if RadNud activated?

Look at the log file report on the grid ... ANA_GRID - bathymetry at RHO-points: h (Grid = 01, Min = 0.00000000E+00 Max = 0.00000000E+00) The water depth is zero everywhere! Which explains why the vertical grid spacing is zero ... Metrics information for Grid 01: =============================== ... ...
by wilkin
Wed Nov 13, 2019 2:50 pm
Forum: ROMS Problems
Topic: Nudging time scales for RadNud boundaries
Replies: 4
Views: 933

Re: Nudging time scales for RadNud boundaries

Running a recursive grep query for Tobc_in will guide you to where open boundary nudging time scales are set. In subroutine inp_par.F you find ... DO itrc=1,NT(ng) IF (LBC(ibry,isTvar(itrc),ng)%nudging) THEN Tobc_out(itrc,ng,ibry)=Tnudg(itrc,ng) Tobc_in (itrc,ng,ibry)=obcfac(ng)*Tnudg(itrc,ng) END I...
by wilkin
Tue Nov 12, 2019 11:56 am
Forum: ROMS Discussion
Topic: Is it a must to use VolCons if RadNud activated?
Replies: 8
Views: 981

Re: Is it a must to use VolCons if RadNud activated?

You can't mix Periodic and Closed on the same boundary for different variables. Lateral Boundary Conditions: NLM ============================ Variable Grid West Edge South Edge East Edge North Edge --------- ---- ---------- ---------- ---------- ---------- zeta 1 Closed Chapman Imp Chapman Imp Chapm...
by wilkin
Wed Oct 23, 2019 7:01 pm
Forum: ROMS Source
Topic: Huon_eastward and Hvom_northward
Replies: 9
Views: 1086

Re: Huon_eastward and Hvom_northward

Kate's point is quite correct. If you want to accurately compute volume flux through an arbitrary section you shouldn't separately rotate and interpolating the velocity components and grid metrics. The zig-zag path in the post Kate directs you to i(step [13]) illustrates the exact flux between two p...
by wilkin
Tue Oct 22, 2019 1:00 pm
Forum: ROMS Source
Topic: Huon_eastward and Hvom_northward
Replies: 9
Views: 1086

Re: Huon_eastward and Hvom_northward

The volume transport is the *sum* of Huon (in m^2/s) over the k index (that's the vertical integral) divided by pm (i.e. times dy). That gives you m^3/s. The "H" in Huon is really Hz which is what we call the elemental cell layer thickness. Alternatively, for your purposes, calculate ubar times (h+z...
by wilkin
Tue Oct 22, 2019 10:32 am
Forum: ROMS Source
Topic: Huon_eastward and Hvom_northward
Replies: 9
Views: 1086

Re: Huon_eastward and Hvom_northward

Huon and Hvom are defined at u and v points (cell faces) respectively. They are cell face average transports such that the time varying dz due to the time dependent s-coordinate is fully accounted for in the time average. The vertical *sum* of Huon is the vertical *integral* of u dz. They, and espec...
by wilkin
Sun Sep 29, 2019 4:44 pm
Forum: ROMS Problems
Topic: Problem reading input files
Replies: 1
Views: 488

Re: Problem reading input files

ROMS usually reads meteorology surface forcing after rivers and before boundaries. Is this skipped in your case because of the idealized config? Can you force ROMS to confirm it has opened the boundary file, say by giving in the wrong name in roms.in to trigger a 'file not found'. That was you know ...
by wilkin
Thu Sep 12, 2019 2:02 pm
Forum: ROMS Bugs
Topic: DIAG speed trouble / gridbuilder
Replies: 3
Views: 668

Re: DIAG speed trouble / gridbuilder

With a minimum grid cell size of ~4 km you should be well within CFL stability with such a small time step, so that's not your problem. The log indicates a 3rd record was written to the restart file on blow-up, so you should plot what's in there and look for a location that is causing trouble. It co...
by wilkin
Sat Sep 07, 2019 11:58 am
Forum: ROMS Discussion
Topic: The xi_position and eta_position of rivers.nc input
Replies: 4
Views: 544

Re: The xi_position and eta_position of rivers.nc input

There is a detailed explanation of the conventions for specifying river sources here in WikiROMS:

https://www.myroms.org/wiki/River_Runof ... _Eposition
by wilkin
Wed Aug 28, 2019 10:55 pm
Forum: ROMS Discussion
Topic: Lagrangian Drifters stick to the boundary.
Replies: 4
Views: 590

Re: Lagrangian Drifters stick to the boundary.

Are the sticky floats always stuck? i.e. did they move at all? It's hard to tell for sure from the images you posted, but I get a sense that many of the stuck floats are in one-cell wide bays or corners, and it is very hard to generate a flow inside a one-cell wide bay that will move a float out of ...
by wilkin
Wed Aug 28, 2019 6:40 am
Forum: ROMS Discussion
Topic: Lagrangian Drifters stick to the boundary.
Replies: 4
Views: 590

Re: Lagrangian Drifters stick to the boundary.

Are you using the online #define FLOATS option in ROMS, or doing the particle tracking yourself from archived ROMS model output?
by wilkin
Fri Aug 23, 2019 11:22 am
Forum: ROMS Discussion
Topic: Shortwave and Longwave radiation.
Replies: 3
Views: 651

Re: Shortwave and Longwave radiation.

Yes, you need to subtract 'Upward Solar Radiation flux' from 'Downward solar radiation flux' to get net shortwave radiation. For longwave you have two options and you can prepare for both. When using #define BULK_FLUXES the default is to read net longwave radiation from variable lwrad (the name that...
by wilkin
Wed Aug 14, 2019 1:59 pm
Forum: ROMS Sediment
Topic: Calculating sediment flux across transect
Replies: 4
Views: 1067

Re: Calculating sediment flux across transect

The Huon_* quantities are defined on cell faces, i.e. respective u or v faces, because this is the way ROMS does fluxes internally. The divergence in "x" of fluxes on two neighboring "u" faces gives the cell centered "rho" (or "sand") point flux. So following a wiggly path of u and v faces will give...
by wilkin
Sat Aug 03, 2019 1:00 pm
Forum: ROMS Problems
Topic: Error using loaddap
Replies: 1
Views: 446

Re: Error using loaddap

loaddap.m is very old contributed code to Matlab.

These days the Matlab ncread and related functions will read OPeNDAP data directly. You don't need to use loaddap. Whatever software you were given to read SODA output you need to update or find something else newer to do the task.
by wilkin
Fri Aug 02, 2019 1:28 am
Forum: ROMS Discussion
Topic: Question about tidal forcing in the nesting application
Replies: 5
Views: 702

Re: Question about tidal forcing in the nesting application

Update your code. Those boundary condition #define(s) have been superseded by logical switches in ocean.in.
by wilkin
Thu Aug 01, 2019 6:54 pm
Forum: ROMS Discussion
Topic: Question about tidal forcing in the nesting application
Replies: 5
Views: 702

Re: Question about tidal forcing in the nesting application

If indeed the TIDENAME is where it is supposed to be ...
! Input tidal forcing file name.
TIDENAME == ../Data/my_test_tides_a.nc
then the message ...
NETCDF_OPEN - unable to open existing NetCDF file:
my_test_tides_a.nc
presumably means the permissions on the file are denying read access.
by wilkin
Thu Aug 01, 2019 3:15 pm
Forum: ROMS Problems
Topic: ROMS different src version leading to unalike results
Replies: 7
Views: 1284

Re: ROMS different src version leading to unalike results

The rotation of the mixing tensor to "isopycnal" coordinates should really be done with respect to the slope of potential density surfaces referenced to the local depth, not the sea surface. I checked on this yesterday with Trevor McDougall, just to be sure. So neither option (not in-situ density or...
by wilkin
Thu Aug 01, 2019 2:17 pm
Forum: ROMS Discussion
Topic: Question about tidal forcing in the nesting application
Replies: 5
Views: 702

Re: Question about tidal forcing in the nesting application

NETCDF_OPEN - unable to open existing NetCDF file: my_test_tides_a.nc This suggests ROMS did not find your tides file. The path to the file that you specified in ocean.in (or roms.in these days) may be incorrect or, if it is a relative path, not consistent with the directory in which you are runnin...
by wilkin
Thu Jul 18, 2019 2:01 pm
Forum: ROMS Problems
Topic: ROMS different src version leading to unalike results
Replies: 7
Views: 1284

Re: ROMS different src version leading to unalike results

There are a lot of changes since version 783 (3 or more years ago?) so it is going to be tedious to track down. As Kate suggests, you can do intermediate updates to successively newer versions and see when changes in your solution arise. This will be a bit messy because you may need to thoughtfully ...
by wilkin
Sat Jun 29, 2019 8:26 pm
Forum: ROMS Discussion
Topic: Alongshore currents with periodic alongshore boundaries
Replies: 9
Views: 1370

Re: Alongshore currents with periodic alongshore boundaries

I described a way to do this in an old forum post https://www.myroms.org/forum/viewtopic.php?f=1&t=2412 If you #define ATM_PRESS and introduce a linearly varying along-channel air pressure gradient (using ana_pair.h for example), then the pressure gradient calculation will convert this grad(p) into ...
by wilkin
Wed Jun 26, 2019 4:55 am
Forum: ROMS Discussion
Topic: ROMS 1D for Mac needed
Replies: 2
Views: 494

Re: ROMS 1D for Mac needed

See the test case BIO_TOY.

External/roms_bio_toy.in
Include/bio_toy.h

This is a 4x4 doubly-periodic set-up which degenerates to a horizontally uniform solution.

Just #undef BIO_FENNEL to turn off the biology.

build.sh should take care of compiling on MacOS if you configure it correctly.
by wilkin
Wed Jun 12, 2019 10:47 am
Forum: ROMS Discussion
Topic: Time type in nc file
Replies: 5
Views: 759

Re: Time type in nc file

I extracted the zeta variable to compare to the published tidal constituents from NOAA stations in the Gulf of Maine. ...
Whose ROMS model output did you analyze?
by wilkin
Thu Jun 06, 2019 8:14 pm
Forum: ROMS Problems
Topic: NESTING RUNTIME ERROR code 59
Replies: 5
Views: 814

Re: NESTING RUNTIME ERROR code 59

The error ... forrtl: severe (59): list-directed I/O syntax error, unit -5, file Internal List-Directed Read ... indicates a problem reading the ocean.in file. Make sure you are executing the program correctly: mpirun ... ocean.in not mpirun ... < ocean.in Check that the syntax in ocean.in is correc...
by wilkin
Fri May 24, 2019 6:56 am
Forum: ROMS Discussion
Topic: ad passive tracer
Replies: 10
Views: 1346

Re: ad passive tracer

Your roms_upwelling.in has 4 passive tracers, not one. You have set NPT=4. Your roms_upwelling.in has also set "closed" as the options for open boundary conditions on passive tracers: LBC(isTvar) == Per Clo Per Clo \ ! temperature Per Clo Per Clo \ Clo Clo Clo Clo \ Clo Clo Clo Clo \ Clo Clo Clo Clo...
by wilkin
Sun May 12, 2019 1:06 pm
Forum: ROMS Problems
Topic: Segmentation fault with floats
Replies: 6
Views: 1020

Re: Segmentation fault with floats

When does the seg fault occur?

At model initialization, at first float release, or midway in the run?
by wilkin
Sat May 11, 2019 12:47 pm
Forum: ROMS Installation
Topic: benchmark case compile problem
Replies: 3
Views: 673

Re: benchmark case compile problem

Delete the oceanM you have and redo the build.

