from sortedcontainers import SortedKeyList
import random
[docs]
class GuidedExchangeOperator:
def __init__(self, environment_energies, feature_key):
self.n_envs = int(len(environment_energies)/2)
self.env_energy_differences = [environment_energies[i] - environment_energies[i + self.n_envs] for i in range(self.n_envs)]
self.neigh_energy_difference = [environment_energies[i+1] - environment_energies[i] for i in range((self.n_envs*2)-1)] + [-1000]
self.feature_key = feature_key
self.symbol1_exchange_energies = dict()
self.symbol2_exchange_energies = dict()
self.symbol1_indices = SortedKeyList(key=lambda x: self.symbol1_exchange_energies[x])
self.symbol2_indices = SortedKeyList(key=lambda x: self.symbol2_exchange_energies[x])
self.n_symbol1_atoms = 0
self.n_symbol2_atoms = 0
[docs]
def env_from_feature(self, x):
return x % self.n_envs
[docs]
def guided_exchange(self, particle):
symbol1_index = self.symbol1_indices[0]
symbol2_index = self.symbol2_indices[0]
particle.swap_symbols([(symbol1_index, symbol2_index)])
return symbol1_index, symbol2_index
[docs]
def basin_hop_step(self, particle):
expected_energy_gain = -1
index = -1
random_indices = random.sample(range(max(self.n_symbol1_atoms, self.n_symbol2_atoms)), max(self.n_symbol1_atoms, self.n_symbol2_atoms))
while expected_energy_gain <= 0 and index < min(self.n_symbol1_atoms, self.n_symbol2_atoms):
index += 1
symbol1_index = self.symbol1_indices[random_indices[index] % self.n_symbol1_atoms]
symbol1_energy = self.symbol1_exchange_energies[symbol1_index]
symbol2_index = self.symbol2_indices[random_indices[index] % self.n_symbol2_atoms]
symbol2_energy = self.symbol2_exchange_energies[symbol2_index]
expected_energy_gain = symbol1_energy + symbol2_energy
if expected_energy_gain > 0:
particle.swap_symbols([(symbol1_index, symbol2_index)])
return symbol1_index, symbol2_index
symbol1_index = self.symbol1_indices[random_indices[index] % self.n_symbol1_atoms]
symbol2_index = self.symbol2_indices[random_indices[index] % self.n_symbol2_atoms]
particle.swap_symbols([(symbol1_index, symbol2_index)])
return symbol1_index, symbol2_index
[docs]
def bind_particle(self, particle):
symbols = sorted(particle.atoms.get_all_symbols())
symbol1 = symbols[0]
symbol2 = symbols[1]
symbol1_indices = particle.get_indices_by_symbol(symbol1)
symbol2_indices = particle.get_indices_by_symbol(symbol2)
self.n_symbol1_atoms = len(symbol1_indices)
self.n_symbol2_atoms = len(symbol2_indices)
atom_features = particle.get_atom_features(self.feature_key)
for index in symbol1_indices:
feature = atom_features[index]
energy_change = 0
for neigh_idx in particle.get_coordination_atoms(index):
neigh_feature = atom_features[neigh_idx]
energy_change -= self.neigh_energy_difference[neigh_feature-1]
self.symbol1_exchange_energies[index] = (-self.env_energy_differences[self.env_from_feature(feature)] + energy_change)
self.symbol1_indices.add(index)
for index in symbol2_indices:
feature = atom_features[index]
energy_change = 0
for neigh_idx in particle.get_coordination_atoms(index):
neigh_feature = atom_features[neigh_idx]
energy_change += self.neigh_energy_difference[neigh_feature]
self.symbol2_exchange_energies[index] = (+self.env_energy_differences[self.env_from_feature(feature)] + energy_change)
self.symbol2_indices.add(index)
[docs]
def update(self, particle, indices, exchange_indices):
symbols = sorted(particle.atoms.get_all_symbols())
symbol1 = symbols[0]
atom_features = particle.get_atom_features(self.feature_key)
for index in indices:
if index in exchange_indices:
if particle.get_symbol(index) == symbol1:
self.symbol2_indices.remove(index)
else:
self.symbol1_indices.remove(index)
else:
if particle.get_symbol(index) == symbol1:
self.symbol1_indices.remove(index)
