Ocean Modeling Discussion

jcwarner

ok. i see your earlier post on the coawst forum. I see that you are running ROMS with WEC on, but you are not coupled to a wave model. You must be reading in a netcdf forcing file with the wave info? I have not run that type of application in a long time. The waves are difficult to prescribe in a ...

jcwarner

this really should be posted on the coawst forum here:
https://github.com/DOI-USGS/COAWST/issues
please post it there with the full output.
thanks

jcwarner

ok. well you need to look around a bit.
I have it here:
COAWST/Data/ROMS/Grid/bio_toy_grd.nc
and Rutgers has it here
roms_test/bio_toy/Data/bio_toy_grd.nc

jcwarner

i think the path needs to be
Data/ROMS/grid/bio_toy.nc

jcwarner

Ah! ok , yes i gave you the k-e. And we dont see those wiggles with k-e. I dont typically use the k-gen settings. Wonder if you can adjust any parameters to get rid of that noise. try this: Generic length-scale turbulence closure parameters. GLS_P == 2.0d0 ! GLS_M == 1.0d0 GLS_N == -0.67d0 GLS_Kmin ...

jcwarner

give this a try ! Generic length-scale turbulence closure parameters. GLS_P == 3.0d0 ! K-epsilon GLS_M == 1.5d0 GLS_N == -1.0d0 GLS_Kmin == 7.6d-6 GLS_Pmin == 1.0d-12 GLS_CMU0 == 0.5477d0 GLS_C1 == 1.44d0 GLS_C2 == 1.92d0 GLS_C3M == -0.4d0 GLS_C3P == 1.0d0 GLS_SIGK == 1.0d0 GLS_SIGP == 1.30d0

jcwarner

i dont normally see that kind of noise.
what are the ocean.in gls settings?

jcwarner

you need to make sure the flow is coming into the domain.
it can be tricky to identify the u- or v- locations for the inflows. the river point sources need to be at u- or v- masked points.
do you see the velocities increase at the discharge locations?

jcwarner

as i look thru the ini_fields, i see set_zeta_timeavg, but it is inside a solve3d loop, for example: 925 # ifdef SOLVE3D 926 ! 927 !----------------------------------------------------------------------- 928 ! Initialize fast-time averaged free-surface (Zt_avg1) with the inital 929 ! free-surface ...

jcwarner

can you type
grep -nir set_zeta_timeavg ROMS/*
and find out what folder that var is in?

jcwarner

Dear Help Desk- I found an issue in ROMS/Utility/def_diags.F. The variable zeta is now written out to the diagnostics file for CF compliance. It works fine for a new run. But when we do a restart, the variable zeta is not given a varid. I fixed this in def_diags.F Here is the section that needs to ...

jcwarner

What is the horizontal white box across the middle-top of the cross-section plots? Maybe try these switches on/off: #define SPLINES_VVISC try with this off #define SPLINES_VDIFF try with this off #define UV_VIS2 #define MIX_GEO_UV < --- try mix_s_uv #define TS_DIF2 #define MIX_GEO_TS < --- try mix_s ...

jcwarner

i think it is telling you to set NRREC=1, because there is only 1 time record in that file.
you set it to 4 and there are not 4 time records.

jcwarner

i see what you are saying, but the full section of code is: ! Compute dissipation of turbulent energy (m3/s3). Add in vertical ! mixing term. ! Qdiss=dt(ng)*SQRT(tke(i,j,k,nstp))/(my_B1*Ls_unlmt) cff=Ls_unlmt*(1.0_r8/(z_w(i,j,N(ng))-z_w(i,j,k))+ & & 1.0_r8/(z_w(i,j,k)-z_w(i,j,0))) Wscale=1.0_r8+cff3 ...

jcwarner

the newest code version should have 5 digits there.

jcwarner

set NRREC = 1 or = 2

jcwarner

i think you are using an older version of code. if you look here: https://github.com/myroms/roms/blob/develop/ROMS/Nonlinear/bulk_flux.F We do: Uair(i,j)=Uwind(i,j)- & & 0.5_r8*(u(i,j,N(ng),nrhs)+u(i+1,j,N(ng),nrhs)) not Uwind(i,j)=Uwind(i,j)-0.5_r8* ... can you do an update. thanks j

jcwarner

the reason is that your time step starts at 2123781120 and you want a new his file every 2880 steps. So 2123781120/2880 = 737424 files. and right now the roms his file has 5 digits. roms_his_00001.nc up to roms_his_99999.nc so roms can not make a his file with this name: roms_his_737424.nc Maybe ...

jcwarner

N-S periodic means that field values on the northern edge will be copied to the southern edge, and also the other way. So the thin line along the bottom is the pressure from the northern edge, if you set periodic in the ocean.in file. for a continuous gradient, periodic may not be the best choice ...

jcwarner

this looks like COAWST and it is probably best to post an issue over there. but it looks to me that the model ran for a few hours, then ROMS computed Inf for SST. So i suggest you look in the rst file, save the roms his every 20 minutes, look at the his file and see where an issue is developing. You ...

jcwarner

1) in ana_pair, near the top you have
USE mod_param
USE mod_forces
USE mod_ncparam

you need to add mod_grid, so make it look like:
USE mod_param
USE mod_forces
USE mod_grid
USE mod_ncparam

jcwarner

I dont think it got 'deleted', but it never showed up. I wrote it, thought i hit the 'submit' button, and then it never showed up.
I am sure it was me, not pushing the correct post button and then closing the window.
Hopefully the main intent of my post is there.
-j

jcwarner

So i wrote a long post here, but it somehow got deleted. I will try to recover what i essence of what i wrote. In summary, i ran your case and i see the salt decrease for the LwSrc as it should, with the source of water coming in at salt=0. I ran your case with LuvSrc and i see the salt increase ...

jcwarner

ok. this looks like a simple test case.
can you tar up the ocean.in, *.h, and any files someplace that i can get?

jcwarner

where are you putting the rivers in at? are they from the lateral boundary or in the interior of the domain?
the LuvSrc need to come from masked areas, you cant just add them into an active grid cell.
If you want to add the source to an active grid cell, then try LwSrc.