Watch the output to screen during the build process - there is a lot of information there about what ROMS is actually doing as opposed to watch you thought you'd asked for.
by wilkin
Thu May 02, 2019 3:54 pm
Forum: ROMS Discussion
Topic: COARE 3.5 bulk flux parameterizations
Replies: 0
Views: 552

COARE 3.5 bulk flux parameterizations

Has anyone written a new bulk_flux.F for COARE3.5 Edson et al.,2013? Edson, J.B., V. Jampana, R.A. Weller, S.P. Bigorre, A.J. Plueddemann, C.W. Fairall, S.D. Miller, L. Mahrt, D. Vickers, and H. Hersbach, 2013: On the Exchange of Momentum over the Open Ocean. J. Phys. Oceanogr., 43, 1589–1610, https...
by wilkin
Thu May 02, 2019 1:28 pm
Forum: ROMS Discussion
Topic: cppdefs for BULK_FLUX
Replies: 11
Views: 1845

Re: cppdefs for BULK_FLUX

My task is to simulate sea level height in future 50 or 100 years. First, simulating the climatology condition for my study area until model is stable. ... Second, simulating the history period forced by CMIP5 history output data. ... Third, simulating the future condition based on CMIP5 future out...
by wilkin
Wed Apr 24, 2019 12:56 am
Forum: ROMS Problems
Topic: roms preprocessing tools (d_mercator2roms.m)
Replies: 4
Views: 1042

Re: roms preprocessing tools (d_mercator2roms.m)

Thank you for your replies. Isn't it has similar data format? Similar, yes, but the script is expecting certain names and conventions for the coordinates and dimensions. Code doesn't do similar . By the way, I interpolated the WOA data (1 x 1 degree) to my grid (5 x 5 km), which might be the proble...
by wilkin
Tue Apr 23, 2019 10:54 am
Forum: ROMS Problems
Topic: roms preprocessing tools (d_mercator2roms.m)
Replies: 4
Views: 1042

Re: roms preprocessing tools (d_mercator2roms.m)

Looks to me like you're using a World Ocean Atlas climatology as input.

Code: Select all

Tfile   = 'woa18_ann_temp.nc';
Sfile   = 'woa18_ann_salt.nc';
This script is designed to process Mercator-Océan data from Copernicus.eu.
by wilkin
Tue Apr 16, 2019 1:15 pm
Forum: ROMS Discussion
Topic: CF compliant units attributes in Varinfo.dat
Replies: 7
Views: 1232

Re: CF compliant units attributes in Varinfo.dat

Do not separate the units "seconds" from the reference date. Read the CF Conventions standard:

http://cfconventions.org/cf-conventions ... coordinate
by wilkin
Fri Mar 15, 2019 11:34 am
Forum: ROMS Discussion
Topic: parameter hc and Tcline
Replies: 2
Views: 689

Re: parameter hc and Tcline

The parameters Tcline and hc are explained here:
https://www.myroms.org/wiki/Vertical_S-coordinate

The page concludes with some example stretching generated with scoord.m which is in the Matlab repository available on myroms.org.
by wilkin
Fri Mar 08, 2019 10:55 am
Forum: ROMS Usage
Topic: BLOWING UP during nesting
Replies: 11
Views: 1842

Re: BLOWING UP during nesting

Metrics information for Grid 02:
===============================

...
Minimum Z-grid spacing, DZmin = -2.33860479E-01 m
Maximum Z-grid spacing, DZmax = 9.27954758E+35 m
You have negative depths.
by wilkin
Thu Mar 07, 2019 2:01 am
Forum: ROMS Bugs
Topic: A small bug in ana_srflux.h
Replies: 12
Views: 4548

Re: A small bug in ana_srflux.h

Can you clarify which lines you are referring to in which version of the code: For me the division by 15.0 on line 176 is a definite bug: 1) It breaks periodicity over 360 degrees change in lonr 2) It is inconsistent with lines 205 and 213 They don't align with the version of ana_srflux.h I'm lookin...
by wilkin
Wed Feb 27, 2019 12:40 pm
Forum: ROMS Problems
Topic: Shortwave radiation and net surface heat flux inconsistency
Replies: 6
Views: 1556

Re: Shortwave radiation and net surface heat flux inconsiste

COAWST handles the humidity slightly differently (in ana_srflux.h): # ifdef SPECIFIC_HUMIDITY ! With this directive specific humidity is input as kg/kg vap_p=Pair(i,j)*Hair(i,j)/(0.62197_r8+0.378_r8*Hair(i,j)) # else vap_p=e_sat*Hair(i,j) ! water vapor pressure (hPa=mbar) # endif and in bulk_flux.F:...
by wilkin
Fri Feb 15, 2019 4:32 pm
Forum: ROMS Discussion
Topic: Calculation of Geostrophic Current
Replies: 2
Views: 1209

Re: Calculation of Geostrophic Current

That is a script designed to do what it says in the help: % Compute u,v geostrophic from a standard level t,s,ssh climatology It does not operate on ROMS output. If it were a function designed specifically for ROMS I would have called it roms_(something).m. There has never been an "old version of RO...
by wilkin
Mon Feb 11, 2019 2:31 pm
Forum: ROMS Tools and Techniques
Topic: Soundspeed for ROMS output
Replies: 4
Views: 1070

Re: Soundspeed for ROMS output

There is also code in the CSIRO seawater toolbox for Matlab (function sw_svel) though seawater has been superseded by the Gibbs SeaWater (GSW) toolbox for TEOS-10
http://www.teos-10.org/pubs/gsw/html/gsw_contents.html
and in there it is function gsw_sound_speed
by wilkin
Mon Feb 04, 2019 11:29 am
Forum: ROMS Discussion
Topic: z level
Replies: 5
Views: 2116

Re: z level

If you click on that very old http://romsmatlab.tiddlyspot.com link you need to click on Download which opens up the entry: As of 7 Apr 2008 I now manage changes to the Matlab functions documented here using svn (SubVersion) for version control. There is some help on using Subversion on the ROMS Wik...
by wilkin
Sun Jan 27, 2019 11:20 pm
Forum: ROMS Source
Topic: My ROMS
Replies: 9
Views: 4053

Re: My ROMS

The CPP flag should be more explicit that this is solely a modification to the open boundary data, like ADD_IB_TO_OBC_ZETA (!). Since it requires Pair, which is typically only loaded for BULK_FLUXES, it might need some trickery in globaldefs and get_data.F to load Pair in the event that BULK_FLUXES ...
by wilkin
Wed Jan 23, 2019 2:38 pm
Forum: ROMS Discussion
Topic: Weights in VSHAPE and layers thickness?
Replies: 6
Views: 2270

Re: Weights in VSHAPE and layers thickness?

Parker, In WikiROMS at https://www.myroms.org/wiki/Vertical_S-coordinate there is a note to the effect that the coordinate tends to a uniform σ coordinate in shallow water: Transformation (2) has been available in UCLA-ROMS since 2005. It is activated by setting Vtransform = 2 in ocean.in. Notice th...
by wilkin
Wed Dec 12, 2018 12:13 pm
Forum: ROMS Documentation
Topic: About the case LATTE
Replies: 2
Views: 1280

Re: About the case LATTE

That's a 10-year old test case that has not been updated ...
https://www.myroms.org/wiki/ROMS_UNSW2008
You can probably find a better starting point for your project.
by wilkin
Sat Dec 08, 2018 2:07 am
Forum: ROMS Discussion
Topic: Virtual salt flux sea surface boundary condition
Replies: 4
Views: 1663

Re: Virtual salt flux sea surface boundary condition

By no means am I an expert in air-sea radiative transfer, so I can't give you an authoritative answer. I don't understand the Dickey et al. (1994) eqn. (15) at all. Why should there be a contribution to upwelling longwave radiation that scales with downwelling longwave according to emmisivity ? It's...
by wilkin
Fri Dec 07, 2018 6:27 pm
Forum: ROMS Discussion
Topic: Virtual salt flux sea surface boundary condition
Replies: 4
Views: 1663

Re: Virtual salt flux sea surface boundary condition

Parker, If using BULK_FLUXES without EMINUSP the rain data will not be used in the salt flux. You will see that stdout reports the rain data were read - which may mislead you into thinking that rain is used somehow in the salt flux condition. It is not. Bulk fluxes uses rain in the momentum flux - t...
by wilkin
Wed Dec 05, 2018 4:52 am
Forum: ROMS Discussion
Topic: magnitude of viscosities used in GOFS and RELO
Replies: 1
Views: 675

Re: magnitude of viscosities used in GOFS and RELO

There is a HYCOM google group and forum. https://groups.google.com/a/hycom.org/f ... orum/forum

You might read the documentation there and post a query.
by wilkin
Fri Nov 30, 2018 9:41 pm
Forum: ROMS Usage
Topic: Accessing forcing data from NCEP NOMADS
Replies: 1
Views: 856

Accessing forcing data from NCEP NOMADS

Just a heads-up ... for those of you who use the NCEP NOMADS server http://nomads.ncep.noaa.gov to access NAM, GFS etc. meteorology and other data. NOAA is migrating all HTTP traffic from HTTP to HTTPS. Beginning Dec 3, 2018, all HTTPS URLs will be available alongside HTTP. Starting on December 7, 2...
by wilkin
Fri Nov 30, 2018 11:32 am
Forum: ROMS Problems
Topic: 'nfast' and 'ndtfast' on Barotropic time step
Replies: 5
Views: 1505

Re: 'nfast' and 'ndtfast' on Barotropic time step

Read this explanation on WikiROMS:
https://www.myroms.org/wiki/Numerical_S ... g_Overview
and the Shchepetkin papers.
by wilkin
Wed Nov 28, 2018 12:34 pm
Forum: ROMS Documentation
Topic: SeaGrid Tutorial Link dead
Replies: 1
Views: 967

Re: SeaGrid Tutorial Link dead

You'd probably be better off using GridBuilder (see the last post at viewtopic.php?f=23&t=3839&p=17148&hilit ... der#p17148) than Seagrid.
by wilkin
Wed Nov 07, 2018 12:32 pm
Forum: ROMS Problems
Topic: Transport adjustment on the boundary
Replies: 6
Views: 1477

Re: Transport adjustment on the boundary

I'm not clear on why you are checking volume conservation in ROMS - I'm pretty sure we've had that working correctly for the last 10 years! So really you're checking your own code and logic. You had a post earlier about using Huon etc to compute transport, and you said you vertically integrated thes...
by wilkin
Thu Nov 01, 2018 2:49 pm
Forum: ROMS Usage
Topic: How to generate contact netcdf?
Replies: 7
Views: 1729

Re: How to generate contact netcdf?

