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 >> >> >
