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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D-Flow Flexible Mesh
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Cohesive sediments & muddy systems

 

 

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Sediment layer thickness in *.mor file vs *.sed file

CH
Claire Hughes, modified 5 Years ago.

Sediment layer thickness in *.mor file vs *.sed file

Youngling Posts: 7 Join Date: 1/6/14 Recent Posts
Hi everyone,
I am new here and have recently started to play with the D3D model.

I have some quick questions. I will use the example in the related webinar to try and make it as clear as possible.

For the setup given below:

-------------------------------------------------------------------------------------------------------------------------------------------------------------

*.mor file

[Underlayer]
IUnderLyr = 2 [-] Flag for underlayer concept
TTLForm = 1 [-] Transport layer thickness formulation
ThTrLyr = 0.01 [m] Thickness of the transport layer
MxNULyr = 10 [-] Number of underlayers (excluding final well mixed layer)
ThUnLyr = 0.01 [m] Thickness of each underlayer
UpdBaseLyr = 1 [-] Composition and thickness integer (1-4)
IniComp = mor.ini

Mor.ini file

[Layer]
Type = mass fraction
Fraction1 = 1.0
Fraction2 = 0.0
Thick = 0.01

[Layer]
Type = mass fraction
Fraction1 = 0.0
Fraction2 = 1.0
Thick = 0.99

-------------------------------------------------------------------------------------------------------------------------------------------------------------

What should be in the *.sed file (and the mdf file) ?

my take:

sed file:

[SedimentFileInformation]

[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 = 2.0000000e-003 [m] Median sediment diameter (D50)
CDryB = 1.6000000e+003 [kg/m3] Dry bed density
IniSedThick = ??????? [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]
[Sediment]
Name = #Sediment-Mud# Name of sediment fraction
SedTyp = mud Must be "sand", "mud" or "bedload"
RhoSol = 2.6500000e+003 [kg/m3] Specific density
SalMax = 0.0000000e+000 [ppt] Salinity for saline settling velocity
WS0 = 4.5000000e-004 [m/s] Settling velocity fresh water
WSM = 4.5000000e-004 [m/s] Settling velocity saline water
TcrSed = 1.0000000e+003 [N/m2] Critical bed shear stress for sedimentation (uniform value or filename)
TcrEro = 1.3000000e-001 [N/m2] Critical bed shear stress for erosion (uniform value or filename)
EroPar = 1.0000000e-004 [kg/m2/s] Erosion parameter (uniform value or filename)
CDryB = 5.0000000e+002 [kg/m3] Dry bed density
IniSedThick = ?????? [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]

mdf file
Namc1 = #Sediment-Sand #
Namc2 = #Sediment-Mud #

So some questions on this:
1-Does the order of fractions in mor.ini file follows the same order in the *.sed file, i.e., fraction1 now refers to Sediment-Mud and fraction 2 refers to Sediment sand ? Or maybe do I need to use the same names?

2-What about the IniSedThick defined here? If I put 5m as InisedThick for both Sediments defined in this sed file, is it ignored because I already defined the thicknesses in the mor file?

As you can see I am a little bit confused on how to setup my bed here. If you can give me a complete map of the steps I would appreciate it.
Thanks
Richard Measures, modified 5 Years ago.

RE: Sediment layer thickness in *.mor file vs *.sed file

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

To answer your questions:
  • I think the order of the fractions in the initial bed composition file (*.inb file in the manual but I think this is what your Mor.ini file is) should match the order of the fractions in the *.sed file i.e. Fraction1 does refer to Sediment-Sand in your example. This has always worked for me correctly ( but in my models I have always had the fractions arranged from fine to coarse in the *.sed file so not sure if this makes a difference?). I attach some example files from one of my models if this helps - they're coarse sediments but the principles are the same.
  • IniSedThick is overruled by whatever is written in the initial bed composition file so it doesn't matter what value you put in the *.sed file.
Also, incase you hadn't already discovered them you should note the additional output options you can turn on in the *.mor file which can help diagnose if your bed is set up as you intended. e.g.
[Output]
   Frac             = true                 [-]      Output sediment fraction in top layer
   Dm               = false                [-]      Output arithmetic mean sediment diameter
Hope that helps,

Richard
CH
Claire Hughes, modified 5 Years ago.

RE: Sediment layer thickness in *.mor file vs *.sed file

Youngling Posts: 7 Join Date: 1/6/14 Recent Posts
Thanks Richard,

regarding my second question, apparently I miss this on page 556 of the manual emoticon

IniComp: file containing initial bed composition (1 string) usage of this keyword overrules the IniSedThick (or older SdBUni) values given in the sed file (see Section B.9.9)


for the first part; thanks for the files it helps a lot.
If you don't mind answering some new questions for me, that'd be great emoticon

1-definition of MxNULyr says: Number of underlayers (excluding final well mixed layer) - I'm assuming the "final well mixed layer' is the base layer (as you also named it in the inb file).
So is the last layer defined in the inb file always the base layer?
If so should I define MxNulyr and ThUnLyr in a way that (MxNulyr xThUnLyr)> Layer 1 thickness to bookeep into the base layer.