Problems we have seen with other users starting from old grids is that the parent grid is missing the psi points coordinates. You may need to add the psi points if they are absent because the grid subsetting is defined in terms of the psi-points corners. If you need a Matlab function to compute the ...
by wilkin
Mon Oct 08, 2018 3:45 pm
Forum: ROMS Problems
Topic: Error reading wetdry mask at psi points
Replies: 8
Views: 1459

Re: Error reading wetdry mask at psi points

Does you varinfo.dat have the metadata for the psi points wet/dry mask? Line 270 of def_his.f90 will be pretty close to the step defining the mask, for which it needs the Vinfo data leaded fro varinfo.dat. Generally speaking, just switching in a subroutine (here get_wetdry.F) from another repository...
by wilkin
Sat Oct 06, 2018 3:53 pm
Forum: ROMS Problems
Topic: Error reading wetdry mask at psi points
Replies: 8
Views: 1459

Re: Error reading wetdry mask at psi points

I don't think the problem is in GET_WETDRY because the message to the log file that it read the V-points mask indicates it ran past reading the psi-ponts mask and went on to DEF_HIS. So the error is in DEF_HIS or a subsequent WRT_HIS. This a 2D horizontal configuration and I have no experience with ...
by wilkin
Sat Oct 06, 2018 12:13 pm
Forum: ROMS Problems
Topic: Error reading wetdry mask at psi points
Replies: 8
Views: 1459

Re: Error reading wetdry mask at psi points

Kate ... This is your branch of code - can you help? There is no revision number in the previous version log.
by wilkin
Mon Oct 01, 2018 2:25 pm
Forum: ROMS Discussion
Topic: Parameter Theta s and theta b don't work
Replies: 2
Views: 846

Re: Parameter Theta s and theta b don't work

s_rho is not the final dimensional vertical coordinate. s_rho depends on the choice of TRANSFORM and the final z depths depend on the STRETCHING applied to s_rho. Read https://www.myroms.org/wiki/Vertical_S-coordinate There are Matlab and Python routines to compute z offline from the Vtransform, Vst...
by wilkin
Tue Sep 25, 2018 3:26 pm
Forum: ROMS Discussion
Topic: ROMS history file has suddenly included restart record
Replies: 7
Views: 1435

Re: ROMS history file has suddenly included restart record

There have been some changes to the time handling that might have altered the model behavior, e.g.: https://www.myroms.org/projects/src/ticket/778 But the changes were to make ROMS behave more according to how it is supposed to. Read the GLOSSARY at the end of ocean.in for a description of how NRREC...
by wilkin
Sun Sep 23, 2018 1:41 pm
Forum: ROMS Discussion
Topic: How to set Coriolis parameter f in x-y coordinates?
Replies: 2
Views: 753

Re: How to set Coriolis parameter f in x-y coordinates?

Look at the examples in ana_grid.h (which you are presumably using to create your x/y grid). Follow one of these, like UPWELLING: Xsize=1000.0_r8*REAL(Lm(ng),r8) Esize=1000.0_r8*REAL(Mm(ng),r8) depth=150.0_r8 f0=-8.26E-05_r8 beta=0.0_r8 and set f0 to the value you want. Then there is code later in a...
by wilkin
Wed Sep 19, 2018 2:26 pm
Forum: ROMS Bugs
Topic: can't find revision #751 in new source code
Replies: 2
Views: 1053

Re: can't find revision #751 in new source code

Joao, Even if the Timeline in trac https://www.myroms.org/projects/src/timeline does not go back far enough in time you can choose any Changeset and edit the browser URL to enter the number you want. So for revision 751 you want: https://www.myroms.org/projects/src/changeset/751 A LOT has changed in...
by wilkin
Sat Sep 15, 2018 12:28 pm
Forum: ROMS Usage
Topic: Running ROMS error
Replies: 2
Views: 1083

Re: Running ROMS error

You are probably specifying the path incorrectly.

Just try copying varinfo.dat to the directory where you have oceanS and ocean_upwelling.in, and remove any path information to the file in ocean_upwelling.in, i.e. have:

VARNAME = varinfo.dat
by wilkin
Tue Sep 04, 2018 10:53 am
Forum: ROMS Installation
Topic: ./build.bash error:Can't open tmp file at ROMS/Bin/cpp_clean
Replies: 5
Views: 1442

Re: ./build.bash error:Can't open tmp file at ROMS/Bin/cpp_c

Could you have run out of disk space? That might prevent cpp_clean from writing. I doubt the problem is in cpp_clean itself. Your directory listing of Build_roms shows only 5 files. Is that all there is? There should be many more files processed before make gets to def_diags.f90. What release number...
by wilkin
Thu Aug 30, 2018 2:27 pm
Forum: ROMS Tools and Techniques
Topic: How to "ls" filenames on thredds / opendap catalog
Replies: 2
Views: 938

Re: How to "ls" filenames on thredds / opendap catalog

John L., There is no standard way that people set up their opendap catalogs that would make this straightforward. If you are in control of the THREDDS service, then my suggestion would be to set up a time aggregation. Then you can request a data subset from a single stable URL by searching a range o...
by wilkin
Tue Aug 21, 2018 2:10 pm
Forum: ROMS Discussion
Topic: d_ecmwf2roms.m
Replies: 9
Views: 1616

Re: d_ecmwf2roms.m

'PAR' is not a variable in the suite of forcing data used by ROMS distributed at myroms.org, so it has no entry in in the associated roms_metadata.m.
by wilkin
Mon Aug 13, 2018 2:14 pm
Forum: ROMS Discussion
Topic: blowing up on nested grid
Replies: 4
Views: 1289

Re: blowing up on nested grid

When I checked Grid02 by itself. It works well. Please give me some suggestion. By this do you mean you get the same extreme DXmin, DYmin and DZmax yet it runs? If so, then the issues you are having (this is a guess) may be associated with a poor match of land/sea mask in the contact points region....
by wilkin
Sat Jul 14, 2018 5:06 am
Forum: ROMS Sediment
Topic: Wave-current BBL drag coefficient as output
Replies: 4
Views: 2911

Re: Wave-current BBL drag coefficient as output

Parker, I think your approach is reasonable in the 'deeper' case where the assumption underpinning the quadratic drag formulation holds; namely, that the flow at level k=1 is the free stream velocity outside the boundary layer. But where k=1 might be inside a modeled boundary layer you have problems...
by wilkin
Sat Jul 14, 2018 12:43 am
Forum: ROMS Discussion
Topic: Blowing up problem using GLS mixing
Replies: 8
Views: 2088

Re: Blowing up problem using GLS mixing

As John Warner says, you should save output nearing the time of blow-up and try to catch where and for what reason the model is going awry. I suggest capturing the same time for the case that does not blow-up, and compare. Perhaps repeat the Richardson number calculation offline to visualize the dif...
by wilkin
Wed Jun 27, 2018 9:43 am
Forum: ROMS Problems
Topic: ROMS 2-way nesting
Replies: 7
Views: 2107

Re: ROMS 2-way nesting

Does the parent grid run on its own (without any nesting)? You have open boundary conditions (Chapman/Flather/gradient) for velocities but closed for tracers. That might give you stability problems at the boundary. You also have explicit horizontal mixing on tracers in s-coordinates (MIX_S_TS) rathe...
by wilkin
Tue May 29, 2018 8:26 am
Forum: ROMS Discussion
Topic: Set a land mask on the sea in SeaGrid
Replies: 22
Views: 5183

Re: Set a land mask on the sea in SeaGrid

Try the tool editmask which is in the myroms/landmask folder of Matlab tools
by wilkin
Fri May 11, 2018 7:27 am
Forum: ROMS Bugs
Topic: all result = 0?
Replies: 22
Views: 4315

Re: all result = 0?

Reading the log file output your quoted WRT_HIS - wrote history fields (Index=2,2) into time record = 0000082 82 0 00:00:01 0.000000E+00 9.608405E+01 9.608405E+01 4.601201E ... that says to me the model has run for only 1 second of simulated time. If so, you're not going to see much action. What is ...
by wilkin
Mon Apr 30, 2018 4:37 pm
Forum: ROMS Discussion
Topic: river discharge river_Vshape or Multiple rive file
Replies: 9
Views: 1867

Re: river discharge river_Vshape or Multiple rive file

If you search the code for other occurrences of LuvSrc you'll find it also in step2d_LF_AM3.h. Looks you need to hack the barotropic velocity also at line 2438 in step2d_LF_AM3.h. There is also code in step3d_t.F but unless you have different salinity and temperature in conjunction with the discharg...
by wilkin
Sun Apr 29, 2018 10:01 am
Forum: ROMS Discussion
Topic: river discharge river_Vshape or Multiple rive file
Replies: 9
Views: 1867

Re: river discharge river_Vshape or Multiple rive file

Because of same location of river, The last 5 rivers replace the first 5 rivers (I think That's why the model only show the high discharge) Yes, your problem is in step3d_uv.F, where if you look at the code around line 967 ... !-----------------------------------------------------------------------...
by wilkin
Wed Apr 25, 2018 4:45 am
Forum: ROMS Problems
Topic: Grid is not recognized by ROMS
Replies: 2
Views: 1263

Re: Grid is not recognized by ROMS

When you say ROMS does not recognize the grid, do you mean it did not read it at all or that it gave an error. If it did not even read perhaps you have #define ANA_GRID by mistake.
by wilkin
Fri Apr 20, 2018 4:10 pm
Forum: ROMS Problems
Topic: Problem generating contact file with three refined grids
Replies: 5
Views: 1551

Re: Problem generating contact file with three refined grids

I just took a look at my 3-level nested setup and I agree you should have netcdf contactfile_doppio_pioneer_array_v3 { dimensions: Ngrids = 3 ; Ncontact = 4 ; In my case I have a factor of 3 refinement at both levels. Would it be trouble to test whether this is a bug with refinement factors - i.e. c...
by wilkin
Fri Apr 13, 2018 10:17 am
Forum: ROMS Problems
Topic: Fjord tidal test case
Replies: 6
Views: 2147

Re: Fjord tidal test case

You say I only see rdrag instead of rdrag2 There are a few things to check here. First, be very careful about spelling of #define directives. Are you sure you have all the right characters (I'm sure you do, for some directives 0 and o or 1 and l can be confused. Second, be careful about the placemen...
by wilkin
Tue Mar 27, 2018 10:44 am
Forum: ROMS Adjoint
Topic: question about the caculating of om_p, om_u, on_p, on_u
Replies: 5
Views: 1789

Re: question about the caculating of om_p, om_u, on_p, on_u

You are quite right Kate - my mistake. Two wrongs don't make a right, but three rights make a left. So one over one over DX is DX.
by wilkin
Tue Mar 27, 2018 5:13 am
Forum: ROMS Adjoint
Topic: question about the caculating of om_p, om_u, on_p, on_u
Replies: 5
Views: 1789

Re: question about the caculating of om_p, om_u, on_p, on_u

Those comments ! om_r RHO-grid spacing (meters) in the XI-direction. ! should read ! om_r reciprocal of RHO-grid spacing (meters^-1) in the XI-direction.! The "o" is for "over" as in "one over m" (1/m). You will see this usage throughout the code. The way these terms are computed at points other tha...
by wilkin
Thu Feb 22, 2018 4:39 am
Forum: ROMS Source
Topic: My ROMS
Replies: 9
Views: 4053

Re: My ROMS

We'd be interested to know more about your PRESS_COMPENSATE. To use Mercator-Ocean sea level as open boundary conditions to our model we make our own ad hoc adjustment to the sea level to impose an inverse barometer response. Our regional model has the ATM_PRESS effect driving local "storm surge" - ...
by wilkin
Tue Feb 20, 2018 10:35 pm
Forum: ROMS Problems
Topic: Regarding the option TIDENAME
Replies: 8
Views: 1936

Re: Regarding the option TIDENAME

There was a change made in July 2017 to remove tide forcing from the regular list of forcing files given in FRCNAME. Here is the ticket: https://www.myroms.org/projects/src/ticket/736 This was to facilitate using the same list of meteorological forcing files for every nest in nesting downscaling app...
by wilkin
Fri Feb 02, 2018 4:49 am
Forum: ROMS Discussion
Topic: high u_hvisc near the surface at the masked regions
Replies: 2
Views: 880