jcwarner

so the river inflows have salt = 0, correct?
are there any undershoots of sal? is the sal < 14 anywhere?
depending on the advection scheme, you can get over and under shoots, but the total mass should be correct.

jcwarner

are you nudging to a clm field?

jcwarner

so this is an issue with COAWST. Please post this here:
https://github.com/DOI-USGS/COAWST/issues
we dont use svn anymore.
and it built ok
"make: 'Build' is up to date."

jcwarner

REGRID - input gridded data does not contain model grid: Gridded: LonMin = 50.0000 LonMax = 58.0000 LatMin = 8.0000 LatMax = 14.0000 Model: LonMin = 50.0715 LonMax = 58.3698 LatMin = 8.5862 LatMax = 14.8747 the model goes to 58.3698, but the data only extends to 58.00 you need to have the data span ...

jcwarner

you can modify those m files as needed. and you can certainly search around for other tools. for the wave forcing, as i said already, we used to run swan, save the data, create a roms forc file, and then run roms. in theory it used to work, and it might now. but i dont run the modeling system that ...

jcwarner

these are settings for surface flux of tke due to wave breaking, see
https://www.sciencedirect.com/science/a ... 0312000042

jcwarner

look at
line 307 of file inp_decode.f90
and see what the code is trying to read.

jcwarner

1- i am not sure what is causing the blips at the coast. not sure i have seen this before. is it also in u and v? i would think so. are you nudging to ubar vbar? if not, then it is not an issue. 3 - we used to run roms forced with the output from swan. to do that, we would run swan, make a roms forc ...

jcwarner

it would be best to post this on the coawst issue site:
https://github.com/DOI-USGS/COAWST/issues
and include the full output, not just those last few lines.

jcwarner

you need to do something there.
not sure what the bath looks like. maybe a little smoothing there. maybe increase visc2 a little.
maybe decrease time step. try a few things.

jcwarner

"WRT_RST_NF90 - wrote re-start fields (Index=2,2) in record = 1"

have you viewed the rst file?
use ncview or similar tool to quickly look in the file, see where the problem exists.

jcwarner

yes sorry.
i was changing the way to compute the metrics to be more in line with gridbuilder and i messed up the x y values used to compute dx dy and angle.
sorry.
i reverted my method back to what i had before. if you do a git pull it should be better now.

-j

jcwarner

sorry for the late reply on this one.
are you still trying to incorporate the sediment.?
You can use the coawst model for now, we have more updated methods there. we are working to include all the sediment into the rutgers version now.
-j

jcwarner

ok. here is some 'no responsibility' guidance. Look in ROMS/Nonliear/set_vbc.F and there is a section for the bottom stress near line 637 or so: # elif defined UV_QDRAG ! ! Set quadratic bottom stress. ! DO j=Jstr,Jend DO i=IstrU,Iend cff1=0.25_r8*(v(i ,j ,1,nrhs)+ & & v(i ,j+1,1,nrhs)+ & & v(i-1,j ...

jcwarner

ok. So does this term need to be added throughout the water column, or just as an extra term that could be added to the bottom stress?

jcwarner

This could be added as a body force, or it could be the same way we added vegetation drag throughout the water column.
What is the T?

jcwarner

ok. now you know what is happening. next is to figure out why it is happening. it blew up in 12 time steps, so save every his step, and watch what happens in that corner. what are the sal and temp in your bc files? I personally do not use A4 advection, i use U3. maybe try different advection or diff ...

jcwarner

12 2022-07-01 12:18:00.00 2.693400E-02 5.341908E+03 5.341935E+03 4.910017E+13 (588,005,03) 4.670190E-01 2.073180E-01 2.452327E+00 2.479567E+01 DIAG speed trouble 24.795668439173749 DIAG speed ijk 20.680908753216158 589 5 1 1 Blowing-up: Saving latest model state into RESTART file REASON: MaxSpeed ...

jcwarner

i think you can start out by first adjusting the time step. and see if you can get the configuration you have to run.

jcwarner

192 ntimes Number of timesteps for 3-D equations. 900.000 dt Timestep size (s) for 3-D equations. 30 ndtfast Number of timesteps for 2-D equations between each 3D timestep. roms time step should be a lot smaller. i see you have ~1km spacing. try 90 sec or something like that to start.

jcwarner

here is some help.
viewtopic.php?t=2930

jcwarner

keep looking in your file, it says

"INQUIRY - unable to find requested variable: EminusP
in file:
Projects/UPWELLING/ROMS_forcing.nc"

jcwarner

GET_NGFLD - free-surface western boundary condition, 1947-12-12 00:00:00.00 (Grid= 01, Rec=12, Index=2, File: croco_bry.nc) (Tmin= 15.0000 Tmax= 345.0000) t = 345.0000 (Min = NaN Max = NaN) GET_NGFLD - free-surface northern boundary condition, 1947-12-12 00:00:00.00 (Grid= 01, Rec=12, Index=2, File ...

jcwarner

this is best to post a message on the coawst forum:
https://github.com/DOI-USGS/COAWST/issues
and the answer is yes, it should work.

jcwarner

for coawst issues, specific to compiling or running multiple models together, it is best to post an issue here: https://github.com/DOI-USGS/COAWST/issues your issue is that you selected a compiler for openmp and mpi. (dm+sm) For cowast, you can only use mpi. if you have further issues please post a ...

jcwarner

can you just set the u-mask to be zero at a point and that would prevent the flow across that interface (similar for v). ? .

jcwarner

look at the temp and salt, they might be contributing.
what did you set for the bc's in the ocean.in file.

jcwarner

a couple of things here. 1 - there is a depth in your grid exactly = 0 (h(52,4) ==0) and that caused some troubles in the routine to comute ubar and vbar cc=roms_zint_mw(u,gn); ubar=rho2u_2d_mw(u2rho_2d_mw(cc)./gn.h); cc=roms_zint_mw(v,gn); vbar=rho2v_2d_mw(v2rho_2d_mw(cc)./gn.h); %== Rotate the ...

jcwarner

The USGS - Woods Hole Coastal and Marine Science Center (WHCMSC) is seeking a coastal ocean modeler. The USGS conducts a wide range of interdisciplinary research activities in marine, estuarine, lacustrine, and terrestrial regions of the United States, including the Atlantic Ocean, Pacific Ocean ...

