Source code for

import logging
from typing import List, Tuple

import numpy as np
from ase import Atoms
from import cut

from import logger
logger = logger.getChild('structure_mapping')

[docs]def map_structure_to_reference(input_structure: Atoms, reference_structure: Atoms, tolerance_mapping: float, vacancy_type: str = None, inert_species: List[str] = None, tolerance_cell: float = 0.05, tolerance_positions: float = 0.01) \ -> Tuple[Atoms, float, float]: """Maps a relaxed structure onto a reference structure. The function returns a tuple comprising * the ideal supercell most closely matching the input structure, * the largest deviation of any input coordinate from its ideal coordinate, and * the average deviation of the input coordinates from the ideal coordinates. Parameters ---------- input_structure relaxed input structure reference_structure reference structure, which can but need not represent the primitive cell tolerance_mapping maximum allowed displacement for mapping an atom in the relaxed (but rescaled) structure to the reference supercell *Note*: A reasonable choice is up to 20-30% of the first nearest neighbor distance (`r1`). A value above 50% of `r1` will most likely lead to atoms being multiply assigned, whereby the mapping fails. vacancy_type If this parameter is set to a non-zero string unassigned sites in the reference structure will be assigned to this type. *Note 1*: By default (``None``) the method will fail if there are *any* unassigned sites in the reference structure. *Note 2*: ``vacancy_type`` must be a valid species as enforced by the :class:`ase.Atoms` class. inert_species List of chemical symbols (e.g., ``['Au', 'Pd']``) that are never substituted for a vacancy. Used to make an initial rescale of the cell and thus increases the probability for a successful mapping. Need not be specified if ``vacancy_type`` is ``None``. tolerance_cell tolerance factor applied when computing permutation matrix to generate supercell tolerance_positions tolerance factor applied when scanning for overlapping positions in Angstrom (forwarded to :func:``) Example ------- The following code snippet illustrates the general usage. It first creates a primitive FCC cell, which is latter used as reference structure. To emulate a relaxed structure obtained from, e.g., a density functional theory calculation, the code then creates a 4x4x4 conventional FCC supercell, which is populated with two different atom types, has distorted cell vectors, and random displacements to the atoms. Finally, the present function is used to map the structure back the ideal lattice:: from import bulk reference = bulk('Au', a=4.09) atoms = bulk('Au', cubic=True, a=4.09).repeat(4) atoms.set_chemical_symbols(10 * ['Ag'] + (len(atoms) - 10) * ['Au']) atoms.set_cell(atoms.cell * 1.02, scale_atoms=True) atoms.rattle(0.1) mapped_atoms = map_structure_to_reference(atoms, reference, 1.0) """ assert np.all(input_structure.pbc == reference_structure.pbc), \ ('The periodic boundary conditions differ' ' between input and reference structure') if logger.isEnabledFor(logging.DEBUG): np.set_printoptions(suppress=True, precision=6) # Scale input cell and construct supercell of the reference structure scaled_cell = _get_scaled_cell(input_structure, reference_structure, vacancy_type=vacancy_type, inert_species=inert_species) P = _get_transformation_matrix(scaled_cell, reference_structure.cell, tolerance_cell=tolerance_cell) logger.debug('P:\n {}'.format(P)) scaled_structure, ideal_supercell = \ _rescale_structures(input_structure, reference_structure, P, tolerance_positions=tolerance_positions) assert len(ideal_supercell) == len(scaled_structure) or \ vacancy_type is not None, \ ('Number of atoms in ideal supercell does not match ' 'input structure.