Re: high u_hvisc near the surface at the masked regions

Sonaljit, It looks like you're using the CariCOOS model configuration but with several modifications to the set-up (like MIX_GEO_UV that Kate noted, and I see biharmonic friction also). The CariCOOS model was running quite reliably in its configuration as of a few months ago, so any changes should b...
by wilkin
Mon Jan 29, 2018 12:00 am
Forum: ROMS Discussion
Topic: Curvilinear grid, (Uwind,Vwind) and (sustr,svstr) angles
Replies: 8
Views: 1737

Re: Curvilinear grid, (Uwind,Vwind) and (sustr,svstr) angles

If you have saved the output sustr,svstr you can plot those with roms_quivergrd - they are on the staggered grid and are in ROMS coordinates. What not just give it a simple netCDF file with uniform winds - it can be a 1-D (function of time only) file and the regrid step will automatically propagate ...
by wilkin
Sun Jan 28, 2018 11:24 pm
Forum: ROMS Discussion
Topic: Curvilinear grid, (Uwind,Vwind) and (sustr,svstr) angles
Replies: 8
Views: 1737

Re: Curvilinear grid, (Uwind,Vwind) and (sustr,svstr) angles

roms_quivergrd is not the function for what you are trying to do. roms_quivergrd plots vectors that are already in ROMS xi,eta coordinates and separated out onto their respective u,v points of the staggered Arakawa-C grid. You are asking it to plot vectors that are centered on the common rho-points ...
by wilkin
Sun Jan 28, 2018 12:37 am
Forum: ROMS Discussion
Topic: Curvilinear grid, (Uwind,Vwind) and (sustr,svstr) angles
Replies: 8
Views: 1737

Re: Curvilinear grid, (Uwind,Vwind) and (sustr,svstr) angles

You must #define CURVGRID or you won't have the correct nonlinear momentum terms that arise from non-Cartesian coordinates. Without knowing how you made those Matlab vector plots and whether you have showing output sustr,svstr vectors or output Uwind,Vwind, it's hard to be sure where the issue lies,...
by wilkin
Sun Jan 14, 2018 2:50 am
Forum: ROMS Adjoint
Topic: wind stress
Replies: 2
Views: 1474

Re: wind stress

In bulk_flux.F the components Uwind,Vwind are defined at rho points, not the staggered u,v points, so better code would be: Uwind(i,j)=Uwind(i,j)-0.5_r8* & & (u(i,j,N(ng),nrhs)+u(i+1,j,N(ng),nrhs)) Vwind(i,j)=Vwind(i,j)-0.5_r8* & & (v(i,j,N(ng),nrhs)+v(i,j+1,N(ng),nrhs)) Also, it is better to modify...
by wilkin
Wed Dec 27, 2017 9:45 pm
Forum: ROMS Bugs
Topic: Problems about pCO2 and CO2_flux output results under Wetdry
Replies: 4
Views: 1395

Re: Problems about pCO2 and CO2_flux output results under We

Looking in the source code I have downloaded I see no occurrence of the variable rmask_io in fennel.h. So I went into the source code "trac" tool https://www.myroms.org/projects/src/wiki intending to look at the sequence of changes to fennel.h. But first I did a search on "rmask_io" which led me dir...
by wilkin
Wed Dec 20, 2017 4:59 am
Forum: ROMS Problems
Topic: double refinement with diferent refinement factors
Replies: 2
Views: 1073

Re: double refinement with diferent refinement factors

In principle you can use different ratios in the different grids, but I will confess I don't know that we ever tested that. Quick question - is this 2-way or 1-way nesting? If it's not 2-way, please give that a try. We did notice some odd volume conservation issues in earlier versions of the code, b...
by wilkin
Sat Dec 16, 2017 2:20 pm
Forum: ROMS Bugs
Topic: WTYPE=9 causes division by zero in lmd_swfrac.F
Replies: 2
Views: 1577

Re: WTYPE=9 causes division by zero in lmd_swfrac.F

Here's the ticket for when that change was introduced:
https://www.myroms.org/projects/src/ticket/609
Maybe you can figure out what the parameters should be - probably a very small but finite value not zero.
by wilkin
Mon Dec 11, 2017 10:12 pm
Forum: ROMS Problems
Topic: CPU time and MPI issues with nested grids
Replies: 16
Views: 6092

Re: CPU time and MPI issues with nested grids

It would be interesting to see the elapsed time profile and message passage profile reports at the end of the log file.

Can you share those?
by wilkin
Tue Dec 05, 2017 1:15 pm
Forum: ROMS Installation
Topic: LtracerSrc LuvSrc can make a problem " insufficient virtual"
Replies: 6
Views: 2837

Re: LtracerSrc LuvSrc can make a problem " insufficient virt

There are templates for all netcdf files in your source code in Data/ROMS/CDL
by wilkin
Sat Dec 02, 2017 1:58 pm
Forum: ROMS Problems
Topic: CPU time and MPI issues with nested grids
Replies: 16
Views: 6092

Re: CPU time and MPI issues with nested grids

should I set the tiling so that both the coarse and fine grids use all the cores?
Yes, this is required. The product NtileI times NtileJ must be the same in every nest.
by wilkin
Thu Nov 30, 2017 3:42 pm
Forum: ROMS Installation
Topic: LtracerSrc LuvSrc can make a problem " insufficient virtual"
Replies: 6
Views: 2837

Re: LtracerSrc LuvSrc can make a problem " insufficient virt

Roms can run sucessfully when I do not turn on "LuvSrc " and "LtracerSrc ". But I got a error "insufficient virtual memory" when I set "LuvSrc " and "LtracerSrc " were ture. You probably have something misconfigured in your river source file, so you should check that it follows the correct netcdf t...
by wilkin
Sun Nov 19, 2017 5:40 pm
Forum: ROMS Discussion
Topic: Flow runs to fast in ideal domain
Replies: 8
Views: 1789

Re: Flow runs to fast in ideal domain

As Kate pointed out, the fastest wave in your uniform depth ocean will be the surface gravity wave with speed sqrt(gh) which for 160 m depth is 39.6 m/s. To travel 200 km at this speed takes:

200e3/sqrt(9.81*160) = 5e3 seconds = 1.4 hours.

So that's what's going on in the start of your simulation.
by wilkin
Mon Nov 13, 2017 2:17 pm
Forum: ROMS Ecosystem
Topic: PhyIS units in Fennel
Replies: 5
Views: 3788

Re: PhyIS units in Fennel

This was fixed at revision 741 in October 2014.
by wilkin
Fri Nov 10, 2017 3:10 pm
Forum: ROMS Usage
Topic: Is CFSR server is down
Replies: 3
Views: 7294

Re: Is CFSR server is down

Over a year ago all US Federal web services were required to switch to secure http, so at the very least your script needs updating to access opendap using https://... But you should double-check to URL to the CFSR data online at https://nomads.ncdc.noaa.gov/thredds/catalog/modeldata/cmd_flxf/catalo...
by wilkin
Sat Sep 23, 2017 11:56 am
Forum: ROMS Tools and Techniques
Topic: D_ECMWF2ROMS Matlab scripts
Replies: 7
Views: 3915

Re: D_ECMWF2ROMS Matlab scripts

I wrote this code a long time ago so my memory of the details is a biz fuzzy, but it required some awkward programming to get the ECMWF results into the form ROMS expects. The challenging thing is that several of the values in the ECMWF raw data files are reported as a cumulative sum over the foreca...
by wilkin
Fri Sep 22, 2017 3:33 pm
Forum: ROMS Discussion
Topic: Climatology as open boundary
Replies: 6
Views: 2014

Re: Climatology as open boundary

Code: Select all

LBC(isUbar) == Clo Shc Shc Shc ! 2D U-momentum
The Shchepetkin condition for 2-D velocity requires boundary data.
by wilkin
Thu Sep 21, 2017 10:10 am
Forum: ROMS Discussion
Topic: Climatology as open boundary
Replies: 6
Views: 2014

Re: Climatology as open boundary

If you use Rad instead of RadNud you will not require a boundary conditions file. If the climatology nudging is effective, it hardly matters there's no nudging at the perimeter. I'd be cautious with the climatology nudging for both 2-D and 3-D velocity. You'll want to be very sure they are consisten...
by wilkin
Wed Aug 23, 2017 2:06 pm
Forum: ROMS Bugs
Topic: Non-zero horizontal advection across land-sea interface
Replies: 1
Views: 1733

Re: Non-zero horizontal advection across land-sea interface

Thanks for this detailed and thoughtful summary of the problem you've encountered. While global conservation doesn't seem to be violated in this case, I can see that the weak outflow of tracer at depth is unsettling. It may be that the mass inflow/outflow in step3d_uv.F in the block at line 964: ! !...
by wilkin
Mon Aug 14, 2017 4:27 pm
Forum: ROMS Problems
Topic: Short wave radiation
Replies: 5
Views: 2478

Re: Short wave radiation

GET_2DFLD - solar shortwave radiation flux, 2012-01-01 00:00:00.00 (Grid=01, Rec=0000001, Index=1, File: NWS_meteo_SWR_forcing.nc) (Tmin= 0.0000 Tmax= 181.7500) t = 0.0000 (Min = 1.00000000E+35 Max = -1.00000000E+35) regrid = T Tmin/Tmax are the times in days. The values are the Min/Max and you hav...
by wilkin
Fri Aug 11, 2017 3:22 pm
Forum: ROMS Problems
Topic: Short wave radiation
Replies: 5
Views: 2478

Re: Short wave radiation

How do you know you are running with a semidiurnal cycle in shortwave radiation? Is it because you have Hout(idSrad) == T ! swrad shortwave radiation flux and relatively frequent output intervals (set with NHIS). That's the quickest way to see what ROMS is reading or computing internally. There are ...
by wilkin
Wed Aug 09, 2017 7:47 pm
Forum: ROMS Discussion
Topic: Virtual salt flux sea surface boundary condition
Replies: 4
Views: 1663

Virtual salt flux sea surface boundary condition

Those of you working with large discharge river point sources have probably experienced over/under-shooting of the salt concentration due to poor performance of the advection near to the point source when using 3rd-order upwind, Akima, or other schemes (not MPDATA). These extremes usually mix away q...
by wilkin
Thu Jul 20, 2017 11:03 am
Forum: ROMS Discussion
Topic: Large deviation between history output and average output
Replies: 2
Views: 1225

Re: Large deviation between history output and average outpu

Are you sure you are comparing time series with the same time coordinate?
by wilkin
Mon Jul 17, 2017 2:00 pm
Forum: ROMS Adjoint
Topic: Offline Heat Budget calculations from ROMS model output
Replies: 13
Views: 8521

Re: Offline Heat Budget calculations from ROMS model output

The diagnostics calculations are throughout the code. Search for the CPP directive DIAGNOSTICS_TS (or DIAGNOSTICS_UV) and you will find snippets of code everywhere. For example ... queequeg:ROMS wilkin$ grep DIAGNOSTICS_TS Nonlinear/* | more grep: Nonlinear/Biology: Is a directory grep: Nonlinear/Se...
by wilkin
Sat Jul 15, 2017 11:58 am
Forum: ROMS Problems
Topic: AVERAGES_DETIDES result problem
Replies: 7
Views: 3951

Re: AVERAGES_DETIDES result problem

Do you have write permission on NetCDF file: ./Projects/RAVI_EXP_8/tide_ravi_exp_8.nc ?

