"""
Honeycomb
=========
"""
import numpy as np
from stk._internal.topology_graphs.edge 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, 0.0, 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),
),
)