jcwarner

1. Look in ROMS/Nonlinear/set_vbc.F The bottom stress for a 2D application is # if defined UV_LDRAG ! ! Set linear bottom stress. ! DO j=Jstr,Jend DO i=IstrU,Iend bustr(i,j)=0.5_r8*(rdrag(i-1,j)+rdrag(i,j))* & & ubar(i,j,krhs) ... etc and for 3D it is # elif defined UV_LDRAG ! ! Set linear bottom ...

jcwarner

not sure, but it looks like you put ! in front of a lot of lines. Even if you are not using that info, the inp script looks for that data. for example ! NestLayers = 1 < this line needs to be read ! Number of grids in each nesting layer [1:NestLayers]. ! GridsInLayer = 1 < this line needs to be read ...

jcwarner

ROMS/TOMS: Wrong choice of grid 01 partition or number of parallel nodes. NtileI * NtileJ = 2 must be equal to the number of parallel processes = 1 Change -np value to mpirun or change domain partition in input script. if you set to run with -np X, where X is an integer, then you need to change ...

jcwarner

I had a mix of options that were not correct and it caused an issue. There is a catch in mod_arrays to prevent my problem: IF (LuvSrc(ng).or.LwSrc(ng).or.ANY(LtracerSrc(:,ng))) THEN CALL allocate_sources (ng) END IF so this is all good. sorry to raise the flag. happy modeling. -j

jcwarner

I am having an issue with a memory allocation, and it came back to the init for the var Nsrc. In ROMS/Modules/mod_sources.F we have #ifndef ANA_PSOURCE .... Nsrc(mg)=var_Dsize(1) ! first dimension .... #else ... Msrc(ng)=200 Nsrc(ng)=Msrc(ng) #endif ... ! Allocate point Sources/Sinks variables ...

jcwarner

ok do me a favor.
cd ROMS/Nonlinear
mv gls_corstep.F gls_corstep.F_orig
go here:
https://myroms.org/forum/viewtopic.php?p=24570#p24570
and download their alt_gls_corstep.F,
mv alt_gls_corstep.F gls_corstep.F
then recompile and see if that helps.
-j

jcwarner

if you set the coefficients to use k-e or k-gen, does the spots still appear?

jcwarner

what kind of vertical mixing do you have on?
do you have any wave-ocn coupling?

jcwarner

those are about the same dynamics that we simulated for H Ivan.
Zambon, J.B., He, R., and Warner, J.C. (2014). Investigation of Hurricane Ivan using the Coupled Ocean-Atmosphere-Wave-Sediment Transport (COAWST) Model, Ocean Dynamics, 64, 1535-1554. doi:10.1007/s10236-014-0777-7.

jcwarner

i think it has to deal with the time stepping and the Hz grid cell thickness. in prestep3d we have cff1=Hz(i,j,k)*t(i,j,k,nstp,itrc) ... # ifdef DIAGNOSTICS_TS DiaTwrk(i,j,k,itrc,iTrate)=cff1 so the iTrate is t(nstp)*Hz ~= told*Hzold in step3dt we do 2 things: DO idiag=1,NDT DiaTwrk(i,j,k,itrc,idiag ...

jcwarner

the last line of your file says "Could not read valid record axe from file" i had to search for this one. it is in SWAN, call agnc_set_error( 'Could not read valid record axe from file') looks like you are trying to read a netcdf file. I suggest you use SWAN by itself, try to run that application ...

jcwarner

For compile errors with coawst, please submit them to https://github.com/jcwarner-usgs/COAWST/issues i took a quick look at your compile log. there are lots of issues. first, it shows "f951: Warning: Nonexistent include directory ‘/main’ [-Wmissing-include-dirs] f951: Warning: Nonexistent include dir ...

jcwarner

We are using ROMS to simulate rainfall and urban flooding during hurricanes. Currently the 'rain' input from the surface forcing is used for several physics such as a BC for salinity. This will allow the water to get fresher. But the volume of that rain is not accounted for. The LwSrc point source ...

jcwarner

if you have a uniform current on a non-uniform grid, the stress would be uniform because the current is uniform.
the areas are taken into account when the time stepping of the full equations.
you can dig into the details here:
https://www.myroms.org/wiki/Documentation_Portal

jcwarner

Do you think it is due to the vegetation, or just that the water is shallow? you could use the VEGETATION option that we have in coawst. it extracts momentum from the water column up to the veg height, and this has been shown to reduce flow in those areas. Beudin, A., Kalra, T. S., Ganju, N. K., and ...

jcwarner

i think 0 is at the lower left psi point. maybe Hernan is better to answer. if so,then int(track(ixgrd)) would give the left side of the box at a u-point, and int(track(ixgrd))+1 would be the right side u-point. but you have i1 = MIN(INT (track(ixgrd,nfp1,1)+0.5_r8) ,Lm(ng)+1) i2 = MAX(i1 + 1,0) so ...

jcwarner

yes, use coawst for roms+swan coupling, and that system also has the option to also use wrf. Rutgers has WRF coupling and that is with ESMF. i have not used that yet, but it will be happening soon. Also, Rutgers is looking to couple WAVEWATCH III to ROMS via ESMF, but that is just starting. So for ...

jcwarner

if you are using coawst, please post a message here:
https://github.com/jcwarner-usgs/COAWST/issues

you would need to use coawst.bash
we include a user manual.doc that has lots of info.
thanks
j

jcwarner

looks like model is taking longer to ebb, that could be due to friction too high on the landward side of this site.
you need to look at an animation and see how the flow looks.

jcwarner

when you made the child grid, did you use coarse2fine:

Istr=22; Iend=60; Jstr=26; Jend=54;
ref_ratio=3;
roms_child_grid='Sandy_roms_grid_ref3.nc';
F=coarse2fine('Sandy_roms_grid.nc','Sandy_roms_grid_ref3.nc', ...
ref_ratio,Istr,Iend,Jstr,Jend);

jcwarner

in ROMS/Utility/def_his.F I see # ifdef LMD_SKPP ! ! Define depth of surface boundary layer. ! IF (Hout(idHsbl,ng)) THEN ......... status=def_var(ng, iNLM, HIS(ng)%ncid, HIS(ng)%Vid(idHsbl), & & NF_FOUT, nvd3, t2dgrd, Aval, Vinfo, ncname) IF (FoundError(exit_flag, NoError, __LINE__, MyFile)) RETURN ...

