import numpy as np
from stk._internal.topology_graphs.edge 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),
),
)