Hi Benjy,
The demo on https://sand-atlas.scigem.com/sands/LECA-598-sand/
<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
<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 <mailto: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
<mailto:dannyvdhaven@xxxxxxxxx>>
*Sent:* Wednesday, 31 July 2024 3:38 AM
*To:* Bruno Chareyre <bruno.chareyre@xxxxxxxxxxxxxxx
<mailto:bruno.chareyre@xxxxxxxxxxxxxxx>>
*Cc:* yade-dev@xxxxxxxxxxxxxxxxxxx
<mailto:yade-dev@xxxxxxxxxxxxxxxxxxx> <yade-dev@xxxxxxxxxxxxxxxxxxx
<mailto:yade-dev@xxxxxxxxxxxxxxxxxxx>>; Ilija Vego
<ilija.vego@xxxxxxxxxxxxx <mailto:ilija.vego@xxxxxxxxxxxxx>>; Benjy
Marks <benjy.marks@xxxxxxxxxxxxx <mailto: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
<mailto: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>
<mailto:benjy.marks@xxxxxxxxxxxxx>
To: Bruno Chareyre <bruno.chareyre@xxxxxxxxxxxxxxx>
<mailto:bruno.chareyre@xxxxxxxxxxxxxxx>,
Bruno.Chareyre@xxxxxxxxxxxxxxxxxxxxxx
<mailto:Bruno.Chareyre@xxxxxxxxxxxxxxxxxxxxxx>
<Bruno.Chareyre@xxxxxxxxxxxxxxxxxxxxxx>
<mailto:Bruno.Chareyre@xxxxxxxxxxxxxxxxxxxxxx>
CC: Ilija Vego <ilija.vego@xxxxxxxxxxxxx>
<mailto: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>
<mailto:bruno.chareyre@xxxxxxxxxxxxxxx>
*Sent:* Thursday, July 25, 2024 1:10:28 AM
*To:* Benjy Marks <benjy.marks@xxxxxxxxxxxxx>
<mailto:benjy.marks@xxxxxxxxxxxxx>;
Bruno.Chareyre@xxxxxxxxxxxxxxxxxxxxxx
<mailto:Bruno.Chareyre@xxxxxxxxxxxxxxxxxxxxxx>
<Bruno.Chareyre@xxxxxxxxxxxxxxxxxxxxxx>
<mailto:Bruno.Chareyre@xxxxxxxxxxxxxxxxxxxxxx>
*Cc:* Ilija Vego <ilija.vego@xxxxxxxxxxxxx>
<mailto: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*
/Associate Professor
/
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engineering and management**
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<https://url.au.m.mimecastprotect.com/s/0aooCROND2unXjA4OUPiPtvIJ4r?domain=grenoble-inp.fr>
/
/*3SR Lab**
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/
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