yade-dev team mailing list archive

[Danny van der Haven <dannyvdhaven@xxxxxxxxx>]

Hi Benjy,

The demo on https://sand-atlas.scigem.com/sands/LECA-598-sand/ looks great!
Earlier, you asked for feedback on the website. I really like the visual
examples and that you can adjust the graph. I think it would be nice to
have the units in the axis labels as well (particularly for the diameter,
whose label now gets cut off). Is "area" the surface area of the particle,
one of the projected areas, or the sphere-equivalent area? Adding a shape
classification such as the modified Zingg plots may be helpful (
https://doi.org/10.1016/j.powtec.2021.11.027), because the intermediate
axis is also important. My last comment would be that it may be nice to add
particle volumes, since it is quite common to plot e.g. the particle
diameter as a function of the total volume (a CFD plot with volume fraction
on the y axis and diameter on the x axis). Hope this helps you.

Thank you also for following up. For us to be able to use the level-set
models, it should be 1) possible to load the level-set into Python, 2) the
level set be a regular grid, and 3) turn the level set into a native-Python
nested list, which is needed to feed it to the underlying C++ engine.

I see that OpenVDB has a Python interface, which is very helpful. This
meets the first requirement, but I'm not sure about 2 and 3. If you could
help answer those questions, that would be very helpful.

Thank you,
With kind regards,
Danny van der Haven


Op vr 13 sep 2024 om 08:13 schreef Benjy Marks <benjy.marks@xxxxxxxxxxxxx>:

