calculating distance R from xyz data file

Question

I am trying to work with .xyz file, and I have got it to opening up and reading the file. I need to calculate r (distance) for each row of xyz data ( by doing r^2 = x^2+y^2+z^2). However, I failed to separate each xyz value in a row because it recognizes the data as a single column ex([-3.657420e-01 -1.434236e+00 1.086713e+00]) is a single row, when ideally it should be separated by x,y,z value.

I am attaching the script to opening/ showing the xyz file, and the sample output. Can anyone help me out with calculating 'r' for each row of data?

Thank you

import numpy as np
filename = "lj-0200.xyz"
xyz_file = np.genfromtxt(fname=filename,skip_header=2,dtype='unicode')
xyz = open(filename)

atom_coordinates = (xyz_file[:,1:])
atom_coordinates = atom_coordinates.astype(float)
atom_quantity = int(xyz.readline())
title = xyz.readline()

print("Input filename is",filename, "Title is", title,"There are",atom_quantity,"atoms in this file")
print(atom_coordinates)

output

Input filename is lj-0200.xyz Title is A Box of Atoms
 There are 200 atoms in this file
[[-3.657420e-01 -1.434236e+00  1.086713e+00]
 [ 1.758085e+00 -2.733505e+00 -4.553970e-01]
 [-2.777260e+00  8.659730e-01 -9.788090e-01]
 [-8.509290e-01  8.053680e-01 -1.050607e+00]
 [ 4.697280e-01 -1.262455e+00  1.770134e+00]
 [ 1.776954e+00  2.284919e+00  2.691217e+00]
 [ 1.564369e+00  2.100387e+00 -3.898060e-01]
 [ 2.153646e+00  1.233546e+00  1.145661e+00]
 [ 2.373994e+00  2.372510e+00  1.522204e+00]...

Answer 1

Read the Numpy indexing documentation here

r = np.linalg.norm(atom_coordinates, axis= 1)