Source code for stk.molecular.topology_graphs.topology_graph.optimizers.mchammer



import mchammer as mch

from .optimizer import Optimizer
from .utilities import get_long_bond_ids, get_mch_bonds, get_subunits

[docs]class MCHammer(Optimizer): """ Performs Monte Carlo optimisation of long-bonds in molecules [1]_. Examples -------- *Structure Optimization* Using :class:`.MCHammer` will lead to :class:`.ConstructedMolecule` structures without long bonds. .. testcode:: structure-optimization import stk bb1 = stk.BuildingBlock('NCCN', [stk.PrimaryAminoFactory()]) bb2 = stk.BuildingBlock('O=CCC=O', [stk.AldehydeFactory()]) polymer = stk.ConstructedMolecule( topology_graph=stk.polymer.Linear( building_blocks=(bb1, bb2), repeating_unit='AB', num_repeating_units=6, optimizer=stk.MCHammer(), ), ) Optimisation with :mod:`stk` simply collects the final position matrix. The optimisation's trajectory can be output using the :mod:`MCHammer` implementation if required by the user [1]_. The open-source optimization code :mod:`MCHammer` specializes in the `collapsing` of molecules with long bonds like those constructed by :mod:`stk`. This code is entirely nonphysical and is, therefore, completely general to any chemistry. References ---------- .. [1] """
[docs] def __init__( self, step_size=0.25, target_bond_length=1.2, num_steps=500, bond_epsilon=50, nonbond_epsilon=20, nonbond_sigma=1.2, nonbond_mu=3, beta=2, random_seed=1000, ): """ Initialize an instance of :class:`.MCHammer`. Parameters ---------- step_size : :class:`float`, optional The relative size of the step to take during step. target_bond_length : :class:`float`, optional Target equilibrium bond length for long bonds to minimize to in Angstrom. num_steps : :class:`int`, optional Number of MC moves to perform. bond_epsilon : :class:`float`, optional Value of epsilon used in the bond potential in MC moves. Determines strength of the bond potential. nonbond_epsilon : :class:`float`, optional Value of epsilon used in the nonbond potential in MC moves. Determines strength of the nonbond potential. Larger values lead to a larger building block repulsion. nonbond_sigma : :class:`float`, optional Value of sigma used in the nonbond potential in MC moves. Larger values lead to building block repulsion at larger distances. nonbond_mu : :class:`float`, optional Value of mu used in the nonbond potential in MC moves. Determines the steepness of the nonbond potential. beta : :class:`float`, optional Value of beta used in the in MC moves. Beta takes the place of the inverse Boltzmann temperature. random_seed : :class:`int` or :class:`NoneType`, optional Random seed to use for MC algorithm. If ``None`` a system-based random seed will be used and results will not be reproducible between invocations. """ self._optimizer = mch.Optimizer( step_size=step_size, target_bond_length=target_bond_length, num_steps=num_steps, bond_epsilon=bond_epsilon, nonbond_epsilon=nonbond_epsilon, nonbond_sigma=nonbond_sigma, nonbond_mu=nonbond_mu, beta=beta, random_seed=random_seed, )
[docs] def optimize(self, state): # Define MCHammer molecule to optimize. mch_mol = mch.Molecule( atoms=( mch.Atom( id=atom.get_id(), element_string=atom.__class__.__name__, ) for atom in state.get_atoms() ), bonds=tuple(get_mch_bonds(state)), position_matrix=state.get_position_matrix(), ) # Run optimization. mch_mol, results = self._optimizer.get_result( mol=mch_mol, bond_pair_ids=tuple(get_long_bond_ids(state)), subunits=get_subunits(state), ) return state.with_position_matrix( position_matrix=mch_mol.get_position_matrix(), )