Hey Viral: sure, I'll keep you posted on how it spans out. On Wed, Jan 28, 2015 at 8:29 PM, Viral Shah <[email protected]> wrote:
> Amuthan, > > Off-topic, but do let us know any issues you face in parallelization. Any > inputs on API design, performance, documentation, etc. will be greatly > useful. > > -viral > > > On Wednesday, January 28, 2015 at 8:12:19 PM UTC+5:30, Amuthan A. > Ramabathiran wrote: >> >> Hi Guillaume: >> >> This looks good -- thanks for the package! I have a basic question >> regarding the force computation: I had a quick look at the code and it >> appears to me that the current code uses an O(N^2) algorithm (direct sum) >> for this. Is my understanding correct? Software like LAMMPS use very >> efficient algorithms for short and long range potentials and this might >> possibly account for the fact that the benchmark is 80x slower. >> >> I had developed a serial MD code using neighbor lists last year and I'm >> currently in the process of parallelizing it to study the suitability of >> Julia for developing (reasonably) parallel research codes. Is >> parallelization something you're looking into? I would be very interested >> in hearing about this. Thanks! >> >> Cheers, >> Amuthan >> >> On Tuesday, January 27, 2015 at 2:46:59 PM UTC-8, Luthaf wrote: >>> >>> Hi julians ! >>> >>> I am very happy to announce the release of Jumos, a Julia package for >>> molecular simulations. >>> >>> You can find the code here: https://github.com/Luthaf/Jumos.jl, and the >>> documentation is hosted by readthedocs : http://jumos.readthedocs.org/ >>> en/latest/. >>> >>> This package aims at being as extensible as possible. Every algorithm is >>> a type that can be subtyped and changed at runtime, during the simulation. >>> This makes it easy to write new algorithms, experiment with them, and >>> combine algorithms in all the fancy ways you can imagine. >>> >>> Presently, only molecular dynamic is implemented, but I am planning to >>> add energy minimisation, and trajectory replay from files (maybe >>> monte-carlo simulations if I find some time). A handful of tools are >>> already implemented : >>> - Velocity-Verlet and Verlet integrator; >>> - Lennard-Jones and Harmonic potential; >>> - User-defined potentials; >>> - RDF and density profile analysis; >>> - Berendsen thermostat; >>> - Velocity-rescale thermostat; >>> - Temperature and energy computations. >>> >>> And a lot more are planned: https://github.com/Luthaf/Jumos.jl/issues. >>> If you want to help, contributions are very welcome ! Just pick up an >>> issue or create a new one as a feature request. >>> The first benchmark (against LAMMPS) gives me a speed 80 times slower >>> than LAMMPS. This is already great for a dynamic language, but there is >>> still room for improvement ! >>> >>> Any feedback on the implementation is also very welcome. >>> >>> Regards >>> Guillaume >>> >>> PS: What does the ANN in the title mean ? It seems to be everywhere, >>> but I don't have any clue about its meaning >>> >>> >>
