Other functions

Self-consistent phonons

hiphive.self_consistent_phonons.self_consistent_harmonic_model(atoms_ideal, calc, cs, T, alpha, n_iterations, n_structures, parameters_start=None)[source]

Constructs a set of self-consistent second-order force constants that provides the closest match to the potential energy surface at a the specified temperature.

Parameters:
  • atoms_ideal (ase.Atoms) – ideal structure
  • calc (ASE calculator object) – calculator to be used as reference potential
  • cs (ClusterSpace) – clusterspace onto which to project the reference potential
  • T (float) – temperature in K
  • alpha (float) – stepsize in optimization algorithm
  • n_iterations (int) – number of iterations in poor mans
  • n_structures (int) – number of structures to use when fitting
  • parameters_start (numpy.ndarray) – parameters from which to start the optimization
Returns:

sequence of parameter vectors generated while iterating to self-consistency

Return type:

list(numpy.ndarray)

Utilities

This module contains various support/utility functions.

class hiphive.utilities.Shell(types, distance, count=0)[source]

Neighbor Shell class

Parameters:
  • types (list or tuple) – atomic types for neighbor shell
  • distance (float) – interatomic distance for neighbor shell
  • count (int) – number of pairs in the neighbor shell
hiphive.utilities.get_displacements(atoms, atoms_ideal)[source]

Computes the smallest possible displacements from positions and ideal positions given a cell metric.

Notes

Parameters:
Returns:

wrapped displacements

Return type:

numpy.ndarray

hiphive.utilities.get_neighbor_shells(atoms, cutoff, dist_tol=1e-05)[source]

Gets list of neighbor shells.

Distances are grouped into shells via the following algorithm:

  1. Find smallest atomic distance d_min
  2. Find all pair distances in the range d_min + 1 * dist_tol
  3. Construct a shell from these and pop them from distance list
  4. Go to 1.
Parameters:
  • atoms (ase.Atoms) – Atoms used for finding shells
  • cutoff (float) – exclude neighbor shells which have a distance larger than cutoff
  • dist_tol (float) – distance tolerance
Returns:

neighbor shells

Return type:

list(Shell)

hiphive.utilities.prepare_structures(structures, atoms_ideal, calc)[source]

Prepares a set of structures in the format suitable for a StructureContainer.

Note: Changes the structures in place.