AVERAGES_DETIDE is going to modify that file. ROMS reports it read successfully, so it must be in the correct path. But opening it to write there is a problem.
by wilkin
Wed Jul 12, 2017 7:16 am
Forum: ROMS Bugs
Topic: when I use LtracerSponge , LuvSponge , something wrong
Replies: 2
Views: 1841

Re: when I use LtracerSponge , LuvSponge , something wrong

Hernan Arango's add_sponge.m function in the myroms.org Matlab tools will add (or overwrite) the sponge to an existing grid file: add_sponge: Adds sponge data to a ROMS Grid NetCDF file add_sponge(ncfile, visc_factor, diff_factor) Adds enhanced viscosity and diffusion scaling variables (visc_factor ...
by wilkin
Fri May 26, 2017 6:00 pm
Forum: ROMS Tools and Techniques
Topic: roms_matlab plotting and analysis routines
Replies: 88
Views: 57657

Re: roms_matlab plotting and analysis routines

This is a Matlab problem, not ROMS or Matlab tools for ROMS issue. Get some help from someone in your group or department to get started. Try the Matlab "peaks" command to test your plotting:

>> peaks
by wilkin
Fri May 26, 2017 10:41 am
Forum: ROMS Tools and Techniques
Topic: roms_matlab plotting and analysis routines
Replies: 88
Views: 57657

Re: roms_matlab plotting and analysis routines

If you enter

>> help roms_wilkin

that should direct you to some old documentation on this code at http://romsmatlab.tiddlyspot.com/ that explains that I use snctools (which has nc_varget etc.) for the netcdf read.
by wilkin
Wed May 24, 2017 1:00 pm
Forum: ROMS Discussion
Topic: different history files
Replies: 1
Views: 706

Re: different history files

Use NDEFHIS: ! NDEFHIS Number of time-steps between the creation of new HISTORY file. ! If NDEFHIS=0, the model will only process one HISTORY file. ! This feature is useful for long simulations when HISTORY file ! get too large; it creates a new file every NDEFHIS time-steps.
by wilkin
Tue May 23, 2017 11:01 am
Forum: ROMS Bugs
Topic: Upwelling Channel with 4 Open Boundaries
Replies: 6
Views: 2180

Re: Upwelling Channel with 4 Open Boundaries

If you are trying to set-up something that is effectively 1-dimensional in the vertical (you have no horizontal variation in density or wind forcing) then you might want a small double periodic domain. See the BIO_TOY and SED_TOY examples for guidance on how to do this.
by wilkin
Tue May 16, 2017 11:01 am
Forum: ROMS Ecosystem
Topic: about nutrient concentration in river
Replies: 3
Views: 2104

Re: about nutrient concentration in river

There are logical flags in bio_Fennel.in that activate/deactivate tracers in the river file. ! Logical switches (TRUE/FALSE) to activate biological tracers point ! Sources/Sinks (like river runoff) and to specify which tracer variables ! to consider: [NBT,Ngrids] values are expected. See glossary be...
by wilkin
Wed May 10, 2017 1:38 pm
Forum: ROMS Discussion
Topic: zgrid boundaries in floats output file
Replies: 1
Views: 708

Re: zgrid boundaries in floats output file

What turbulence closure scheme are you using? That affects how Akt is computed that sets the random velocity. Is FLOAT_STICKY #defined? That affects whether floats reflect from the surface and bottom. You might experiment with setting this to see what happens - it could help diagnose the issue. Arou...
by wilkin
Tue May 09, 2017 10:01 am
Forum: ROMS Discussion
Topic: Error while reading variable Uwind
Replies: 7
Views: 2565

Re: Error while reading variable Uwind

We need to know your value for spherical to know if that is that problem. If you have the NCO tools http://nco.sourceforge.net/ (i.e. command line utilities ncks, ncap2 etc.) this is easily determined. Show the value of spherical : ncks -v spherical grdfile.nc Reset the value of spherical if it is n...
by wilkin
Thu May 04, 2017 6:30 am
Forum: ROMS Problems
Topic: Donor grid identification-assignment problem
Replies: 4
Views: 1651

Re: Donor grid identification-assignment problem

INP_PAR - Unable to open ROMS/TOMS input script file. In distributed-memory applications, the input script file is processed in parallel. The Unix routine GETARG is used to get script file name. For example, in MPI applications make sure that command line is something like: mpirun -np 4 ocean ocean...
by wilkin
Tue Apr 25, 2017 6:51 am
Forum: ROMS Usage
Topic: Question about coarse2fine
Replies: 4
Views: 2159

Re: Question about coarse2fine

nc_inq.m is in the myroms Matlab tools in the subdirectory netcdf which is at the same level in the Matlab hierarchy at the subdirectory grid where you have coarse2fine.m . You can download with a similar svn command to what you used to get grid/coarse2fine.m etc. None of the nesting Matlab tools n...
by wilkin
Fri Apr 21, 2017 8:50 pm
Forum: ROMS Ecosystem
Topic: Climatology and nudging in ecosystem models
Replies: 17
Views: 7375

Re: Climatology and nudging in ecosystem models

Is there some place in varinfo.dat that allows salt and temp climatology to be read? What changed with that ticket was that ROMS now propagates the definitions in varinfo.dat for the tracer state variables (temp, salt, NO3 ...) to corresponding climatology variables without having to define entries...
by wilkin
Fri Apr 21, 2017 6:37 pm
Forum: ROMS Ecosystem
Topic: Climatology and nudging in ecosystem models
Replies: 17
Views: 7375

Re: Climatology and nudging in ecosystem models

This works fine for the velocities, and for salt and temp, but the run crashes without comment during initialization right at the moment I believe it should be trying to read the first bio variable climatology field. It is reading it from the same .nc file as where it gets salt and temp. Make sure ...
by wilkin
Mon Apr 17, 2017 1:05 pm
Forum: ROMS Problems
Topic: The model does not read the Forcing file for the Child grid
Replies: 6
Views: 2670

Re: The model does not read the Forcing file for the Child g

The stdout ("log file") reports a list of Output/Input Files: for each grid, e.g. Physical Parameters, Grid: 02 ============================= all the other parameters, then ... Output/Input Files: Output Restart File: r11/pioneer_rst.nc Prefix for History Files: r11/pioneer_his Prefix for Averages F...
by wilkin
Sat Apr 15, 2017 1:37 pm
Forum: ROMS Problems
Topic: The model does not read the Forcing file for the Child grid
Replies: 6
Views: 2670

Re: The model does not read the Forcing file for the Child g

To the best of my knowledge we did not code any option to interpolate forcing data of the parent grid onto the child grid other than by explicitly repeating the name(s) of the parent forcing file(s) in the FRCNAME input. Look closely at your stdout (the "log file") because it reports all the forcing...
by wilkin
Tue Apr 04, 2017 6:12 am
Forum: ROMS Sediment
Topic: Wave-current BBL drag coefficient as output
Replies: 4
Views: 2911

Re: Wave-current BBL drag coefficient as output

If you are using a bottom boundary layer model you should not have UV_QDRAG defined. The bottom boundary layer model is computing the stress itself so you don't want to override that with a quadratic drag law. Whatever your choice of bottom boundary layer model (which affects the .h file included in...
by wilkin
Wed Mar 15, 2017 8:03 pm
Forum: ROMS Tools and Techniques
Topic: Problem refining with coarse2fine on a complex-shaped grid
Replies: 1
Views: 1567

Re: Problem refining with coarse2fine on a complex-shaped gr

If the coordinates you used for lon_rho and lat_rho have duplicates - even if they are NaN - TriScatteredInterp will throw an error.
by wilkin
Tue Feb 28, 2017 12:06 pm
Forum: ROMS Discussion
Topic: I want to add river to the model
Replies: 2
Views: 1538

Re: I want to add river to the model

Read the WikiROMS page all about it
https://www.myroms.org/wiki/River_Runoff
by wilkin
Fri Feb 24, 2017 10:03 am
Forum: ROMS Problems
Topic: ecmwf2roms
Replies: 10
Views: 5576

Re: ecmwf2roms

That code modification is going to give you the wrong values. For data that are integrated over time during the analysis interval, like precipitation, you must unravel the time accumulation. The only way to do this it to start the input data from the 3-hour step in ERA files. In this case, the loop ...
by wilkin
Thu Feb 23, 2017 7:36 am
Forum: ROMS Problems
Topic: ecmwf2roms
Replies: 10
Views: 5576

Re: ecmwf2roms

Did you download 3 hour interval data as discussed previously in this thread?
by wilkin
Tue Feb 14, 2017 12:35 pm
Forum: ROMS Tools and Techniques
Topic: SEAGRID.m with MATLAB R2014b
Replies: 12
Views: 13000

Re: SEAGRID.m with MATLAB R2014b

No one has updated seagrid. It's too hard and there are other tools.

We keep an old version of Matlab on our system just for this purpose.
by wilkin
Tue Jan 24, 2017 12:05 pm
Forum: ROMS Ecosystem
Topic: Correction to fennel.h
Replies: 2
Views: 1902

Re: Correction to fennel.h

What's the provenance of the version of fennel.h you are working with? I can't find lines matching those you describe.

Can you give line numbers in a fresh version of fennel.h from the trunk code, or from browsing at
https://www.myroms.org/projects/src/bro ... y/fennel.h
by wilkin
Fri Jan 13, 2017 2:49 pm
Forum: ROMS Discussion
Topic: Doubt regarding the vertical levels distribution in model
Replies: 4
Views: 2966

Re: Doubt regarding the vertical levels distribution in mo

There is a relatively detailed explanation on WikiROMS of how stretching alters with the different transform and parameter options:

https://www.myroms.org/wiki/Vertical_S-coordinate
by wilkin
Fri Dec 16, 2016 7:13 pm
Forum: ROMS Ecosystem
Topic: Climatology and nudging in ecosystem models
Replies: 17
Views: 7375

Re: Climatology and nudging in ecosystem models

John, What you say here all sounds correct, but let me reiterate for others: If you are nudging to climatological data that are provided in a netcdf file then it is very straightforward. The climatology file need only include the variables you wish to nudge, and they have the same names as the ROMS ...
by wilkin
Thu Dec 15, 2016 8:51 am
Forum: ROMS Ecosystem
Topic: Climatology and nudging in ecosystem models
Replies: 17
Views: 7375

Re: Climatology and nudging in ecosystem models

I suspect you need to update your varinfo.dat and/or bio_Fennel.in. When we introduced the more generic handling of optional nudging for additional tracers those files had to change.
by wilkin
Mon Oct 03, 2016 9:09 pm
Forum: ROMS Discussion
Topic: Quetions about solar radiation as ROMS input forcing
Replies: 7
Views: 2437

Re: Quetions about solar radiation as ROMS input forcing

If you wish the net shortwave radiation to penetrate into the ocean then you #define SOLAR_SOURCE This effectively the causes the net shortwave to be separated from the total heat flux, and for it to be successively absorbed going down into the water column. The vertical scale over which the shortwa...
by wilkin
Wed Sep 28, 2016 1:39 pm
Forum: ROMS Discussion
Topic: Quetions about solar radiation as ROMS input forcing
Replies: 7
Views: 2437

Re: Quetions about solar radiation as ROMS input forcing

You should use net solar radiation. This is what enters the ocean and heats it. Atmospheric models frequently output downward and upward solar radiation separately, and in that case you need to compute the difference to get the net. Using downward flux only would neglect the fact that some of that r...
by wilkin
Tue Sep 27, 2016 11:07 am
Forum: ROMS Problems
Topic: ecmwf2roms
Replies: 10
Views: 5576

Re: ecmwf2roms

I wrote the script assuming that 3-hour interval data were downloaded for processing. Hence the step==3 condition is true on the first pass through and field_previous gets initialized with the hour 3 data. The comments at the start note that ... % The following parameters are used to extract ERA-Int...
by wilkin
Thu Sep 22, 2016 11:04 am
Forum: ROMS Tools and Techniques
Topic: How to decrease nc file bulk using mexnc
Replies: 2
Views: 2330