jcwarner

yes i saw your post on the other site and just responded the same thing there. The Sandy test case is a test case. I do that for purposes to demonstrate a procedure for setting up and running the coupled system. The grids are very coarse, and the simulation is short, just to show how to do things ...

jcwarner

i updated the script (get_ijrg.m) a few months ago (?) to use: % % Read HYCOM lon lat depth % display(['getting HYCOM grid data from ', url]) lonlat_fullgrid=1; try numX=ncread(url,'X'); numY=ncread(url,'Y'); hycom_lon=ncread(url,'Longitude'); hycom_lat=ncread(url,'Latitude'); hycom_depth=ncread(url ...

jcwarner

ok thanks for digging in that deep. it helps a lot.
let me look into it. I do remember those min values were only suggestions, from the literature. But if there is an issue with the min being applied to tke*Hz and not to tke (and gls), then that needs to be resolved.
-j

jcwarner

this is a coawst issue that has been resolved.
please do a git pull.
in the future please post these issues on the coawst site here:
https://github.com/jcwarner-usgs/COAWST/issues

thanks
j

jcwarner

i see the mud_time is the same as salt_time. but i dont think that is the problem. you should be able to list any name, as long as the dimension information is correct. you also need to look in the varinfo.dat. the mud vars should be listed as using mud_time. maybe try to change varinfo from mud ...

jcwarner

what does this give:
ncdisp('D:\Data\NC\coase_1010\out_4m\coase_21_bry_nonorth_sed05.nc')

jcwarner

are these 2 files the same:

D:\Data\NC\coase_1010\out_4m\coase_21_bry_nonorth_sed05.nc
and
/public1/home/sc90163/project_hzhy/coase_21/4m_in/coase_21_bry_nonorth_sed05.nc

jcwarner

"The run seems to stop halfway when ninfo is too small, but I'll try to make it as small as possible." When you set Ninfo == 1, roms will make a call to Nonlinear/diag.F every time step IF (MOD(iic(ng)-1,ninfo(ng)).eq.0) THEN in here , roms computes max values for vel and dens, compares them to some ...

jcwarner

yes i figured that. run the job for a short duration and look at the diagnositcs.nc file. you will need to spend some time, start with the depth avg terms. they are easier to figure out. try to add up the terms at one of the time steps: ubar_accel = ubar_sustr+ubar_bustr+ubar_prsgrd+ubar_cor+ubar ...

jcwarner

the wiki does not have a full explanation, but there are other sources to get the meaning of the diagnostics. https://www.myroms.org/wiki/Model_Diagnostics here is a list of the equations https://www.myroms.org/wiki/Numerical_Solution_Technique Kates manual has a nice more full expansion of the ...

jcwarner

this can get complicated in the code. Suggest you use the diagnostics, they are set up to compute all this for you.

jcwarner

ok but can you still try my other suggestions: 1- set Ninof to be 1, so we can see if there is more information. 3 what it the temp coming in for this point source? 4- what is the time series of Qin (river flow) at the problematic point? can you plot that? 5- use KANTHA_CLAYSON, not CANUTO. my ...

jcwarner

so i can offer a few suggestions again 1- set Ninof to be 1, so we can see if there is more information. 2- use HSIMT for all the tracers including salt + temp 3 you say "Another note: forcing for vertical sources varies on a monthly basis. Thus, the input transport, temperature, biogeochem, etc. on ...

jcwarner

at the top of your coawst.bash you have
parallel=0
clean=1
dprint=0
cleanwrf=0
cleanwrfhydro=0
cleanww3=0

switch that to
parallel=0
clean=1
dprint=0
cleanwrf=1
cleanwrfhydro=1
cleanww3=1

this should fix it.

jcwarner

ok now i see your log file.
but that log file is for "william_onlyroms.h"
And that built correctly.
So that is not the correct log file for me to look at.

jcwarner

the problem probably occurred way near the beginning of the build. and then it got to the end and all the modules were not there. When WRF builds, if it gets an error, it keeps going. So you need to scroll way up to the top and start from there to look for the 'error'. You can output the build using ...

jcwarner

the bathy in that test case is very crude. it is only intended as a guide.
Strongly suggest you use a different source for the bathy.
here is one source: https://download.gebco.net/
here is another: https://www.ncei.noaa.gov/products/etop ... lief-model

-j

jcwarner

here are a few thoughts / suggestions. 1 what are the magnitudes of mass transport for the LwSRC? i see: GET_NGFLD_NF90 - river runoff mass transport, 2021-02-20 12:00:00.00 (Grid= 01, Rec=5, Index=2, File: rivers.nc) (Tmin= 18674.5000 Tmax= 18681.5000) t = 18678.5000 (Min = -9.00360189E+03 Max = 1 ...

jcwarner

you really should post this on the coawst site here: https://github.com/jcwarner-usgs/COAWST/issues because Rutgers ROMS does not have all the wave physics yet. We are porting them over but it will take some time. Suggest you look at the COAWST user manual, test cases of Inlet_test, Rip_current ...

jcwarner

this post is about SWAN, and it would best placed on the coawst ticket site
https://github.com/jcwarner-usgs/COAWST/issues
as a short reply, you need to look at any Err* or PRINT* files for more info.
if you are going to follow up, post a new instance on the coawst issues.
-j

jcwarner

Can you look at the different components of the heat budget: lwrad, swrad, latent, sens, and compare the coupled to uncoupled of those 4 terms?

jcwarner

ok, that figure looks better and i can see what you are talking about. Suggest you look at the different components of the heat budget: lwrad, swrad, latent, sens, and compare the coupled to uncoupled of those 4 terms. Try undef ANA_SRFLUX, although i dont think that is the problem. i am not ...

jcwarner

yes i understand what T2 is.
I see an image, with lots of colors, i dont know geographically where it is.
I dont know where the 'anamoly' is, etc. Do the temp issue appear right away, is it on land, on the ocean,
I do not have enough info to understand the issue.

