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

"""
Honeycomb
=========

"""

import numpy as np

from ..topology_graph import Edge
from .cof import Cof
from .vertices import LinearVertex, NonLinearVertex


[docs]class Honeycomb(Cof): """ Represents a 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.Honeycomb( 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() ), ) ``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.Honeycomb( 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() ), ) 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 See :class:`.Cof` for more details and examples. """ _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), ) )