I am trying to calculate voronoi volume of a water surronded by nearest oxygen. This is my code.

from numpy import *

import glob

box = 3.73014

list_of_files = glob.glob('./npt11.txt')

for file_name in list_of_files:

f = loadtxt(file_name, float)

g = zeros(3)

# Specify a Donor water molecule's coordinate

for i in range(0,5181,3):

# Donor Oxygen vector

x_DO = f[i, 0]

y_DO = f[i, 1]

z_DO = f[i, 2]

r_DO = [x_DO, y_DO, z_DO]

# Specify an around water molecules

# DOAO vector list included in cut-off

list_of_DOAO = []

for j in range(i+3,5184,3):

x_AO = f[j,0]

y_AO = f[j,1]

z_AO = f[j,2]

# DO-AO vector using periodic boundary condition

x_DOAO = x_AO - x_DO

x_DOAO = x_DOAO - box*round(x_DOAO/box)

y_DOAO = y_AO - y_DO

y_DOAO = y_DOAO - box*round(y_DOAO/box)

z_DOAO = z_AO - z_DO

z_DOAO = z_DOAO - box*round(z_DOAO/box)

r_DOAO = [x_DOAO, y_DOAO, z_DOAO]

r_DOAO_rev = [-x_DOAO, -y_DOAO, -z_DOAO]

# DO-AO vector length

rc = sqrt(dot(r_DOAO, r_DOAO))

# Cut-off calculation

# 1. Spherical searching of DO-AO distance

if rc < 0.35:

# Store the list of AO within the cut-off distance

list_of_DOAO.append(r_DOAO)

points = array(list_of_DOAO)

ConvexHull(points)

At this point, I got an error like

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QhullError Traceback (most recent call last)

in ()

98 list_of_DOAO.append(r_DOAO)

99 points = array(list_of_DOAO)

--> 100 ConvexHull(points)

101

qhull.pyx in scipy.spatial.qhull.ConvexHull.__init__()

qhull.pyx in scipy.spatial.qhull._Qhull.__init__()

QhullError: QH6214 qhull input error: not enough points(3) to construct initial simplex (need 4)

While executing: | qhull i Qt

Options selected for Qhull 2015.2.r 2016/01/18:

run-id 1666097638 incidence Qtriangulate _pre-merge _zero-centrum

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How could I fix them?