jcwarner

not sure what i am looking at here.
what does the SST in roms look like?

jcwarner

i remember setting this up. there was some trial-and-error to keep the salt where i wanted it. there is a balance between bathy, Qriver, and mixing (basically the tidal forcing). So as you adjust that balance, the salt field will evolve. For that particular very idealized case (constant dh/dx) the ...

jcwarner

EGU2023 - OS1.2/AS2: Air-sea interactions through modeling and observation on multiple temporal and spatial scales. We would like to invite submissions to session OS1.2/AS2: Air-sea interactions through modeling and observation on multiple temporal and spatial scales. This session aims to gather ...

jcwarner

so i just tried the second one you have, and it worked for me: disp('getting roms grid, hycom grid, and overlapping indices') [gn, clm]=get_ijrg(url, modelgrid, theta_s, theta_b, Tcline, N, Vtransform, Vstretching); getting roms grid, hycom grid, and overlapping indices getting roms grid dimensions ...

jcwarner

there is a lot of info in the COAWST_User manual.doc. if you only select the roms model, then coawstM is essentially romsM. if you select additional other models, only 1 executable is created, coawstM. That would run roms + wrf, or whatever. this is a different approach than what Rutgers does, so if ...

jcwarner

use the coawst.bash file in the main dir. I have modified the build to be able to compile all the different models.
if you have more issues please post here:
https://github.com/jcwarner-usgs/COAWST/issues
thanks, j

jcwarner

seems odd.
when you did the test with the extra time step in the middle, what did roms report out when it read the file?
it always reports out the min, max, times, etc. check that.

jcwarner

DIAG speed trouble 93.106400122773167 DIAG speed ijk 131.67231528779021 96 64 1 1 Found Error: 01 Line: 341 Source: ROMS/Nonlinear/main3d.F Found Error: 01 Line: 331 Source: ROMS/Drivers/nl_ocean.h, ROMS_run Blowing-up: Saving latest model state into RESTART file REASON: MaxSpeed = 9.3E+01 WRT_RST ...

jcwarner

I see still: GET_GRID - bathymetry at RHO-points: h (Grid = 01, File: Projects/Katrina/roms_grid_Katrina.nc) (Min = 5.95202990E-03 Max = 3.35037820E+03) that is a min of 0.005 m . I dont think you need a min of 5 mm. try again. in the grid file to set h to have a minimum depth. maybe something like ...

jcwarner

for gls i typically use

# define GLS_MIXING
# ifdef GLS_MIXING
# define RI_SPLINES
# define KANTHA_CLAYSON
# define N2S2_HORAVG
# endif

it can get more options, for surface mixing etc, not sure what type of applications you are using.

for LMD i will let someone else answer.

jcwarner

gls and tke will only be output if you activate GLS_MIXING or maybe also MY25_MIXING.

for the hsbl, those go with the LMD options.

-j

jcwarner

GET_GRID - bathymetry at RHO-points: h (Grid = 01, File: Projects/Katrina/roms_grid_Katrina.nc) (Min = -2.15744419E+02 Max = 3.33282292E+03) you need to activate wet dry if you have negative h values. Suggest you take a look at your grid and decide if you are really resolving wet/dry processes. if ...

jcwarner

how many time steps did you run it for?

jcwarner

where are the locations for the : LwSrc == T

jcwarner

we have MAIN: Abnormal termination: BLOWUP. REASON: MaxDensity = 3.4E+02 can you look in the ocean_rst.nc and see where that density is large? is it at the open boundary? at a river location? maybe try to turn off the rivers, and turn off clm nudging. see if it runs without them to help diagnose the ...

jcwarner

ok so this is a different user on the same post. to zhaoyun- all you are telling us is that it blows up on first time step. You need to provide more information. Look at the std out and see if there is any information like h<0 and no wetdry, or nans in input forc fields, etc. the warnings are ok ...

jcwarner

did you also update your ocean.in file to include the BC's and advection choices?
-j

jcwarner

there can be many reasons why the model is not starting. i remember seeing this GET_GRID - bathymetry at RHO-points: h (Grid = 02, File: Projects/Mangkhut/Mangkhut_roms_grid_ref3.nc) (Min = 0.00000000E+00 Max = 3.49541846E+03) if your min depth is 0, you need to define wet_dry. -j

jcwarner

looks like the simulation starts with zeta = -0.5 but the obs are at +0.5. so it will take a while for that barotropic mode to slosh out of the model. after 2 days the water levels look like they are starting to get into phase. if that storm at time 40 is your main interest, i suggest you start the ...

jcwarner

oops, not enough coffee yet. those ecmwf is for bulk fluxes. there are other posts on getting hycom data, such as: https://www.myroms.org/forum/viewtopic.php?p=23944&hilit=hycom#p23944 https://www.myroms.org/forum/viewtopic.php?p=23938&hilit=hycom#p23938 https://www.myroms.org/forum/viewtopic.php?p ...

jcwarner

doing griddata u for HYCOM level 1 ... doing griddata u for HYCOM level 2 catch u Unable to download HYCOM u data at17-Jul-2022 23:08:30 if it worked for level 1, but not for level 2, that is an internet or Thredds issue. this is common. you can try again, or try some other way. Also, if you want to ...

jcwarner

the tools we have there are for aggregated data

https://tds.hycom.org/thredds/catalog.html
i dont see the 60.5 on that list.

