date:20170511

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

2017-05-11 Thread Alan Gauld via Tutor

On 11/05/17 20:46, Stephen P. Molnar wrote:

>> 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.

I'm glad you found the problem but please, when you post,
do NOT summarize the error.

Always, always, send the full error trace, there is a wealth
of data in those messages and if we only get your best guess
at what they mean we are deprived of essential clues in
diagnosing problems.

> Problem solved: np.savetxt(name_s,I_z) should be np.savetxt(name_s,[I_z])

-- 
Alan G
Author of the Learn to Program web site
http://www.alan-g.me.uk/
http://www.amazon.com/author/alan_gauld
Follow my photo-blog on Flickr at:
http://www.flickr.com/photos/alangauldphotos


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

2017-05-11 Thread Stephen P. Molnar


On 05/11/2017 02:26 PM, Stephen P. Molnar wrote:

  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  ZAFRAG MASS X   Y   Z
0 C 6.012.0110.000.000.00
1 H 1.0 1.0082.0598010.000.00
2 Br   35.079.900   -1.2031263.4029530.00
3 Cl   17.035.453   -1.108639   -1.5678532.715601
4 F 9.018.998   -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.



Problem solved: np.savetxt(name_s,I_z) should be np.savetxt(name_s,[I_z])

--
Stephen P. Molnar, Ph.D.Life is a fuzzy set
www.molecular-modeling.net  Stochastic and multivariate
(614)312-7528 (c)
Skype: smolnar1
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[Tutor] python 3 np.savetxt(name_s, I_z) produces IndexError: tuple index out of range

2017-05-11 Thread 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  ZAFRAG MASS X   Y   Z
   0 C 6.012.0110.000.000.00
   1 H 1.0 1.0082.0598010.000.00
   2 Br   35.079.900   -1.2031263.4029530.00
   3 Cl   17.035.453   -1.108639   -1.5678532.715601
   4 F 9.018.998   -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
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Re: [Tutor] Fwd: Re: While Loop Question

2017-05-11 Thread Rafael Skovron

Thank you all I finally understood that the while code traps j and runs
independently of the for loop until while is false and a new i is picked.



On Thu, May 11, 2017 at 10:19 AM Abdur-Rahmaan Janhangeer <
arj.pyt...@gmail.com> wrote:

> sorry j is set to zero. grave typo
>
> Abdur-Rahmaan Janhangeer,
> Mauritius
> https://abdurrahmaanjanhangeer.wordpress.com
>
> On 11 May 2017 12:29 pm, "Abdur-Rahmaan Janhangeer" 
> wrote:
>
> >
> >
> > -- Forwarded message --
> > From: "Abdur-Rahmaan Janhangeer" 
> > Date: 11 May 2017 12:26 pm
> > Subject: Re: [Tutor] While Loop Question
> > To: "Rafael Skovron" 
> > Cc:
> >
> > i modified your code to make it look like that :
> >
> > for i in range(1, 5):
> >
> > j=0
> > print("outer,  i=",i)
> > while j < i:
> >  print("inner, j=",j)
> >
> >  j += 1
> >
> > so it shows that each time the outer loop is reexecuted, i is set to
> zero.
> >
> > putting j at the begining completely, it is not reset to zero
> >
> > Abdur-Rahmaan Janhangeer,
> > Mauritius
> > https://abdurrahmaanjanhangeer.wordpress.com
> >
> >
> >
> >
> ___
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Re: [Tutor] While Loop Question

2017-05-11 Thread George Fischhof

2017-05-11 3:53 GMT+02:00 Rafael Skovron :

> Sorry I left out the indents in my previous email. It seems like j is
> always reset to zero. Why does j vary?
>
> Are there two different instances of j going on?
>
>
> for i in range(1, 5):
>
> j=0
>
>while j < i:
>
>  print(j, end = " ")
>
>  j += 1
> ___
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>



Hi,

As there is a j = 0 statement in the for cycle, it will be set to 0 every
time the while cycle finishes. (The while cycle will then increment j, then
if j == i j will be set to 0 again).

