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

Spatially varying grain size

Ben Williams, modified 8 Years ago.

Spatially varying grain size

Jedi Knight Posts: 114 Join Date: 3/23/11 Recent Posts
Hello.

I'd like to ask a question about including spatially varying grain size within a Delft3D simulation.

My interpretation of how you do this is as follows:

1) Run a simulation to give a map file.
2) Use Quickplot to export a variable (e.g. bed level) at water level points (as opposed to velocity points) as a .grd and .dep file. I say at water level points because the FLOW manual (pg 542) specifies that the .d50 file must give values at cell centers.
3) Use QUICKIN to impose zones of whatever grain size you want (in units of metres, and assuming that the grain sizes are valid for the transport formula you are using).
4) Change the extension name of the modified .dep file to .d50
5) In the *.sed file, change the following line:
(from) SedDia = 1.0000000e-003 [m] Median sediment diameter (D50)
(to) SedDia = <name>.d50 [m] Median sediment diameter (D50)

Am I correct in outlining the proceedure?

Kind regards,

Ben
Ben Williams, modified 8 Years ago.

RE: Spatially varying grain size (Answer)

Jedi Knight Posts: 114 Join Date: 3/23/11 Recent Posts
Issue solved.

For those of you who may also wonder how to do this, change the following line in the .sed file:

(from) SedDia = 1.0000000e-003 [m] Median sediment diameter (D50)
(to) SedDia = #<name>.d50# [m] Median sediment diameter (D50)

In order for the file to be read in, it must be enclosed by ## This is not at all obvious in the manual.

Ben
Bert Jagers, modified 8 Years ago.

RE: Spatially varying grain size (Answer)

Jedi Knight Posts: 201 Join Date: 12/22/10 Recent Posts
Hi Ben,

Two posts, two responses:

1a) You are correct when you say that the file format of a spatially varying grain diameter file is equal to that of a depth .dep file; changing the extension from .dep to .d50 is not necessary for the program but helps the user (i.e. yourself, colleagues and support) to understand what the purpose is of the various files is (minimum amount of metadata). By default QUICKIN is set to generate values at the corner points of the grid. If you check Operations -> Data in Cell Centre then QUICKIN will generate a depth file with data in cell centres (i.e. in water level points) what you need for the grain diameter or bed composition in general. It's not necessary to follow the approach you describe. Note that you can also provide the initial depth at those points; in that case you will need to select Numerical Parameters -> Depth specified at: Grid cell centres in the FLOW-GUI (dpsopt = #dp# in the .mdf file).

1b) You write "Use Quickplot to export a variable (e.g. bed level) at water level points (as opposed to velocity points)" The text "as opposed to velocity points" is not correct. Traditionally Delft3D (in the days of Delft3D-MOR the predecessor of Delft3D-FLOW with online sediment transport and morphology) computed the bed levels at the corner points of the grid (i.e. the intersections of the grid lines). This is the same place where QUICKIN interpolates the depth values to by default. The edges of the grid are the locations where the velocities are computed.

2) Concerning the use of numbers and strings in the Delft3D input files. One can do either:
SedDia = #<name>.d50# [m] Median sediment diameter (D50)
or
SedDia = <name>.d50
That is, if you want to add comments to the line with the keyword and value then you need to highlight which part of the line represents the value. One cannot identify where a string ends if more characters follow (file names may contain spaces), so therefore you need to encompass a string value between hash-signs. The hash-signs are not necessary if all characters to the right of the equal sign is the value. For a number there is some logic to identify it so hash-signs are not necessary but it's still allowed, so
SedDia = #1.0000000e-003# [m] Median sediment diameter (D50)
would be perfectly acceptable.

General warning: Delft3D will first check whether it can find a file with the name specified. If it cannot find such a file then it will try to identify the number in the line; but the number does not have to be at the start of the line. So,
SedDia = 0.05
would read a file called "0.05" if that exists in the current directory, and
SedDia = #missingfile.d50# [m] Median sediment diameter (D50)
would result in a grain diameter of 50 metre if the missingfile.d50 isn't found (since 50 is the first - and only - number between the hash-signs).

Success,

Bert
Ben Williams, modified 8 Years ago.

RE: Spatially varying grain size

Jedi Knight Posts: 114 Join Date: 3/23/11 Recent Posts
Hello Bert,

Thank you for the information and also for the clarification on technical points. I appreciate your input.

Kind regards,

Ben
AR
Andi Ramli, modified 6 Years ago.

RE: Spatially varying grain size

Youngling Posts: 5 Join Date: 6/17/13 Recent Posts
Hi Ben and Bert,


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
Qinghua Ye, modified 6 Years ago.

