Ocean Modeling Discussion

hello,
I think they are the same units, because either NO₃ or NH₄ has only one nitrogen per molecule.

Hello,
You may check the units attribute of the time variable (such as "ocean_time") in "zjw_ini.nc". If it starts with "days since", you may change it to "hours since"; Or reset its value correctly. For instance, you may need 58362/3600=16.2117 (days since 2018-09-01).
PS: This is not a bug.

Thanks! Sometimes, my NTIMES is not integer multiples of NDEFAVG, which causes the problem. :shock:
Moreover, when I checked the output.F, it says:
Line 399-402
IF (((iic(ng).gt.ntstart(ng)).and. &
& (MOD(iic(ng)-1,nAVG(ng)).eq.0)).or. &
& ((iic(ng).ge.ntsAVG(ng)).and.(nAVG(ng).eq.1))) THEN ...

(1) mod_arrays.F
Line 67
& deallocate_seabed, &
Line 266
CALL allocate_sedbed (ng)
should be

& deallocate_sedbed, &
CALL deallocate_sedbed (ng)

(2) read_phypar.F
Block of "#ifdef AVERAGES" from line 4095
Line 4097
OutFiles=ntimes(ng)/ndefAVG(ng)

should add the same process as other ...

(1) wrt_tides.F
line 91
SUBROUTINE wrt_tides_nf90 (ng, tile)
line 367
SUBROUTINE wrt_tides_pio (ng, tile)
should be

SUBROUTINE wrt_tides_nf90 (ng, tile, LBi, UBi, LBj, UBj)
SUBROUTINE wrt_tides_pio (ng, tile, LBi, UBi, LBj, UBj)
(2) def_tides.F
line 64
CALL def_tides_nf90 (ng)
line 68 ...

Yes, I omitted it.
Thank you!

Hello,
From line 183 to 223, the fennel_mod.h says:
#ifdef CARBON
# ifdef OXYGEN
# if defined PO4 && defined RIVER_DON
NBT=15
# elif defined RIVER_DON && !defined PO4
NBT=14
# elif defined PO4 && !defined RIVER_DON
NBT=13
# else
NBT=12
# endif
# else
# if defined PO4 && defined RIVER_DON
NBT ...

bkresning found a bug in the Matlab script "nc_read.m", line 430.
it should be
case {netcdf.getConstant('nc_int'), ...
netcdf.getConstant('nc_short'), ...
netcdf.getConstant('nc_byte')}
f = double(f).*scale+offset;
the original post is in:
https://www.myroms.org/forum/viewtopic.php?f=23&t=4677

Undefined function or variable 'nc_int'.

Error in nc_read>nc_read_matlab (line 430)
case {nc_int, nc_short, nc_byte}

Error in nc_read (line 95)
f = nc_read_matlab(ncfile,Vname,Tindex,ReplaceValue,PreserveType,Info);

Error in d_ecmwf2roms_na (line 476)
field = nc_read(InpFile, Vecmwf, Rec ...

Maybe you did not compile NetCDF with a suitable HDF library?

Sometimes, it's tricky to compile NetCDF and HDF4/5 completely. Therefor, creating all nc files under format of "classic" or "64bit" which is "Original NetCDF format" could be an easier way to bypass re-compiling NetCDF and other ...

I have similar problem with dates in my Input climatology file. Did you maybe solve your problem or not yet?
As mentioned in the post, it was the false attribute in a time variable (such as in the "river_time") that caused my problem. If ROMS does not find an attribute of "units", it will use ...

There may be a little bug in "check_multifile.F".

When my river force file encountered a problem (owing to a missing "s" of "units" in attribute :? ), said:
CHECK_MULTIFILE - Error while checking input Sources/Sinks Data file:
../input_const/ECS_N1_1_rvr.nc
last data time record available is for ...

I always use
[lon_rho, lat_rho, ~, ~, ~] = wlgrid('read', 'd3d_all.grd');
to get the full grid without deleting any land point.

And then
[tmp_lon_mask, ~, ~, ~, ~] = wlgrid('read', 'd3d_water.grd');
mask_rho = ones(size(lon_rho));
mask_rho(tmp_lon_mask == 0 | isnan(tmp_lon_mask)) = 0;
to ...

In general, ROMS reads Coriolis factor "f" from the grid file. If using Matlab to create a grid file, you may find a function-"sw_f" provided by authority, which calculates it on every points. Or do you not offer your own grid but use an analytical one?

function f = sw_f(lat)

% SW_F Coriolis ...

Thanks for your correction!

In my opinion, if the added judgement works, the 1st record is the only bad one and should be discarded, is that right?

if (F(n).scale < 0),
step = rem(frc_time,0.5)*24;
if step == 3
fieldfinal = field;
elseif step == 0

fieldfinal = field - field_previous; % At other steps subtract
end % the previous accumulation

frc_time = frc_time - 1.5/24; % Center forcing time on the
% accumulation interval

field ...

0) before applying your own netcdf 4.3.3, maybe its "make check" should be passed through at first.
1) since a certain version, netcdf-fortran is splitted out, therefor the environment parameter "LIBS" should be set like this:
"LIBS := -L$(NETCDF_LIBDIR) -lnetcdf -lnetcdff" instead of
"LIBS := -L ...

There may be some bugs in netcdf when doing "make check", and a possible solution is "make" firstly, means "make; make check". As mentioned in the document of netcdf, it is complicated and without "check", there may hide some risks :twisted: (Generally, "install" will never check the capability but ...

Could you please post the output of command: "make install" or "make check", rather than "configure"?

There are many tips about Segmentation fault in FAQ https://www.myroms.org/wiki/Frequently_Asked_Questions#Segmentation_fault
It's a copy:
Segmentation fault
There is more than one way to get a seg fault. Ways I know of include (a) running out of memory or some other system limit, (b) accessing ...

I met a similar problem. Maybe it can give you a small hint or nothing .
My fault was giving a wrong time unit in boundary file, says the 'units' attribute of "zeta_time". viewtopic.php?f=19&t=3450&hilit=time+unit

For example, if this is netCDF file including two days data, time array is 0 12 24 36 48 3 6 9 15 18 21 27 30 33 39 42 45.

Thank you very much to hbzong. I was struggling from a while with internal times of ERA-interim netcdf's extracted from the data portal and now finally I have understood.
For ...