-j

jcwarner

i dont think GLS has changed much in several years, so it should be the same.
-j

jcwarner

ok. First of all let's tackle the AKV_limit issue. This option is intended to prevent the values of Akt and Akv from getting very large. I do a lot of estuary work with lots of mixing, so I recommend setting these limiter values be at something like AKV_limit=1.0d0 and Akt_limit=1.0d0. IF you are ...

jcwarner

Is anyone else using obc_roms2roms.m? I am getting a size mismatch at lines 720-723 B.(ufield) = u .* cos(angle.(edge)) - ... v .* sin(angle.(edge)); the ufield = 'u_west' size(u) = 2 327 40 size(cos(angle.(edge))) = 2 327 40 size(v) = 2 326 40 size(sin(angle.(edge))) = 2 327 40 obviously u and v ...

jcwarner

the variable names change over the years. I have no control in that. I just pushed out an update to the m files. please do an update and try again. thanks. if you have more troubles, please post a message on the coawst git site, as this issue for those tools. https://github.com/jcwarner-usgs/COAWST ...

jcwarner

For the LwSrc, in step3d_t.F near lines 1146 we need to change cff=dt(ng)*pm(i,j)*pn(i,j) to cff=dt(ng)*pm(Isrc,Jsrc)*pn(Isrc,Jsrc) and the same near lines 1343 from cff=dt(ng)*pm(i,j)*pn(i,j) to cff=dt(ng)*pm(Isrc,Jsrc)*pn(Isrc,Jsrc) -j

jcwarner

what bottom stress are you using? UV_LOGDRAG?
what is your Zob?

jcwarner

i think you need more Volume to be filled on the flood, and then this will allow increased flows on the ebb. I was hoping to see more overtides in that water level time series (ie quicker rise to peak water level and longer tail to lower water level). do you see that further into the estuary? i see ...

jcwarner

some quick looks: -how long did you run this for? looks like the salt is getting better as time goes on. -in the attached ppt, the vel in Charcoal bay does not get as strong (peaky) as the observations. So the salt will not get advected as far at those peaks, and that is exactly what you see in the ...

jcwarner

you need to look at how the temperature is evolving over time. does it get warmer from the surface net fluxes and then mix downwards? does it get warmer from the offshore boundary and then propagate in? i see: GET_3DFLD - potential temperature climatology, t = 45 15:45:04 (Rec=0000002, Index=2, File ...

jcwarner

glad it is working for you!
-j

jcwarner

not exactly sure what is going on from that information. but it looks like you are doing a restart, and the model is looking for fields in that restart file. did you do a run with sediment and now restarting that? or did the first run not have sediment? if the first run did not have sediment, then ...

jcwarner

ok i spent some time on this. I think the issue is a bathy mismatch between the child and the parent, especially near the boundary. At the location of that vortex, the child grid has a bathymetric rise, but the parent grid did not see it. So i recommend that you use average child bathy to replace ...

jcwarner

I looked at the grids and they seem ok. the bathy matches well. the dmde looks large in the parent grid. are you running with curvgrid on? also the parent has spherical ='T' and the child has spherical = 1. this is probably not an issue. how did you set the init conditions? are the T/S fields ...

jcwarner

the turbulence and the sediment should be separate. Both MY25 and GLS will output tke and gls. IF you use MY25, then tke is 0.5q^2 (i think, it has been a while) and gls will be the q^2l. IF you use GLS , then tke is tke and gls will be the set depending on the p m n parameters (gls can be ...

jcwarner

looks like the only differences for roms is along the southern boundary.
with nesting, does the vortex start and grow, is it formed during the experiment at the boundary and advect in?
does the child bathy match the parent?
i assume this probably gets deep along that child southern boundary.
-j

jcwarner

Akima is hiring a Technician V position to support the USGS Woods Hole Coastal and Marine Science Center (WHCMSC), Woods Hole, Massachusetts. The Technician V will assist the WHCMSC in developing, implementing, testing, and applying a coupled ocean-atmosphere-wave-sediment transport modeling system ...

jcwarner

if you are having trouble getting hycom data, suggest that you use ECMWF data. John Wilkin has a nice set of tools to do this:
roms_get_era5_NCARds633_bulkflux.m
and
roms_write_era5_NCARds633_frcfile.m
from here:
https://github.com/johnwilkin/roms_wilkin

jcwarner

i am not worried about the free surface, if that is all dry anyway. do you have wet dry on? did you set hmin = 5 in both the parent and child? is this vortex created at the boundary and advected in? can you do me a favor, i made a change to my version of nesting.F, Are you using COAWST? if so please ...

jcwarner

all those 'mem leaks' are for calls to allocate state variables such as allocate ( OCEAN(ng) % rubar(LBi:UBi,LBj:UBj,2) ) allocate ( OCEAN(ng) % rvbar(LBi:UBi,LBj:UBj,2) ) allocate ( OCEAN(ng) % rzeta(LBi:UBi,LBj:UBj,2) ) allocate ( OCEAN(ng) % ubar(LBi:UBi,LBj:UBj,3) ) allocate ( OCEAN(ng) % vbar ...

jcwarner

ok i need another one. Build/mod_ocean.f90
-j

jcwarner

not sure what these are, but if you got a netcdf output file, then the model ran fine.
can you post
Build/mod_arrays.f90
that seems to come up a lot.
thanks
j

jcwarner

I think this person is using COAWST. And yes they should add SST to cover non-Roms areas, and they probably are. We have had this option since the beginning of the coupling. What we do is use the SST from the WRFlow file, and replace that with ROMS data wherever the ocean is. We do that for each ...

jcwarner

is this the nest or the parent grid?
if this is the nest, are the vortices advected into the nest from the parent?
what do the temp and salt fields look like? you are using radnudge on the south, so what are you nudging to?

jcwarner

it is not possible for me to tell what is going on. The issue is with the array sizes. You will need to put in break points, see what the arrays are, the sizes, the values, and follow the arrays as they are passed to each routine. it is not that hard, just put in break points. when matlab stops at ...

jcwarner

for example here https://tds.hycom.org/thredds/dodsC/GLBy0.08/expt_93.0/FMRC/runs/GLBy0.08_930_FMRC_RUN_2022-05-05T12:00:00Z.html the variable list will show for time: units: hours since 2022-04-30 12:00:00.000 UTC so the 120 is hours since that time. You need to look for these attributes on the ...

jcwarner

sorry. i think you posted a message on the coawst issues and i did not get back to you.
i think you have a misspelled cpp def

define ATM2OCE_FLUXES
should be
define ATM2OCN_FLUXES

then do a ./coawst.bash and see if that compiles better.
-john

jcwarner

https://www.myroms.org/wiki/River_Runof ... _Eposition
is a good description of the river locations.
it needs to be coming out of the land masked cell.

jcwarner

it could be i, j, or transport.
make sure the Q is positive for flow to the right.
look at the u values and ensure the rivers are coming from the correct locations.
those locations should be masked points. the river flow will overwrite the zero values at the masked locations.

