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23 """Module for functions relating to the paramagnetic centre."""
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26 from numpy.linalg import norm
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30 """Calculate the electron spin to nuclear spin unit vectors and distances.
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32 This assumes that there is one paramagnetic centre per state of the system.
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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 """
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46 for i in range(len(atomic_pos)):
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48 for c in range(len(atomic_pos[i])):
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50 vect = atomic_pos[i, c] - paramag_centre[c]
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53 r[i, c] = norm(vect)
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56 unit_vector[i, c] = vect / r[i, c]
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59 r[i, c] = r[i, c] * 1e-10
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63 """Calculate the electron spin to nuclear spin unit vectors and distances.
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65 This assumes that there is only one paramagnetic centre for all states of the system.
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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 """
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79 for i in range(len(atomic_pos)):
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81 for c in range(len(atomic_pos[i])):
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83 vect = atomic_pos[i, c] - paramag_centre
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86 r[i, c] = norm(vect)
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89 unit_vector[i, c] = vect / r[i, c]
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92 r[i, c] = r[i, c] * 1e-10
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