feat: implement Verlet neighbour list#65
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romainljsimon merged 11 commits intomainfrom Feb 3, 2026
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**Summary** This PR removes the validation subdirectory and moves its content to example. I initially felt like a validation subdir had some sense, as it shows that the code actually does what it should. With #65 that adds a thorough example, I feel like it makes more sense to put everything as examples. Maybe at some point add a README to explain that the results were validated, with a link to the LJ mixture example?
romainljsimon
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Feb 3, 2026
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Summary
This PR implements a flavor of Verlet list. It addresses #63.
The VerletList object contains for each particle in the system, an array of all its neighbours (defined as all particles within the interaction cutoff + some arbitrary parameter dr).
These arrays of neighbours are updated only when a given particle moves a distance greater than dr/2, ensuring that the list of neighbours always contains all particles within the interaction cutoff radius.
Test plan
The CI was updated to check over a trajectory that the energy is identical to that obtained using different neighbour list methods.
Performances
The VerletList implementation was compared to the LinkedList one, for a system of ortho-terphenyl molecules, at density 1.2 and temperature 2.
In the attached plot, the simulation time is reported for different values of the parameter dr. The dashed line at the top is the timing with the LinkedList implementation. For reference, the interaction cutoff is 1.23.
The timing is done once for each Verlet list, and 4 times for the LinkedList, with values ranging from 75s to 105s.
There's quite a lot of variability between repeats, but we still have a ~2x speedup for this system, for 0.3 < dr < 0.6.