Source code for hiphive.utilities

This module contains various support/utility functions.

import numpy as np
from ase.geometry import find_mic
from .io.logging import logger

logger = logger.getChild('utilities')

[docs]def get_displacements(atoms, atoms_ideal): """ Computes the smallest possible displacements from displaced atoms relative to ideal atoms. Notes ----- * uses :func:`ase.geometry.find_mic` * assumes `pbc=[True, True, True]`. Parameters ---------- atoms : ase.Atoms configuration with displaced atoms atoms_ideal : ase.Atoms ideal configuration relative to which displacements are computed Returns ------- numpy.ndarray displacements """ if not np.array_equal(atoms.numbers, atoms_ideal.numbers): raise ValueError('Atomic numbers do not match.') displacements = [] for pos, ideal_pos in zip(atoms.positions, atoms_ideal.positions): v_ij = np.array([pos - ideal_pos]) displacements.append(find_mic(v_ij, atoms_ideal.cell, pbc=True)[0][0]) return np.array(displacements)
[docs]def prepare_structures(structures, atoms_ideal, calc): """ Prepares a set of structures in the format suitable for a :class:`StructureContainer <hiphive.StructureContainer>`. **Note:** Changes the structures in place. """ for atoms in structures: atoms.set_calculator(calc) forces = atoms.get_forces() displacements = get_displacements(atoms, atoms_ideal) atoms.positions = atoms_ideal.get_positions() atoms.new_array('forces', forces) atoms.new_array('displacements', displacements)
[docs]def get_neighbor_shells(atoms, cutoff, dist_tol=1e-5): """ 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 ------- list(Shell) neighbor shells """ # TODO: Remove this once this feature have been in ASE long enough try: from ase.neighborlist import neighbor_list except ImportError: raise ImportError('get_neighbor_shells uses new functionality from ASE' ', please update ASE in order to use this function.') # get distances ijd = neighbor_list('ijd', atoms, cutoff) ijd = list(zip(*ijd)) ijd.sort(key=lambda x: x[2]) # sort into shells symbols = atoms.get_chemical_symbols() shells = [] for i, j, d in ijd: types = tuple(sorted([symbols[i], symbols[j]])) for shell in shells: if abs(d - shell.distance) < dist_tol and types == shell.types: shell.count += 1 break else: shell = Shell(types, d, 1) shells.append(shell) shells.sort(key=lambda x: (x.distance, x.types, x.count)) # warning if two shells are within 2 * tol for i, s1 in enumerate(shells): for j, s2 in enumerate(shells[i+1:]): if s1.types != s2.types: continue if not s1.distance < s2.distance - 2 * dist_tol: logger.warning('Found two shells within 2 * dist_tol') return shells
[docs]class Shell: """ 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 """ def __init__(self, types, distance, count=0): self.types = types self.distance = distance self.count = count def __str__(self): s = '{}-{} distance: {:10.6f} count: {}'.format( *self.types, self.distance, self.count) return s __repr__ = __str__