Ellipsoids superballs and polyhedra

[Bradleydi]

Since DynamO only supports sphere at present, I strongly suggest that Marcus could add more features of ellipsoids and other kinds of polyhedra into DynamO in the near future.

[Bradleydi]

Donev only shared its hard-sphere codes, but not ellipsoid ones (precompiled executables). If you have related codes, I would like to be a helper to develop DynamO!

[toastedcrumpets]

Donev spells out the algorithm in two publications: http://cims.nyu.edu/~donev/Packing/EDMD.pdf The second publication is key here, as the Neighbour List implementations (NNL) are another topic entirely.

The key definition are the overlap potentials for ellipsoids (section C of the second paper). The difficulty is that they use a maple script for the determinant and adjoint calculation of the polynomial coefficients used in Eq. 17. The numerical routines are not a problem, but the implementation of these expressions will take some time to do neatly. If you can implement these and design a "unit test" (a method to check that the implementation is correct), the rest I think is relatively straightforward.

[Bradleydi]

Thank you! I looked through it and, sadly, find it is not easy for me to make some contribution to DynamO. My plan is to understand developed DynamO's code first. BTW, HOOMD-blue is also a pretty good tool for simulation.

[toastedcrumpets]

Hi, OK, no problem. I'll leave this issue open as a feature request and I'll close it once ellipsoids are implemented in the future.

Just to let you know, if you want to learn more about the use and applications of DynamO we have a workshop coming up in January: https://eventbooking.stfc.ac.uk/news-events/dynamo2015

[Bradleydi]

Oh that's good! It will be better if you can upload workshop videos online for potential users. BTW, I noticed that there is a new polynomial class added. Is that a part for ellipsoids? I am really looking forward to that! Best!

[toastedcrumpets]

Yeah the new polynomial class is a start on a very small Computer Algebra library to support the implementation of complex overlap functions. The first work will be on reimplementing sphere-torus, sphere-oscillating plates, and so on, before I get to around to ellipsoids.

The recording of the workshop is a good idea, I'll put this forward to the workshop organisers to see if it can be done.

[Suvendu86]

Hello Marcus, I am also looking forward this new feature of ellipsoids in 3D and 2D including shear.

Best Regards, Suvendu

PS: I have seen that you are simulating thin needles. Is it possible for you to add some tutorials on it?

[toastedcrumpets]

Hi Suvendu, I missed your question when you first posted this. Thin needles are available in DynamO (there is a dynamod mode to demonstrate this:

dynamod -m 13

However, I plan to rework the way rotation is specified in the configuration file, so at the moment I don't want to write tutorials on systems with rotational degrees of freedom. Marcus

[Suvendu86]

Hi Marcus,

Thanks for the update. I will wait for the update.

Bests, Suvendu

[Bradleydi]

Hi Marcus,

Recently I am wondering whether "bullet physics engine" can be incorporated into the Dynamo for simulation of convex polyhedra.

https://github.com/bulletphysics/bullet3

Thank you Best