[Tutor] python 3 np.savetxt(name_s, I_z) produces IndexError: tuple index out of range

[Stephen P. Molnar]

  0
down vote
favorite
	

I am using Spyder3.1.4 with Python 3.6.0 | Anaconda 4.3.0 (64-bit) | and 
IPython 6.0.0.

My script is rather long and calculates a series of molecular indices 
using the same formula and a series of different coefficients. The 
script uses the np.savetxt() quite a few times, but one use generates 
the title error. The offending line is np.savetxt(name_s,I_z) where I_z 
is a single number of type float64 with a size of 1.

If I comment out the line containing the np.savetxt statement the script 
runs to completion and np.savetxt(name_s,I_oe) where I_oe is a float64 
number except it has a size of (1,).

Now, it would seems to me that the different size of the name in the 
np.savetxt statement causes the error, but how do I correct it? Google 
has not resulted in a solution.

Here is an abbreviated copy of the script:

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Sat Apr  8 15:17:07 2017

@author: comp

Copyright (c) 2017 Stephen P. Molnar, Ph.D.

"""
import matplotlib.pyplot as plt
import numpy as np


start=1
finish=31
points=300

s = np.linspace(start, finish, points)
np.savetxt('s',s)

name = input("Enter Molecule ID: ")

name_in = name+'.dat'

dtype = [('NO', int), ('LB', 'S2'), ('ZA', float), ('FRAG', int),
          ('MASS', float), ('X', float), ('Y', float), ('Z', float)]
data = np.genfromtxt(name_in, dtype=dtype, skip_header=3)

N =  data.shape[0]
a = np.array([data['X'], data['Y'], data['Z']])
anrows, ancols = np.shape(a)
a_new = a.reshape(anrows, 1, ancols)

diff = a_new - a

D = (diff ** 2).sum(2)
D = np.sqrt(D)
r = D

def eq7(a, s, Z):
     """
     Computes equation 7 in Molnar & King (2001)
     """
     N = r.shape[0]
     I = np.zeros(s.shape)
     for i in range(1, N):
         for j in range(i):
             I += Z[i] * Z[j] * np.sin(s * r[i, j])/(s * r[i, j])

     return I

I = eq7(r, s, data['ZA'])

name_s = name+'-Iz'
np.savetxt(name_s,I)

I_sq = []
I_sq = I**2
Area = []

name_s = name+'-Iz'

Area = np.trapz(I_sq,x=None,dx=0.01,axis=-1)
I_z = np.sqrt(Area)

fig = plt.figure()
ax = fig.add_subplot(111)
ax.plot(s.T, I)
fig.gca().set_xlabel("Distance (Å)")
plt.ylabel('Atomic Number Transform (FT$_z$)')
plt.show()
print('FTz: ',I_z)
name_s = name+'-FTz'
print(name_s)
np.savetxt(name_s,I_z)


#--------------------------------------------------------------------------
# MASS Mollecular Transform  FT_m


I = eq7(r, s, data['MASS'])

name_s = name+'-Im'

np.savetxt(name_s,I)
fig = plt.figure()
ax = fig.add_subplot(111)
ax.plot(s.T, I)
fig.gca().set_xlabel("Distance (Å)")
plt.ylabel('MASS Transform (FT$_m$)')
plt.show()

I_sq = I**2
Area = np.trapz(I_sq,x=None,dx=0.01,axis=-1)
np.savetxt('I_m',I,delimiter=' ')
I_m = np.sqrt([Area])

print('FTm: ',I_m)
name_s = name+'-FTm'
np.savetxt(name_s,I_m)

"""
#------------------------------------------------------------------------------

name_in = name+'.mpa.dat'

dtype_1 = [('NO', int), ('ATOM', 'S2'), ('NA', float), ('ZA', float),
          ('QA', float), ('VA', float), ('BVA', float), ('FA', float)]

data_1 = np.genfromtxt(name_in, dtype=dtype_1, skip_header=11)

qa = []
qa = np.array(data_1['QA'])
va = []
va = np.array([data_1['VA']])
bva =[]
bva = np.array([data_1['BVA']])
fa = []
fa = np.array([data_1['FA']])

#------------------------------------------------------------------------------
#Charge Molecular Transform  FT_c

I = eq7(r, s, data_1['QA'])
I_c = I

name_s = name+'-Ic'

np.savetxt(name_s,I)
fig = plt.figure()
ax = fig.add_subplot(111)
ax.plot(s.T, I)
fig.gca().set_xlabel("Distance (Å)")
plt.ylabel('Charge Transform (FT$_C$)')
plt.show()

I_sq = I_c**2
Area = np.trapz(I_sq,x=None,dx=0.01,axis=-1)
np.savetxt(name_s,I,delimiter=' ')
I_c = np.sqrt([Area])

print('FTc: ',I_c)
name_s = name+'-FTc'

np.savetxt(name_s,I_c)


"""

And here is the input file:

CARTESIAN COORDINATES (A.U.)
----------------------------
   NO LB      ZA    FRAG     MASS         X           Y           Z
    0 C     6.0000    0    12.011    0.000000    0.000000    0.000000
    1 H     1.0000    0     1.008    2.059801    0.000000    0.000000
    2 Br   35.0000    0    79.900   -1.203126    3.402953    0.000000
    3 Cl   17.0000    0    35.453   -1.108639   -1.567853    2.715601
    4 F     9.0000    0    18.998   -0.938564   -1.327330   -2.299003

The last line in the script is causing the problem.

A pointer towards the solution to the problem will be much apprecialted.

Thanks in advance.

-- 
Stephen P. Molnar, Ph.D.		Life is a fuzzy set
www.molecular-modeling.net		Stochastic and multivariate
(614)312-7528 (c)
Skype: smolnar1