RE: Spatially varying grain size

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

As Ben mentioned,

SedDia = #sed50.D50# [m] Median sediment diameter (D50), the filename needs to be in ##.

Regards,

Qinghua
ZM
zhina mohammed, modified 5 Years ago.

RE: Spatially varying grain size

Youngling Posts: 23 Join Date: 12/14/15 Recent Posts
Hi everyone
I am setting up sediment transport model in a river
I have some questions if could help me with
1. I want to input multiple grain size in sediment part
what I have done, is in process part, I input 6 sediment type, Now for every sediment ask for density and d50, I wonder if my step is correct? and for inputting concentration for each fraction, I will multiply percent to a total concentration like Fraction 1, concentration=3%* total concentration, and so on

2. can I indicate 2 different type of sediment in the simulation, for example, I want to one of my fraction to be sand and the other to be mud, is that possible by choosing different type sediment?

3. I wonder why the model asks for the concentration at downstream, why the model can not estimate the concentration at downstream?



Your help is appreciated
Thank you in advance
Zhina
Richard Measures, modified 5 Years ago.

RE: Spatially varying grain size

Jedi Knight Posts: 178 Join Date: 3/23/11 Recent Posts
Hi Zhina,

It sounds like you are on the right track. In answer to your questions:
  • It is correct that you will have to supply density and size for each sediment fraction. If all the sediment is from the same source it may well be that the density is the same for all fractions but the size is different. However if you have multiple rock types it may be useful to have sediment with different densities also. I'm not sure I fully understand the second half of this question.
  • Yes you can have two different sediment types in your simulation.
  • The model needs a concentration for all boundaries in case water flows in from that boundary. Your downstream boundary condition is most likely a water level boundary condition of some kind. In your model (of a river) it only experiences outflow, but in a different model the same type of boundary could experience flow reversals (e.g. in a tidal situation) and the model would need to know what concentration to impose at the boundary. For your case it doesn't matter what concentration you put at the downstream boundary as it will never be used.


Hope that helps,
Richard
ZM
zhina mohammed, modified 5 Years ago.

RE: Spatially varying grain size

Youngling Posts: 23 Join Date: 12/14/15 Recent Posts
Hi Richard;
Thank you for your answer.
now, my model is working well.



Best Regards
Zhina
MK
Manuela König, modified 3 Years ago.

RE: Spatially varying grain size

Youngling Posts: 4 Join Date: 6/12/17 Recent Posts
Hej,

I am trying to build a D50 file to specify my grain size diameter for my sand fraction.
I followed all the discribed steps but getting the ERROR message: *** ERROR Sediment diameters must be positive!

I checked my d50 file, but there are no negative values in it.

Hope you might help.
Attached you find my .d50 and .sed file.

Thanks,
Manuela
KO
Kyssyanne Oliveira, modified 3 Years ago.

RE: Spatially varying grain size

Youngling Posts: 13 Join Date: 9/4/13 Recent Posts
Hi All,
I'm trying to model the resuspension of mixed (cohesive plus noncohesive) sediment in a continental shelf that has carbonate and terrigenous sediment. Basically, I have to vary spatially four classes of sediment: terrigenous mud, terrigenous sand, carbonate sand and carbonate gravel.

I saw that spatial varying D50 (SedDia file) can only be used with one sediment fraction in the model. So my doubt is how I can set all these sediments in my model. I also saw that the .sdb file would be used, but I'm a little confused on how to do this.


Cheers,
Kyssyanne Samihra
Ahmed Elkut, modified 6 Months ago.

