Add displacement plots

[stefsmeets]

This PR adds an implementation for the displacement plots (Figure 1-3) using pymatgen. Takes ~1s to calculate displacements for 75k x 104 sites. Could be faster with a better implementation using np.einsum.

Known problems

• Calculating displacements element wise is SLOW. Better make a huge matrix of all coordinates and perform the operation at once.
• Account for sites jumping to different unit cells. The matlab codes for whether the jump in fractional coordinates is larger than 0.5.

Todo

• Vasprun.get_trajectory() is a giant array of all fractional coordinates. Use this as a basis for displacement calculations.

Essentially:

1. Put all coordinates in giant array (Vasprun.get_trajectories())
2. Identify cell jumps per time step
3. Calculate distance between coordinates at t=0 and t=last
   • Use lattice.metric_tensor for generatlized distance calculation between fractional coordinates (Dunitz p227)
   • xyz.T.dot(lattice.metric_tensor).dot(xyz)

Figures

[v1kko]

Great work, didn't went into the details of all the plots but they look good.

One issue is that I cannot import GEMDAT.plot_xxx or import GEMDAT.analyze_md anymore, but we can fix that later