Merge branch 'cgnr'

CHANGELOG.md

@@ -12,11 +12,16 @@ we hit release version 1.0.0.
 - enabled `Grid.to|new` with the most basic stuff
   str|Path|Grid|pyamg
 - `Shape.translate`, to easily translate entire shape constructs, #655
+- Creation of chiral GNRs (`kind=chiral` in `sisl.geom.nanoribbon`/`sisl.geom.graphene_nanoribbon`
+  as well as `sisl.geom.cgnr`)
+- Creation of [n]-triangulenes (`sisl.geom.triangulene`)
 
 ### Fixed
 - enabled slicing in matrix assignments, #650
 - changed `Shape.volume()` to `Shape.volume` 
 
+### Changed
+- `vacuum` is now an optional parameter for all ribbon structures
 
 
 ## [0.14.3] - 2023-11-07

docs/api/default_geom.rst

@@ -42,6 +42,15 @@ Surfaces (slabs)
    fcc_slab
    rocksalt_slab
 
+0D materials
+============
+
+.. autosummary::
+   :toctree: generated/
+
+   honeycomb_flake
+   graphene_flake
+   triangulene
 
 1D materials
 ============
@@ -52,6 +61,7 @@ Surfaces (slabs)
    nanoribbon
    agnr
    zgnr
+   cgnr
    graphene_nanoribbon
    nanotube
    heteroribbon
@@ -67,8 +77,6 @@ Surfaces (slabs)
    honeycomb
    bilayer
    graphene
-   honeycomb_flake
-   graphene_flake
 
 
 Helpers

src/sisl/geom/flat.py

@@ -8,11 +8,11 @@
 
 from ._common import geometry_define_nsc
 
-__all__ = ["honeycomb", "graphene", "honeycomb_flake", "graphene_flake"]
+__all__ = ["honeycomb", "graphene", "honeycomb_flake", "graphene_flake", "triangulene"]
 
 
 @set_module("sisl.geom")
-def honeycomb(bond: float, atoms, orthogonal: bool = False):
+def honeycomb(bond: float, atoms, orthogonal: bool = False) -> Geometry:
     """Honeycomb lattice with 2 or 4 atoms per unit-cell, latter orthogonal cell
 
     This enables creating BN lattices with ease, or graphene lattices.
@@ -65,7 +65,7 @@ def honeycomb(bond: float, atoms, orthogonal: bool = False):
 
 
 @set_module("sisl.geom")
-def graphene(bond: float = 1.42, atoms=None, orthogonal: bool = False):
+def graphene(bond: float = 1.42, atoms=None, orthogonal: bool = False) -> Geometry:
     """Graphene lattice with 2 or 4 atoms per unit-cell, latter orthogonal cell
 
     Parameters
@@ -204,3 +204,40 @@ def graphene_flake(
     if atoms is None:
         atoms = Atom(Z=6, R=bond * 1.01)
     return honeycomb_flake(shells, bond, atoms, vacuum)
+
+
+@set_module("sisl.geom")
+def triangulene(
+    n: int, bond: float = 1.42, atoms=None, vacuum: float = 20.0
+) -> Geometry:
+    """Construction of an [n]-triangulene geometry
+
+    Parameters
+    ----------
+    n :
+       size of the triangulene
+    bond :
+       bond length between atoms (*not* lattice constant)
+    atoms :
+        the atom (or atoms) that the honeycomb lattice consists of.
+        Default to Carbon atom.
+    vacuum:
+        Amount of vacuum to add to the cell on all directions
+    """
+    if atoms is None:
+        atoms = Atom(Z=6, R=bond * 1.01)
+    geom = graphene(bond=bond, atoms=atoms) * (n + 1, n + 1, 1)
+    idx = np.where(geom.xyz[:, 0] <= geom.cell[0, 0] + 0.01)[0]
+    geom = geom.sub(idx[1:])
+
+    # Set the cell according to the requested vacuum
+    size = geom.xyz.max(axis=0) - geom.xyz.min(axis=0)
+    geom.cell[:] = np.diag(size + vacuum)
+
+    # Center the molecule in cell
+    geom = geom.move(geom.center(what="cell") - geom.center())
+
+    # Set boundary conditions
+    geometry_define_nsc(geom, [False, False, False])
+
+    return geom