RE: Spatially varying grain size

Youngling Posts: 11 Join Date: 5/20/14 Recent Posts
Hi everyone I am running a long-term morphology simulation. I have been using constant value for the d50 throughout the model. However, now I am implementing some nourishment scenarios and I needed to use a spatially varying d50 file. 
I used the QUICKIN and followed the recommended procedure to generate the file as a depth file and then change it to .d50 file. The model itself seemed to be running without any issues, but the results were completely different. The current pattern and sediment transport pattern have significantly changed, which does not make any sense. The alongshore transport rate has diminished drastically, (from about 600,000 m^3/3year to less than 200,000 m^3/3years).
I tried to use a constant d50 value but using the same file and obtained the same results (very odd results in the sediment pattern). 
It looks like the model does not read the file correctly, or it does not read the file at all and assumed another value for the d50 from elsewhere. However, I check the diagnostics files and the model do reads the file.
*** Start  of sediment input
Ref concentration             :  0.1600E+04
Option Dss                    :           0
Uniform mud content           :  0.0000E+00
Sediment number               :           1
  Name                        : Sediment_Sand
  Type                        :        sand
  RHOSOL                      :  0.2650E+04
  RHOSOL                      :  lognormal
  geom. st. dev.              :  0.1340E+01
  SedD50                      :  d50.d50
  CDRYB                       :  0.1600E+04
  Uniform IniThick            :  0.5000E+01 [m]
  FACDSS                      :  0.1000E+01
  Flocculation factor GamFloc :  0.1000E+01
So my questions are,
1) How to make sure that the model is reading the file of d50 correctly?
2) Is there any way to get the d50 value in the output so we can make sure that the model is reading the file correctly?
3)  What I might be doing wrong so that the model behaves this way? I cannot figure any issues with the file and the model is behaving very well with constant value of d50.
Note: I am running the model parallel on 22 cores. Could this make any issues the the file?
I cannot attach the d50 file because it is larger that 50KB. So, I have attached the files on the dropbox using the link below. If any additional file is necessary, please let me know.
https://www.dropbox.com/sh/6jv19x0auasclwi/AADvSSj43x36joVziKQkWkxsa?dl=0

Sincerely,
Ahmed Elkut
Richard Measures, modified 6 Months ago.

RE: Spatially varying grain size

Youngling Posts: 1 Join Date: 9/16/19 Recent Posts
Hi Ahmed,
To help investigate what is happening it is possible to output spatial maps of grain size by inserting additional keywords into the mor file - see table B.6 in appendix B.9.2 of the FLOW manual. I think you will need to insert something like the below into your mor file:
[Output]
Dm   = true


I'm not sure exactly what is causing the model to read the d50 incorrectly (I haven't had time to look at your model in detail) but a couple of ideas you could try are:
  1. Surrounding your file name with hashes so that delft3D knows it is text i.e.
    SedD50 = #d50.d50#

  2. Using the keyword SedDia rather than SedD50 in the sed file (see table B.3 in appendix section B.9.1 of the manual) i.e.
    SedDia = #d50.d50#
Hopefully that helps?
Richard
Ahmed Elkut, modified 6 Months ago.

RE: Spatially varying grain size

Youngling Posts: 11 Join Date: 5/20/14 Recent Posts
Dear Richard
Thank you for your response.
I checked if the model is reading the D50 file in good order and it seems that it does. However, the model still behaves strangely with odd sediment and morphology patterns. 
I have used SedD50 and SedDia and both are working fine.
In the attached files below you will kindly fine the difference between using constant D50 as just a uniform value (0.00024 m) and as the same value but using a FILE.
Of course the two runs should present the same results except they don't. In addition, the rate of alongshore sediment transport will drop in the second run (with the file.d50) and these changes are associated with changes in the alongshore current pattern.I do not know how the *.d50 file affects the current pattern this way.I Hope you can help.
Best regards,
Ahmed Elkut
NA
Nora Asa, modified 5 Months ago.

