Extension for Python - Generate neighbour list
This code was written to allow for the faster generation of neighbour lists, given a list of elements in n-dimensions. It uses a supplied cutoff radius, and currently brute-forces the calculation. Further iterations will allow for more efficient methods.
Simply place the .so or .pyd file in the same directory as your code, depending on if you're using linux or windows respectively, then import.
import neigh
from random import random
X, Y, Z = 100, 100, 100
O_x, O_y, O_z = 0, 0, 0
N = 100
CUTOFF = 1.5
POSITION_ARRAY = [None for i in range(N)]
for i in range(N):
x, y, z = random()*X+O_x, random()*Y+O_y, random()*Z+O_z
positions[i] = [x, y, z]
neighbour_list = neigh.get_neigh(POSITION_ARRAY, CUTOFF, PBC=[X, Y, Z], origin = [O_x, O_y, O_z])
The function neigh.get_neigh takes in:
- POSITION_ARRAY = A list of lists, each holding floats describing your system
- CUTOFF = A float that gives a cutoff radius
- PBC = A list of floats describing your box
- origin = A list of floats describing where your origin is
NOTE! In theory the code allows for n-dimensions; however, if you use PBC, then it only allows for dim <= 3.