Add implementation for calculating site transitions

[stefsmeets]

This PR adds an implementation to calculate site transitions.

This code covers everything until line 156 in find_sites.m.

Data are loaded from a cif file, which means they cannot be compared directly to the matlab data (the order of the sites and thus coordinates is different).

The result differs slightly, I think because of rounding errors.

Todo

• Generate succes array
• Generate transitions array
• Generate occupancy array
• Generate occupancy_parts array
• Generate atom_sites array
• Refine and refactor code
• Load vibration_amplitude from some sort of cache or calculate it on-the-fly (Maybe a preprocess(Data) to get everything at once?) -> Structure the calculations, data now has a calculate_all function #20

[stefsmeets]

These coordinates correspond to the sites in the known_materials.md.

site_coords = np.array(
[
    [0.183,  0.183,  0.024],
    [0.183,  0.683,  0.524],
    [0.683,  0.183,  0.524],
    [0.683,  0.683,  0.024],
    [0.817,  0.817,  0.024],
    [0.817,  0.317,  0.524],
    [0.317,  0.817,  0.524],
    [0.317,  0.317,  0.024],
    [0.817,  0.183,  0.976],
    [0.817,  0.683,  0.476],
    [0.317,  0.183,  0.476],
    [0.317,  0.683,  0.976],
    [0.183,  0.817,  0.976],
    [0.183,  0.317,  0.476],
    [0.683,  0.817,  0.476],
    [0.683,  0.317,  0.976],
    [0.024,  0.183,  0.183],
    [0.024,  0.683,  0.683],
    [0.524,  0.183,  0.683],
    [0.524,  0.683,  0.183],
    [0.024,  0.817,  0.817],
    [0.024,  0.317,  0.317],
    [0.524,  0.817,  0.317],
    [0.524,  0.317,  0.817],
    [0.976,  0.817,  0.183],
    [0.976,  0.317,  0.683],
    [0.476,  0.817,  0.683],
    [0.476,  0.317,  0.183],
    [0.976,  0.183,  0.817],
    [0.976,  0.683,  0.317],
    [0.476,  0.183,  0.317],
    [0.476,  0.683,  0.817],
    [0.183,  0.024,  0.183],
    [0.183,  0.524,  0.683],
    [0.683,  0.024,  0.683],
    [0.683,  0.524,  0.183],
    [0.817,  0.024,  0.817],
    [0.817,  0.524,  0.317],
    [0.317,  0.024,  0.317],
    [0.317,  0.524,  0.817],
    [0.183,  0.976,  0.817],
    [0.183,  0.476,  0.317],
    [0.683,  0.976,  0.317],
    [0.683,  0.476,  0.817],
    [0.817,  0.976,  0.183],
    [0.817,  0.476,  0.683],
    [0.317,  0.976,  0.683],
    [0.317,  0.476,  0.183],
])