2-Do you know what you called active layer in the inb file, is actually the "active (transport) layer in the model? so in your file do you have ThTrLyr = 0.025 ? I'm trying to understand the correct way to set this up. If the first layer is always the transport layer , what happens if I set the ThTrLyr > Layer 1 thickness ? I guess I shouldn't do that.

wow, sorry if my questions are so confusing emoticon)
cheers
Claire
Richard Measures, modified 5 Years ago.

RE: Sediment layer thickness in *.mor file vs *.sed file

Jedi Knight Posts: 178 Join Date: 3/23/11 Recent Posts
Hi Claire,
  • My example files might have been a bit confusing here because I don't have any storage layers (e.g. MxNuLyr=0, I'm only using an active layer and a base layer/final well mixed layer). I'm not exactly sure I follow your question but I think (hopefully someone will correct me if I'm wrong) that in the *.inb file the layers start from the top and work down and that you should have MxNuLyr+2 layers in your *.inb file (the active layer + MxNuLyr storage layers + the base layer). If your storage layers start with nothing in you can specify them as zero thickness in the *.inb file but still list them.
  • In my file I do have a 0.25m thick active layer - this is because I'm simulating very coarse cobbles on a gravel bed river! I think (again, hopefully someone will correct me if I'm wrong) if your ThTrLyr is set differently to your Layer 1 thickness in the *.inb file then delft3D exchanges sediment between the active layer and the layer below in order to revert the Layer 1 thickness to ThTrLyr. For example if ThTrLyr > Layer 1 thickness then sediment from the underlying layer will be mixed up into the active layer to bring it's thickness up to ThTrLyr - this will potentially change the composition of the active layer and reduce the thickness of the underlying storage layer. I've always tried to set layer 1 thickness equal to ThTrLyr
Does that help?

Richard
CH
Claire Hughes, modified 5 Years ago.

RE: Sediment layer thickness in *.mor file vs *.sed file

Youngling Posts: 7 Join Date: 1/6/14 Recent Posts
Thank you Richard,
the discussion is really helpful.

Hopefully, someone will confirm the parts you weren't sure.

that in the *.inb file the layers start from the top and work down

This is correct, it's been mentioned in the webinar.

that you should have MxNuLyr+2 layers in your *.inb file (the active layer + MxNuLyr storage layers + the base layer). If your storage layers start with nothing in you can specify them as zero thickness in the *.inb file but still list them.


I did not know this. From the webinar, I thought the underlayers are just for bookkeeping and the number and thickness defines the resolution only. So what I was thinking, is that we have transport layer on top, which does not have to be defined in the *inb file because it's already part of Layer1. I am just not sure about the base layer now.

Well, hopefully someone will clarify things for us.
thanks
Claire
Emiel Moerman, modified 5 Years ago.

RE: Sediment layer thickness in *.mor file vs *.sed file

Padawan Posts: 84 Join Date: 3/10/11 Recent Posts
Hi Claire (/Richard),

During my thesis a couple years back I had a look at the Bed Composition in Delft3D in a bit more detail.
Back then, I made a sort of summary of the process. I attached the document to this post for your convenience.
Perhaps it is of some help to you as well.

Regards,

Emiel Moerman
CH
Claire Hughes, modified 5 Years ago.

RE: Sediment layer thickness in *.mor file vs *.sed file

Youngling Posts: 7 Join Date: 1/6/14 Recent Posts
Emiel,

I think it's a huge contribution to the discussion. Thanks for sharing.

I fully understand the base layer concept now.
Just to clarify something about the Transport Layer:

On Page 4 of the document you attached, in the "Examples of a layered bed composition subjected to deposition and erosion" section, you wrote:

Consider a stratigraphied bed with a total thickness of 3.5 m. The bed consist of 3 different layers. The first layer is considered to be the tranport layer and has an assigned thickness of 0.5 m. The second layer has a thickness of 2 m and the bottom layer has a thickness of 1 m.


In this case, you define 3 different [Layer]s in your inb file right? So your ThTrLyr (thickness of the transport layer) was 0.5m and in the inb file you have:
[layer]
thick = 0.5
fracs etc
[layer]
thick = 2
fracs etc
[layer]
thick = 1
fracs

In a case where I define two layers, where first layer is 2.5m thick, layer 2 is 1m thick and ThTrLyr = 0.5m
[layer]
thick = 2.5
fracs etc
[layer]
thick = 1
fracs etc

did I end up having a 4m stratigraphied bed? or since I only have 2 layers defined Transport layer is the first 0.5m portion of layer 1 making my total bed depth 3.5m?

