consider adding PBC warning

[tpchuckles]

I encountered a system with atoms "jumping" from the top to the bottom of the system, due to PBC in MD, and no automatic haircutting/etc in PySlice, meaning these atoms "light up" at all frequencies.

If we're not going to implement automatic haircutting (and I don't think we should, because this would be a surprising modification to your system if you didn't ask for it), then we should at least have a warning: "hey we noticed you have atoms jumping around, dz/dt = huge, consider haircutting"?

[tpchuckles]

io/loader.py > _load_via_ovito uses the UnwrapTrajectoriesModifier, so this should not be happening.

furthermore, something like the following inside trajectory turns up nothing of particular interest:

    def checkPBC(self):
        if len(self.positions)>1:
            dxdt = np.absolute( self.positions[1:,:,:]-self.positions[:-1,:,:] ) # nt,na,xyz
            print(np.diag(self.box_matrix),np.amax(dxdt))
            where = np.where(dxdt>np.diag(self.box_matrix)[None,None,:]/2)
            print(where)

[tpchuckles]

it is likely that surface atoms "light up" in a highly-convergent beam case (e.g. 30 mrad) because the probe is more focused and the signal intensity is inversely proportional to spot size. this is separate from dynamic and channeling effects

you see this in other types of experiments: in laser-based pump-probe experiments, the highest magnitude signal occurs when the pump/probe lasers are focused at the sample (and people use this effect as part of their procedure to ensure the lasers are focused).

I will test this by changing the defocus in PySlice and watching different layers of atoms light up. will report back when the SI are finished running.