Source code for stk.molecular.topology_graphs.cof.periodic_honeycomb

"""
Periodic Honeycomb
==================

"""


import numpy as np

from ...reactions import GenericReactionFactory
from ..topology_graph import Edge, NullOptimizer
from .cof import Cof
from .vertices import LinearVertex, NonLinearVertex


[docs]class PeriodicHoneycomb(Cof): """ Represents a periodic honeycomb COF topology graph. Unoptimized construction .. moldoc:: import moldoc.molecule as molecule import stk bb1 = stk.BuildingBlock('BrCCBr', [stk.BromoFactory()]) bb2 = stk.BuildingBlock('BrCC(CBr)CBr', [stk.BromoFactory()]) cof = stk.ConstructedMolecule( topology_graph=stk.cof.PeriodicHoneycomb( building_blocks=(bb1, bb2), lattice_size=(3, 3, 1), ), ) moldoc_display_molecule = molecule.Molecule( atoms=( molecule.Atom( atomic_number=atom.get_atomic_number(), position=position, ) for atom, position in zip( cof.get_atoms(), cof.get_position_matrix(), ) ), bonds=( molecule.Bond( atom1_id=bond.get_atom1().get_id(), atom2_id=bond.get_atom2().get_id(), order=( 1 if bond.get_order() == 9 else bond.get_order() ), ) for bond in cof.get_bonds() if all(p == 0 for p in bond.get_periodicity()) ), ) ``Collapser(scale_steps=False)`` optimized construction .. moldoc:: import moldoc.molecule as molecule import stk bb1 = stk.BuildingBlock('BrCCBr', [stk.BromoFactory()]) bb2 = stk.BuildingBlock('BrCC(CBr)CBr', [stk.BromoFactory()]) cof = stk.ConstructedMolecule( topology_graph=stk.cof.PeriodicHoneycomb( building_blocks=(bb1, bb2), lattice_size=(3, 3, 1), optimizer=stk.Collapser(scale_steps=False), ), ) moldoc_display_molecule = molecule.Molecule( atoms=( molecule.Atom( atomic_number=atom.get_atomic_number(), position=position, ) for atom, position in zip( cof.get_atoms(), cof.get_position_matrix(), ) ), bonds=( molecule.Bond( atom1_id=bond.get_atom1().get_id(), atom2_id=bond.get_atom2().get_id(), order=( 1 if bond.get_order() == 9 else bond.get_order() ), ) for bond in cof.get_bonds() if all(p == 0 for p in bond.get_periodicity()) ), ) Building blocks with three and two functional groups are required for this topology graph. When using a :class:`dict` for the `building_blocks` parameter, as in :ref:`cof-topology-graph-examples`: *Multi-Building Block COF Construction*, a :class:`.BuildingBlock`, with the following number of functional groups, needs to be assigned to each of the following vertex ids: | 3-functional groups: 0 to 1 | 2-functional groups: 2 to 4 Note that optimizers may not optimize the :class:`.PeriodicInfo`. The documentation of the optimizer will state if it does. See :class:`.Cof` for more details and examples. """
[docs] def __init__( self, building_blocks, lattice_size, vertex_alignments=None, reaction_factory=GenericReactionFactory(), num_processes=1, optimizer=NullOptimizer(), ): """ Initialize a :class:`.PeriodicHoneycomb` instance. Parameters ---------- building_blocks : :class:`tuple` or :class:`dict` Can be a :class:`tuple` of :class:`.BuildingBlock` instances, which should be placed on the topology graph. Can also be a :class:`dict` which maps the :class:`.BuildingBlock` instances to the ids of the vertices it should be placed on. A :class:`dict` is required when there are multiple building blocks with the same number of functional groups, because in this case the desired placement is ambiguous. lattice_size : :class:`tuple` of :class:`int` The size of the lattice in the x, y and z directions. vertex_alignments : :class:`dict`, optional A mapping from the id of a :class:`.Vertex` to an :class:`.Edge` connected to it. The :class:`.Edge` is used to align the first :class:`.FunctionalGroup` of a :class:`.BuildingBlock` placed on that vertex. Only vertices which need to have their default edge changed need to be present in the :class:`dict`. If ``None`` then the default edge is used for each vertex. Changing which :class:`.Edge` is used will mean that the topology graph represents different structural isomers. The edge is referred to by a number between ``0`` (inclusive) and the number of edges the vertex is connected to (exclusive). reaction_factory : :class:`.ReactionFactory`, optional The reaction factory to use for creating bonds between building blocks. num_processes : :class:`int`, optional The number of parallel processes to create during :meth:`construct`. optimizer : :class:`.Optimizer`, optional Used to optimize the structure of the constructed molecule. Raises ------ :class:`AssertionError` If the any building block does not have a valid number of functional groups. :class:`ValueError` If the there are multiple building blocks with the same number of functional_groups in `building_blocks`, and they are not explicitly assigned to vertices. The desired placement of building blocks is ambiguous in this case. :class:`~.cof.UnoccupiedVertexError` If a vertex of the COF topology graph does not have a building block placed on it. :class:`~.cof.OverlyOccupiedVertexError` If a vertex of the COF topology graph has more than one building block placed on it. """ super().__init__( building_blocks=building_blocks, lattice_size=lattice_size, periodic=True, vertex_alignments=vertex_alignments, reaction_factory=reaction_factory, num_processes=num_processes, optimizer=optimizer, )
_lattice_constants = _a, _b, _c = ( np.array([1., 0., 0.]), np.array([0.5, 0.866, 0]), np.array([0, 0, 5/1.7321]) ) _non_linears = ( NonLinearVertex(0, (1/3)*_a + (1/3)*_b + (1/2)*_c), NonLinearVertex(1, (2/3)*_a + (2/3)*_b + (1/2)*_c), ) _vertex_prototypes = ( *_non_linears, LinearVertex.init_at_center( id=2, vertices=(_non_linears[0], _non_linears[1]), ), LinearVertex.init_at_shifted_center( id=3, vertices=(_non_linears[0], _non_linears[1]), cell_shifts=((0, 0, 0), (0, -1, 0)), lattice_constants=_lattice_constants, ), LinearVertex.init_at_shifted_center( id=4, vertices=(_non_linears[0], _non_linears[1]), cell_shifts=((0, 0, 0), (-1, 0, 0)), lattice_constants=_lattice_constants, ) ) _edge_prototypes = ( Edge(0, _vertex_prototypes[2], _vertex_prototypes[0]), Edge(1, _vertex_prototypes[2], _vertex_prototypes[1]), Edge(2, _vertex_prototypes[3], _vertex_prototypes[0]), Edge( id=3, vertex1=_vertex_prototypes[3], vertex2=_vertex_prototypes[1], periodicity=(0, -1, 0), ), Edge(4, _vertex_prototypes[4], _vertex_prototypes[0]), Edge( id=5, vertex1=_vertex_prototypes[4], vertex2=_vertex_prototypes[1], periodicity=(-1, 0, 0), ) )