\n' 'ideal: {}\ninput: {}'.format(len(ideal_supercell), len(scaled_structure))) logger.debug('Number of atoms in reference structure:' ' {}'.format(len(reference_structure))) logger.debug('Number of atoms in input structure:' ' {}\n'.format(len(input_structure))) logger.debug('Reference cell metric:\n' '{}'.format(reference_structure.cell)) logger.debug('Input cell metric:\n' '{}\n'.format(input_structure.cell)) logger.debug('Transformation matrix connecting reference structure' ' and idealized input structure:\n {}'.format(P)) logger.debug('Determinant of transformation matrix:' ' {:.3f}\n'.format(np.linalg.det(P))) logger.debug('Cell metric of ideal supercell:\n' '{}'.format(ideal_supercell.cell)) logger.debug('Cell metric of rescaled input structure:\n' '{}\n'.format(scaled_structure.cell)) # map atoms in input structure to closest site in ideal supercell dr_max = 0.0 dr_sum = 0.0 dr_sumsq = 0.0 # per-atom-list for keeping track of mapped atoms mapped = [-1] * len(ideal_supercell) # distances between ideal and input sites drs = [None] * len(ideal_supercell) for ideal_site in ideal_supercell: for atom in scaled_structure: # in order to compute the distance the current atom from # the input structure is temporarily added to the # ideal supercell. This allows one to simply use the ASE # Atoms method for computing the interatomic distance ideal_supercell.append(atom) dr = ideal_supercell.get_distance(ideal_site.index, ideal_supercell[-1].index, mic=True) del ideal_supercell[-1] if dr < tolerance_mapping: if mapped[ideal_site.index] >= 0: raise Exception('More than one atom from the relaxed' ' (and rescaled) structure have been' ' mapped onto the same ideal site.\n' ' Try reducing `tolerance_mapping`.') mapped[ideal_site.index] = atom.index drs[ideal_site.index] = dr ideal_site.symbol = atom.symbol dr_max = max(dr, dr_max) dr_sum += dr dr_sumsq += dr * dr break else: assert vacancy_type is not None, \ ('Failed to assign an atom from the relaxed (and' ' rescaled) structure to the ideal lattice.' ' Try increasing `tolerance_mapping`.\n' ' {}'.format(ideal_site)) ideal_site.symbol = vacancy_type dr_avg = dr_sum / len(ideal_supercell) dr_sdv = np.sqrt(dr_sumsq / len(ideal_supercell) - dr_avg ** 2) # check that not more than one atom was assigned to the same site for k in set(mapped): assert k < 0 or mapped.count(k) <= 1, \ ('Site {} has been assigned more than once.'.format(k)) # check that the chemical composition of input and ideal supercell matches for symbol in set(input_structure.get_chemical_symbols()): n1 = input_structure.get_chemical_symbols().count(symbol) n2 = ideal_supercell.get_chemical_symbols().count(symbol) assert n1 == n2, ('Number of atoms of type {} differs between' ' input structure ({}) and ideal' ' supercell ({}).'.format(symbol, n1, n2)) if logger.isEnabledFor(logging.DEBUG): logger.debug('Maximum, average and standard deviation of atomic' ' displacements: {} {} {}'.format(dr_max, dr_avg, dr_sdv)) logger.debug('{:52} {:}'.format('Input structure:', 'Scaled structure:')) for k, (input_atom, scaled_atom) in enumerate(zip(input_structure, scaled_structure)): msg = '{:4} {:2}'.format(k, input_atom.symbol) msg += (3 * ' {:12.6f}').format(*input_atom.position) msg += ' -->' msg += (3 * ' {:12.6f}').format(*scaled_atom.position) logger.debug(msg) logger.debug('\n') logger.debug('{:52} {}'.format('Ideal supercell:', 'Scaled structure:')) for ideal_atom, k, dr in zip(ideal_supercell, mapped, drs): msg = ' {:2}'.format(ideal_atom.symbol) msg += (3 * ' {:12.6f}').format(*ideal_atom.position) msg += ' -->' msg += ' {:4}'.format(k) if k >= 0: scaled_pos = scaled_structure[k].position msg += (3 * ' {:12.6f}').format(*scaled_pos) msg += ' --> {:.4f}'.format(dr) logger.debug(msg) return ideal_supercell, dr_max, dr_avg
def _get_scaled_cell(input_structure: Atoms, reference_structure: Atoms, vacancy_type: str = None, inert_species: List[str] = None) -> np.ndarray: """ The input structure needs to be scaled in order to match the lattice structure of the reference structure. The reference structure can be a primitive cell, in which case the input structure would usually be a supercell thereof. Also, we need an ideal supercell that matches the input structure. Parameters ---------- input_structure relaxed input structure reference_structure: ASE Atoms object reference structure, which can but need not represent the primitive cell vacancy_type if not None, the cell is scaled if and only if `inert_species` is not None inert_species list of chemical symbols(e.g., `['Au', 'Pd']`) that are never substituted