Adding additional stuff

[matteobecchi]

Requested Reviewers: @andrewtarzia @SimoneMartino98

• The 2-nn intrinsic dimension estimator is some old code that I found and thought could be useful.
• At the moment, I implemented the "array -> xyz file" function in utilities because to pass through a Trj object you need to add a lot of stuff (atoms topology, tilmestep) that could be unnecessary for someone simply wanting to save some coordinates and open it with Ovito (es, for a toy model or CG simulation).

[matteobecchi]

The plan now is:

• We add this simple function that does array -> xyz without passing from a Trj, to keep things simple
• We also add a Trj method that saves an extended xyz with the trajectory and a series of Insights passed by the user.

[SimoneMartino98]

i think we need some pytests more for this ? + a comment

overall great job, this is super useful.

[SimoneMartino98]

Maybe make a point more on the fact that we mean position coordinate (that must be (frame, atoms ,3)?
Or extend the function to create a general XYZ with fewer or more than 3 columns? The user in that case must specify the identity of each column (like Ovito).

[SimoneMartino98]

just a thought: In this case using pandas could help

[matteobecchi]

I specified better what this function is for, and added a note suggesting to use Trj if the system has more complexity.

[matteobecchi]

Surely pandas give more control but I don't want to force the user to use pandas... for instance I have no idea how to use it. Is this bad? -.-"

[SimoneMartino98]

It's not so difficult to use, and it contains some useful utilities for organizing datasets (remove cols, add cols, add rows). But anyway, it was just a possibility, keep this one.

[andrewtarzia]

Let's not bring pandas into this, and if we do, we will use polars (pandas in rust).

[matteobecchi]

There's always another, better version of everything...

[SimoneMartino98]

everything ok for me now; good job 👍

[andrewtarzia]

njit == numba.jit?

[SimoneMartino98]

not sure but:
@njit is short for @jit(nopython=True).

so, to be sure, i would add the argument.

but let's check it

[matteobecchi]

Yes. I'll make it consistent with the lens.py file.