intro story Coast / Estuary

Coast / Estuary

Coastal systems are among the most dynamic physical systems on earth and are subject to a large variety of forces. The morphodynamic changes occurring to coastlines worldwide are of great interest and importance. These changes occur as a result of the erosion of sediments, its subsequent transport as bed load or suspended load, and eventual deposition. 
 
Estuaries are partly enclosed water bodies that have an open connection to the coast. Estuaries generally have one or more branching channels, intertidal mudflats and/or salt marshes. Intertidal areas are of high ecological importance and trap sediments (sands, silts, clays and organic matter).
Within the Delft3D modelling package a large variation of coastal and estuarine physical and chemical processes can be simulated. These include waves, tidal propagation, wind- or wave-induced water level setup, flow induced by salinity or temperature gradients, sand and mud transport, water quality and changing bathymetry (morphology). Delft3D can also be used operationally e.g. storm, surge and algal bloom forecasting. 
 
On this discussion page you can post questions, research discussions or just share your experience about modelling coastal and/or estuarine systems with Delft3D FM. 
 

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Sub groups
D-Flow Flexible Mesh
DELWAQ
Cohesive sediments & muddy systems

 

 

Message Boards

Problems with *.d50 and *.sdb files

SI
Sasha Izru, modified 8 Years ago.

Problems with *.d50 and *.sdb files

Youngling Posts: 20 Join Date: 9/16/12 Recent Posts
Hi everyone!
I am feeling a little silly for the questions that I’m going to do, but I hope that someone can help me to clear my doubts.

I am doing morphodynamic simulations, using the on-line option (WAVE+FLOW). The way, that I am running WAVE+FLOW, is trough script/command line (I did a *.bat file) and I have had success when I have ran my cases. In some of my test cases and talking about sediment transport formulations, I have used the Van Rijn and Bijker.

First question:
In all my cases, I used uniform values in all the parameters. But now, I would like to vary spatially values such as d50 and initial sediment layer thickness. In order to do this, I did the *.sbd and *.d50 files, following the tips of Ben Williams and Bert Jagers:


Later, I got d50 and initial sediment layer thickness files, I changed all the negatives values on these files in order to avoid messages about negatives data. About the last lines of both files, the block of lines where appear -999.00 (NaN), I copied the previous block of lines with different value of -999.00.

My *.sed file has the next lines:

[SedimentFileInformation]
FileCreatedBy = Sasha
FileCreationDate = Thu Dec 05 2012, 18:39:32
FileVersion = 01.00
[SedimentOverall]
IopSus = 0 :
Cref = 1.6000000e+003
[Sediment]
Name = #Sediment sand#
SedTyp = sand
RhoSol = 2.600000e+003
SedDia = d50.d50
CDryB = 1.7000000e+003
IniSedThick = tsv.sdb
FacDSS = 1.0000000e+000

When I try to run the simulation, WAVE starts to compute the first iteration and when the iteration ends, FLOW begins to compute, but suddenly, the FLOW window is closed automatically.
I checked the tri-diag file and I didn’t find some message which tells me what it was the error.

I have enormous doubts about the correct format of *.d50 and .sdb files.
Is there anyone that could give me some suggestion in order to know what happen in my simulation?

I’m attaching my *.sbd and *.d50 files to this post.

Second question:
In one of my morfodynamic simulations where I had “partially” success (using uniform values on SedDia and IniSedThick), in the tri-diag file, I found five error lines with these messages:
*** WARNING Bed change exceeds 5.0 % of waterdepth after 1443 timesteps, location (m,n) = (581,2)
*** WARNING Bed change exceeds 5.0 % of waterdepth after 1444 timesteps, location (m,n) = (581,2)
Sediment erosion shortage at NM 42343 Fraction: 1 Mass available : -0.2220E+02 Mass to be eroded: -0.4177E+02
Sediment erosion shortage at NM 42344 Fraction: 1 Mass available : -0.2897E+02 Mass to be eroded: -0.4192E+02
Sediment erosion shortage at NM 42345 Fraction: 1 Mass available : -0.3213E+02 Mass to be eroded: -0.4200E+02

To avoid these messages, should I increase the uniform value of my initial sediment layer thickness?

Thanks for any suggestion!

Cheers.

Sasha
Qinghua Ye, modified 8 Years ago.

RE: Problems with *.d50 and *.sdb files (Answer)

Jedi Council Member Posts: 610 Join Date: 3/2/11 Recent Posts
Hi Sasha,

For the sediment diameter file *.d50, did you notice that the values are quite big? Like there are some values like 4.9950463E+00. I am not sure what it is, but do have a check.

For the 2nd question, yes. The sediment erosion is bigger than the sediment available.

Hope this help a bit.

Qinghua
SI
Sasha Izru, modified 8 Years ago.