for a vacancy. Needless if `vacancy_type` is `None` """ modcell = input_structure.get_cell() if vacancy_type is None: # Without scale factor we can just rescale with number of atoms atvol_in = input_structure.get_volume() / len(input_structure) atvol_ref = reference_structure.get_volume() / len(reference_structure) scale = atvol_in / atvol_ref if vacancy_type is not None: if inert_species is None: scale = 1.0 else: # We cannot use the number of atoms since there may be vacancies # in the input_structure. Instead we count the species that we # know should always be present. n_in = 0 n_ref = 0 symbols_in = input_structure.get_chemical_symbols() symbols_ref = reference_structure.get_chemical_symbols() for species in inert_species: n_in += symbols_in.count(species) n_ref += symbols_ref.count(species) atvol_in = input_structure.get_volume() / n_in atvol_ref = reference_structure.get_volume() / n_ref scale = atvol_in / atvol_ref modcell *= (1.0 / scale) ** (1.0 / 3.0) return modcell def _get_transformation_matrix(input_cell: np.ndarray, reference_cell: np.ndarray, tolerance_cell: float = 0.05) -> np.ndarray: """ Obtains the (in general non-integer) transformation matrix connecting the input structure to the reference structure L=L_p.P - -> P=L_p ^ -1.L Parameters ---------- input_cell cell metric of input structure(possibly scaled) reference_cell cell metric of reference structure tolerance_cell tolerance for how much the elements of P are allowed to deviate from the nearest integer before they are rounded Returns ------- transformation matrix P of integers """ logger.debug('reference_cell:\n {}'.format(reference_cell)) logger.debug('input_cell:\n {}'.format(input_cell)) logger.debug('inv(reference_cell):\n {}' .format(np.linalg.inv(reference_cell))) P =, np.linalg.inv(reference_cell)) logger.debug('P:\n {}'.format(P)) # ensure that the transformation matrix does not deviate too # strongly from the nearest integer matrix if np.linalg.norm(P - np.around(P)) / 9 > tolerance_cell: print('reference:\n {}\n'.format(reference_cell)) print('input:\n {}\n'.format(input_cell)) print('P:\n {}\n'.format(P)) print('det P = {}\n'.format(np.linalg.det(P))) print('P_round:\n {}\n'.format(np.around(P))) print('Deviation: {}\n'.format(np.linalg.norm(P - np.around(P)) / 9)) raise Exception('Failed to map structure to reference structure' ' (tolerance_cell exceeded). If there are vacancies,' ' one can try specifying `inert_species`. Otherwise,' ' one can try raising `tolerance_cell`.') # reduce the (real) transformation matrix to the nearest integer one P = np.around(P) logger.debug('P:\n {}'.format(P)) return P def _rescale_structures(input_structure: Atoms, reference_structure: Atoms, P: np.ndarray, tolerance_positions: float = 0.01) \ -> Tuple[Atoms, Atoms]: """ Rescales `input_structure` with `P` so that it matches `reference_structure`, and creates a supercell of `reference_structure` using `P` Parameters ---------- input_structure relaxed input structure reference_structure reference structure, which can but need not represent the primitive cell P transformation matrix of integers tolerance_positions tolerance factor applied when scanning for overlapping positions in Angstrom(forwarded to ``) Returns ------- a tuple with the scaled version of `input_structure` and the supercell of `reference_structure` matching cell metric of `scaled_structure` """ scaled_structure = input_structure.copy() scaled_structure.set_cell(, reference_structure.cell), scale_atoms=True) # generate supercell of (presumably primitive) reference structure ideal_supercell = cut(reference_structure, *P, tolerance=tolerance_positions) n_mapped = int(np.round(len(reference_structure) * np.linalg.det(P))) if len(ideal_supercell) != n_mapped: print('len(reference_structure)', len(reference_structure)) print('det(P)', np.linalg.det(P)) print('len(ideal_supercell)', len(ideal_supercell)) print('n_mapped', n_mapped) raise Exception('Supercell construction of reference structure failed' ' (number of atoms do not match).\n' 'Permutation matrix used:\n{}'.format(P) + '\nYou can try to change tolerance_positions.') return scaled_structure, ideal_supercell