-j

jcwarner

if you are using coawst, you can post a message here:
https://github.com/jcwarner-usgs/COAWST/issues

also i suggest you look at the Inlet_test case and the User manual for descriptions on how to set these up.
-j

jcwarner

ok. if you min depth = 5 meters, and then wet/dry helped, i suggest you look at the zeta values to make sure the tides are ok. what is the tide range in this area? for the next problem, that is probably a density issue. closely look at what is being put along that boundary for temp salt u v etc. you ...

jcwarner

you could look at
At line 322 of file inp_decode.f90
and see what is trying to be read. looks like it wants a real but getting an integer or something like that.

jcwarner

what is the bathy in that corner? i see you have 2 Vtransform S-coordinate transformation equation. 4 Vstretching S-coordinate stretching function. 5.0000E+00 theta_s S-coordinate surface control parameter. 4.0000E-01 theta_b S-coordinate bottom control parameter. 50.000 Tcline S-coordinate surface ...

jcwarner

not sure if this is the correct answer, but you need to be consistent with salinity and NT value settings.

If you use
#define SALINITY
then make sure ocean.in has NAT = 2

If you use
#undef SALINITY or not even mention salinity,
then make sure ocean.in has NAT = 1

-j

jcwarner

not sure what you mean by the visc values. Are you using horiz viscosity: #define UV_VIS2 #define MIX_S_UV then you can set VISC2 == 2.0d0 ! m2/s ??? or something like that Perhaps the tracer horiz diffusivity is more what you need: # define TS_DIF2 # define MIX_GEO_TS TNU2 == 0.5d0 ! m2/s ??? or ...

jcwarner

oh ok. let me look at that glossary, it might not be worded clearly.
can you paste that part of the glossary here?
if you choose k-e coeffs, then gls will be e (dissipation).

jcwarner

here is a good paper with lots of info: Warner, J.C., Sherwood, C., Arango, H., and Signell, R. (2005). “Performance of Four Turbulence Closure Models Implemented Using a Generic Length Scale Method.” Ocean Modelling, v. 8/1-2, p. 81-113. the GLS scheme is a method that transports tke and 'gls' = ...

jcwarner

that is only a warning.
For WRF you need to
export NETCDF=/location/of/netcdf
did you set that?

jcwarner

this is more of a coawst configuration issue, and should be posted here:
https://github.com/jcwarner-usgs/COAWST/issues
can you post this and the coupling.in file over there.
-j

jcwarner

i had a little trouble following your logic, but it is not really clear what is causing the differences in the tke. Can you look at fields of temp, u, v, AKv, etc to see if there is something noticeably different in the runs? like something happening along the open boundary. Are there rivers (with ...

jcwarner

this is a common issue with gfortran
you need to edit the Makefile.conf (i think) and add a fflag
-fallow-argument-mismatch

-j

jcwarner

your executable is created here: -o ./scrip_coawst so it does not have a .exe on the end. do a ls -ltr and do you see ..... -rw-rw-r-- 1 jwarner domain users 103960 Jan 10 2020 remap_write.o -rw-rw-r-- 1 jwarner domain users 19413 Jan 10 2020 scrip.fpp -rw-rw-r-- 1 jwarner domain users 20302 Jan 10 ...

jcwarner

make sure you have
c:/cygwin64/usr/include/mpif.h
if not then you missed something during the setup, like libopenmpifh40 or something like that

jcwarner

can you post this message here:
https://github.com/jcwarner-usgs/COAWST/issues

jcwarner

All the boundary condition options have been moved to the ocean.in file. You dont need the boundary cpp options like EW_PERIODIC or FSCLAMPED etc. it is all in the ocean.in For Example: ! Set lateral boundary conditions keyword. Notice that a value is expected ! for each boundary segment per nested ...

jcwarner

Sunny up here but looks like rain coming your way Hernan. Enjoy the day! -j

jcwarner

viewtopic.php?p=23617#p23617

not sure if this was fixed yet or not.
-j

jcwarner

maybe you could help a bit and track that message, what is on

/mnt/c/Users/lyras/OneDrive/install_roms/folder_tes/Build_romsG/mod_scalars.f90:2595

jcwarner

i am not sure the difference between those 2 output files. the server.log has - bathymetry at RHO-points: h (Grid = 01, File: bowl_grid.nc) (Min = 2.00018817E-02 Max = 1.00000000E+03) Minimum Z-grid spacing, DZmin = 6.53658218E-04 m that is a small dz somewhere. you have thetas =10. maybe adjust the ...

jcwarner

both the Netcdf libs and roms need to be built with the same compiler and version of that compiler.

type this:
nf-config --all

and this
mpif90 -v

find out what compiler was used to build the Netcdf libs, or have someone rebuild the netcdf with the same mpif90 that you are using.

jcwarner

how about you post the whole output, not just the last part.
there might be something wrong with the init conditions.

jcwarner

I am nots really sure what all to suggest here. A few images back , you had zeta on the west side at -8m. Can you figure out why that happened? Even a super strong wind would have trouble to do that. I thought the winds might not be rotated to the grid correctly. Suggest you set roms to write out ...

jcwarner

do you have
#define CURVGRID
that might help with some of the advection.
take a look at the winds in that ncviewer. how strong are they on the west side?

