should cropping update the positions of atoms?

[tpchuckles]

suppose i have a 50 unit cell long structure (25 uc of material A, 25 uc of material B). That's a pretty big area though, and i'm just doing HAADF in the middle, so i can crop it to save memory (and not need to compute such a large potential):

trajectory=trajectory.slice_positions( x_range=[18*a,32*a] ) # crops 25|25 into 7|7 unit cells

when i do the full-length ADF, i get a periodic structure, as expected:

probe_xs = np.linspace(0,50*a,16*8,endpoint=False)

but what i did not expect was to find my interface still at 25*a. in other words, we cropped the system, but atom positions are still referenced to the original origin of the system, not the new origin of the system. is this weird?

this is more apparent if I try to do HAADF over a smaller region, e.g. a 4|4 unit cell length area, i need to choose coordinates centered on the original system:

probe_xs = np.linspace(21*a,29*a,16*8,endpoint=False)

and NOT coordinates centered on the new system:

probe_xs = np.linspace(3*a,11*a,16*8,endpoint=False)

i don't know if this is surprising behavior to anyone else?

[tpchuckles]

discussed offline: yes, we think this should be expected behavior.

• The user who is, for example, opening their MD results in ovito or some other tool might actually be confused to find their features at different coordinates (my interface is at 136 in the second figure above, so it's good our ADF plot shows that!)
• Needing to remember to adjust the positions (if we were to change the origin, or subtract off x1,y1,z1 from all atomic positions) is confusing.
• We don't consider crop_positions to be changing the system, but rather, selecting a smaller region of the whole (so further selecting within that down-sized region should be done using the original coordinate system).