> Hi Danny, all,
>
> Thank you for the detailed description of how you are dealing with level
> set particles in YADE. Since you indicated that you dont have a file
> storage format, we have decided for our repository to store the level set
> data using the open standard openVDB <https://www.openvdb.org/>. It would
> be great to know if this data can be used with YADE. We also have mesh data
> available as STL files if anyone is using meshes.
>
> If there are other file formats or data types which would make this
> information more accessible to you or your users we are willing to
> implement them, we just need clear direction.
>
> thank you,
> benjy
> ------------------------------
> *From:* Danny van der Haven <dannyvdhaven@xxxxxxxxx>
> *Sent:* Wednesday, 31 July 2024 3:38 AM
> *To:* Bruno Chareyre <bruno.chareyre@xxxxxxxxxxxxxxx>
> *Cc:* yade-dev@xxxxxxxxxxxxxxxxxxx <yade-dev@xxxxxxxxxxxxxxxxxxx>; Ilija
> Vego <ilija.vego@xxxxxxxxxxxxx>; Benjy Marks <benjy.marks@xxxxxxxxxxxxx>
> *Subject:* Re: [Yade-dev] Fwd: The Sand Atlas
>
> Dear Bruno,
>
> Thank you for forwarding, that sounds like a very interesting and useful
> project!
>
> I have been chatting to Vasileios about this as well, but I'm working on a
> generalised package for making level set particles / objects and hope to
> finish it in a month or two. I have also had some success in scanning in
> some powders with microCT to get particle shapes.
>
>    - The importing of level-set particles into YADE is currently
>    something that I don't have a proper file format for; I just write things
>    to a .csv file and load that using YADE's python interface. I will publish
>    my script for this together with the package I am building.
>    - Generating level-set particles from microCT is not a trivial task.
>    If they want to supply these in their database, I recommend they wait until
>    I have published the package (open source) and use that code.
>    - For the package, I can deal with a lot of different input data
>    already, as long as the individual particles are clearly labelled. Given
>    the starting data is from microCT, the easiest input data is a single file
>    per particle containing the binary voxel image of that particle. (The same
>    applies to Vasileios' CLUMP library, I think.) Clumps, triangular meshes,
>    and potential particles can all be converted to level sets. Converting an
>    improper mesh to a level-set object will automatically close the mesh in an
>    intuitive way.
>    - I think Vasileios' CLUMP library also has a way to make
>    meshed/polyhedral particles from images. Not sure if it works for concave
>    particles, but an easy way to do this (maybe with a bit of overkill on the
>    resolution) is to binarise the image and then apply marching cubes.
>
> Are the people from Sand Atlas already involved with the ON-DEM project (
> https://www.cost.eu/actions/CA22132/
> <https://url.au.m.mimecastprotect.com/s/62FUCYW8NockXEzV9S3CrtzXzi4?domain=cost.eu>)
> ?
>
> With kind regards,
> Danny
>
>
> Op di 30 jul 2024 om 14:20 schreef Bruno Chareyre <
> bruno.chareyre@xxxxxxxxxxxxxxx>:
>
>
> Dear Yade devs,
>
> Benjy Marks/Sydney is providing grain shape data from CT on Sand Atlas
> website
> <https://url.au.m.mimecastprotect.com/s/xMz0CQnMBZfBLM5vRFPhXt1c10E?domain=sand-atlas.scigem.com/>
> and he is interested in making that data compatible with direct imports in
> shape models. It seems to me in requires a bit of work on either Yade or
> Sand Atlas sides, or both.
>
> IIRC Vasileios developed a tool to convert images into shape models
> already, Jérôme/Dany may have ideas for the case of level sets too. Others?
>
> 1/ Which would be the most basic and generic data format for raw data?
> (presumably voxel data)
> 2/ Which are the *available* functionalities to convert raw data into a
> DEM shape model?
> 3/ Which are the *unavailable* functionalities needed to convert raw data
> into a DEM shape model?
>
> Cheers
>
> Bruno
>
>
>
> -------- Forwarded Message --------
> Subject: Re: The Sand Atlas
> Date: Wed, 24 Jul 2024 18:54:53 +0000
> From: Benjy Marks <benjy.marks@xxxxxxxxxxxxx> <benjy.marks@xxxxxxxxxxxxx>
> To: Bruno Chareyre <bruno.chareyre@xxxxxxxxxxxxxxx>
> <bruno.chareyre@xxxxxxxxxxxxxxx>, Bruno.Chareyre@xxxxxxxxxxxxxxxxxxxxxx
> <Bruno.Chareyre@xxxxxxxxxxxxxxxxxxxxxx>
> <Bruno.Chareyre@xxxxxxxxxxxxxxxxxxxxxx>
> CC: Ilija Vego <ilija.vego@xxxxxxxxxxxxx> <ilija.vego@xxxxxxxxxxxxx>
>
> Hi Bruno,
>
> Essentially we have the 3D data from CT scans of the particles and we are
> willing to convert them into whatever shape models yade developers would
> prefer. I'm impressed that yade accepts 5 different shape models! We can
> certainly produce 5 different file types and have them all available if the
> yade team thinks that will be useful. The main point for us is to make all
> of this existing data available and useful for as many people as possible.
>
> Benjy
>
> ------------------------------
> *From:* Bruno Chareyre <bruno.chareyre@xxxxxxxxxxxxxxx>
> <bruno.chareyre@xxxxxxxxxxxxxxx>
> *Sent:* Thursday, July 25, 2024 1:10:28 AM
> *To:* Benjy Marks <benjy.marks@xxxxxxxxxxxxx> <benjy.marks@xxxxxxxxxxxxx>;
> Bruno.Chareyre@xxxxxxxxxxxxxxxxxxxxxx
> <Bruno.Chareyre@xxxxxxxxxxxxxxxxxxxxxx>
> <Bruno.Chareyre@xxxxxxxxxxxxxxxxxxxxxx>
> *Cc:* Ilija Vego <ilija.vego@xxxxxxxxxxxxx> <ilija.vego@xxxxxxxxxxxxx>
> *Subject:* Re: The Sand Atlas
>
>
> Dear Benjy,
>
>
> Thank you for the suggestion, it sounds interesting. It seems it all
> depends on which shape model would be used:
>
> - multisphere approximation
> - raw polyhedron
> - Minkowski polyhedron
>
> - potential particle
>
> - level set
>
> - (other things I can't imagine and which aren't implemented in Yade
> a.t.m.)
>
>
> That's five different "download for" already. :)
> Do I miss something?
>
>
> I'm not the most active in shape models actually. I should probably
> forward your proposition to other devs, or directly to yade mailing list.
>
> But before that could you clarify what sort of data you would provide /
> how close to shape models it would be?
>
> Kind Regards
>
>
> Bruno
>
>
>
> On 23/07/2024 00:51, Benjy Marks wrote:
>
> Hi Bruno,
>
> How are you? I hope you're well.
>
> We are putting together an open source repository called the Sand Atlas
> <https://url.au.m.mimecastprotect.com/s/xMz0CQnMBZfBLM5vRFPhXt1c10E?domain=sand-atlas.scigem.com/>.
> It is a website for hosting 3d models of particles, so that they can be
> used in DEM codes etc. I was wondering if this would be useful for YADE? If
> so, I would like to make it just a single click on our website where users
> can click "Download for YADE" and it gives them correctly formatted files
> so that they can be used seamlessly. We will try to do the same for other
> open source DEM codes too.
>
> The website now is more of a tech demo, many of the links dont work and
> the particles arent meshed that nicely, but this will all hopefully be
> sorted out in the next month. We also have asked around to a bunch of
> researchers and hope to have 50+ particle types available by September.
>
> If you have any feedback about the website, or ways that this kind of data
> might be useful to you or others, please let me know!
>
> thanks,
> benjy
>
> --
>
> *Bruno Chareyre*
>
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>
>
>
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