Re: How to decrease nc file bulk using mexnc

The built-in netcdf utility in more recent releases of Matlab is what you want: >> help netcdf.create netcdf.create Create new netCDF file. ncid = netcdf.create(filename, mode) creates a new netCDF file according to the file creation mode. The return value is a file ID. The type of access is describ...
by wilkin
Thu Sep 15, 2016 1:48 pm
Forum: ROMS Discussion
Topic: Blowing-up problem: Bulk_fluxes
Replies: 6
Views: 2422

Re: Blowing-up problem: Bulk_fluxes

One odd thing I see in your configuration (by reading the log file) is that you have set DIURNAL_SRFLUX but you are using 6-hourly swrad. This is a contradiction. DIURNAL_SRFLUX is designed to take daily average net shortwave and modulate that over the course of a day using the analytical diurnal cy...
by wilkin
Tue Sep 13, 2016 6:09 pm
Forum: ROMS Discussion
Topic: Error MAIN: Abnormal termination: BLOWUP
Replies: 1
Views: 1536

Re: Error MAIN: Abnormal termination: BLOWUP

That you have NaN for the energy and volume before the run even starts suggests that you input initial conditions contained NaN. View the standard output where it reads initial conditions. You'll see something like: NLM: GET_STATE - Read state initial conditions, t = 00 00:00:00 (Grid 01, File: your...
by wilkin
Wed Sep 07, 2016 1:48 pm
Forum: ROMS Discussion
Topic: Difficulty with two-way deep water nested grids
Replies: 5
Views: 2798

Re: Difficulty with two-way deep water nested grids

I don't expect there is likely to be an issue with time-stepping (the difference between your "sync" case and the other). What distinguishes 1-way and 2-way nesting is the treatment of points in the contact region where the coarse grid is the receiver and the fine grid is the donor (which is everywh...
by wilkin
Wed Sep 07, 2016 11:07 am
Forum: ROMS Discussion
Topic: Difficulty with two-way deep water nested grids
Replies: 5
Views: 2798

Re: Difficulty with two-way deep water nested grids

You've only run for 0.3 days. Do the waves dissipate in a few inertial periods? There might be some adjustment to initial conditions going on.
by wilkin
Tue Sep 06, 2016 10:47 am
Forum: ROMS Discussion
Topic: assimilate TSLA into the restart fields of my ROMS model
Replies: 6
Views: 3076

Re: assimilate TSLA into the restart fields of my ROMS model

The point of having a PERFECT RESTART option in ROMS is to be able to be able to restart a run as if it were never interrupted. To do so it needs all levels that are carried for the 3td-order predictor-corrector time stepping. Since you propose to change the ocean state with an offline analysis, per...
by wilkin
Wed Aug 24, 2016 5:46 pm
Forum: ROMS Tools and Techniques
Topic: wind vector direction in NAM and NARR data
Replies: 5
Views: 3652

wind vector direction in NAM and NARR data

The Matlab script nam_narr_2roms.m in the coawst/Tools/mfiles/mtools distribution reads meteorology analysis fields from the NCDC NOMADS analysis archives and makes meteorology forcing files for ROMS. It's a very handy piece of code and easily customized to a new user domain. But the wind components...
by wilkin
Wed Aug 10, 2016 5:36 pm
Forum: ROMS Discussion
Topic: atmospheric forcing time problem
Replies: 3
Views: 2605

Re: atmospheric forcing time problem

Do the wind variables in your file have an attribute "time:"?

That would direct ROMS to try reading that variable as the time coordinate instead of wind_time (which is the default name set in varinfo.dat).
by wilkin
Wed Aug 10, 2016 1:40 pm
Forum: ROMS Information
Topic: grid points for defining FORCES
Replies: 5
Views: 2703

Re: grid points for defining FORCES

It depends. If ROMS has to interpolate and rotate the winds, it wants them at rho points. If you have already interpolated and rotated them, then Uwind is at u-points and Vwind is at v-points. I don't think that's correct. Stresses sustr,svstr are at the corresponding u,v points, but the wind compo...
by wilkin
Sun Aug 07, 2016 3:45 pm
Forum: ROMS Problems
Topic: netcdf.mod : No such file or directory
Replies: 3
Views: 4448

Re: netcdf.mod : No such file or directory

You may have installed netcdf in a directory that ROMS is not finding. Read in the comments in the build script ... # If the USE_MY_LIBS is activated above, the path of the libraries # required by ROMS can be set here using environmental variables # which take precedence to the values specified in t...
by wilkin
Fri Jul 22, 2016 12:57 pm
Forum: ROMS Discussion
Topic: doubt regarding unit conversion of evaporation
Replies: 2
Views: 2634

Re: doubt regarding unit conversion of evaporation

It's in the code in bulk_flux.F. ! For EMINUSP option, EVAP = LHeat (W/m2) / Hlv (J/kg) = kg/m2/s ! PREC = rain = kg/m2/s ! ! To convert these rates to m/s divide by freshwater density, rhow. ! ... # ifdef EMINUSP evap(i,j)=LHeat(i,j)/Hlv(i,j) Divide latent flux in W/m2 by the latent heat of vaporiz...
by wilkin
Sun Jul 17, 2016 12:22 pm
Forum: ROMS Problems
Topic: time unit conversion
Replies: 1
Views: 2004

Re: time unit conversion

Since you are not changing the base date (1800-01-01 in both files) only the units from hours to days, you can make the conversion with the NCO tool ncap ncap -s 'time=time/24' orig_file new_file then update the units attributes to keep the metadata accurate ncatted -a units,time,c,c,"days since 180...
by wilkin
Tue Jul 12, 2016 8:53 pm
Forum: ROMS Tools and Techniques
Topic: roms_matlab plotting and analysis routines
Replies: 88
Views: 57657

Re: roms_matlab plotting and analysis routines

There is something funky going on with my nc_vinfo.m. I downloaded it yesterday from https://github.com/dcherian/tools/blob/ ... nc_vinfo.m. Is there a better place to get it? That distribution by Deepak Cherian on github of Hernan Arango's netcdf utilities for ROMS is woefully out of date. You sho...
by wilkin
Tue Jul 12, 2016 11:04 am
Forum: ROMS Tools and Techniques
Topic: roms_matlab plotting and analysis routines
Replies: 88
Views: 57657

Re: roms_matlab plotting and analysis routines

The result of Iv = nc_vinfo(file,var) should look like: K>> Iv = nc_vinfo(file,var) Iv = Filename: 'http://tds.marine.rutgers.edu/thredds/dodsC/roms/espresso/2013_d...' Name: 'temp' Dimensions: [1x4 struct] Size: [130 82 36 27684] Attributes: [1x8 struct] Cgridtype: [1x1 struct] Datatype: 'single' n...
by wilkin
Tue Jul 05, 2016 4:07 pm
Forum: ROMS Discussion
Topic: i have a question
Replies: 11
Views: 2988

Re: i have a question

You say you removed the cycle_length attribute: I use the BULK_FLUX. and the line 100 of get_data.f90 want to get wind component.I also remove the cycle attribute.But canot run. But the traceback indicates that inquire found the attribute and therefore called get_cycle . oceanG 0000000001CD4A8F Unkn...
by wilkin
Sun Jul 03, 2016 11:56 am
Forum: ROMS Information
Topic: Curvilinear Coordinates
Replies: 13
Views: 28625

Re: Curvilinear Coordinates

These are the attributes I add to my ROMS grid files to remind me how angle is defined. double angle(eta_rho, xi_rho) ; angle:long_name = "angle ROMS xi axis is rotated anticlockwise from due east" ; angle:equation = "u(roms)=Real((Ueast+i*Vnorth)*exp(-i*angle)) and v(roms)=Imag((Ueast+i*Vnorth)*exp...
by wilkin
Tue Jun 28, 2016 5:11 am
Forum: ROMS Usage
Topic: facing Error:ROMS/TOMS - Blows up ......... exit_flag: 1
Replies: 8
Views: 5115

Re: facing Error:ROMS/TOMS - Blows up ......... exit_flag:

Basin information for Grid 01: Maximum grid stiffness ratios: rx0 = NaN (Beckmann and Haidvogel) rx1 = NaN (Haney) Initial basin volumes: TotVolume = 0.0000000000E+00 m3 MinVolume = 0.0000000000E+00 m3 MaxVolume = 0.0000000000E+00 m3 Max/Min = 0.0000000000E+00 Your ocean depth is zero everywhere. R...
by wilkin
Wed Jun 22, 2016 1:08 pm
Forum: ROMS Discussion
Topic: tide problem
Replies: 9
Views: 3756

Re: tide problem

In the FAQ https://www.myroms.org/wiki/Frequently_Asked_Questions#What_are_the_ways_that_ROMS_can_receive_tides_on_the_boundaries.3F note point (3): You can specify other 2-d currents and surface elevation signals as coming in, plus have tides ... if you #define ADD_FSOBC and #define ADD_M2OBC. I no...
by wilkin
Sat Jun 18, 2016 12:51 pm
Forum: ROMS Usage
Topic: problem with atmospheric forcing.
Replies: 13
Views: 5529

Re: problem with atmospheric forcing.

You can't have evaporation and precipitation separately in the output if you're not using BULK FLUXES. Evaporation is only computed if latent heat exchange is computed.

You are imposing surface net freshwater flux and net heat flux as inputs. There is no way to separation the rain from the net.
by wilkin
Fri Jun 17, 2016 7:22 pm
Forum: ROMS Usage
Topic: problem with atmospheric forcing.
Replies: 13
Views: 5529

Re: problem with atmospheric forcing.

Although the ROMS information output showing that I had input the files. That list only echoes the forcing files that ROMS identified from your ocean.in. What you need to look for is the report to stdout as to the data read from those files by GET_2DLFD, e.g. something like: GET_2DFLD - surface u-w...
by wilkin
Fri Jun 17, 2016 1:38 pm
Forum: ROMS Usage
Topic: problem with atmospheric forcing.
Replies: 13
Views: 5529

Re: problem with atmospheric forcing.

After that, I changed surface forcing parameterization from my original header file with Bulk FLUXES to this one. /* surface forcing */ # undef BULK_FLUXES /*# define BULK_FLUXES*/ /* original set up */ # ifdef BULK_FLUXES # define LONGWAVE_OUT # define EMINUSP # define SOLAR_SOURCE # undef DIURNAL...
by wilkin
Wed Jun 15, 2016 1:35 pm
Forum: ROMS Discussion
Topic: Losing tracer as time progresses
Replies: 9
Views: 3639

Re: Losing tracer as time progresses

The logic of the climatology nudging is explained in this release note from 2014: https://www.myroms.org/projects/src/ticket/627 (scroll down about half way to the climatology information - after the sponges). In a nutshell, the LtracerCLM switch controls whether ROMS needs to read climatology (for ...
by wilkin
Sun Jun 12, 2016 2:33 pm
Forum: ROMS Usage
Topic: MAIN: Abnormal termination: BLOWUP.
Replies: 18
Views: 6939

Re: MAIN: Abnormal termination: BLOWUP.

You need to figure out where ROMS is blowing up in order to begin taking rational remedial steps. But you are not saving any output that would help you do that. Physical Parameters, Grid: 01 ============================= 8784 ntimes Number of timesteps for 3-D equations. 600.000 dt Timestep size (s)...
by wilkin
Sat Jun 11, 2016 1:08 pm
Forum: ROMS Usage
Topic: MAIN: Abnormal termination: BLOWUP.
Replies: 18
Views: 6939

Re: MAIN: Abnormal termination: BLOWUP.