George
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Re: [Tutor] Fwd: Re: While Loop Question

2017-05-11 Thread Abdur-Rahmaan Janhangeer

sorry j is set to zero. grave typo

Abdur-Rahmaan Janhangeer,
Mauritius
https://abdurrahmaanjanhangeer.wordpress.com

On 11 May 2017 12:29 pm, "Abdur-Rahmaan Janhangeer" 
wrote:

>
>
> -- Forwarded message --
> From: "Abdur-Rahmaan Janhangeer" 
> Date: 11 May 2017 12:26 pm
> Subject: Re: [Tutor] While Loop Question
> To: "Rafael Skovron" 
> Cc:
>
> i modified your code to make it look like that :
>
> for i in range(1, 5):
>
> j=0
> print("outer,  i=",i)
> while j < i:
>  print("inner, j=",j)
>
>  j += 1
>
> so it shows that each time the outer loop is reexecuted, i is set to zero.
>
> putting j at the begining completely, it is not reset to zero
>
> Abdur-Rahmaan Janhangeer,
> Mauritius
> https://abdurrahmaanjanhangeer.wordpress.com
>
>
>
>
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[Tutor] Fwd: Re: While Loop Question

2017-05-11 Thread Abdur-Rahmaan Janhangeer

-- Forwarded message --
From: "Abdur-Rahmaan Janhangeer" 
Date: 11 May 2017 12:26 pm
Subject: Re: [Tutor] While Loop Question
To: "Rafael Skovron" 
Cc:

i modified your code to make it look like that :

for i in range(1, 5):

j=0
print("outer,  i=",i)
while j < i:
 print("inner, j=",j)

 j += 1

so it shows that each time the outer loop is reexecuted, i is set to zero.

putting j at the begining completely, it is not reset to zero

Abdur-Rahmaan Janhangeer,
Mauritius
https://abdurrahmaanjanhangeer.wordpress.com
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Re: [Tutor] While Loop Question

2017-05-11 Thread Steven D'Aprano

On Wed, May 10, 2017 at 06:53:21PM -0700, Rafael Skovron wrote:
> Sorry I left out the indents in my previous email. It seems like j is
> always reset to zero. Why does j vary?

Because you run code that adds 1 to j.

> Are there two different instances of j going on?

No. Try to run the code in your head and see what happens. See below:

> for i in range(1, 5):
> j=0
> while j < i:
>  print(j, end = " ")
>  j += 1

We start by setting i = 1, then the body of the for-loop begins. That 
sets j = 0, and since 0 < 1, we enter the while-loop.

Inside the while-loop, we print j (0), then add 1 to j which makes it 1. 
Then we return to the top of the while-loop. Since 1 is NOT less than 1, 
we exit the while-loop and return to the top of the for-loop.

Now we set i = 2, and continue into the body of the for-loop. That sets 
j = 0 (again!) and since 0 < 2, we enter the while-loop.

Inside the while-loop, we print j (0), then add 1 to j which makes it 1. 
Then we return to the top of the while-loop. Since 1 < 2, we continue 
inside the body, print j (1), then add 1 to j which makes it 2. Since 2 
is not LESS than 2, we exit the while-loop and return to the top of the 
for-loop.

Now we set i = 3, and continue into the body of the for-loop. That sets 
j = 0 (again!) and since 0 < 3, we enter the while-loop.

Inside the while-loop, we follow the same steps and print 0, then 1, 
then 2, then exit the while-loop and return to the top of the for-loop.

Now we set i = 4, and again continue into the while-loop to print 0, 1, 
2 and finally 3, then exit the while-loop and return to the top of the 
for-loop, which is now complete.

-- 
Steve
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Re: [Tutor] Simple while loop question

2017-05-11 Thread Alan Gauld via Tutor

On 11/05/17 02:50, Rafael Skovron wrote:
> I dont understand why j can have any value other than zero in this:
> 
> for i in range(1, 5):
  j = 0
  while j < i:
 print(j, end = " ")
 j += 1


Because i can go as high as 4 (from range(1,5)->1,2,3,4).
So lets consider that final case:

i->4
j->0
j True
print 0
j->1
jTrue
print 1
j->2
jTrue
j->3
print 3
j->4
j<4->False


So you'd expect the output to go like this:

i=1, j->0
i=2, j->0,1
i=3, j->0,1,2
i=4, j->0,1,2,3

And since you set the print end to be  a
space it will all run into one line:

0 0 1 0 1 2 0 1 2 3

Is that what you see?

-- 
Alan G
Author of the Learn to Program web site
http://www.alan-g.me.uk/
http://www.amazon.com/author/alan_gauld
Follow my photo-blog on Flickr at:
http://www.flickr.com/photos/alangauldphotos


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[Tutor] Simple while loop question

2017-05-11 Thread Rafael Skovron

I dont understand why j can have any value other than zero in this:

for i in range(1, 5):

j = 0

while j < i:

print(j, end = " ")

j += 1
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Re: [Tutor] python 3 np.savetxt(name_s, I_z) produces IndexError: tuple index out of range

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

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

Re: [Tutor] Fwd: Re: While Loop Question

Re: [Tutor] While Loop Question

Re: [Tutor] Fwd: Re: While Loop Question

[Tutor] Fwd: Re: While Loop Question

Re: [Tutor] While Loop Question

Re: [Tutor] Simple while loop question

[Tutor] Simple while loop question

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