-j

jcwarner

does it run without the clm nudging?
look at the entire output file, there might have been more info before the nan.

jcwarner

1581120 2008-07-02 00:00:00.00 0.000000E+00 1.453619E+04 1.453619E+04 1.282427E+15 (000,000,00) 0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00 DEF_HIS - creating history file, Grid 01: Ev08_his_coupled_00184.nc WRT_HIS - wrote history fields (Index=1,1) in record = 0000001 DEF_AVG - creating ...

jcwarner

think you are changing too many things here. ERA winds should not affect the tides. and dont rely on ncview to give you the max/min. click at a point and get a time series. try this: You have this: Variable Grid West Edge South Edge East Edge North Edge ...

jcwarner

on this page, top figure, what is 'wrong' with the zeta?

jcwarner

looking better.
there are 'extrapolation' options, which need to be used with caution.
but give that a try.
maybe someone else has a better idea.

jcwarner

it just wants you to enter the data as a column. lets say this is a 2D field in x and z. lets also say that you have 10 vertical layers and we are looking at the y index of 35 (just picking any number here). N=10; yidx=35; X=repmat(lon_rho(:,yidx),N); Z=z_rho(:,yidx,:); S=squeeze(salt(:,yidx,:,tidx ...

jcwarner

" linear interpolation over one column at the time" - that is probably not a good idea.
try a 2D interpolation scheme. Are you using matlab?
help scatteredInterpolant
F = scatteredInterpolant(x_rho,z_rho,salt);
saltnew= F(xnew,znew);

jcwarner

take a look at the file Build/mod_ncparam.f90 at line 1039 and see what it is looking for.

romsS 00000000005696B9 mod_ncparam_mp_in 1039 mod_ncparam.f90

jcwarner

"forrtl: severe (408): fort: (2): Subscript #2 of the array FRC has value 1 which is greater than the upper bound of -1" i looked in your ocean.in and you have: !NFFILES = 1 ! number of unique forcing files !FRCNAME == /disk3/chenzhixing/ROMS/cases/laizhou/laizhou-frc.nc ! forcing file 1, grid 1 ...

jcwarner

this configuration is for ROMS by itself. the model runs for a while, as you say, and then 13510 2010-01-04 03:03:20.00 5.896200E-02 1.757339E+04 1.757345E+04 1.160390E+16 (127,016,32) 1.571469E-02 1.362909E-02 7.575998E+00 2.012555E+01 DIAG speed trouble 20.125553145124616 ... Blowing-up: Saving ...

jcwarner

" Cha for free-surface and Rad for momentum in 2D and 3D mode, the boundary file is not read" Yes, those BC's do not need any external data. so a file does not need to be read. " RadNud for free-surface or Fla mode for momentum in 2D mode, the input boundary file is usually read" Yes, RadNud needs ...

jcwarner

difficult to assess why the model would blow up with that limited information. if you want to run the simulation and have the blow up occur, look at the rst file, his file time steps right before the blow up, etc. that can help to diagnose what may have been going on. look at water levels, currents ...

jcwarner

what does the grid angle look like?
also, when you make those pcolor plots, are they
pcolorjw(lon_rho,lat_rho,angle)
and use
pcolorjw(lon_u,lat_u,ubar)
etc

You said the u and v are ok, but the u_east and v_north are not? so that might be an angle issue.

jcwarner

small but tricky bug when #define SINGLE_PRECISION 1) in get_idata we have real(r8) :: time_save = 0.0_r8 but it needs to be real(dp) :: time_save = 0.0_dp 2) And then there are multiple uses of: time_save=time(ng) time(ng)=8640000.0_r8 .... call get2d.. time(ng)=time_save I think this should be ...

jcwarner

you need to be careful in here, as some routines (like MPDATA) are a little different than others.
but at the bottom of step3d_t is where the units become Tracer only. it can happen in the diffusion step, and here again you need to be careful if splines are on or not.

jcwarner

i just downloaded the code the other day, and the RIVERPLUME1 test case worked fine for me. give that a try. i dont understand if you are using RIVERPLUME1 or trying to use that as a guide. if it is a guide, then you need to define your own application in ana_psource and copy those lines of code to ...

jcwarner

sorry for the very long delay on this response. i had lost this thread. when coupled to swan, the wec breaking is the wave dissipation from swan. it comes from swan as a variable DISSURF and put into roms variable Dissip_break. That Dissip_break is used: - #define WEC_VF then it is used to drive ...

jcwarner

starting with the most recent version of Rutgers code, I used the RIVER_PLUME1 test case because it has 1 UV_Psource location for a river entering a N-S Periodic domain with East and West walls. Therefore, the entire volume change within the domain is due to the river inflow. I ran the test case 'as ...

jcwarner

if you want to use a coupled roms+swan, then you need to use COAWST
https://github.com/jcwarner-usgs/COAWST
-j

jcwarner

i did a grep -nir hbbl ROMS/* and got a lot of results, but i think the most relevant is in ROMS/Nonlinear/lmd_bkpp.F and it says "This routine determines the depth of bottom oceanic boundary ! ! layer, hbbl, as the deepest depth where the bulk Richardson ! ! number is equal to the critical value ...

jcwarner

if you are going to use ROMS + SWAN coupling, then please use the COAWST code here:
https://github.com/jcwarner-usgs/COAWST

that should run 'as is' and give the outputs, this is an example test case.
thanks,
john

jcwarner

there are probably a few things not correct here, you will need to try and figure them out. for swan Err file01 -001 : this is for grid 1, tile 1 (so probably left side) it has Error : invalid boundary point Error : ( -99 -99) is outside computational grid so most likely one of the Boundspec ...

jcwarner

half right, half not. for ini and clm: you can use the parent ini and clm to make the first child ini and clm. Then use those first child ini and clm to make the files for the 3rd grid. for the contact: roms only wants 1 contact file, so to create a contact file for 3 grids you need to make all 3 ...

jcwarner

this is now a SWAN error. I see in Errfile02-001 (this is for swan grid 2, tile partition 1) Error : invalid boundary point Error : ( -99 -99) is outside computational grid Error : invalid boundary point Error : ( -99 -99) is outside computational grid Error : File is already opened: Projects/Tembin ...

jcwarner

this is for ROMS.
It looks like your ocean.in has

Ngrids = 2
NestLayers = 2

but it must have been compiled without nesting. the error is saying that you can only have NestLayers = 1 for non-nesting.
think you need to add
#define NESTING
to *.h file and recompile.
-j

jcwarner

wow! thanks for diggin in. But i see in mod_ncparam.F

ic=5
DO i=1,MT
ic=ic+1
isTvar(i)=ic
END DO
....
isWvel=ic+1

are you saying ifort can not do "DO i=1,0" ?

there still should be a value for ic =5.

jcwarner

what is on line 904 of mod_ncparam.f90
(the f90, not the F)
mod_ncparam_mp_in 904 mod_ncparam.f90

jcwarner

can you post the issue here:
https://github.com/jcwarner-usgs/COAWST/issues
and include the output during the run or during the build?
thanks,
j

Search found 1200 matches