On Jan 23, 2017, at 4:54 PM, Kaido Reivelt <kaido....@gmail.com> wrote:Kaido ReiveltWith best regards,BTW, Next-Generation Molecular Workbench engine, is it an open-source software platform?Yes, we have technical persons around, please send the instructions.Hi Dan and thank you for the reply,Right now we would like to embed the simulations in our web platform. The multi-page/step activities have to wait a while.2017-01-23 16:18 GMT+02:00 Daniel Damelin <ddam...@concord.org>:Hi Kaido,It would be great if you would be interested in translating some of our materials. When you mention simulations and activities I assume you mean both the individual simulations and some of the multi-page activities? Are there specific ones you are interested in?Regarding simulation translation, is there someone on your end that has some technical capability. It won’t require actual programming, but someone who is familiar with Git file version management and has some technical facility would be required to make that possible.If you have access to someone like that, then I can send more detailed instructions about how to move forward.Thanks for your interest.-Dan DamelinOn Jan 23, 2017, at 7:25 AM, Kaido Reivelt <kaido....@gmail.com> wrote:Estonian Physical Society, UT Centre of Physics EducationKaido ReiveltWith best regards,Is it possible to become your partner? Our primary interest is to translate your materials for Estonian physics teachers. But there might be other means for cooperation.Dear AllEstonian Physical Society and Institute of Physics, University of Tartu aknowledges your work on physics simulations and activities in http://mw.concord.org/nextgen/.
> Otherwise, what would be the best way of implementing it? I tried creating a modified version of bounceParticleOffWalls and it works reasonably well, but I realize I have to implement minimum image convention in the interactions between particles as well, and probably modify how the neighbor lists are treated.
I believe you are on the right track here. Piotr Janik worked on the neighbor list implementation as part of engine optimization, so he may have some advice on which parts of MD2D need to be modified to achieve this new feature.
Thanks Piotr for these pointers. So far I have modified bounceParticleOffWalls, getNeighboringCells, and calculateLJInteraction, and I think it works as it should, for atomistic systems. I also implemented a non-elegant way to get out the "true" coordinates (not limited to the box) so one can compute e.g. mean displacement. Here are a few examples:
The neighbor list is a mystery to me, but it seems to work
I would say that obstacles and shapes are incompatible with
periodic boundary conditions for fundamental reasons, at least I
will not try to implement it. Systems with charges would require
Ewald summation, which unfortunately I don't think I'm capable of
implementing. Molecules would be nice, but I think that might be
much more difficult than atoms.
So, my question is, would this very limited functionality
(neutral atoms in rectangular boxes without obstacles) be of
interest to anyone else, so that I should try to contribute these
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