[image] GitHub - m3g/CellListMap.jl: Flexible implementation of cell lists to map the... Flexible implementation of cell lists to map the calculations of particle-pair dependent functions, such as forces, energies, neighbor lists, etc. - GitHub - m3g/CellListMap.jl: Flexible implementa..…

I am happy to announce that the article describing this package is now published, and available for free access for 50 days here: CellListMap.jl: Efficient and customizable cell list implementation for calculation of pairwise particle properties within a cutof . Computer Physics Communications, Volu…

[image] Raf: How much do you think will be usable inside a GPU kernel? I have absolutely no experience with programming for GPUs, but almost certainly the algorithm can adapted for that (since the best molecular dynamics simulations codes run on GPUs and this is a subset of what they do). I a…

No worries. I’ve been looking though the code and wikipedia example. It seems like what I need, but just the kernel algorithm really… It will have to be hacked a lot to fit DynamicGrids and GPUs. But I’ll use your code as a reference.

Please let me know when/if you do that, so I can see what you did and port it back :slight_smile:

For sure! It will be integrated with this - so probably pretty convoluted… DynamicGrids.jl/agents.jl at agents · cesaraustralia/DynamicGrids.jl · GitHub Hopefully this idea will work with it… it’s organised around tracking cell counts for doing radix style agent sorts.

Updated some results and example API syntax for a new version (0.4.1).

Indeed, that could improve the performance of this loop . In a simulation probably we need a smart way to update the lists without having to compute them all again, considering the fact that most of the atoms will only move slightly from one step to the next. (my main goal with this package is to pr…

Yes, I agree. Cell lists are a key missing feature in Molly.jl. I am moving to a position this autumn which will let me focus on Molly full time, hopefully it will progress quickly after that and become useful for serious work. The topology tools are barebones at the minute but I’m hoping to depend …

[image] jgreener64: Julia version of Packmol the goal here will be not just better performance and scaling, and arbitrary periodic boundary conditions (I could do that in Fortran), but to provide an interface in which the user can provide its own geometric spacial restrictions to the molecule…

Sounds cool, and could open up research directions using autodiff to tune those functions to give certain resultant properties.

[ANN] CellListMap.jl: short-ranged particle pairwise computations (lennard-jones, gravitational, etc)

Package Announcements

jgreener64 June 18, 2021, 10:58am 8

Looks like a really useful package! I’d like to use something like this in Molly.jl in the future.

Topic		Replies	Views
Accelerate pairwise Lennard-Jones force computation Performance	87	4077	February 12, 2022
CellListMap.jl: Is it suitable for detecting collision of particles? General Usage celllistmap	5	675	September 21, 2021
Pairwise computation slower than Python (Cython) code (BallTree very slow!) Performance question , tree	27	2367	June 18, 2021
[ANN] SpatialHashTables.jl Package Announcements package , gpu	8	1070	May 20, 2024
Cell list algorithm is slower than double for loop Performance	18	2489	April 2, 2020

[ANN] CellListMap.jl: short-ranged particle pairwise computations (lennard-jones, gravitational, etc)

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