vec_euclid.py

from scipy.spatial.distance import euclidean
import numpy as np
from __future__ import division

def periodic_distance(a, b, period=12):
    """
    Euclidean distance w/ periodic boundaries.
    
    >>> A = np.array([1, 12, 1])
    >>> B = np.array([12, 1, 1])
    >>> periodic_distance(A, B)
    array([ 0.51763809,  0.51763809,  0.        ])
    """
    A = 2 * np.math.pi * (a / period)
    B = 2 * np.math.pi * (b / period)
    rA = np.array((np.sin(A), np.cos(A)))
    rB = np.array((np.sin(B), np.cos(B)))
    return np.linalg.norm(rA - rB, axis=0)