jmarshrossney / vicsek Goto Github PK

At the moment this project is fine for making fun little animations of small systems (which was what it was originally made for!), but it's useless to anyone who might want to do some quantitative work.

The reason is that the main loop vicsek.model.VicsekModel.step, via scipy.spatial.distance.squareform, calculates the distances between all particle pairs at every timestep, which is a colossal waste.

I should really try to improve this before even thinking about adding any new models, which means looking into efficient implementations of molecular dynamics...something I have zero familiarity with. I assume particle neighbour lists will be required. Other possibilities are:

• Write the interaction calculation in C/C++ and use e.g. SWIG to make a Python wrapper. Pros: could be fun.
• Use Numba. Pros: don't have to leave Python.
• Another implementation uses this package for 'scalable' neighbour lists.

Is the file named environment.yml from the Linux system? I use the "conda env create -f environment.yml" for windows, but it raised error .