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Unstructured mesh tools and optimisation

Ben Williams, modified 7 Years ago.

Unstructured mesh tools and optimisation

Youngling Posts: 7 Join Date: 3/23/11 Recent Posts
Hi there,

May I ask what kind of tools there will be to construct flexible meshes in the FM version of Delft3D? And if the code for reading data in and out of the binary files will be a little more straight forward than presently exists in the purely curvilinear version? For example, I am not aware of any built-in Matalb functions that will let you undertake an interpolation for meshes with an arbitrary number of vertices. Quickplot is OK for plotting data but obviously in situations when you need to start really digging in to simulation results you need to be reading the data directly from the binary files. The 'vs_use' are fast but I sometimes find them a little obtuse in the way information contained in the binary file is provided to you. Unless the new FM version will use entirely NetCDF files? Will the qp_read functions work with the new FM version, for example.

I was also wondering if the developer team are aware of the excellent open-source mesh-optimisation tools that are available on the DHI website. One of the issues with flexible mesh models is that it becomes very easy to make elements that are so small that they drastically limit the maximum stable time step you can achieve with the model. It is normal to achive a 4 or 5-fold increase in model speed by optimising the mesh in such a way as to remove say the 20 most problematic elements in the domain.

http://mikebydhi.com/Download/DocumentsAndTools/Tools/DHIMatLabToolbox2011.aspx

Also, are there any references and case studies for the numerics of the new model? So one may start planning how best the new FM version may be utilised when it becomes available to the open source community. For example, will the structure (calls from batch files etc) of the cuvilinear version of Delft3D be retained in the new FM version? In particular for running on clusters or multicore workstations? Is the structure of the source code in the FM version of Delft3D significantly different to the curvilinear version?

Kind regards,

Ben
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Wim van Balen, modified 7 Years ago.

RE: Unstructured mesh tools and optimisation (Answer)

Hi Ben,

You touch upon quite some aspects. I shall respond to some issues:

1. The familiar RGFGRID software is currently being made suitable to construct flexible meshes. With the new RGFGRID version you will soon be able to construct either curvilinear and unstructured meshes and to use a bunch of useful tools (several types of refinement techniques, snapping meshes to landboundaries, new utilities to construct a curvilinear mesh directly from splines, etc. etc.).

2. D-Flow FM will use entirely NetCDF files. The new QUICKPLOT shall be able to read these NetCDF files and to visualize data on either curvilinear and unstructured meshes. In the OpenEarth repository (see https://publicwiki.deltares.nl/display/OET/Tools), some Matlab-scripts are already available to read and visualize mesh-files (_net.nc), his-files (_his.nc) and map-files (_map.nc).

3. The toolbox you refer to is closely related to working with DHI related data files. Within D-Flow FM quite some very efficient mesh optimalization methods are already present as well as several sophisticated refinement techniques for structured as well as unstructured meshes.

4. Currently we develop the manuals and documentation in which the necessary informating regarding numerics, batch files, running on multicore stations, and so on. Recently, we have made considerable progress in developing the parallel version of D-Flow FM using MPI.

Regards, Wim
Chiranjeevi Ambati, modified 7 Years ago.

RE: Unstructured mesh tools and optimisation

Youngling Posts: 0 Join Date: 3/23/11 Recent Posts
Dear Ben,

How can i get the new RGFGRID software in which the unstructured mesh generation option is available?

Please send the link to download the new RGFGRID.

Thanks and kind regards
Chiru
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Wim van Balen, modified 7 Years ago.

RE: Unstructured mesh tools and optimisation (Answer)

Hi Chiru,

The RGFGRID version with unstructured mesh functionalities has not yet been released. The expected release date is February / March 2013. In February, further details will be announced.

Regards, Wim
AL
Angie Lee, modified 7 Years ago.

RE: Unstructured mesh tools and optimisation

Youngling Posts: 0 Join Date: 2/3/12 Recent Posts
Wim van Balen:
Hi Chiru,

The RGFGRID version with unstructured mesh functionalities has not yet been released. The expected release date is February / March 2013. In February, further details will be announced.

Regards, Wim


Hi Wim,

Can you assist me where should I get the latest version of RGFGRID? Currently my licensed RGFGRID is Version 4.18.01.18383. But i would like to try out the flexi mesh tool in latest RGFGRID.
Besides, is it possible i can get a copy of latest Delft3D-GUI? My current version is 4.00.02.

Thanks.
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Wim van Balen, modified 7 Years ago.

RE: Unstructured mesh tools and optimisation

Hi Angie Lee,

Some Flexible Mesh related features are already available in the version of January. Lately, some major improvements have been implemented regarding the unstructured grid functionality. These new features are expected to be available mid September, from the website http://oss.deltares.nl/web/delft3d/source-code. The service pack release with RGFGRID including Flexible Mesh functionality is expected mid October.

Regards, Wim
Bert Jagers, modified 7 Years ago.

RE: Unstructured mesh tools and optimisation

Youngling Posts: 0 Join Date: 12/22/10 Recent Posts
Hi Ben,

As a small addition to Wim's reply, I would like to say that:

1) Yes, the qp_read functions will wrap the netcdf functions such that you can access the new and old files in the same way if you like. This layer should deal with all the netCDF meta data. However, accessing the data directly via the netCDF interface will of course also be possible.

2) We'll be using netCDF and follow as much as possible the CF (Climate & Forecasting) conventions for meta-data. Since there was no international standard yet for storing unstructured grids in netCDF we have been active in defining such a standard. You can find a description on our Deltares wiki site. We have been in touch with various groups and several groups are gradually implementing this new convention. Slowly also tools start to emerge that support (part of) this standard.

Bert
MA
Md Bin, modified 6 Years ago.

RE: Unstructured mesh tools and optimisation

Youngling Posts: 0 Join Date: 12/17/12 Recent Posts
Recently Deltars open new module for unstructured grid which name flexible mesh. But I am not sure that where i can found source code of Flexible Mesh. Can you help me please ? Or which RGFGrid version including Flexible mesh
WH
wei huang, modified 6 Years ago.

RE: Unstructured mesh tools and optimisation

Youngling Posts: 0 Join Date: 5/20/13 Recent Posts
In the manual of D-flow flexible mesh, there is instruction of installation. However, I can not find the files mentioned in the manual. Who can tell me where I can get the files such as<unstruc.exe>, <netcdf.dll>, <libiomp5md.dll>, <unstruc.ini>, <interact.ini>, <isocolour.hls>. or as an alternative file <rununstruc.bat> batch file.
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Wim van Balen, modified 6 Years ago.

RE: Unstructured mesh tools and optimisation

Hi,

The files associated with D-Flow FM are not generally released and are hence not generally available. An open source release is planned to take place in 2014. For the time being, the files mentioned in the manual are only incidentally made available to be used for dedicated pilot cases.

Wim
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Wim van Balen, modified 6 Years ago.

RE: Unstructured mesh tools and optimisation

Hi,

The Flexible Mesh source code is not yet available. A first D-Flow FM open source release is planned for 2014. By the end of 2013, an RGFGRID version within Delft3D will be available that will be able to generate and manipulate unstructured meshes.

Wim