mc_rattle

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mc_rattle#

autoplex.data.common.utils.mc_rattle(structure, n_structures=5, rattle_std=0.003, min_distance=1.5, rattle_seed=42, rattle_mc_n_iter=10)[source]#

Take in a pymatgen Structure object and generates rattled structures.

Randomly draws displacements with a MC trial step that penalises displacements leading to very small interatomic distances. Displacements generated will roughly be n_iter**0.5 * rattle_std for small values of n_iter. See https://hiphive.materialsmodeling.org/moduleref/structures.html?highlight=generate_mc_rattled_structures for more details.

Parameters:

  • structure (Structure.) – Pymatgen structures object.

  • n_structures (int.) – Number of rattled structures to generate.

  • rattle_std (float.) – Rattle amplitude (standard deviation in normal distribution). N.B. this value is not connected to the final average displacement for the structures. Default= 0.003.

  • min_distance (float.) – Minimum separation of any two atoms in the rattled structures. Used for computing the probability for each rattle move. Default= 1.5A.

  • rattle_seed (int.) – Seed for setting up NumPy random state from which random numbers are generated. Default= 42.

  • rattle_mc_n_iter (int.) – Number of Monte Carlo iterations. Larger number of iterations will generate larger displacements. Default=10.

Returns:

Monte-Carlo rattled structures.

Return type:

Response.output.

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