Ocean Modeling Discussion

wilkin

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

wilkin

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...

wilkin

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...

wilkin

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/...

wilkin

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 ...

wilkin

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...

wilkin

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.

wilkin

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...

wilkin

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...

wilkin

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...

wilkin

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 ...

wilkin

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.

wilkin

(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: !-----------------------------------------------------------------...

wilkin

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 ...

wilkin

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...

wilkin

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...

wilkin

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.

wilkin

# 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...

wilkin

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?

wilkin

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.

wilkin

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...

wilkin

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...

wilkin

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...

wilkin

...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...

wilkin

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...

wilkin

What do you have for LEVBFRC?

wilkin

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...

wilkin

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...

wilkin

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...

wilkin

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 ...

wilkin

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...

wilkin

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...

wilkin

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...

wilkin

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: =============================== ... ...

wilkin

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...

wilkin

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...

wilkin

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...

wilkin

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...

wilkin

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...

wilkin

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 ...

wilkin

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...

wilkin

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

https://www.myroms.org/wiki/River_Runof ... _Eposition

wilkin

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 ...

wilkin

Are you using the online #define FLOATS option in ROMS, or doing the particle tracking yourself from archived ROMS model output?

wilkin

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...

wilkin

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...

wilkin

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.

wilkin

Update your code. Those boundary condition #define(s) have been superseded by logical switches in ocean.in.

wilkin

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.

wilkin

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...

wilkin

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...

wilkin

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 ...

wilkin

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 ...

wilkin

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.

wilkin

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?

wilkin

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...

wilkin

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...

wilkin

When does the seg fault occur?

At model initialization, at first float release, or midway in the run?

wilkin

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.

wilkin

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...

wilkin

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...

wilkin

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...

wilkin

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.

wilkin

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

http://cfconventions.org/cf-conventions ... coordinate

wilkin

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.

wilkin

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.

wilkin

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...

wilkin

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:...

wilkin

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...

wilkin

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

wilkin

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...

wilkin

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 ...

wilkin

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...

wilkin

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.

wilkin

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...

wilkin

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...

wilkin

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.

wilkin

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...

wilkin

Read this explanation on WikiROMS:
https://www.myroms.org/wiki/Numerical_S ... g_Overview
and the Shchepetkin papers.

wilkin

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.

wilkin

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...

wilkin

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 ...

wilkin

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...

wilkin

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 ...

wilkin

Kate ... This is your branch of code - can you help? There is no revision number in the previous version log.

wilkin

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...

wilkin

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...

wilkin

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...

wilkin

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...

wilkin

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

wilkin

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...

wilkin

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...

wilkin

'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.

wilkin

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....

wilkin

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...

wilkin

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...

wilkin

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...

wilkin

Try the tool editmask which is in the myroms/landmask folder of Matlab tools

wilkin

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 ...

wilkin

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...

wilkin

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 ... !-----------------------------------------------------------------------...

wilkin

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.

wilkin

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...

wilkin

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...

wilkin

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.

wilkin

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...

wilkin

Do you know about this post regarding minimum TKE ...
viewtopic.php?f=17&t=2310&p=8441&hilit= ... ully#p8458

wilkin

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" - ...

wilkin

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...

wilkin

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...

wilkin

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 ...

wilkin

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 ...

wilkin

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,...

wilkin

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...

wilkin

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...

wilkin

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...

wilkin

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.

wilkin

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?

wilkin

There are templates for all netcdf files in your source code in Data/ROMS/CDL

wilkin

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.

wilkin

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...

wilkin

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.

wilkin

This was fixed at revision 741 in October 2014.

wilkin

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...

wilkin

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...

wilkin

Code: Select all

LBC(isUbar) == Clo Shc Shc Shc ! 2D U-momentum

The Shchepetkin condition for 2-D velocity requires boundary data.

wilkin

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...

wilkin

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: ! !...

wilkin

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...

wilkin

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 ...

wilkin

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...

wilkin

Are you sure you are comparing time series with the same time coordinate?

wilkin

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...

wilkin

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.

wilkin

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 ...

wilkin

This post might help
viewtopic.php?f=14&t=965&hilit=tide_start#p3342
and the WikiROMS page it links to
https://www.myroms.org/wiki/tide_start

wilkin

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

wilkin

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.

wilkin

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.

wilkin

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.

wilkin

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...

wilkin

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...

wilkin

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...

wilkin

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...

wilkin

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...

wilkin

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...

wilkin

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 ...

wilkin

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...

wilkin

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...

wilkin

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...

wilkin

If the coordinates you used for lon_rho and lat_rho have duplicates - even if they are NaN - TriScatteredInterp will throw an error.

wilkin

Read the WikiROMS page all about it
https://www.myroms.org/wiki/River_Runoff

wilkin

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 ...

wilkin

Did you download 3 hour interval data as discussed previously in this thread?

wilkin

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.

wilkin

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

wilkin

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

wilkin

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 ...

wilkin

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.

wilkin

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...

wilkin

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...

wilkin

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...

wilkin

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...

wilkin

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...

wilkin

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...

wilkin

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...

wilkin

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.

wilkin

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...

wilkin

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...

wilkin

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).

wilkin

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...

wilkin

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...

wilkin

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...

wilkin

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...

wilkin

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...

wilkin

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...

wilkin

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...

wilkin

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...

wilkin

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...

wilkin

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...

wilkin

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.

wilkin

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...

wilkin

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...

wilkin

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 ...

wilkin

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)...

wilkin

Why we cannot have zero bathymetry:
https://www.myroms.org/wiki/Frequently_ ... .3D0.29.3F

wilkin

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...

wilkin

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...

wilkin

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...

wilkin

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 ...

wilkin

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...

wilkin

# 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...

wilkin

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...

wilkin

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

wilkin

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...

wilkin

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...

wilkin

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...

wilkin

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

That's from December 2011. You might want to update your code.

wilkin

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wilkin

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