RE: Spatially varying grain size

Youngling Posts: 6 Join Date: 11/20/19 Recent Posts
Hi, I am running a sediment transport model using a wave-flow coupling. The upstream boundary is river inflow as well as sediment flux, and the downstream boundary condition is tides and waves. I am using d50 file as suggested above to define spatially varying grain size. I am using a hash sign to define it in .sed file. when I open the mdf file in GUI it says it can not read it but the model runs with no error about this file.
My problem is my model crashes after a while with the following error message, while without using the d50 file the model ran with no issues. The cells which are shown with the warning are where my river boundary. Is it because the d50 file is not being read properly? Any help would be appreciated. Nora
*** WARNING Source and sink term sediment 1 reduced with factor 39649084.62 (m,n)=(18,404), after 24795 timesteps. 
*** WARNING Source and sink term sediment 1 reduced with factor  8947330.00 (m,n)=(19,404), after 24795 timesteps. 
*** WARNING Source and sink term sediment 1 reduced with factor  1965438.47 (m,n)=(20,404), after 24795 timesteps. 
*** WARNING Source and sink term sediment 1 reduced with factor   323952.92 (m,n)=(21,404), after 24795 timesteps. 
*** WARNING Source and sink term sediment 1 reduced with factor   157720.61 (m,n)=(22,404), after 24795 timesteps. 
*** WARNING Source and sink term sediment 1 reduced with factor    39635.95 (m,n)=(23,404), after 24795 timesteps. 
*** WARNING Source and sink term sediment 1 reduced with factor     9784.94 (m,n)=(24,404), after 24795 timesteps. 
*** WARNING Source and sink term sediment 1 reduced with factor     2382.62 (m,n)=(25,404), after 24795 timesteps. 
*** WARNING Source and sink term sediment 1 reduced with factor      591.37 (m,n)=(26,404), after 24795 timesteps. 
*** WARNING Source and sink term sediment 1 reduced with factor      139.47 (m,n)=(27,404), after 24795 timesteps. 
*** WARNING Bed change exceeds   5.0 % of waterdepth after 24795 timesteps, location (m,n) = (14,403)
*** WARNING Bed change exceeds   5.0 % of waterdepth after 24795 timesteps, location (m,n) = (15,403)
*** WARNING Bed change exceeds   5.0 % of waterdepth after 24795 timesteps, location (m,n) = (16,403)
*** WARNING Bed change exceeds   5.0 % of waterdepth after 24795 timesteps, location (m,n) = (17,403)
*** WARNING Bed change exceeds   5.0 % of waterdepth after 24795 timesteps, location (m,n) = (18,403)
*** WARNING Bed change exceeds   5.0 % of waterdepth after 24795 timesteps, location (m,n) = (19,403)
*** WARNING Bed change exceeds   5.0 % of waterdepth after 24795 timesteps, location (m,n) = (20,403)
*** WARNING Bed change exceeds   5.0 % of waterdepth after 24795 timesteps, location (m,n) = (21,403)
Sediment erosion shortage at NM 5668 Fraction: 1 Mass available   :          -0.3647E+08 Mass to be eroded:          -0.3648E+08
Sediment erosion shortage at NM 6883 Fraction: 1 Mass available   :          -0.3848E+09 Mass to be eroded:          -0.3848E+09
Sediment erosion shortage at NM 8503 Fraction: 1 Mass available   :          -0.1210E+07 Mass to be eroded:          -0.1218E+07
*** WARNING Source and sink term sediment 1 reduced with factor259529792.66 (m,n)=(17,404), after 24795 timesteps. 
*** WARNING Source and sink term sediment 1 reduced with factor   345580.16 (m,n)=(21,404), after 24795 timesteps. 
*** WARNING Source and sink term sediment 1 reduced with factor   157103.06 (m,n)=(22,404), after 24795 timesteps. 
*** WARNING Source and sink term sediment 1 reduced with factor    39288.39 (m,n)=(23,404), after 24795 timesteps. 
*** WARNING Source and sink term sediment 1 reduced with factor     9656.34 (m,n)=(24,404), after 24795 timesteps. 
*** WARNING Source and sink term sediment 1 reduced with factor     2341.81 (m,n)=(25,404), after 24795 timesteps. 
*** WARNING Source and sink term sediment 1 reduced with factor      577.19 (m,n)=(26,404), after 24795 timesteps. 
*** WARNING Source and sink term sediment 1 reduced with factor      135.03 (m,n)=(27,404), after 24795 timesteps. 
*** ERROR Water level change too high >      25.00 m (per 0.5 DT) after 24796 timesteps in the following points: 
           (m,n) = (15,404), s0, s1, abs(s0-s1):    0.371E+01 ,    0.301E+06 ,    0.301E+06
           (m,n) = (16,404), s0, s1, abs(s0-s1):    0.370E+01 ,    0.725E+06 ,    0.725E+06
           (m,n) = (18,404), s0, s1, abs(s0-s1):    0.371E+01 ,    0.559E+06 ,    0.559E+06
           (m,n) = (19,404), s0, s1, abs(s0-s1):    0.371E+01 ,    0.232E+06 ,    0.232E+06
           (m,n) = (20,404), s0, s1, abs(s0-s1):    0.371E+01 ,    0.462E+05 ,    0.462E+05
*** ERROR Flow exited abnormally 
LB
Linnea Blåfield, modified 27 Days ago.

RE: Spatially varying grain size

Youngling Posts: 1 Join Date: 2/3/21 Recent Posts
Hi,
I'm trying to model with spatially varying grain size. I have interpolated the D50 grain sizes in QUICKIN (sedtest2.dep and tried also with .d50). I have modified the .sed file seddia part as 
SedDia           =  #sedtest2.d50#      [m]      Median sediment diameter (D50)
or  
SedDia           =  #sedtest2.dep#      [m]      Median sediment diameter (D50)
All the file are in the same directory, I have checked the files for minus (-) marks, spaces etc. and tried with one empty row in the end and without it.
I still get the "Error reading file at sediment1, key SedDia.... Import rejected!"
Does someone have ideas what to try next? I have my files attatched.
Kind regards,
Linnea