Why we cannot have zero bathymetry:
https://www.myroms.org/wiki/Frequently_ ... .3D0.29.3F
by wilkin
Fri Jun 10, 2016 1:18 pm
Forum: ROMS Installation
Topic: Blowing-up: Saving latest model state into RESTART file
Replies: 11
Views: 4903

Re: Blowing-up: Saving latest model state into RESTART file

According to your stdout file std_bio_tsmpdata_kpp.txt you have Chapman open boundary conditions for the biological tracers. There is no such option for tracers, so I don't know what ROMS will have actually done in this situation. Viewing the logic in t3dbc_im.F I suspect it applies no open boundary...
by wilkin
Wed Jun 08, 2016 11:18 am
Forum: ROMS Usage
Topic: MAIN: Abnormal termination: BLOWUP.
Replies: 18
Views: 6939

Re: MAIN: Abnormal termination: BLOWUP.

Check your grid. It looks like there is a point somewhere where the water depth is 25 m above 0: Vertical S-coordinate System, Grid 01: level S-coord Cs-curve Z at hmin at hc half way at hmax 15 0.0000000 0.0000000 -0.000 0.000 0.000 0.000 14 -0.0666667 -0.0004989 2.218 -3.358 -7.757 -9.257 13 -0.13...
by wilkin
Fri Jun 03, 2016 2:48 pm
Forum: ROMS Discussion
Topic: Losing tracer as time progresses
Replies: 9
Views: 3639

Re: Losing tracer as time progresses

There is a note at: https://www.myroms.org/wiki/Numerical_Solution_Technique#Time_Stepping:_Internal_Velocity_Modes_and_Tracers to say Warning: The preceeding notes on tracer advection refer to all but the MPDATA option. The MPDATA algorithm has its own predictor-corrector with emphasis on not allow...
by wilkin
Fri Jun 03, 2016 4:55 am
Forum: ROMS Discussion
Topic: Losing tracer as time progresses
Replies: 9
Views: 3639

Re: Losing tracer as time progresses

Your tracer might not have reached the boundaries, but if the boundaries are open the open boundary conditions (e.g. radiation) could introduce some small amplitude noise that affects your global tracer budget. To get a precise budget, in your vertical integral step be sure you use the time varying ...
by wilkin
Fri Jun 03, 2016 4:50 am
Forum: ROMS Discussion
Topic: Radiation temporal resolution and overheating problem.
Replies: 1
Views: 1991

Re: Radiation temporal resolution and overheating problem.

The solar and thermal radiation was computed from the 12 hour accumulated values, which we only use the 12 and 00 value in the heat flux for ROMS to do the interpolation. The vertical mixing scheme was Mellor-Yamada 2.5 in the model run. Be careful working with "accumulated" values in that data set...
by wilkin
Thu Jun 02, 2016 9:11 am
Forum: ROMS Installation
Topic: problems in runing Roms with tidal forcing
Replies: 16
Views: 8221

Re: problems in runing Roms with tidal forcing

# define SSH_TIDES # define ANA_FSOBC That will do what you want. What happened in your case was that: * You defined ADD_FSOBC: this tells ROMS it needs information on zeta_north etc. * The default, with no other instruction, is for ROMS to attempt to acquire zeta_north etc. from the boundary condi...
by wilkin
Thu Jun 02, 2016 3:16 am
Forum: ROMS Installation
Topic: problems in runing Roms with tidal forcing
Replies: 16
Views: 8221

Re: problems in runing Roms with tidal forcing

I change "define ADD_M2OBC" into "define ANA_M2OBC" in my *h file and the model can run successfully What that did was turn off reading your boundary conditions file and use the analytical default (which is zero), so though the model runs it's not using the data you wanted it do. The CHECK_MULTIFIL...
by wilkin
Tue May 31, 2016 11:15 pm
Forum: ROMS Installation
Topic: problems in runing Roms with tidal forcing
Replies: 16
Views: 8221

Re: problems in runing Roms with tidal forcing

Mark makes a good point about TAB characters in the ocean.in. This trips up a lot of people.

You can test for the existence of TABs in a file called ocean.in with grep:

Code: Select all

grep $'\t' ocean.in 
by wilkin
Tue May 31, 2016 6:24 am
Forum: ROMS Discussion
Topic: blowing up with ubar and vbar with min and max as NaNs
Replies: 9
Views: 3419

Re: blowing up with ubar and vbar with min and max as NaNs

You say: I've checked my ubar e vbar and both have values except in the borders which are masked with NAN values. You can't have NaNs anywhere, not even on the perimeter, because ROMS computes with all values then applies land mask and boundary conditions. So NaNs anywhere propagate to NaNs everywhe...
by wilkin
Mon May 30, 2016 12:44 pm
Forum: ROMS Installation
Topic: problems in runing Roms with tidal forcing
Replies: 16
Views: 8221

Re: problems in runing Roms with tidal forcing

You're getting a error in check_multifile.f90, which handles the processing of the list of forcing files. This says to me there is something wrong with that list or one of the files in it. Check that you have the correct NNFILES parameter, and that you have followed the instructions for the syntax f...
by wilkin
Fri May 20, 2016 2:55 pm
Forum: ROMS Tools and Techniques
Topic: problem of roms_zview roms_bview and roms_quivergrd
Replies: 3
Views: 2914

Re: problem of roms_zview roms_bview and roms_quivergrd

You have that error regarding dnum because it is unassigned at line 119. roms_bview would actually have also given you the following warning: "Problem parsing date from (name of your boundary file) for time index (the requested time index)" This is your clue that your boundary file does not have a t...
by wilkin
Thu May 12, 2016 11:15 am
Forum: ROMS Installation
Topic: Error abou NPZD_IRON
Replies: 3
Views: 3047

Re: Error abou NPZD_IRON

It looks like you are building -D'SVN_REV="583M"'

That's from December 2011. You might want to update your code.
by wilkin
Wed May 04, 2016 1:18 pm
Forum: Job Opportunities
Topic: Marine System Modeler (2 vacancies) at Plymouth Marine Lab
Replies: 0
Views: 6866

Marine System Modeler (2 vacancies) at Plymouth Marine Lab

We are looking to appoint two enthusiastic and highly motivated individuals to join our marine system modelling team. If successful you will work on the development and application of marine ecosystem, biogeochemical and/or physical models, within a range of ongoing programmes. Full details here: ht...
by wilkin
Tue May 03, 2016 7:39 pm
Forum: Job Opportunities
Topic: U Miami (RSMAS) Post-doctoral in ocean modeling & prediction
Replies: 0
Views: 6951

U Miami (RSMAS) Post-doctoral in ocean modeling & prediction

The University of Miami, Rosenstiel School of Marine and Atmospheric Science (RSMAS) invites applications for a Post-doctoral position in ocean modeling and prediction. The successful candidate will be part of a team that conducts interdisciplinary research toward the understanding of ocean processe...
by wilkin
Thu Apr 14, 2016 7:12 pm
Forum: ROMS Tools and Techniques
Topic: roms_matlab plotting and analysis routines
Replies: 88
Views: 57657

Re: roms_matlab plotting and analysis routines

Error in roms_zslice (line 51) time_variable = Iv.Dimensions(end).Name; Error in roms_zview (line 163) [data,x,y,t,grd] = roms_zslice(file,var,time,depth,grd); Error in untitled3 (line 11) roms_zview(file,'temp',1,2,g,3,0.1,'k') The error is being thrown when roms_zslice tries to determine the name...
by wilkin
Wed Mar 09, 2016 4:03 pm
Forum: ROMS Discussion
Topic: roms river LwSrc problem
Replies: 8
Views: 2658

Re: roms river LwSrc problem

Frank, Hernan and I have looked in to this a bit further, and this has raised concerns that the LwSrc option is not implemented correctly. In the LwSrc option a modification should be made to the vertical advective flux in such a way that the subsequent flux divergence introduces the corresponding t...
by wilkin
Sun Feb 28, 2016 10:59 pm
Forum: ROMS Discussion
Topic: Reading ROMS files in R (R-project)
Replies: 4
Views: 2784

Reading ROMS files in R (R-project)

Can anyone point me to help on code/utilities that will correctly interpret the ROMS ocean_s_coordinate_g1 and ocean_s_coordinate_g2 (defined in CF conventions) when reading ROMS output netcdf files in "R" (https://www.r-project.org)?
by wilkin
Wed Feb 17, 2016 2:37 pm
Forum: ROMS Discussion
Topic: MOD_NCPARAM - Unable to open variable information file
Replies: 4
Views: 1777

Re: MOD_NCPARAM - Unable to open variable information file

You are using a very old test case. The svn $Id in your files shows this. !svn $Id: ocean_latte_c.in 272 2007-05-08 14:59:06Z zhang $ !svn $Id: varinfo.dat 273 2007-05-08 15:03:59Z zhang $ These files are unlikely to work with a recent version of the code. I recommend you use a more up to date test ...
by wilkin
Tue Feb 16, 2016 5:58 pm
Forum: Meetings/Workshops
Topic: AGU Ocean Sciences Town Hall on "Future of Ocean Models ..."
Replies: 0
Views: 3881

AGU Ocean Sciences Town Hall on "Future of Ocean Models ..."

For those of you in New Orleans next week (Feb 22-26, 2016) for the AGU Ocean Sciences Meeting you might be interested in attending the Town Hall "Discussion on the Future of Ocean Models in the U.S" Monday, February 22, 2016 06:30 PM - 07:30 PM Ernest N. Morial Convention Center - 203-205 https://a...
by wilkin
Wed Feb 03, 2016 8:30 am
Forum: ROMS Problems
Topic: error while running model as saving output w.r. to ntimes
Replies: 3
Views: 2068

Re: error while running model as saving output w.r. to ntime

DEF_HIS - creating history file, Grid 01: /Land/tanuja_exp_27_onwards_results_backup/output_38_hmin_10_dl_0.0416degree_ecco2bry_era_tropflux_somali/ocean_his_0001.nc DEF_VAR - error while defining attribute: interpolate-land/ROMS_style/svstr_2011.nc,o/Ocean/tropflux_forcings_somali_coast_1995_2014-...
by wilkin
Wed Jan 06, 2016 2:54 pm
Forum: Job Opportunities
Topic: NOAA NOS Coastal Modeling Silver Spring MD
Replies: 0
Views: 3459

NOAA NOS Coastal Modeling Silver Spring MD

Job Title: Physical Scientist ZP-1301-04, DE/CR (1301) Department: Department Of Commerce Agency: National Oceanic and Atmospheric Administration National Ocean Service (NOS) Center for Operational Oceanographic Products and Services (CO-OPS) Silver Spring, MD Job Announcement Number: NOS-COOPS-2016...
by wilkin
Tue Jan 05, 2016 4:43 am
Forum: ROMS Ecosystem
Topic: Problems with npzd_Powell
Replies: 4
Views: 8966

Re: Problems with npzd_Powell

Your log file shows the following: Metrics information for Grid 01: =============================== Minimum X-grid spacing, DXmin = 0.00000000E+00 km Maximum X-grid spacing, DXmax = 2.97235216E+00 km Minimum Y-grid spacing, DYmin = 0.00000000E+00 km Maximum Y-grid spacing, DYmax = 2.97199962E+00 km ...
by wilkin
Wed Dec 09, 2015 2:38 pm
Forum: ROMS Problems
Topic: Checkerboard instability
Replies: 7
Views: 3906

