Force calculation suggestion about molly.jl

[jgreener64]

Thanks for the advice, I'll add it to the to-do list.

[BradenDKelly]

It is probably worth noting that the degrees of freedom are only 3*N, where N is number of particles, for the Andersen thermostat. DF are different for stochastic or deterministic thermostats, and this rippled to kinetic energy. The difference is small, but nonetheless, worth accounting for.

[jgreener64]

Thanks, let me know as you see anything else, it's useful.

[ehsanirani]

I think @BradenDKelly suggestion would enhance the performance and simplicity of the api. The suggested table can also have a r_cutoff field for each pair of particle types. Then something like negative values can be set to it to exclude that pair of particle types from force calculation (or neighbor searching). That's the method that HOOMD-Blue uses.

[jgreener64]

I think it's a good idea but will wait to see how the GPU kernel work (#60) progresses as this may require a refactor of other parts of the API too.