Source Code for Module lib.alignment.paramag_centre

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 2  #                                                                             # 
 3  # Copyright (C) 2010-2011 Edward d'Auvergne                                   # 
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 5  # This file is part of the program relax (http://www.nmr-relax.com).          # 
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21   
22  # Module docstring. 
23  """Module for functions relating to the paramagnetic centre.""" 
24   
25  # Python imports. 
26  from numpy.linalg import norm 
27   
28   
29 -def vectors_centre_per_state(atomic_pos, paramag_centre, unit_vector, r): 
30      """Calculate the electron spin to nuclear spin unit vectors and distances. 
31   
32      This assumes that there is one paramagnetic centre per state of the system. 
33   
34   
35      @param atomic_pos:      The atomic positions in Angstrom.  The first index is the spins, the second is the structures, and the third is the atomic coordinates. 
36      @type atomic_pos:       numpy rank-3 array 
37      @param paramag_centre:  The paramagnetic centre position in Angstrom. 
38      @type paramag_centre:   numpy rank-2, Nx3 array 
39      @param unit_vector:     The structure to fill with the electron spin to nuclear spin unit vectors. 
40      @type unit_vector:      numpy rank-3 array 
41      @param r:               The structure to fill with the electron spin to nuclear spin distances. 
42      @type r:                numpy rank-2 array 
43      """ 
44   
45      # Loop over the spins. 
46      for i in range(len(atomic_pos)): 
47          # Loop over the states. 
48          for c in range(len(atomic_pos[i])): 
49              # The vector. 
50              vect = atomic_pos[i, c] - paramag_centre[c] 
51   
52              # The length. 
53              r[i, c] = norm(vect) 
54   
55              # The unit vector. 
56              unit_vector[i, c] = vect / r[i, c] 
57   
58              # Convert the distances from Angstrom to meters. 
59              r[i, c] = r[i, c] * 1e-10 
60   
61   
62 -def vectors_single_centre(atomic_pos, paramag_centre, unit_vector, r): 
63      """Calculate the electron spin to nuclear spin unit vectors and distances. 
64   
65      This assumes that there is only one paramagnetic centre for all states of the system. 
66   
67   
68      @param atomic_pos:      The atomic positions in Angstrom.  The first index is the spins, the second is the structures, and the third is the atomic coordinates. 
69      @type atomic_pos:       numpy rank-3 array 
70      @param paramag_centre:  The paramagnetic centre position in Angstrom. 
71      @type paramag_centre:   numpy rank-1, 3D array 
72      @param unit_vector:     The structure to fill with the electron spin to nuclear spin unit vectors. 
73      @type unit_vector:      numpy rank-3 array 
74      @param r:               The structure to fill with the electron spin to nuclear spin distances. 
75      @type r:                numpy rank-2 array 
76      """ 
77   
78      # Loop over the spins. 
79      for i in range(len(atomic_pos)): 
80          # Loop over the states. 
81          for c in range(len(atomic_pos[i])): 
82              # The vector. 
83              vect = atomic_pos[i, c] - paramag_centre 
84   
85              # The length. 
86              r[i, c] = norm(vect) 
87   
88              # The unit vector. 
89              unit_vector[i, c] = vect / r[i, c] 
90   
91              # Convert the distances from Angstrom to meters. 
92              r[i, c] = r[i, c] * 1e-10 
93