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

"""
Hexagonal
=========

"""

import numpy as np

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


[docs]class Hexagonal(Cof): """ Represents a hexagonal COF topology graph. Unoptimized construction .. moldoc:: import moldoc.molecule as molecule import stk bb1 = stk.BuildingBlock('BrCCBr', [stk.BromoFactory()]) bb2 = stk.BuildingBlock( smiles='Brc1c(Br)c(Br)c(Br)c(Br)c1Br', functional_groups=[stk.BromoFactory()], ) cof = stk.ConstructedMolecule( topology_graph=stk.cof.Hexagonal( building_blocks=(bb1, bb2), lattice_size=(2, 2, 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=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( smiles='Brc1c(Br)c(Br)c(Br)c(Br)c1Br', functional_groups=[stk.BromoFactory()], ) cof = stk.ConstructedMolecule( topology_graph=stk.cof.Hexagonal( building_blocks=(bb1, bb2), lattice_size=(2, 2, 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=bond.get_order(), ) for bond in cof.get_bonds() ), ) Building blocks with six 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: | 6-functional groups: 0 to 3 | 2-functional groups: 4 to 15 See :class:`.Cof` for more details and examples. """ _lattice_constants = _a, _b, _c = ( np.array([1.0, 0.0, 0.0]), np.array([0.5, 0.866, 0]), np.array([0, 0, 5 / 1.7321]), ) _non_linears = ( NonLinearVertex(0, (1 / 4) * _a + (1 / 4) * _b + (1 / 2) * _c), NonLinearVertex(1, (1 / 4) * _a + (3 / 4) * _b + (1 / 2) * _c), NonLinearVertex(2, (3 / 4) * _a + (1 / 4) * _b + (1 / 2) * _c), NonLinearVertex(3, (3 / 4) * _a + (3 / 4) * _b + (1 / 2) * _c), ) _vertex_prototypes = ( *_non_linears, LinearVertex.init_at_center( id=4, vertices=(_non_linears[0], _non_linears[1]), ), LinearVertex.init_at_center( id=5, vertices=(_non_linears[0], _non_linears[2]), ), LinearVertex.init_at_center( id=6, vertices=(_non_linears[1], _non_linears[2]), ), LinearVertex.init_at_center( id=7, vertices=(_non_linears[1], _non_linears[3]), ), LinearVertex.init_at_center( id=8, vertices=(_non_linears[2], _non_linears[3]), ), LinearVertex.init_at_shifted_center( id=9, vertices=(_non_linears[0], _non_linears[2]), cell_shifts=((0, 0, 0), (-1, 0, 0)), lattice_constants=_lattice_constants, ), LinearVertex.init_at_shifted_center( id=10, 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=11, vertices=(_non_linears[0], _non_linears[3]), cell_shifts=((0, 0, 0), (0, -1, 0)), lattice_constants=_lattice_constants, ), LinearVertex.init_at_shifted_center( id=12, vertices=(_non_linears[2], _non_linears[1]), cell_shifts=((0, 0, 0), (1, -1, 0)), lattice_constants=_lattice_constants, ), LinearVertex.init_at_shifted_center( id=13, vertices=(_non_linears[2], _non_linears[3]), cell_shifts=((0, 0, 0), (0, -1, 0)), lattice_constants=_lattice_constants, ), LinearVertex.init_at_shifted_center( id=14, vertices=(_non_linears[1], _non_linears[3]), cell_shifts=((0, 0, 0), (-1, 0, 0)), lattice_constants=_lattice_constants, ), LinearVertex.init_at_shifted_center( id=15, vertices=(_non_linears[3], _non_linears[0]), cell_shifts=((0, 0, 0), (1, 0, 0)), lattice_constants=_lattice_constants, ), ) _edge_prototypes = ( Edge(0, _vertex_prototypes[4], _vertex_prototypes[0]), Edge(1, _vertex_prototypes[4], _vertex_prototypes[1]), Edge(2, _vertex_prototypes[5], _vertex_prototypes[0]), Edge(3, _vertex_prototypes[5], _vertex_prototypes[2]), Edge(4, _vertex_prototypes[6], _vertex_prototypes[1]), Edge(5, _vertex_prototypes[6], _vertex_prototypes[2]), Edge(6, _vertex_prototypes[7], _vertex_prototypes[1]), Edge(7, _vertex_prototypes[7], _vertex_prototypes[3]), Edge(8, _vertex_prototypes[8], _vertex_prototypes[2]), Edge(9, _vertex_prototypes[8], _vertex_prototypes[3]), Edge(10, _vertex_prototypes[9], _vertex_prototypes[0]), Edge( id=11, vertex1=_vertex_prototypes[9], vertex2=_vertex_prototypes[2], periodicity=(-1, 0, 0), ), Edge(12, _vertex_prototypes[10], _vertex_prototypes[0]), Edge( id=13, vertex1=_vertex_prototypes[10], vertex2=_vertex_prototypes[1], periodicity=(0, -1, 0), ), Edge(14, _vertex_prototypes[11], _vertex_prototypes[0]), Edge( id=15, vertex1=_vertex_prototypes[11], vertex2=_vertex_prototypes[3], periodicity=(0, -1, 0), ), Edge(16, _vertex_prototypes[12], _vertex_prototypes[2]), Edge( id=17, vertex1=_vertex_prototypes[12], vertex2=_vertex_prototypes[1], periodicity=(1, -1, 0), ), Edge(18, _vertex_prototypes[13], _vertex_prototypes[2]), Edge( id=19, vertex1=_vertex_prototypes[13], vertex2=_vertex_prototypes[3], periodicity=(0, -1, 0), ), Edge(20, _vertex_prototypes[14], _vertex_prototypes[1]), Edge( id=21, vertex1=_vertex_prototypes[14], vertex2=_vertex_prototypes[3], periodicity=(-1, 0, 0), ), Edge(22, _vertex_prototypes[15], _vertex_prototypes[3]), Edge( id=23, vertex1=_vertex_prototypes[15], vertex2=_vertex_prototypes[0], periodicity=(1, 0, 0), ), )