I need to know which because in my model, first layer will have varying thickness. If the first layer defined in inb file is assigned to be transport layer, then my transport layer will have varying thickness (which is not possible). I am just worried that the varying thickness of my first layer will be ignored and ThTrLyr will be used instead and the transport layer will be fed by Layer2.

Hope I could explain what's in my mind.
cheers
Claire
Richard Measures, modified 5 Years ago.

RE: Sediment layer thickness in *.mor file vs *.sed file

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

Thanks - I like the pictures - perhaps some of your examples could be merged into the manual?

Claire,

Could you do something like this to explicitly describe your active/transport layer and the layer underneath it?
[layer]
thick = 0.5
fracs etc
[layer]
thick = QuickinTypeFileDescribingSpatiallyVaryingThicknessOfLayer.thk
fracs etc
[layer]
thick = 1
fracs etc

Richard
Emiel Moerman, modified 5 Years ago.

RE: Sediment layer thickness in *.mor file vs *.sed file

Padawan Posts: 84 Join Date: 3/10/11 Recent Posts
Hi Claire,

I am now (thinking about it, reading this discussion) to be honest not sure anymore whether or not you need to define the Transport Layer in your initial bed composition file or not.
Perhaps somebody else can comment on this? It seems to me that it is not necessary. You could simply run 2 simulation one with and one without to verify. You can check whether the method you apply is used correctly by Delft3D by using Quickplot to visualize the available sediment volume per fraction in a cross-section (see attached figure). If I find time I will have a look myself as well to verify.

The last time I used the concept I did do it, but it might have been superfluous.

I attached the files I used in my application back then.

sea.grd = grid file
sea.enc = grid enclosure file
sand.sdb = spatially varying bed thickness file (25 m), applied for both fractions, so total thickness of 50m (you can load this file on the grid through Quickin by importing a depth file).
sea.sed = sediment file (2 fractions)
sea.mor = morphology file, referencing to the sea.ini file
sea.ini = initial bed composition file made up out of 10 layers:
lyr1 = 0.1m (set equal to transport layer)
lyr2 = lyr9 = 5m
lyr10 = 4.9m (total sums up to 50m as defined in sand.sdb files)

fraca.frc = spatially varying fraction file, fraction 1 (you can load this file on the grid through Quickin by importing a depth file).
fracb.frc = spatially varying fraction file, fraction 2 (you can load this file on the grid through Quickin by importing a depth file).

Good luck and keep us posted on any results,

Emiel
Emiel Moerman, modified 5 Years ago.

RE: Sediment layer thickness in *.mor file vs *.sed file

Padawan Posts: 84 Join Date: 3/10/11 Recent Posts
Emiel Moerman, modified 5 Years ago.

RE: Sediment layer thickness in *.mor file vs *.sed file

Padawan Posts: 84 Join Date: 3/10/11 Recent Posts
Hi Claire,

I have had a look with a test-run.
You don't need to define the transport layer in the Initial Bed file.
The transport layer is added on top of the layers defined in the initial bed file.

Regards,

Emiel
CH
Claire Hughes, modified 5 Years ago.

RE: Sediment layer thickness in *.mor file vs *.sed file

Youngling Posts: 7 Join Date: 1/6/14 Recent Posts
Hi Emiel,

thanks for the follow up and testing it out. I am not setup to test these out yet, I just want to be sure of the concepts.

So the transport layer is filled with whatever was defined as Layer1 in the ini file up to the defined ThTrLyr.

In that case, in the example files you sent earlier you could have your ini file starting as:

[Layer]
   Type             = mass fraction
   Fraction1        = fraca.frc
   Fraction2        = fracb.frc
   Thick            = 5

with a total of 10 layers defined (instead of 11) with the last layer also having 5m thickness (instead of 4.9). Please correct me if I am wrong on this.

If this is the case, I attached a doc with the initial bed and transport layer figure, might help others.

PS: I think the thickness in the sand.sdb files you defined in the sea.sed file are not read into the model. I mean, I think, you have a total bed thickness of 50m everywhere because you created 10 underlayers at the beginning with 5m thickness each and not because you have sand.sdb for sediment 1 and sediment 2. Can you clarify if there is something I'm missing here?

pg 556 of manual
IniComp: file containing initial bed composition (1 string) usage of this keyword overrules the IniSedThick (or older SdBUni) values given in the sed file (see Section B.9.9)


This has been a great discussion, I want to thank you both Emiel and Richard. I hope someone from Deltares will seal this discussion soon emoticon
I'll update if I find out more.
Claire