Source code for mchammer.configuration_manager

import copy
import random
from numpy import array
from typing import Dict, List, Tuple, Union
from ase import Atoms

class SwapNotPossibleError(Exception):

[docs]class ConfigurationManager(object): """ The ConfigurationManager owns and handles information pertaining to a configuration being sampled in a Monte Carlo simulation. Parameters ---------- atoms : ASE Atoms configuration to be handled strict_constraints : list of list of int strictest form of the allowed occupations sites_by_sublattice : list of list of int sites (inner list) that belong to each sublattice (outer list) occupation_constraints : list of list of int optional occupation constraint to enfore a more stricter species occupation than what is allowed from the Calculator Todo ---- * occupation constraint not implemented * add check that all sites in the different sublattices all have the same occupation constraint. * revise docstrings * clarify "occupation_constraints" vs "strict_constraints"; the OccupationConstraints class should help here """ def __init__(self, atoms: Atoms, strict_constraints: Union[List[List[int]], List[int]], sites_by_sublattice: Union[List[List[int]], List[int]], occupation_constraints: List[List[int]] = None) -> None: self._atoms = atoms.copy() self._occupations = self._atoms.numbers self._sites_by_sublattice = sites_by_sublattice if occupation_constraints is not None: self._check_occupation_constraint( strict_constraints, occupation_constraints) else: occupation_constraints = strict_constraints self._occupation_constraints = occupation_constraints self._allowed_species = self._set_up_allowed_species() self._sites_by_species = self._get_sites_by_species() def _set_up_allowed_species(self) -> List[int]: """ Returns a list of allowed species. """ allowed_species = set() for occ in self._occupation_constraints: for species in occ: allowed_species.add(species) return list(allowed_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 sublattice in self._sites_by_sublattice: species_dict = {key: [] for key in self._allowed_species} for site in sublattice: species_dict[self._occupations[site]].append(site) sites_by_species.append(species_dict) return sites_by_species def _check_occupation_constraint(self, strict_constraints: Union[List[List[int]], List[int]], occupation_constraints: List[List[int]]): """Checks that the user defined occupation constraints are stricter or as strict as the strict constraints. Parameters ---------- strict_constraints additional (stricter) constraints specified for this configuration manager instance occupation_constraints "default" constraints Todo ---- This method should be revised and rewritten once the OccupationConstraints class is available. At least some of this functionality should probably be moved into said class. """ if not len(strict_constraints) == len(occupation_constraints): raise ValueError( 'strict_occupations and occupation_constraints' ' must be equal length') for strict_occ, occ in zip(strict_constraints, occupation_constraints): if not set(occ).issubset(strict_occ): raise ValueError( 'User defined occupation_constraints must be ' 'stricter or as strict as strict_occupations constraints.') @property def occupations(self) -> List[int]: """ occupation vector of the configuration (copy) """ return self._occupations.copy() @property def occupation_constraints(self) ->List[List[int]]: """occupation constraints associated with configuration manager (copy); the outer list runs over sites with each inner list representing the species allowed on this site. """ return copy.deepcopy(self._occupation_constraints) @property def sublattices(self) -> List[List[int]]: """ sites belonging to each sublattice of the configuration (copy) """ return copy.deepcopy(self._sites_by_sublattice) @property def atoms(self) -> Atoms: """ atomic structure associated with configuration (copy) """ atoms = self._atoms.copy() atoms.set_atomic_numbers(self.occupations) return atoms
[docs] def get_swapped_state(self, sublattice: int) -> 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 configuration mananger. Parameters ---------- sublattice sublattice from which to pick sites Todo ---- * profile this method as it is called frequently * look for speed up opportunities * The current implementation assumes all sites in this sublattice to have the same allowed occupations. """ # pick the first site try: site1 = random.choice(self._sites_by_sublattice[sublattice]) except IndexError: raise SwapNotPossibleError('Sublattice {} is empty.' .format(sublattice)) # pick the second site possible_swap_species = \ set(self._occupation_constraints[site1]) - \ set([self._occupations[site1]]) possible_swap_sites = [] for Z in possible_swap_species: possible_swap_sites.extend(self._sites_by_species[sublattice][Z]) possible_swap_sites = array(possible_swap_sites) try: site2 = random.choice(possible_swap_sites) except IndexError: raise SwapNotPossibleError return ([site1, site2], [self._occupations[site2], self._occupations[site1]])
[docs] def get_flip_state(self, sublattice: int) -> Tuple[int, int]: """ Returns a site index and a new species for the site. Parameters ---------- sublattice index of sublattice from which to pick a site """ site = random.choice(self._sites_by_sublattice[sublattice]) species = random.choice(list( set(self._occupation_constraints[site]) - set([self._occupations[site]]))) return site, species
[docs] def update_occupations(self, sites: List[int], species: List[int]): """ 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 _sites_by_sublattice for site, new_Z in zip(sites, species): old_Z = self._occupations[site] for isub, sublattice_sites in enumerate(self._sites_by_sublattice): if site in sublattice_sites: break else: raise ValueError( 'Site {} is not present in any sublattice.'.format(site)) # Remove site from list of sites for old species self._sites_by_species[isub][old_Z].remove(site) # Add site to list of sites for new species try: self._sites_by_species[isub][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