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. 




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



Message Boards

Trouble in initiating storm surge simulation using Delft3D FM (

Yongsu Na, modified 1 Year ago.

Trouble in initiating storm surge simulation using Delft3D FM (

Youngling Posts: 1 Join Date: 10/25/19 Recent Posts
Hello everyone,

I've been trying to simulate storm surge case using Delft3D FM ( However, the program couldn't start the simulation showing a message "Initialization of tst05 has failed." ("tst05" is the name of the case).

I made a single irregular grid by utilizing Delft Dashboard and RGFGRID. A few quadrangular regular grids with different resolution were generated with DDB first, and they were transformed to irregular grids, and then merged together with triangular irregular grids in between. I tried to maintain the orthogonality of the grid below 0.5, even though it increased as I interpolate the grid with *.xyz bed level file (don't know why).As for bed level data, I combined GEBCO 2019, SRTM 4.1 (both obtained via DDB and a high resolution local data (obtained from an external source).Also, I generated a spider web file via DDB using JTWC best track file.

When I ran the model, FM gave me (!) messages, namely "Roughness&Viscosity&Diffusivity contains unspecified points, the calculation kernel will replace these with default values". I thought it was due to a kind of grid and bed level problem since at first the model gave the same message for Bathymetry "Bathymetry contains unspecified points, ~". However, Roughness&Viscosity&Diffusivity message were kept shown even after I modified the grid and solved bathymetry problem.

Because there is no relevant information in the manuals and websites, not to mention that the model does not allow me to look into it closely, I don't know how to solve this.Please take a look at the files I attached. Any help or discussion will be appreciated.

Thank you and Best,
Yongsu Na 

--- - original grid file (w/o bed level). - some grid cells were eliminated (parts of Yeosu, South Korea). - bed level was interpolated.
P.S. I could not add any post at Delft3D FM Form ( There weren't any buttons. Does anybody know?
Dmitry Kushnir, modified 1 Year ago.

RE: Trouble in initiating storm surge simulation using Delft3D FM (

Jedi Knight Posts: 107 Join Date: 11/9/12 Recent Posts
There are some small flow links on the D-Flow FM model mesh, which have to be removed. I've tried to run your test model and it gave me this error (see diagnosis file attached):

** ERROR  :     4 small flow links discarded. Run 'merge circumcenters' to remove small flow links or increase threshold

This was previously discussed in this thread. Solution: merging small circumcenters of the mesh, using RGFGRID: Operations --> Grid --> Merge Circumcenters. 
Kind regards,


Brandon Huntley, modified 7 Months ago.

RE: Trouble in initiating storm surge simulation using Delft3D FM (

Youngling Posts: 1 Join Date: 7/25/20 Recent Posts
The problem is that sometimes the communication between flow and wave does not work immediately after the restart TheFreshMarketSurvey (the problem does not occur in the middle of the tidal cycle), but this happens at a random moment in the simulation (not always during the first restart for example). I cannot figure out what the problem is, and hope that you can help me. When the simulation crashes a com-file is present
William Burch, modified 2 Months ago.

RE: Trouble in initiating storm surge simulation using Delft3D FM (

Youngling Posts: 1 Join Date: 12/15/20 Recent Posts
The coupled Delft3D Flexible Mesh (D3D FM) - SWAN model with an unstructured grid has been developed recently to simulate storm surge and waves; and another open source model, Telemac-Tomawac, has been widely used for storm surge and wave propagation simulation in coastal areas for more than 20 years. However, the choice of a hydrodynamic model for a specific area in terms of cost, efficiency and accuracy is often a dilemma at the beginning of a modeling project. The objective of this research is to examine the effects of two software packages in terms of accuracy and performance with a case study in the Shanghai area of China. Model performance has been assessed based on model configuration, model calibration, grid generation and computational efficiency. Comparing measured water levels with model results, both approaches were able to accurately predict hydrodynamic conditions in a complex estuarine environment. Both models showed that it can efficiently simulate hydrodynamics in the coastal area under various scenarios for further climate adaptation research. Additionally, both models were used to simulate inundation propagation due to hypothetical failures of flood defenses in the coastal area. A comparison of inundation extent and maximum inundation depth showed that they were equally well-suited for overtopping and inundation simulation.