Re: Checkerboard instability

3 ndtfast Number of timesteps for 2-D equations between You only have 3 time steps of the barotropic mode for every baroclinic time step. So the S-shaped time filter that averages fast-time-step (barotropic) zeta to the slow time step has very few weights. Most users have NDTFAST no less than 20, a...
by wilkin
Thu Dec 03, 2015 5:15 pm
Forum: ROMS Bugs
Topic: issue with coarse2fine.m
Replies: 3
Views: 2435

Re: issue with coarse2fine.m

Jamie offers good advice that tracking down the offending attribute would be instructive. In Matlab it's easy to trap the condition with the debugger: >> dbstop if error Then when you run the code Matlab will stop where it fails and you can interrogate the variables and values in the workspace that ...
by wilkin
Wed Nov 25, 2015 6:58 pm
Forum: ROMS Discussion
Topic: AGE_MEAN
Replies: 3
Views: 1188

Re: AGE_MEAN

Look at the placeholder code in ana_passive.h # ifdef AGE_MEAN DO ip=1,NPT,2 itrc=inert(ip) iage=inert(ip+1) DO k=1,N(ng) DO j=JstrT,JendT DO i=IstrT,IendT t(i,j,k,1,itrc)=??? t(i,j,k,2,itrc)=t(i,j,k,1,itrc) t(i,j,k,1,iage)=0.0_r8 t(i,j,k,2,iage)=t(i,j,k,1,iage) END DO END DO END DO END DO # else Yo...
by wilkin
Mon Oct 12, 2015 3:16 pm
Forum: ROMS Discussion
Topic: Rivers in nested grids
Replies: 2
Views: 1149

Re: Rivers in nested grids

Jamie, I have run nested grids with rivers but made a point of choosing my nest perimeter to avoid having a river source in the contact point regions. That just seemed to be asking for trouble because it might require special handling of the fluxes on those faces. You are correct that in two-way nes...
by wilkin
Fri Oct 09, 2015 12:05 pm
Forum: ROMS Usage
Topic: surface mass sources (but not rivers)
Replies: 3
Views: 1744

Re: surface mass sources (but not rivers)

Look at the LwSrc option. I think that does what you want. grep through the code to see what it does, but just be aware that it interacts with it's counterpart option LuvSrc and a logical negation of LuvSrc can be relevant. You'll see in omega.F that the massflux of the sources impacts w, which is w...
by wilkin
Wed Oct 07, 2015 5:57 pm
Forum: ROMS Discussion
Topic: Getting NaN valus in initial and boundary files
Replies: 7
Views: 2172

Re: Getting NaN valus in initial and boundary files

The "flood-fill" into land is what I am meaning by careful extrapolation, but in my experience is it tricky to build a very robust tool for this. Caution is always required. For me, in the Philippine archipelago a lateral flood fill caused absurd values in the deep Sulu Sea because my deepest ROMS p...
by wilkin
Wed Oct 07, 2015 12:51 pm
Forum: ROMS Discussion
Topic: Getting NaN valus in initial and boundary files
Replies: 7
Views: 2172

Re: Getting NaN valus in initial and boundary files

Mercator-Ocean data are reported with netcdf _FillValue assigned to the land area. When interpolating these data to a ROMS grid, points on your ROMS grid near the coast can fall into cells in Mercator-Ocean that are enclosed by at least one _FillValue - which Matlab will interpret as NaN - and propa...
by wilkin
Mon Sep 21, 2015 5:48 pm
Forum: Meetings/Workshops
Topic: AGU Ocean Sciences: Submit abstracts by Wednesday
Replies: 0
Views: 1591

AGU Ocean Sciences: Submit abstracts by Wednesday

The deadline for submitting abstracts to the 2016 AGU Ocean Sciences meeting is this Wednesday, Sept. 23 . To search for sessions where you might submit an abstract (search by topic, chair's name, or keywords) go to https://agu.confex.com/agu/os16/preliminaryview.cgi/start.html If you are submitting...
by wilkin
Tue Sep 08, 2015 4:00 pm
Forum: ROMS Tools and Techniques
Topic: roms_matlab plotting and analysis routines
Replies: 88
Views: 57657

Re: roms_matlab plotting and analysis routines

m_proj('miller','lon',[117 134],'lat',[15 43]); m_grid('linestyle','none','box','fancy','tickdir','in','xtick',117:4:134,'ytick',15:4:43); m_gshhs_i('patch',[.6 .6 .6]) hold on addpath('J:\east\east preference\ROMSprocess\'); file=('G:\mysoftware\bin\delft2roms\case2\smooth_east_grd3_728.nc'); grd=...
by wilkin
Tue Sep 08, 2015 2:30 pm
Forum: ROMS Tools and Techniques
Topic: roms_matlab plotting and analysis routines
Replies: 88
Views: 57657

Re: roms_matlab plotting and analysis routines

Error in ==> roms_get_grid at 91 grd.(vname) = squeeze(... i see nc_varget.m in this nc_varget.m in http://romsmatlab.tiddlyspot.com/ but i don't know how to get it There are instructions at http://romsmatlab.tiddlyspot.com under DownLoad on where to get the snctools that include nc_varget.m. Sorry...
by wilkin
Tue Sep 08, 2015 2:06 pm
Forum: ROMS Tools and Techniques
Topic: roms_matlab plotting and analysis routines
Replies: 88
Views: 57657

Re: roms_matlab plotting and analysis routines

error: >> plot_mesh ??? Undefined function or method 'isnc3' for input arguments of type 'char'. There is no plot_mesh command in my code. If you've received these routines third hand from someone else perhaps they can help you. You can't switch between nc_varget and ncread because those functions ...
by wilkin
Fri Aug 21, 2015 11:12 am
Forum: ROMS Discussion
Topic: Surface heat retention, year-round fake "upwelling"
Replies: 21
Views: 9727

Re: Surface heat retention, year-round fake "upwelling"

You have been a bit careless with the use of C-language style comments. A comment is opened with /* and closed with */. So the /*#define QCORRECTION is not closed until the end of the line for ANA_SMFLUX. Entering a second opening /* is simply treated as literal comment text. /* Surface Boundary Con...
by wilkin
Thu Aug 13, 2015 4:33 pm
Forum: ROMS Problems
Topic: NESTING GRID blow up first step NaN problem
Replies: 9
Views: 3217

Re: NESTING GRID blow up first step NaN problem

Looking over the logfile output you've showed you haven't tried theta_s more than 0.1, so it will have very little effect. Strictly speaking theta_s = 0 is invalid, but the limit theta_s -> 0 is OK. You get regular sigma coordinates. You need theta_s of 3 or more to really see any appreciable stretc...
by wilkin
Wed Aug 12, 2015 5:26 pm
Forum: ROMS Problems
Topic: NESTING GRID blow up first step NaN problem
Replies: 9
Views: 3217

Re: NESTING GRID blow up first step NaN problem

After reading initial conditions for grid 2 ... NLM: GET_STATE - Read state initial conditions, t = 15749 00:00:00 (Grid 02, File: marmenorHR_ini.nc, Rec=0001, Index=1) ROMS goes on to read forcing data for both grids for t = 15749. But if you look immediately prior to the report in your logfile of:...
by wilkin
Wed Aug 12, 2015 11:10 am
Forum: ROMS Problems
Topic: NESTING GRID blow up first step NaN problem
Replies: 9
Views: 3217

Re: NESTING GRID blow up first step NaN problem

Have you run the parent grid stand-alone without nesting to check that the basic set-up is stable? That's a basic sanity check on configuration. Beyond that, a few things I notice in your list of CPP options and the logfile... You have #defined UV_VIS2 but have the parameter nl_visc2=0 in both grids...
by wilkin
Wed Jul 22, 2015 2:13 pm
Forum: Meetings/Workshops
Topic: AGU Ocean Sciences session on shelf-sea/open-ocean exchange
Replies: 0
Views: 1810

AGU Ocean Sciences session on shelf-sea/open-ocean exchange

At the upcoming AGU Ocean Sciences meeting in New Orleans (21-26 February, 2016) we are convening a session related to shelf-sea/open-ocean exchange processes (session ID #9241). We invite you to attend, and consider submitting an oral or poster presentation to the session. Whether your favorite bou...
by wilkin
Fri Jul 17, 2015 11:09 am
Forum: ROMS Problems
Topic: Create a sponge layer
Replies: 5
Views: 3150

Re: Create a sponge layer

One thing to check is analytical.f90 in your Build directory to see if your code was actually activated before compiling.

You do have UV_VIS2 defined, and one of MIX_S_UV or MIX_GEO_UV, right?
by wilkin
Thu Jul 16, 2015 3:58 pm
Forum: ROMS Messages
Topic: AGE_MEAN description
Replies: 0
Views: 8595

AGE_MEAN description

The AGE_MEAN option introduced with ticket #674 https://www.myroms.org/projects/src/ticket/674 implements the mean water age method described by Gordon Zhang in a JPO article on age and residence time in the Hudson River plume. [Zhang et al. (2010): Simulation of water age and residence time in the ...
by wilkin
Tue Jul 14, 2015 1:42 pm
Forum: ROMS Discussion
Topic: Sponge layer
Replies: 2
Views: 1349

Re: Sponge layer

If you are using the myroms.org source code you need to customize Functionals/ana_sponge.h for your application to apply the sponge where and how you what. The code will scale the input viscosity accordingly. But in your ocean.in you have visc2 = 0, so unless you change that the sponge layer is only...
by wilkin
Tue Jun 23, 2015 12:25 pm
Forum: ROMS Discussion
Topic: More than one river
Replies: 3
Views: 1110

Re: More than one river

Last year I wrote a Wiki ROMS entry about rivers because a number of people were having trouble getting them to work easily. That entry is here: https://www.myroms.org/wiki/index.php/River_Runoff The most common mistake that users make (we have all done it) is to misplace a source with the respect t...
by wilkin
Sat Jun 20, 2015 7:02 pm
Forum: ROMS Usage
Topic: Model blowing up using elevation at the boundary
Replies: 12
Views: 5306

Re: Model blowing up using elevation at the boundary

The real-time assimilation system we run for MARACOOS has a reasonable realization of the surge associated with Sandy along the NJ/Delaware coast. The Version 2 output at http://tds.marine.rutgers.edu:8080/thredds/roms/espresso/catalog.html would be the version you want. In this version we never rec...
by wilkin
Wed Jun 17, 2015 1:35 pm
Forum: ROMS Problems
Topic: passive tracer with bry,init conditions & top/bottom fluxes
Replies: 9
Views: 3066

Re: passive tracer with bry,init conditions & top/bottom flu

You say My lateral bry are all set to zero having the same dimension with temp and salt which are open boundary values but what are your open boundary conditions ? Are they clamped, gradient, or radiation on the inert tracers? If you update your code you will have much greater control on these setti...
by wilkin
Mon Jun 15, 2015 1:35 pm
Forum: ROMS Discussion
Topic: passive tracer forcing file error
Replies: 2
Views: 1416

Re: passive tracer forcing file error

In debugging these situations it can be helpful to review the order in which forcing data is processed in subroutine get_data.F Doing this you will see that ROMS is somewhere around line 611 in get_data.F when it fails on you application. Your standard output suggests it successfully read the "passi...
by wilkin
Thu May 28, 2015 2:08 pm
Forum: ROMS Problems
Topic: Problem using M2CLAMPED
Replies: 9
Views: 3535

Re: Problem using M2CLAMPED

Because of the arrangement of the ROMS C-grid, with the last column of zeta points being outside the "physical" domain defined by the last column of normal velocity points (u on an east boundary), setting zeta_east and only zeta_east on the boundary has virtually no impact on the flow. This is becau...