Source code for hiphive.core.atoms

Collection of functions and classes for handling information concerning atoms
and structures, including the relationship between primitive cell and
supercells that are derived thereof.

import pickle
from ase import Atoms as aseAtoms
import numpy as np
from ..input_output.logging_tools import logger

# TODO: Rename logger
logger = logger.getChild('atoms')

[docs]class Atom: # TODO: This class should inherit some immutable to make it clear that # there is no reference to any other obj """Unique representation of an atom in a lattice with a basis Class for storing information about the position of an atom in a supercell relative to the origin of the underlying primitive cell. This class is used for handling the relationship between a primitive cell and supercells derived thereof. Parameters ---------- site : int site index offset : list(float) or numpy.ndarray must contain three elements, offset_x, offset_y, offset_z """ def __init__(self, site, offset): offset = tuple(offset) self._site = site self._offset = offset @property def site(self): """int : index of corresponding site in the primitive basis""" return self._site @property def offset(self): """list(int) : translational offset of the supercell site relative to the origin of the primitive cell in units of primitive lattice vectors""" return self._offset def __repr__(self): return 'Atom({}, {})'.format(, self.offset)
[docs] def spos(atom, basis): return np.add(basis[], atom.offset)
[docs] def pos(atom, basis, cell): spos = atom.spos(basis) return, cell)
[docs] @staticmethod def spos_to_atom(spos, basis, tol=None): # TODO: Why is this simply duplicated spos_to_atom from helper below? if not tol: # TODO: Link to config file tol = 1e-4 for site, base in enumerate(basis): offset = np.subtract(spos, base) diff = offset - np.round(offset, 0) if np.linalg.norm(diff) < tol: offset = np.round(offset, 0).astype(int) atom = Atom(site, offset) assert np.linalg.norm(spos - atom.spos(basis)) < tol, ( '{} with basis {} != {}'.format(atom, basis, spos)) return atom s = '{} not compatible with {} and tolerance {}' raise Exception(s.format(spos, basis, tol))
def __hash__(self): return hash((self._site, *self.offset)) def __eq__(self, other): if not isinstance(other, Atom): return False return == and self.offset == other.offset
[docs]class Atoms(aseAtoms): """Minimally augmented version of the ASE Atoms class suitable for handling primitive cell information. Saves and loads by pickle. """ @property def basis(self): """numpy.ndarray : scaled coordinates of the sites in the primitive basis """ return self.get_scaled_positions().round(12) % 1
[docs] def write(self, f): """ Writes the object to file. Note: Only the cell, basis and numbers are stored! Parameters ---------- f : str or file object name of input file (str) or stream to write to (file object) """ data = {} data['cell'] = self.cell data['basis'] = self.basis data['numbers'] = self.numbers pickle.dump(data, f)
[docs] @staticmethod def read(f): """ Load an hiPhive Atoms object from file. Parameters ---------- f : str or file object name of input file (str) or stream to load from (file object) Returns ------- hiPhive Atoms object """ data = pickle.load(f) atoms = aseAtoms(numbers=data['numbers'], scaled_positions=data['basis'], cell=data['cell'], pbc=True) return Atoms(atoms)
[docs]def atom_to_spos(atom, basis): """Helper function for obtaining the position of a supercell atom in scaled coordinates. Parameters ---------- atom : hiPhive.Atom supercell atom basis : list(list(float)) or numpy.ndarray positions of sites in the primitive basis Returns ------- numpy.ndarray scaled coordinates of an atom in a supercell """ return np.add(atom.offset, basis[])
[docs]def spos_to_atom(spos, basis, tol=1e-4): """Helper function for transforming a supercell position to the primitive basis. Parameters ---------- spos : list(list(float)) or numpy.ndarray scaled coordinates of an atom in a supercell basis : list(list(float)) or numpy.ndarray positions of sites in the primitive basis tol : float a general tolerance Returns ------- hiphive.Atom supercell atom """ # TODO: Fix tolerance # If needed, convert inputs to arrays to make use of numpy vectorization spos = np.asarray(spos) basis = np.asarray(basis) # If the scaled position belongs to this site, the offset is the # difference in scaled coordinates and should be integer offsets = spos - basis # The diff is the difference between the offset vector and the nearest # integer vector. diffs = offsets - np.round(offsets, 0) # It should be close to the null vector if this is the correct site. match_indices = np.nonzero(np.linalg.norm(diffs, axis=1) < tol)[0] # If no atom was found or more than one atoms were found we throw an error if len(match_indices) != 1: raise ValueError(f'{spos} not compatible with {basis} and tolerance {tol}') # This should be the correct atom site = match_indices[0] # If the difference is less than the tol make the offset integers offset = np.rint(offsets[site]) atom = Atom(site, offset) # Just to be sure we check that the atom actually produces the # input spos given the input basis s = ('Atom=[{},{}] with basis {} != {}' .format(, atom.offset, basis, spos)) assert np.linalg.norm(spos - atom_to_spos(atom, basis)) < tol, s return atom