jax_md_mod.custom_quantity.init_local_structure_index

jax_md_mod.custom_quantity.init_local_structure_index#

init_local_structure_index(displacement_fn, r_cut=0.37, reference_box=None, r_init=None, max_pairs_multiplier=3.0)[source]#

Initializes function to compute the local structure index (LSI).

The LSI measures the gap between the first and second solvation shell [1].

Parameters:

  • displacement_fn – Function to compute the particle distances

  • r_cut (float) – Cutoff of second solvation shell

  • reference_box – Reference box to compute particle distances. Necessary if no dynamic box is provided.

  • r_init – Initial coordinates to estimate the number of particles in the shell.

  • max_pairs_multiplier (float) – Multiplies the estimated maximum number of particles in a shell.

References

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