RE: Problems with *.d50 and *.sdb files

Youngling Posts: 20 Join Date: 9/16/12 Recent Posts
Hi Qinghua,

I checked up my *.d50 and *.sbd files and it is true the files have some values which are different to the values that I specified. I have make other *.d50 files, using the QUICKIN, in order to know if I did a mistake, but not. I have seen that QUICKIN handles different values when the cell has M = 1 in all my test cases of QUICKIN.
Is a possible bug of QUICKIN?

Well, I edited the *.d50 and *.sbd files of my morphological simulation and I put the correct values, but again, I ran the simulation and I have the same result that I described in the last post: not error messages. Really, I do not figure out what happen.
Any idea or suggestion?

About the second question, thank you for cleaning my doubt. Now, I am convinced I should use the *.sbd.

Attaching the new *.d50 and *.sbd.

Thanks

Sasha
Qinghua Ye, modified 8 Years ago.

RE: Problems with *.d50 and *.sdb files

Jedi Council Member Posts: 610 Join Date: 3/2/11 Recent Posts
hi Sasha,

I didn't see any thing strange this time... We probably need more information to target the problem.

Is it possible that we get the full input files to reproduce the problem?

Regards,

Qinghua
SI
Sasha Izru, modified 8 Years ago.

RE: Problems with *.d50 and *.sdb files

Youngling Posts: 20 Join Date: 9/16/12 Recent Posts
Hi Qinghua!

I have uploaded to Dropbox, a folder with a *.zip file in which I put all my input files. In this folder, I also put all the files that I got when I tried to run the simulation.
If it is possible, may you tell some email address in order to share the *.zip file via Dropbox or email?

Thank you.

Regards.

Sasha
Qinghua Ye, modified 8 Years ago.

RE: Problems with *.d50 and *.sdb files

Jedi Council Member Posts: 610 Join Date: 3/2/11 Recent Posts
Hi Sasha,

You can send to my email: qinghua.ye@deltares.nl.

Regards,

Qinghua
Qinghua Ye, modified 8 Years ago.

RE: Problems with *.d50 and *.sdb files

Jedi Council Member Posts: 610 Join Date: 3/2/11 Recent Posts
Hi Sasha,

I cannot reproduce your problem.

In my computer, it works fine as the setup and I didn't find anything wrong with your setup as well.

The zip file is attached.

Qinghua
SI
Sasha Izru, modified 8 Years ago.

RE: Problems with *.d50 and *.sdb files

Youngling Posts: 20 Join Date: 9/16/12 Recent Posts
Hi Qinghua,

I ran again my failed case, but now I could get an image of Flow command window with an error message.
I attach the image and I hope this message gives some idea about what it is the problem.
Message says Flow can't open a file, what could it be that file? tabmom?

Regards.

Sasha.
SI
Sasha Izru, modified 8 Years ago.

RE: Problems with *.d50 and *.sdb files

Youngling Posts: 20 Join Date: 9/16/12 Recent Posts
Hi Qinghua,

I followed your advice and now, my simulations are running.

Thank you for all your support!

Happy Holidays!

Sasha
AR
Andi Ramli, modified 6 Years ago.

RE: Problems with *.d50 and *.sdb files

Youngling Posts: 5 Join Date: 6/17/13 Recent Posts
Hi All,

I am trying to use this *.d50 file as the SedDia, which is written in the .sed file as follow:

[SedimentFileInformation]
FileCreatedBy = Delft3D FLOW-GUI, Version: 3.43.05.22651
FileCreationDate = Fri Oct 31 2014, 14:47:41
FileVersion = 02.00
[SedimentOverall]
Cref = 1.6000000e+003 [kg/m3] CSoil Reference density for hindered settling calculations
IopSus = 0 If Iopsus = 1: susp. sediment size depends on local flow and wave conditions
[Sediment]
Name = #Sediment sand# Name of sediment fraction
SedTyp = sand Must be "sand", "mud" or "bedload"
RhoSol = 2.6500000e+003 [kg/m3] Specific density
SedDia = sed50.D50 [m] Median sediment diameter (D50)
CDryB = 1.6000000e+003 [kg/m3] Dry bed density
IniSedThick = 1.5000000e+001 [m] Initial sediment layer thickness at bed (uniform value or filename)
FacDSS = 1.0000000e+000 [-] FacDss * SedDia = Initial suspended sediment diameter. Range [0.6 - 1.0]



but I always get this error in the Flow GUI:

Fatal errors encountered while reading file
...
Import will be aborted!

Error reading file at sediment Sediment sand, key SedDia
+++++++
Import rejected!
+++++++

Hence, I can not use the .sed file with spatially varying sediment grain size.

Could you please advise me what it is wrong here? Thank you in advance.

Cheers,
Nayo Ramli
U
Jack Teo, modified 4 Years ago.

RE: Problems with *.d50 and *.sdb files

Hi Sasha,

I am trying to run a similar simulation as yours and I wanted to ask you for some tip to solve the problem you had.

Hope to hear from you soon if it doesn't take too much of your time mate.

Thank you very much! emoticon



Cheers
Jack