Pymatgen parser - displacements Nan issue

[Harry-Rich]

When parsing Xdatcar files, displacements are not working properly i.e.

x = Xdatcar("XDATCAR_reduced_50_wrapped.vasp")
time_step = 1.0 * sc.Unit('fs')
step_skip = 50 * sc.Unit('dimensionless')
kin = parser.PymatgenParser(x.structures, time_step = time_step, step_skip = step_skip, specie = ['Li','N', 'H'])

This calls the parser and calculates coords, indices, drift_indices etc.
It should also calculate displacements, but

kin.displacements

returns the right dimensions and shape scipp vairable, but everything is nan.

However,

structure, coords, latt = kin.get_structure_coords_latt(x.structures)
kin.calculate_displacements(coords = coords, lattice= latt)

does work and correctly calculates displacements, so it is not the calculation that is broken, so I believe it must be something in here (Parser) :

        disp = self.calculate_displacements(coords, lattice)
        drift_corrected = self.correct_drift(disp)

        self._slice = DIMENSIONALITY[dimension.lower()]
        drift_corrected = drift_corrected['dimension', self._slice]
        self.dimensionality = drift_corrected.sizes['dimension'] * sc.units.dimensionless

        self.displacements = drift_corrected['atom', indices]

I will look into it, be good if someone else could verify with a different xdatcar file as well

[arm61]

Can you try with the XDATCAR that is located in the docs (https://github.com/bjmorgan/kinisi/blob/master/docs/source/example_XDATCAR.gz)?