Add some examples in documentation with figures

[thomasloux]

It would be great to have in the documentation a separate part for:

• Structure optimization (only atomic positons and positions+cell). It would great to have photos so that one can see the difference in the tutorial
• NVE MD: show energy overtime. Possibly a case with energy converged and another with a timestep that is too big so that the energy drifts
• NVT MD: show temperature fluctuations
• NPT MD: show temperature and pressure fluctuations (note that the pressure fluctuations are widely different in the case of NPT Langevin and NPT Nose Hoover)
  For NPT and NVT: show the invariant quantities for Nosé Hoover.

It's better for new users to see the results directly in the tutorials. It also emphasizes the importance to track some properties over the trajectory.
Also I suspect some of the current examples have examples that diverge because of the chosen parameters.
It's the case of https://github.com/TorchSim/torch-sim/blob/main/examples/scripts/3_Dynamics/3.8_MACE_NPT_Nose_Hoover.py
With dt=1fs the temperature diverges, the results are correct with dt=0.5fs, although it seems that the temperature is under estimated.

[thomasloux]

regarding how to add that in the docs, built with sphinx, you can get inspiration from ASE: https://gitlab.com/ase/ase/-/tree/master/doc/tutorials/minimahopping?ref_type=heads

[wwymak]

hi, I can work on this issue. Is there a preference for each example be a separate PR or just one for the issue?

[thomasloux]

As you want, one PR would probably be a relatively large amount of work