else:
self.symbol2_indices.remove(index)
for index in indices:
feature = atom_features[index]
new_exchange_energy = self.env_energy_differences[self.env_from_feature(feature)]
if index in exchange_indices:
if particle.get_symbol(index) == symbol1:
energy_change = 0
for neigh_idx in particle.get_coordination_atoms(index):
neigh_feature = atom_features[neigh_idx]
energy_change -= self.neigh_energy_difference[neigh_feature-1]
self.symbol1_exchange_energies[index] = -new_exchange_energy + energy_change
del self.symbol2_exchange_energies[index]
else:
energy_change = 0
for neigh_idx in particle.get_coordination_atoms(index):
neigh_feature = atom_features[neigh_idx]
energy_change += self.neigh_energy_difference[neigh_feature]
self.symbol2_exchange_energies[index] = new_exchange_energy + energy_change
del self.symbol1_exchange_energies[index]
else:
if particle.get_symbol(index) == symbol1:
energy_change = 0
for neigh_idx in particle.get_coordination_atoms(index):
neigh_feature = atom_features[neigh_idx]
energy_change -= self.neigh_energy_difference[neigh_feature-1]
self.symbol1_exchange_energies[index] = -new_exchange_energy + energy_change
else:
energy_change = 0
for neigh_idx in particle.get_coordination_atoms(index):
neigh_feature = atom_features[neigh_idx]
energy_change += self.neigh_energy_difference[neigh_feature]
self.symbol2_exchange_energies[index] = new_exchange_energy + energy_change
for index in indices:
if particle.get_symbol(index) == symbol1:
self.symbol1_indices.add(index)
else:
self.symbol2_indices.add(index)
# def update(self, particle, indices, exchange_indices):
# symbols = sorted(particle.atoms.get_all_symbols())
# symbol1 = symbols[0]
# atom_features = particle.get_atom_features(self.feature_key)
# for index in indices:
# if index in exchange_indices:
# if particle.get_symbol(index) == symbol1:
# self.symbol2_indices.remove(index)
# #del self.symbol2_exchange_energies[index]
# else:
# self.symbol1_indices.remove(index)
# #del self.symbol1_exchange_energies[index]
# else:
# if particle.get_symbol(index) == symbol1:
# self.symbol1_indices.remove(index)
# else:
# self.symbol2_indices.remove(index)
# for index in indices:
# feature = atom_features[index]
# new_exchange_energy = self.env_energy_differences[self.env_from_feature(feature)]
# if particle.get_symbol(index) == symbol1:
# energy_change = 0
# for neigh_idx in particle.get_coordination_atoms(index):
# neigh_feature = atom_features[neigh_idx]
# energy_change -= self.neigh_energy_difference[neigh_feature-1]
# #self.symbol1_exchange_energies[index] = (-self.env_energy_differences[self.env_from_feature(feature)] + energy_change)
# #elf.symbol1_indices.add(index)
# else:
# energy_change = 0
# for neigh_idx in particle.get_coordination_atoms(index):
# neigh_feature = atom_features[neigh_idx]
# energy_change += self.neigh_energy_difference[neigh_feature+1]
# #self.symbol2_exchange_energies[index] = (+self.env_energy_differences[self.env_from_feature(feature)] + energy_change)
# #self.symbol2_indices.add(index)
# if index in exchange_indices:
# if particle.get_symbol(index) == symbol1:
# self.symbol1_exchange_energies[index] = -new_exchange_energy + energy_change
# del self.symbol2_exchange_energies[index]
# else:
# self.symbol2_exchange_energies[index] = new_exchange_energy + energy_change
# del self.symbol1_exchange_energies[index]
# else:
# if particle.get_symbol(index) == symbol1:
# self.symbol1_exchange_energies[index] = -new_exchange_energy + energy_change
# else:
# self.symbol2_exchange_energies[index] = new_exchange_energy + energy_change
# for index in indices:
# if particle.get_symbol(index) == symbol1:
# self.symbol1_indices.add(index)
# else:
# self.symbol2_indices.add(index)