Source code for clease.montecarlo.observers.move_obs

from __future__ import annotations
from typing import Iterator, List
import ase
from clease.datastructures import MCStep
from clease.calculator import CleaseCacheCalculator
from .mc_observer import MCObserver

__all__ = ("MoveObserver",)

[docs]class MoveObserver(MCObserver): """Store each step from an MC run to reconstruct the individual atoms objects later. The interval must be set to 1 when attaching this observer, as otherwise steps may be lost and the reconstruction may end up being incorrect. Args: base_atoms (ase.Atoms): The base atoms object which is run in the MC. only_accept (bool, optional): Selects whether the only accepted moves or all the attempted moves are saved. If False, every move will be saved. Defaults to False. """ def __init__(self, base_atoms: ase.Atoms, only_accept: bool = False): super().__init__() self.base_atoms = base_atoms.copy() self.only_accept = only_accept self.steps = []
[docs] def observe_step(self, mc_step: MCStep) -> None: """Observe a single step""" if self.only_accept is True and mc_step.move_accepted is False: # Step was rejected, and we only want accepted steps return self.steps.append(mc_step)
[docs] def reset(self) -> None: self.steps = []
[docs] def reconstruct(self) -> List[ase.Atoms]: """Rebuild the atoms objects as defined by the observed changes.""" return list(self.reconstruct_iter())
[docs] def reconstruct_iter(self) -> Iterator[ase.Atoms]: """Iterator which builds the atoms objects 1-by-1.""" atoms = self.base_atoms.copy() for step in self.steps: # Update the current atoms atoms = _apply_step(atoms, step) yield atoms
[docs] def interval_ok(self, interval: int) -> bool: """Missing steps will result in incorrect reconstructions""" return interval == 1
def _apply_step(atoms: ase.Atoms, step: MCStep) -> ase.Atoms: """Helper function to apply a step to an atoms object. Always a returns a copy of the atoms object.""" atoms = atoms.copy() # Apply changes to a copy of the atoms if step.move_accepted: for change in step.last_move: change.apply_change(atoms) # Attach a calculator with the energies calc = CleaseCacheCalculator( atoms.calc = calc return atoms