Geometry collections

[pfebrer]

I though it could be useful to have a class to store multiple geometries.

This came to my mind when I needed to treat an animation, therefore I have also implemented reading multiple geometries from an xyzSile as an example.

My idea here is that you can operate simultaneously on all the geometries, not only independently but also based on some reference geometry (e.g. the first one). You could also use this class to easily track how the geometry is evolving or interpolate steps between geometries, which would be useful for NEB or to render animations with higher fps/resolution, for example.

This is just a sketch to know your opinion about it.

Note: If you believe this is a good idea, I need to find the best way use the methods from the Geometry class on all geometries of the collection, which are stored in a list. One option would be to make GeometryCollection inherit from Geometry and decorate all the methods in the Geometry class so that they check whether they have been called from a geometry instance or from a collection and act accordingly. But I'm not sure if there is a better way to do it.

[codecov[bot]]

Codecov Report

Merging #167 into master will decrease coverage by 0.04%. The diff coverage is 70.45%.

@@            Coverage Diff             @@
##           master     #167      +/-   ##
==========================================
- Coverage   85.23%   85.18%   -0.05%     
==========================================
  Files         115      115              
  Lines       18725    18751      +26     
==========================================
+ Hits        15960    15973      +13     
- Misses       2765     2778      +13

Impacted Files	Coverage Δ
sisl/io/xyz.py	100% <100%> (ø)	:arrow_up:
sisl/geometry.py	86.58% <38.09%> (-0.72%)	:arrow_down:

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[zerothi]

Thanks for the MR, I think this is a good idea. I will give this some thought and probably implement it in another way (to generalize for all objects).

[pfebrer]

Nice, that would definitely be the best scenario. It would be helpful for plots to make animations too (I already implemented it with my own approach, but if there is a general way that would be great).

[zerothi]

Superseeded by #545 thanks for comments and ideas!