In [15]:

    

import numpy as np
import matplotlib.pyplot as plt
def Deff_calc(x,y,t):
    SD = np.zeros(len(x) - 1)
    MSD = np.zeros(len(x) - 1)
    D_eff = np.zeros(len(x) - 1)
    i = 1
    while i <= (len(x) - 1):
        SD[i-1] = (abs(x[0]-x[i]) ** 2 + abs(y[0]-y[i]) ** 2)
        total_SD = 0
        p = i
        while p >= 1:
            total_SD = total_SD + SD[p-1]
            p -= 1
        MSD[i-1] = total_SD
        D_eff[i-1] = MSD[i-1]/4/t[i]
        i += 1
    print(SD)
    print(MSD)
    print(D_eff)
    fig = plt.figure()
    axes = fig.add_subplot(211)
    plt.xlabel("time")
    plt.ylabel("MSD")
    plt.title("MSD vs. time")
    axes.plot(t[1:len(t)],MSD)
    plt.tight_layout()
    axes2 = fig.add_subplot(212)
    plt.xlabel("time")
    plt.ylabel("D_eff")
    plt.title("D_eff vs. time")
    axes2.plot(t[1:len(t)],D_eff)
    plt.tight_layout()
    plt.show()
Deff_calc(np.array([0,-3.00,-0.5,-3.00,2.00,-2.50,2.50]), np.array([0,2.50,3.50,-4.0,0.00,-0.50,2.50]), np.array([0,1,2,3,4,5,6]))


    

    




[ 15.25  12.5   25.     4.     6.5   12.5 ]
[ 15.25  27.75  52.75  56.75  63.25  75.75]
[ 3.8125      3.46875     4.39583333  3.546875    3.1625      3.15625   ]