Source code for mchammer.configuration_manager

import random
import numpy as np
from typing import Dict, List, Tuple
from ase import Atoms
from icet.core.sublattices import Sublattices
from import atomic_number_to_chemical_symbol

class SwapNotPossibleError(Exception):

[docs] class ConfigurationManager(object): """ The ConfigurationManager owns and handles information pertaining to a configuration being sampled in a Monte Carlo simulation. Note ---- As a user you will usually not interact directly with objects of this type. Parameters ---------- structure : Atoms Configuration to be handled. sublattices : :class:`Sublattices <icet.core.sublattices.Sublattices>` Sublattices used to define allowed occupations and handle related information. """ def __init__(self, structure: Atoms, sublattices: Sublattices) -> None: self._structure = structure.copy() self._occupations = self._structure.numbers self._sublattices = sublattices self._sites_by_species = self._get_sites_by_species() def _get_sites_by_species(self) -> List[Dict[int, List[int]]]: """Returns the sites that are occupied for each species. Each dictionary represents one sublattice where the key is the species (by atomic number) and the value is the list of sites occupied by said species in the respective sublattice. """ sites_by_species = [] for sl in self._sublattices: species_dict = {key: [] for key in sl.atomic_numbers} for site in sl.indices: species_dict[self._occupations[site]].append(site) sites_by_species.append(species_dict) return sites_by_species @property def occupations(self) -> np.ndarray: """ Occupation vector of the configuration (copy). """ return self._occupations.copy() @property def sublattices(self) -> Sublattices: """ Sublattices of the configuration. """ return self._sublattices @property def structure(self) -> Atoms: """ Atomic structure associated with configuration (copy). """ structure = self._structure.copy() structure.set_atomic_numbers(self.occupations) return structure
[docs] def get_occupations_on_sublattice(self, sublattice_index: int) -> List[int]: """ Returns the occupations on one sublattice. Parameters --------- sublattice_index Sublattice by index for which the occupations should be returned. """ sl = self.sublattices[sublattice_index] return list(self.occupations[sl.indices])
[docs] def is_swap_possible(self, sublattice_index: int, allowed_species: List[int] = None) -> bool: """ Checks if a swap trial move is possible on a specific sublattice. Parameters ---------- sublattice_index Index of sublattice to be checked. allowed_species List of atomic numbers for allowed species. """ sl = self.sublattices[sublattice_index] if allowed_species is None: swap_symbols = set(self.occupations[sl.indices]) else: swap_symbols = set([o for o in self.occupations[sl.indices] if o in allowed_species]) return len(swap_symbols) > 1
[docs] def get_swapped_state(self, sublattice_index: int, allowed_species: List[int] = None ) -> Tuple[List[int], List[int]]: """Returns two random sites (first element of tuple) and their occupation after a swap (second element of tuple). The new configuration will obey the occupation constraints associated with the :class:`ConfigurationManager` object. Parameters ---------- sublattice_index Sublattice by index from which to pick sites. allowed_species List of atomic numbers for allowed species. """ # pick the first site if allowed_species is None: available_sites = self.sublattices[sublattice_index].indices else: available_sites = [ s for Z in allowed_species for s in self._get_sites_by_species()[sublattice_index][Z]] try: site1 = random.choice(available_sites) except IndexError: raise SwapNotPossibleError(f'Sublattice {sublattice_index} is empty.') # pick the second site if allowed_species is None: possible_swap_species = \ set(self._sublattices.get_allowed_numbers_on_site(site1)) - \ set([self._occupations[site1]]) else: possible_swap_species = \ set(allowed_species) - set([self._occupations[site1]]) possible_swap_sites = [] for Z in possible_swap_species: possible_swap_sites.extend(self._sites_by_species[sublattice_index][Z]) possible_swap_sites = np.array(possible_swap_sites) try: site2 = random.choice(possible_swap_sites) except IndexError: raise SwapNotPossibleError( 'Cannot swap on sublattice {} since it is full of {} species .' .format(sublattice_index, atomic_number_to_chemical_symbol([self._occupations[site1]])[0])) return ([site1, site2], [self._occupations[site2], self._occupations[site1]])
[docs] def get_flip_state( self, sublattice_index: int, allowed_species: List[int] = None, ) -> Tuple[int, int]: """ Returns a site index and a new species for the site. Parameters ---------- sublattice_index Index of sublattice from which to pick a site. allowed_species List of atomic numbers for allowed species. """ if allowed_species is None: available_sites = self._sublattices[sublattice_index].indices else: available_sites = [s for Z in allowed_species for s in self._get_sites_by_species()[sublattice_index][Z]] site = random.choice(available_sites) if allowed_species is not None: species = random.choice(list( set(allowed_species) - set([self._occupations[site]]))) else: species = random.choice(list( set(self._sublattices[sublattice_index].atomic_numbers) - set([self._occupations[site]]))) return site, species
[docs] def update_occupations(self, sites: List[int], species: List[int]) -> None: """ Updates the occupation vector of the configuration being sampled. This will change the state in both the configuration in the calculator and the configuration manager. Parameters ---------- sites Indices of sites of the configuration to change. species New occupations by atomic number. """ # Update sublattices for site, new_Z in zip(sites, species): if 0 > new_Z > 118: raise ValueError('Invalid new species {} on site {}'.format(new_Z, site)) if len(self._occupations) >= site < 0: raise ValueError('Site {} is not a valid site index'.format(site)) old_Z = self._occupations[site] sublattice_index = self.sublattices.get_sublattice_index_from_site_index(site) if new_Z not in self.sublattices[sublattice_index].atomic_numbers: raise ValueError('Invalid new species {} on site {}'.format(new_Z, site)) # Remove site from list of sites for old species self._sites_by_species[sublattice_index][old_Z].remove(site) # Add site to list of sites for new species try: self._sites_by_species[sublattice_index][new_Z].append(site) except KeyError: raise ValueError('Invalid new species {} on site {}'.format(new_Z, site)) # Update occupation vector itself self._occupations[sites] = species