GEMDAT-repos / GEMDAT

Python toolkit for molecular dynamics analysis
https://gemdat.readthedocs.io
Apache License 2.0
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orientations function to return non-normalized cartesian vectors #289

Closed tfamprikis closed 3 months ago

tfamprikis commented 3 months ago

i.e. something like get_unit_vectors_trajectory() that forgoes the normalization to a unit vector, i.e. retains the information of bond/vector lengths.

rn the only way to do this is to go through get_conventional_coordinates() which has the side effect of applying the primitive to conventional transformation that is not always needed.

this function should then be used in all the Orientations transformation functions (e.g. get_symmetric_trajectory()) and plots (rectilinear_plot, bond_length_distribution)

tfamprikis commented 3 months ago

nevermind, was confused because of the name

right now, get_unit_vectors_trajectory() only produces unit vectors if Orientations is called with normalize_trajectory=True. otherwise it doesnt (it does instead what I describe above)

should probably rename to make this clear.

also normalization should probably be a method rather than a parameter of Orientations